Publications

  • A. Best, K. James, C. Dalgliesh, E. Hong, M. Kheirolahi-Kouhestani, T. Curk, Y. Xu, M. Danilenko, R. Hussain, B. Keavney, A. Wipat, R. Klinck, I. Cowell, K. Cheong Lee, C. Austin, J. Venables, B. Chabot, M. Koref, A. Tyson-Capper, and D. Elliott, “Human tra2 proteins jointly control a chek1 splicing switch amongst alternative and constitutive target exons,” Nature communications, vol. [in press], 2014.
    [Bibtex]
    @ARTICLE{Best:2014:NatureComm,
    author = {Best, A and James, K and Dalgliesh, C and Hong, E and Kheirolahi-Kouhestani, M and Curk, T and Xu, Y and Danilenko, M and Hussain, R and Keavney, B and Wipat, A and Klinck, R and Cowell, I and Cheong Lee, K and Austin, C and Venables, JP and Chabot, B and Koref, MS and Tyson-Capper, A and Elliott, DJ},
    title = {Human Tra2 proteins jointly control a CHEK1 splicing switch amongst alternative and constitutive target exons},
    journal = {Nature Communications},
    year = {2014},
    volume = {[in press]}
    }
  • [DOI] G. Misirli, J. Hallinan, R. Röttger, J. Baumbach, and A. Wipat, “Bacillusregnet: a transcriptional regulation database and analysis platform for bacillus species,” J integr bioinform, vol. 11, iss. 2, pp. 244-244, 2014.
    [Bibtex]
    @Article{Misirli:2014:J-Integr-Bioinform:25001169,
    author = "Misirli, G and Hallinan, J and R{\"o}ttger, R and Baumbach, J and Wipat, A",
    title = {BacillusRegNet: A transcriptional regulation database and analysis platform for Bacillus species},
    abstract = {As high-throughput technologies become cheaper and easier to use, raw sequence data and corresponding annotations for many organisms are becoming available. However, sequence data alone is not sufficient to explain the biological behaviour of organisms, which arises largely from complex molecular interactions. There is a need to develop new platform technologies that can be applied to the investigation of whole-genome datasets in an efficient and cost-effective manner. One such approach is the transfer of existing knowledge from well-studied organisms to closely-related organisms. In this paper, we describe a system, BacillusRegNet, for the use of a model organism, Bacillus subtilis, to infer genome-wide regulatory networks in less well-studied close relatives. The putative transcription factors, their binding sequences and predicted promoter sequences along with annotations are available from the associated BacillusRegNet website (http://bacillus.ncl.ac.uk).},
    journal = "J Integr Bioinform",
    year = "2014",
    volume = "11",
    number = "2",
    pages = "244-244",
    month = "",
    pmid = "25001169",
    url = "http://www.hubmed.org/display.cgi?uids=25001169",
    doi = "10.2390/biecoll-jib-2014-244"
    }
  • [DOI] J. Rusakovica, J. Hallinan, A. Wipat, and P. Zuliani, “Probabilistic latent semantic analysis applied to whole bacterial genomes identifies common genomic features,” J integr bioinform, vol. 11, iss. 2, pp. 243-243, 2014.
    [Bibtex]
    @Article{Rusakovica:2014:J-Integr-Bioinform:24980693,
    author = "Rusakovica, J and Hallinan, J and Wipat, A and Zuliani, P",
    title = {Probabilistic latent semantic analysis applied to whole bacterial genomes identifies common genomic features},
    abstract = {The spread of drug resistance amongst clinically-important bacteria is a serious, and growing, problem [1]. However, the analysis of entire genomes requires considerable computational effort, usually including the assembly of the genome and subsequent identification of genes known to be important in pathology. An alternative approach is to use computational algorithms to identify genomic differences between pathogenic and non-pathogenic bacteria, even without knowing the biological meaning of those differences. To overcome this problem, a range of techniques for dimensionality reduction have been developed. One such approach is known as latent-variable models [2]. In latent-variable models dimensionality reduction is achieved by representing a high-dimensional data by a few hidden or latent variables, which are not directly observed but inferred from the observed variables present in the model. Probabilistic Latent Semantic Indexing (PLSA) is an extention of LSA [3]. PLSA is based on a mixture decomposition derived from a latent class model. The main objective of the algorithm, as in LSA, is to represent high-dimensional co-occurrence information in a lower-dimensional way in order to discover the hidden semantic structure of the data using a probabilistic framework. In this work we applied the PLSA approach to analyse the common genomic features in methicillin resistant Staphylococcus aureus, using tokens derived from amino acid sequences rather than DNA. We characterised genome-scale amino acid sequences in terms of their components, and then investigated the relationships between genomes and tokens and the phenotypes they generated. As a control we used the non-pathogenic model Gram-positive bacterium Bacillus subtilis.},
    journal = "J Integr Bioinform",
    year = "2014",
    volume = "11",
    number = "2",
    pages = "243-243",
    month = "",
    pmid = "24980693",
    url = "http://www.hubmed.org/display.cgi?uids=24980693",
    doi = "10.2390/biecoll-jib-2014-243"
    }
  • [DOI] K. Flanagan, S. Cockell, C. Harwood, J. Hallinan, S. Nakjang, B. Lawry, and A. Wipat, “A distributed computational search strategy for the identification of diagnostics targets: application to finding aptamer targets for methicillin-resistant staphylococci,” J integr bioinform, vol. 11, iss. 2, pp. 242-242, 2014.
    [Bibtex]
    @Article{Flanagan:2014:J-Integr-Bioinform:24980620,
    author = "Flanagan, K and Cockell, S and Harwood, C and Hallinan, J and Nakjang, S and Lawry, B and Wipat, A",
    title = {A distributed computational search strategy for the identification of diagnostics targets: Application to finding aptamer targets for methicillin-resistant staphylococci},
    abstract = {The rapid and cost-effective identification of bacterial species is crucial, especially for clinical diagnosis and treatment. Peptide aptamers have been shown to be valuable for use as a component of novel, direct detection methods. These small peptides have a number of advantages over antibodies, including greater specificity and longer shelf life. These properties facilitate their use as the detector components of biosensor devices. However, the identification of suitable aptamer targets for particular groups of organisms is challenging. We present a semi-automated processing pipeline for the identification of candidate aptamer targets from whole bacterial genome sequences. The pipeline can be configured to search for protein sequence fragments that uniquely identify a set of strains of interest. The system is also capable of identifying additional organisms that may be of interest due to their possession of protein fragments in common with the initial set. Through the use of Cloud computing technology and distributed databases, our system is capable of scaling with the rapidly growing genome repositories, and consequently of keeping the resulting data sets up-to-date. The system described is also more generically applicable to the discovery of specific targets for other diagnostic approaches such as DNA probes, PCR primers and antibodies.},
    journal = "J Integr Bioinform",
    year = "2014",
    volume = "11",
    number = "2",
    pages = "242-242",
    month = "",
    pmid = "24980620",
    url = "http://www.hubmed.org/display.cgi?uids=24980620",
    doi = "10.2390/biecoll-jib-2014-242"
    }
  • [DOI] N. Roehner, E. Oberortner, M. Pocock, J. Beal, K. Clancy, C. Madsen, G. Misirli, A. Wipat, H. Sauro, and C. J. Myers, “Proposed data model for the next version of the synthetic biology open language,” Acs synth biol, 2014.
    [Bibtex]
    @Article{Roehner:2014:ACS-Synth-Biol:24896221,
    author = "Roehner, N and Oberortner, E and Pocock, M and Beal, J and Clancy, K and Madsen, C and Misirli, G and Wipat, A and Sauro, H and Myers, C J",
    title = {Proposed Data Model for the Next Version of the Synthetic Biology Open Language},
    abstract = {While the first version of the Synthetic Biology Open Language (SBOL) has been adopted by several academic and commercial genetic design automation (GDA) software tools, it only covers a limited number of the requirements for a standardized exchange format for synthetic biology. In particular, SBOL Version 1.1 is capable of representing DNA components and their hierarchical composition via sequence annotations. This proposal revises SBOL Version 1.1, enabling the representation of a wider range of components with and without sequences, including RNA components, protein components, small molecules, and molecular complexes. It also introduces modules to instantiate groups of components on the basis of their shared function and assert molecular interactions between components. By increasing the range of structural and functional descriptions in SBOL and allowing for their composition, the proposed improvements enable SBOL to represent and facilitate the exchange of a broader class of genetic designs.},
    journal = "ACS Synth Biol",
    year = "2014",
    volume = "",
    number = "",
    pages = "",
    month = "Jun",
    pmid = "24896221",
    url = "http://www.hubmed.org/display.cgi?uids=24896221",
    doi = "10.1021/sb500176h"
    }
  • [DOI] M. Galdzicki, K. P. Clancy, E. Oberortner, M. Pocock, J. Y. Quinn, C. A. Rodriguez, N. Roehner, M. L. Wilson, L. Adam, J. C. Anderson, B. A. Bartley, J. Beal, D. Chandran, J. Chen, D. Densmore, D. Endy, R. Grünberg, J. Hallinan, N. J. Hillson, J. D. Johnson, A. Kuchinsky, M. Lux, G. Misirli, J. Peccoud, H. A. Plahar, E. Sirin, G. B. Stan, A. Villalobos, A. Wipat, J. H. Gennari, C. J. Myers, and H. M. Sauro, “The synthetic biology open language (sbol) provides a community standard for communicating designs in synthetic biology,” Nat biotechnol, vol. 32, iss. 6, pp. 545-550, 2014.
    [Bibtex]
    @Article{Galdzicki:2014:Nat-Biotechnol:24911500,
    author = "Galdzicki, M and Clancy, K P and Oberortner, E and Pocock, M and Quinn, J Y and Rodriguez, C A and Roehner, N and Wilson, M L and Adam, L and Anderson, J C and Bartley, B A and Beal, J and Chandran, D and Chen, J and Densmore, D and Endy, D and Gr{\"u}nberg, R and Hallinan, J and Hillson, N J and Johnson, J D and Kuchinsky, A and Lux, M and Misirli, G and Peccoud, J and Plahar, H A and Sirin, E and Stan, G B and Villalobos, A and Wipat, A and Gennari, J H and Myers, C J and Sauro, H M",
    title = {The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology},
    abstract = {The re-use of previously validated designs is critical to the evolution of synthetic biology from a research discipline to an engineering practice. Here we describe the Synthetic Biology Open Language (SBOL), a proposed data standard for exchanging designs within the synthetic biology community. SBOL represents synthetic biology designs in a community-driven, formalized format for exchange between software tools, research groups and commercial service providers. The SBOL Developers Group has implemented SBOL as an XML/RDF serialization and provides software libraries and specification documentation to help developers implement SBOL in their own software. We describe early successes, including a demonstration of the utility of SBOL for information exchange between several different software tools and repositories from both academic and industrial partners. As a community-driven standard, SBOL will be updated as synthetic biology evolves to provide specific capabilities for different aspects of the synthetic biology workflow.},
    journal = "Nat Biotechnol",
    year = "2014",
    volume = "32",
    number = "6",
    pages = "545-550",
    month = "Jun",
    pmid = "24911500",
    url = "http://www.hubmed.org/display.cgi?uids=24911500",
    doi = "10.1038/nbt.2891"
    }
  • [DOI] S. Pohl, G. Bhavsar, J. Hulme, A. E. Bloor, G. Misirli, M. W. Leckenby, D. S. Radford, W. Smith, A. Wipat, E. D. Williamson, C. R. Harwood, and R. M. Cranenburgh, “Proteomic analysis of bacillus subtilis strains engineered for improved production of heterologous proteins,” Proteomics, vol. 13, iss. 22, pp. 3298-3308, 2013.
    [Bibtex]
    @Article{Pohl:2013:Proteomics:24115457,
    author = "Pohl, S and Bhavsar, G and Hulme, J and Bloor, A E and Misirli, G and Leckenby, M W and Radford, D S and Smith, W and Wipat, A and Williamson, E D and Harwood, C R and Cranenburgh, R M",
    title = {Proteomic analysis of Bacillus subtilis strains engineered for improved production of heterologous proteins},
    abstract = {The use of bacterial systems for recombinant protein production has advantages of simplicity, time and cost over competing systems. However, widely used bacterial expression systems (e.g. Escherichia coli, Pseudomonas fluorescens) are not able to secrete soluble proteins directly into the culture medium. This limits yields and increases downstream processing time and costs. In contrast, Bacillus spp. secrete native enzymes directly into the culture medium at grams-per-litre quantities, although the yields of some recombinant proteins are severely limited. We have engineered the Bacillus subtilis genome to generate novel strains with precise deletions in the genes encoding ten extracytoplasmic proteases that affect recombinant protein secretion, which lack chromosomal antibiotic resistance genes. The deletion sites and presence of single nucleotide polymorphisms were confirmed by sequencing. The strains are stable and were used in industrial-scale fermenters for the production of the Bacillus anthracis vaccine protein, protective antigen, the productivity of which is extremely low in the unmodified strain. We also show that the deletion of so-called quality control proteases appears to influence cell-wall synthesis, resulting in the induction of the cell-wall stress regulon that encodes another quality control protease.},
    journal = "Proteomics",
    year = "2013",
    volume = "13",
    number = "22",
    pages = "3298-3308",
    month = "Nov",
    pmid = "24115457",
    url = "http://www.hubmed.org/display.cgi?uids=24115457",
    doi = "10.1002/pmic.201300183"
    }
  • [DOI] G. Misirli, A. Wipat, J. Mullen, K. James, M. Pocock, W. Smith, N. Allenby, and J. S. Hallinan, “Bacillondex: an integrated data resource for systems and synthetic biology,” J integr bioinform, vol. 10, iss. 2, pp. 224-224, 2013.
    [Bibtex]
    @ARTICLE{Misirli:2013:J-Integr-Bioinform:23571273,
    author = {Misirli, G and Wipat, A and Mullen, J and James, K and Pocock, M
    and Smith, W and Allenby, N and Hallinan, J S},
    title = {BacillOndex: An Integrated Data Resource for Systems and Synthetic Biology},
    journal = {J Integr Bioinform},
    year = {2013},
    volume = {10},
    pages = {224-224},
    number = {2},
    abstract = {BacillOndex is an extension of the Ondex data integration system,
    providing a semantically annotated, integrated knowledge base for
    the model Gram-positive bacterium Bacillus subtilis. This application
    allows a user to mine a variety of B. subtilis data sources, and
    analyse the resulting integrated dataset, which contains data about
    genes, gene products and their interactions. The data can be analysed
    either manually, by browsing using Ondex, or computationally via
    a Web services interface. We describe the process of creating a BacillOndex
    instance, and describe the use of the system for the analysis of
    single nucleotide polymorphisms in B. subtilis Marburg. The Marburg
    strain is the progenitor of the widely-used laboratory strain B.
    subtilis 168. We identified 27 SNPs with predictable phenotypic effects,
    including genetic traits for known phenotypes. We conclude that BacillOndex
    is a valuable tool for the systems-level investigation of, and hypothesis
    generation about, this important biotechnology workhorse. Such understanding
    contributes to our ability to construct synthetic genetic circuits
    in this organism.},
    doi = {10.2390/biecoll-jib-2013-224},
    owner = {n8384838},
    pmid = {23571273},
    timestamp = {2013.05.09},
    url = {http://www.hubmed.org/display.cgi?uids=23571273}
    }
  • [DOI] S. Nakjang, D. A. Ndeh, A. Wipat, D. N. Bolam, and R P. Hirt, “A novel extracellular metallopeptidase domain shared by animal host-associated mutualistic and pathogenic microbes,” Plos one, vol. 7, iss. 1, 2012.
    [Bibtex]
    @ARTICLE{Nakjang:2012:PLoS-One:22299034,
    author = {Nakjang, S and Ndeh, D A and Wipat, A and Bolam, D N and Hirt, R
    P},
    title = {A novel extracellular metallopeptidase domain shared by animal host-associated mutualistic and pathogenic microbes},
    journal = {PLoS One},
    year = {2012},
    volume = {7},
    number = {1},
    abstract = {The mucosal microbiota is recognised as an important factor for our
    health, with many disease states linked to imbalances in the normal
    community structure. Hence, there is considerable interest in identifying
    the molecular basis of human-microbe interactions. In this work we
    investigated the capacity of microbes to thrive on mucosal surfaces,
    either as mutualists, commensals or pathogens, using comparative
    genomics to identify co-occurring molecular traits. We identified
    a novel domain we named M60-like/PF13402 (new Pfam entry PF13402),
    which was detected mainly among proteins from animal host mucosa-associated
    prokaryotic and eukaryotic microbes ranging from mutualists to pathogens.
    Lateral gene transfers between distantly related microbes explained
    their shared M60-like/PF13402 domain. The novel domain is characterised
    by a zinc-metallopeptidase-like motif and is distantly related to
    known viral enhancin zinc-metallopeptidases. Signal peptides and/or
    cell surface anchoring features were detected in most microbial M60-like/PF13402
    domain-containing proteins, indicating that these proteins target
    an extracellular substrate. A significant subset of these putative
    peptidases was further characterised by the presence of associated
    domains belonging to carbohydrate-binding module family 5/12, 32
    and 51 and other glycan-binding domains, suggesting that these novel
    proteases are targeted to complex glycoproteins such as mucins. An
    in vitro mucinase assay demonstrated degradation of mammalian mucins
    by a recombinant form of an M60-like/PF13402-containing protein from
    the gut mutualist Bacteroides thetaiotaomicron. This study reveals
    that M60-like domains are peptidases targeting host glycoproteins.
    These peptidases likely play an important role in successful colonisation
    of both vertebrate mucosal surfaces and the invertebrate digestive
    tract by both mutualistic and pathogenic microbes. Moreover, 141
    entries across various peptidase families described in the MEROPS
    database were also identified with carbohydrate-binding modules defining
    a new functional context for these glycan-binding domains and providing
    opportunities to engineer proteases targeting specific glycoproteins
    for both biomedical and industrial applications.},
    doi = {10.1371/journal.pone.0030287},
    owner = {n8384838},
    pmid = {22299034},
    timestamp = {2013.05.07},
    url = {http://www.hubmed.org/display.cgi?uids=22299034}
    }
  • [DOI] K. Flanagan, S. Nakjang, J. Hallinan, C. Harwood, R. P. Hirt, M. R. Pocock, and A. Wipat, “Microbase2.0: a generic framework for computationally intensive bioinformatics workflows in the cloud,” J integr bioinform, vol. 9, iss. 2, pp. 212-212, 2012.
    [Bibtex]
    @ARTICLE{Flanagan:2012:J-Integr-Bioinform:23001322,
    author = {Flanagan, K and Nakjang, S and Hallinan, J and Harwood, C and Hirt,
    R P and Pocock, M R and Wipat, A},
    title = {Microbase2.0: a generic framework for computationally intensive bioinformatics workflows in the cloud},
    journal = {J Integr Bioinform},
    year = {2012},
    volume = {9},
    pages = {212-212},
    number = {2},
    abstract = {As bioinformatics datasets grow ever larger, and analyses become increasingly
    complex, there is a need for data handling infrastructures to keep
    pace with developing technology. One solution is to apply Grid and
    Cloud technologies to address the computational requirements of analysing
    high throughput datasets. We present an approach for writing new,
    or wrapping existing applications, and a reference implementation
    of a framework, Microbase2.0, for executing those applications using
    Grid and Cloud technologies. We used Microbase2.0 to develop an automated
    Cloud-based bioinformatics workflow executing simultaneously on two
    different Amazon EC2 data centres and the Newcastle University Condor
    Grid. Several CPU years' worth of computational work was performed
    by this system in less than two months. The workflow produced a detailed
    dataset characterising the cellular localisation of 3,021,490 proteins
    from 867 taxa, including bacteria, archaea and unicellular eukaryotes.
    Microbase2.0 is freely available from http://www.microbase.org.uk/.},
    doi = {10.2390/biecoll-jib-2012-212},
    owner = {n8384838},
    pmid = {23001322},
    timestamp = {2013.05.07},
    url = {http://www.hubmed.org/display.cgi?uids=23001322}
    }
  • [DOI] M. Collison, R. P. Hirt, A. Wipat, S. Nakjang, P. Sanseau, and J. R. Brown, “Data mining the human gut microbiota for therapeutic targets,” Brief bioinform, vol. 13, iss. 6, pp. 751-768, 2012.
    [Bibtex]
    @ARTICLE{Collison:2012:Brief-Bioinform:22445903,
    author = {Collison, M and Hirt, R P and Wipat, A and Nakjang, S and Sanseau,
    P and Brown, J R},
    title = {Data mining the human gut microbiota for therapeutic targets},
    journal = {Brief Bioinform},
    year = {2012},
    volume = {13},
    pages = {751-768},
    number = {6},
    month = {Nov},
    abstract = {It is well known that microbes have an intricate role in human health
    and disease. However, targeted strategies for modulating human health
    through the modification of either human-associated microbial communities
    or associated human-host targets have yet to be realized. New knowledge
    about the role of microbial communities in the microbiota of the
    gastrointestinal tract (GIT) and their collective genomes, the GIT
    microbiome, in chronic diseases opens new opportunities for therapeutic
    interventions. GIT microbiota participation in drug metabolism is
    a further pharmaceutical consideration. In this review, we discuss
    how computational methods could lead to a systems-level understanding
    of the global physiology of the host-microbiota superorganism in
    health and disease. Such knowledge will provide a platform for the
    identification and development of new therapeutic strategies for
    chronic diseases possibly involving microbial as well as human-host
    targets that improve upon existing probiotics, prebiotics or antibiotics.
    In addition, integrative bioinformatics analysis will further our
    understanding of the microbial biotransformation of exogenous compounds
    or xenobiotics, which could lead to safer and more efficacious drugs.},
    doi = {10.1093/bib/bbs002},
    owner = {n8384838},
    pmid = {22445903},
    timestamp = {2013.05.07},
    url = {http://www.hubmed.org/display.cgi?uids=22445903}
    }
  • J. Hallinan, S. Park, and A. Wipat, “Bridging the gap between design and reality: a dual evolutionary strategy for the design of synthetic genetic circuits.,” Bioinformatics: the international conference on bioinformatics models, methods and algorithms. algarve, portugal., 2012.
    [Bibtex]
    @ARTICLE{Hallinan:2012p3280,
    author = {J Hallinan and S Park and A Wipat},
    title = {Bridging the gap between design and reality: A dual evolutionary strategy for the design of synthetic genetic circuits.},
    journal = {Bioinformatics: The International Conference on Bioinformatics Models,
    Methods and Algorithms. Algarve, Portugal. },
    year = {2012},
    abstract = {... Genetic Circuits JS Hallinan, S. Park and A. Wipat School of Computing
    Science, Newcastle University, NE7 4RU, Newcastle upon Tyne, UK {jennifer.hallinan,
    sungshic . park , anil.wipat}@newcastle.ac.uk Keywords: Synthetic
    ... },
    date-added = {2012-11-06 17:27:12 +0000},
    date-modified = {2013-05-08 11:14:39 +0100},
    local-url = {file://localhost/Users/spark/Dropbox/workspace1/Papers/staff.ncl.ac.uk%0A%202012%20Hallinan.pdf},
    owner = {n8384838},
    pmid = {related:vNgMM0WuoA8J},
    rating = {0},
    read = {Yes},
    timestamp = {2013.05.08},
    uri = {papers://85714800-3608-429D-85A0-7D00B06F5DFE/Paper/p3280},
    url = {http://www.staff.ncl.ac.uk/j.s.hallinan/pubs/BioinformaticsConf.pdf}
    }
  • [DOI] J. Weile, K. James, J. Hallinan, S. J. Cockell, P. Lord, A. Wipat, and D. J. Wilkinson, “Bayesian integration of networks without gold standards,” Bioinformatics, vol. 28, iss. 11, pp. 1495-1500, 2012.
    [Bibtex]
    @ARTICLE{Weile:2012:Bioinformatics:22492647,
    author = {Weile, J and James, K and Hallinan, J and Cockell, S J and Lord,
    P and Wipat, A and Wilkinson, D J},
    title = {Bayesian integration of networks without gold standards},
    journal = {Bioinformatics},
    year = {2012},
    volume = {28},
    pages = {1495-1500},
    number = {11},
    month = {Jun},
    abstract = {Biological experiments give insight into networks of processes inside
    a cell, but are subject to error and uncertainty. However, due to
    the overlap between the large number of experiments reported in public
    databases it is possible to assess the chances of individual observations
    being correct. In order to do so, existing methods rely on high-quality
    'gold standard' reference networks, but such reference networks are
    not always available.We present a novel algorithm for computing the
    probability of network interactions that operates without gold standard
    reference data. We show that our algorithm outperforms existing gold
    standard-based methods. Finally, we apply the new algorithm to a
    large collection of genetic interaction and protein-protein interaction
    experiments.The integrated dataset and a reference implementation
    of the algorithm as a plug-in for the Ondex data integration framework
    are available for download at http://bio-nexus.ncl.ac.uk/projects/nogold/},
    doi = {10.1093/bioinformatics/bts154},
    owner = {n8384838},
    pmid = {22492647},
    timestamp = {2013.05.09},
    url = {http://www.hubmed.org/display.cgi?uids=22492647}
    }
  • [DOI] K. James, A. Wipat, and J. Hallinan, “Is newer better?–evaluating the effects of data curation on integrated analyses in saccharomyces cerevisiae,” Integr biol (camb), vol. 4, iss. 7, pp. 715-727, 2012.
    [Bibtex]
    @ARTICLE{James:2012:Integr-Biol-Camb:22526920,
    author = {James, K and Wipat, A and Hallinan, J},
    title = {Is newer better?--evaluating the effects of data curation on integrated analyses in Saccharomyces cerevisiae},
    journal = {Integr Biol (Camb)},
    year = {2012},
    volume = {4},
    pages = {715-727},
    number = {7},
    month = {Jul},
    abstract = {Recent high-throughput experiments have produced a wealth of heterogeneous
    datasets, each of which provides information about different aspects
    of the cell. Consequently, integration of diverse data types is essential
    in order to address many biological questions. The quality of any
    integrated analysis system is dependent upon the quality of its component
    data, and upon the Gold Standard data used to evaluate it. It is
    commonly assumed that the quality of data improves as databases grow
    and change, particularly for manually curated databases. However,
    the validity of this assumption can be questioned, given the constant
    changes in the data coupled with the high level of noise associated
    with high-throughput experimental techniques. One of the most powerful
    approaches to data integration is the use of Probabilistic Functional
    Integrated Networks (PFINs). Here, we systematically analyse the
    changes in four highly-curated and widely-used online databases and
    evaluate the extent to which these changes affect the protein function
    prediction performance of PFINs in the yeast Saccharomyces cerevisiae.
    We find that the global trend in network performance improves over
    time. Where individual areas of biology are concerned, however, the
    most recent files do not always produce the best results. Individual
    datasets have unique biases towards different biological processes
    and by selecting and integrating relevant datasets performance can
    be improved. When using any type of integrated system to answer a
    specific biological question careful selection of raw data and Gold
    Standard is vital, since the most recent data may not be the most
    appropriate.},
    doi = {10.1039/c2ib00123c},
    owner = {n8384838},
    pmid = {22526920},
    timestamp = {2013.05.09},
    url = {http://www.hubmed.org/display.cgi?uids=22526920}
    }
  • [DOI] W. Y. Tu, S. Pohl, P. Summpunn, S. Hering, S. Kerstan, and C. R. Harwood, “Comparative analysis of the responses of related pathogenic and environmental bacteria to oxidative stress,” Microbiology, vol. 158, iss. Pt 3, pp. 636-647, 2012.
    [Bibtex]
    @ARTICLE{Tu:2012:Microbiology:22174384,
    author = {Tu, W Y and Pohl, S and Summpunn, P and Hering, S and Kerstan, S
    and Harwood, C R},
    title = {Comparative analysis of the responses of related pathogenic and environmental bacteria to oxidative stress},
    journal = {Microbiology},
    year = {2012},
    volume = {158},
    pages = {636-647},
    number = {Pt 3},
    month = {Mar},
    abstract = {Bacillus anthracis, the causative agent of anthrax, is exposed to
    host-mediated antibacterial activities, such as reactive oxygen species
    (ROS), during the early stages of its disease process. The ability
    to resist these host-mediated stresses is an essential characteristic
    of a successful pathogen while it is generally assumed that non-pathogenic
    environmental bacteria succumb to these antimicrobial activities.
    In order to gain insights into the underlying mechanisms that pathogens
    use to resist host-mediated oxidative stress, we have compared the
    oxidative stress responses of B. anthracis and Bacillus subtilis,
    a well-studied environmental bacterium. Among the four putative catalases
    encoded by B. anthracis we identified KatB as the main vegetative
    catalase. Comparative analysis of catalase production in B. anthracis
    and B. subtilis in response to superoxide and peroxide stress reveals
    different expression profiles, even though both are regulated by
    the PerR repressor, which senses and responds to peroxide stress.
    A B. anthracis perR deletion mutant exhibits enhanced KatB activity
    and is hyper-resistant to peroxide stress. Superoxide dismutase A1
    (SodA1) is the main contributor to the intracellular superoxide dismutase
    activity in vegetative cells and the gene encoding this enzyme is
    constitutively expressed. Although aspects of the ROS detoxifying
    systems of B. anthracis and B. subtilis are similar, their responses
    to superoxide stress are different. The observed differences are
    likely to reflect adaptations to specific environmental niches.},
    doi = {10.1099/mic.0.057000-0},
    owner = {n8384838},
    pmid = {22174384},
    timestamp = {2013.05.24},
    url = {http://www.hubmed.org/display.cgi?uids=22174384}
    }
  • [DOI] W. Y. Tu, S. Pohl, K. Gizynski, and C. R. Harwood, “The iron-binding protein dps2 confers peroxide stress resistance on bacillus anthracis,” J bacteriol, vol. 194, iss. 5, pp. 925-931, 2012.
    [Bibtex]
    @ARTICLE{Tu:2012:J-Bacteriol:22155779,
    author = {Tu, W Y and Pohl, S and Gizynski, K and Harwood, C R},
    title = {The iron-binding protein Dps2 confers peroxide stress resistance on Bacillus anthracis},
    journal = {J Bacteriol},
    year = {2012},
    volume = {194},
    pages = {925-931},
    number = {5},
    month = {Mar},
    abstract = {Iron is an essential nutrient that is implicated in most cellular
    oxidation reactions. However, iron is a highly reactive element that,
    if not appropriately chaperoned, can react with endogenously and
    exogenously generated oxidants such as hydrogen peroxide to generate
    highly toxic hydroxyl radicals. Dps proteins (DNA-binding proteins
    from starved cells) form a distinct class (the miniferritins) of
    iron-binding proteins within the ferritin superfamily. Bacillus anthracis
    encodes two Dps-like proteins, Dps1 and Dps2, the latter being one
    of the main iron-containing proteins in the cytoplasm. In this study,
    the function of Dps2 was characterized in vivo. A B. anthracis Delta
    dps2 mutant was constructed by double-crossover mutagenesis. The
    growth of the Delta dps2 mutant was unaffected by excess iron or
    iron-limiting conditions, indicating that the primary role of Dps2
    is not that of iron sequestration and storage. However, the Delta
    dps2 mutant was highly sensitive to H(2)O(2), and pretreatment of
    the cells with the iron chelator deferoxamine mesylate (DFM) significantly
    reduced its sensitivity to H(2)O(2) stress. In addition, the transcription
    of dps2 was upregulated by H(2)O(2) treatment and derepressed in
    a perR mutant, indicating that dps2 is a member of the regulon controlled
    by the PerR regulator. This indicates that the main role of Dps2
    is to protect cells from peroxide stress by inhibiting the iron-catalyzed
    production of OH.},
    doi = {10.1128/JB.06005-11},
    owner = {n8384838},
    pmid = {22155779},
    timestamp = {2013.05.24},
    url = {http://www.hubmed.org/display.cgi?uids=22155779}
    }
  • [DOI] W. Y. Tu, S. Pohl, J. Gray, N. J. Robinson, C R. Harwood, and K. J. Waldron, “Cellular iron distribution in bacillus anthracis,” J bacteriol, vol. 194, iss. 5, pp. 932-940, 2012.
    [Bibtex]
    @ARTICLE{Tu:2012:J-Bacteriol:22178968,
    author = {Tu, W Y and Pohl, S and Gray, J and Robinson, N J and Harwood, C
    R and Waldron, K J},
    title = {Cellular iron distribution in Bacillus anthracis},
    journal = {J Bacteriol},
    year = {2012},
    volume = {194},
    pages = {932-940},
    number = {5},
    month = {Mar},
    abstract = {Although successful iron acquisition by pathogens within a host is
    a prerequisite for the establishment of infection, surprisingly little
    is known about the intracellular distribution of iron within bacterial
    pathogens. We have used a combination of anaerobic native liquid
    chromatography, inductively coupled plasma mass spectrometry, principal-component
    analysis, and peptide mass fingerprinting to investigate the cytosolic
    iron distribution in the pathogen Bacillus anthracis. Our studies
    identified three of the major iron pools as being associated with
    the electron transfer protein ferredoxin, the miniferritin Dps2,
    and the superoxide dismutase (SOD) enzymes SodA1 and SodA2. Although
    both SOD isozymes were predicted to utilize manganese cofactors,
    quantification of the metal ions associated with SodA1 and SodA2
    in cell extracts established that SodA1 is associated with both manganese
    and iron, whereas SodA2 is bound exclusively to iron in vivo. These
    data were confirmed by in vitro assays using recombinant protein
    preparations, showing that SodA2 is active with an iron cofactor,
    while SodA1 is cambialistic, i.e., active with manganese or iron.
    Furthermore, we observe that B. anthracis cells exposed to superoxide
    stress increase their total iron content more than 2-fold over 60
    min, while the manganese and zinc contents are unaffected. Notably,
    the acquired iron is not localized to the three identified cytosolic
    iron pools.},
    doi = {10.1128/JB.06195-11},
    owner = {n8384838},
    pmid = {22178968},
    timestamp = {2013.05.24},
    url = {http://www.hubmed.org/display.cgi?uids=22178968}
    }
  • [DOI] J. M. Buescher, W. Liebermeister, M. Jules, M. Uhr, J. Muntel, E. Botella, B. Hessling, R. J. Kleijn, L. Le Chat, F. Lecointe, U. Mäder, P. Nicolas, S. Piersma, F. Rügheimer, D. Becher, P. Bessieres, E. Bidnenko, E. L. Denham, E. Dervyn, K. M. Devine, G. Doherty, S. Drulhe, L. Felicori, M. J. Fogg, A. Goelzer, A. Hansen, C. R. Harwood, M. Hecker, S. Hubner, C. Hultschig, H. Jarmer, E. Klipp, A. Leduc, P. Lewis, F. Molina, P. Noirot, S. Peres, N. Pigeonneau, S. Pohl, S. Rasmussen, B. Rinn, M. Schaffer, J. Schnidder, B. Schwikowski, J. M. Van Dijl, P. Veiga, S. Walsh, A. J. Wilkinson, J. Stelling, S. Aymerich, and U. Sauer, “Global network reorganization during dynamic adaptations of bacillus subtilis metabolism,” Science, vol. 335, iss. 6072, pp. 1099-1103, 2012.
    [Bibtex]
    @ARTICLE{Buescher:2012:Science:22383848,
    author = {Buescher, J M and Liebermeister, W and Jules, M and Uhr, M and Muntel,
    J and Botella, E and Hessling, B and Kleijn, R J and Le Chat, L and
    Lecointe, F and M{\"a}der, U and Nicolas, P and Piersma, S and R{\"u}gheimer,
    F and Becher, D and Bessieres, P and Bidnenko, E and Denham, E L
    and Dervyn, E and Devine, K M and Doherty, G and Drulhe, S and Felicori,
    L and Fogg, M J and Goelzer, A and Hansen, A and Harwood, C R and
    Hecker, M and Hubner, S and Hultschig, C and Jarmer, H and Klipp,
    E and Leduc, A and Lewis, P and Molina, F and Noirot, P and Peres,
    S and Pigeonneau, N and Pohl, S and Rasmussen, S and Rinn, B and
    Schaffer, M and Schnidder, J and Schwikowski, B and Van Dijl, J M
    and Veiga, P and Walsh, S and Wilkinson, A J and Stelling, J and
    Aymerich, S and Sauer, U},
    title = {Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism},
    journal = {Science},
    year = {2012},
    volume = {335},
    pages = {1099-1103},
    number = {6072},
    month = {Mar},
    abstract = {Adaptation of cells to environmental changes requires dynamic interactions
    between metabolic and regulatory networks, but studies typically
    address only one or a few layers of regulation. For nutritional shifts
    between two preferred carbon sources of Bacillus subtilis, we combined
    statistical and model-based data analyses of dynamic transcript,
    protein, and metabolite abundances and promoter activities. Adaptation
    to malate was rapid and primarily controlled posttranscriptionally
    compared with the slow, mainly transcriptionally controlled adaptation
    to glucose that entailed nearly half of the known transcription regulation
    network. Interactions across multiple levels of regulation were involved
    in adaptive changes that could also be achieved by controlling single
    genes. Our analysis suggests that global trade-offs and evolutionary
    constraints provide incentives to favor complex control programs.},
    doi = {10.1126/science.1206871},
    owner = {n8384838},
    pmid = {22383848},
    timestamp = {2013.05.24},
    url = {http://www.hubmed.org/display.cgi?uids=22383848}
    }
  • [DOI] P. Nicolas, U. Mäder, E. Dervyn, T. Rochat, A. Leduc, N. Pigeonneau, E. Bidnenko, E. Marchadier, M. Hoebeke, S. Aymerich, D. Becher, P. Bisicchia, E. Botella, O. Delumeau, G. Doherty, E. L. Denham, M. J. Fogg, V. Fromion, A. Goelzer, A. Hansen, E. Härtig, C. R. Harwood, G. Homuth, H. Jarmer, M. Jules, E. Klipp, L. Le Chat, F. Lecointe, P. Lewis, W. Liebermeister, A. March, R. A. Mars, P. Nannapaneni, D. Noone, S. Pohl, B. Rinn, F. Rügheimer, P. K. Sappa, F. Samson, M. Schaffer, B. Schwikowski, L. Steil, J. Stülke, T. Wiegert, K. M. Devine, A. J. Wilkinson, J. M. van Dijl, M. Hecker, U. Völker, P. Bessières, and P. Noirot, “Condition-dependent transcriptome reveals high-level regulatory architecture in bacillus subtilis,” Science, vol. 335, iss. 6072, pp. 1103-1106, 2012.
    [Bibtex]
    @ARTICLE{Nicolas:2012:Science:22383849,
    author = {Nicolas, P and M{\"a}der, U and Dervyn, E and Rochat, T and Leduc,
    A and Pigeonneau, N and Bidnenko, E and Marchadier, E and Hoebeke,
    M and Aymerich, S and Becher, D and Bisicchia, P and Botella, E and
    Delumeau, O and Doherty, G and Denham, E L and Fogg, M J and Fromion,
    V and Goelzer, A and Hansen, A and H{\"a}rtig, E and Harwood, C R
    and Homuth, G and Jarmer, H and Jules, M and Klipp, E and Le Chat,
    L and Lecointe, F and Lewis, P and Liebermeister, W and March, A
    and Mars, R A and Nannapaneni, P and Noone, D and Pohl, S and Rinn,
    B and R{\"u}gheimer, F and Sappa, P K and Samson, F and Schaffer,
    M and Schwikowski, B and Steil, L and St{\"u}lke, J and Wiegert,
    T and Devine, K M and Wilkinson, A J and van Dijl, J M and Hecker,
    M and V{\"o}lker, U and Bessi{\`e}res, P and Noirot, P},
    title = {Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis},
    journal = {Science},
    year = {2012},
    volume = {335},
    pages = {1103-1106},
    number = {6072},
    month = {Mar},
    abstract = {Bacteria adapt to environmental stimuli by adjusting their transcriptomes
    in a complex manner, the full potential of which has yet to be established
    for any individual bacterial species. Here, we report the transcriptomes
    of Bacillus subtilis exposed to a wide range of environmental and
    nutritional conditions that the organism might encounter in nature.
    We comprehensively mapped transcription units (TUs) and grouped 2935
    promoters into regulons controlled by various RNA polymerase sigma
    factors, accounting for \~66% of the observed variance in transcriptional
    activity. This global classification of promoters and detailed description
    of TUs revealed that a large proportion of the detected antisense
    RNAs arose from potentially spurious transcription initiation by
    alternative sigma factors and from imperfect control of transcription
    termination.},
    doi = {10.1126/science.1206848},
    owner = {n8384838},
    pmid = {22383849},
    timestamp = {2013.05.24},
    url = {http://www.hubmed.org/display.cgi?uids=22383849}
    }
  • G. Misirli, J. Hallinan, J. Weile, S. Cockell, and A. Wipat, “Bacillondex: data integration and visualisation for bacillus subtilis,” School of Computing Science, University of Newcastle upon Tyne. 2011.
    [Bibtex]
    @TECHREPORT{,
    author = {Misirli, G. and Hallinan, J. and Weile, J. and Cockell, S. and Wipat,
    A.},
    title = {BacillOndex: Data integration and visualisation for Bacillus subtilis},
    institution = {School of Computing Science, University of Newcastle upon Tyne.},
    year = {2011},
    journal = {Newcastle University Technical Report Series},
    owner = {n8384838},
    timestamp = {2013.05.07}
    }
  • M. Galdzicki, M. L. Wilson, C. A. Rodriguez, L. Adam, A. Adler, C. J. Anderson, J. Beal, D. Chandran, D. Densmore, O. Drory, D. Endy, J. H. Gennari, R. Grünberg, T. S. Ham, A. Kuchinsky, M. W. Lux, C. Madsen, G. Misirli, C. J. Myers, J. Peccoud, H. Plahar, M. R. Pocock, N. Roehner, T. Smith, G. Stan, A. Villalobos, A. Wipat, and H. M. Sauro, “Synthetic biology open language (sbol) version 1.0.0,” 2011.
    [Bibtex]
    @TECHREPORT{,
    author = {Galdzicki, Michal and Wilson, Mandy L. and Rodriguez, Cesar A. and
    Adam, Laura and Adler, Aaron and Anderson, J. Christopher and Beal,
    Jacob and Chandran, Deepak and Densmore, Douglas and Drory, Omri
    A. and Endy, Drew and Gennari, John H. and Gr\"{u}nberg, Raik and Ham,
    Timothy S. and Kuchinsky, Allan and Lux, Matthew W. and Madsen, Curtis
    and Misirli, Goksel and Myers, Chris J. and Peccoud, Jean and Plahar,
    Hector and Pocock, Matthew R. and Roehner, Nicholas and Smith, Trevor
    F. and Stan, Guy-Bart and Villalobos, Alan and Wipat, Anil and Sauro,
    Herbert M.},
    title = {Synthetic Biology Open Language (SBOL) Version 1.0.0},
    year = {2011},
    journal = {Newcastle University Technical Report Series},
    keywords = {SBOL},
    owner = {n8384838},
    timestamp = {2013.05.07}
    }
  • K. James, S. J. Lycett, A. Wipat, and J. S. Hallinan, “Multiple gold standards address bias in functional network integration,” 2011.
    [Bibtex]
    @TECHREPORT{,
    author = {James, K. and Lycett, S. J. and Wipat, A. and Hallinan, J. S.},
    title = {Multiple gold standards address bias in functional network integration},
    year = {2011},
    journal = {Newcastle University Technical Report Series},
    owner = {n8384838},
    timestamp = {2013.03.07},
    volume = {TR1302}
    }
  • [DOI] S. G. Addinall, E. M. Holstein, C. Lawless, M. Yu, K. Chapman, A. P. Banks, H. P. Ngo, L. Maringele, M. Taschuk, A. Young, A. Ciesiolka, A. L. Lister, A. Wipat, D. J. Wilkinson, and D. Lydall, “Quantitative fitness analysis shows that nmd proteins and many other protein complexes suppress or enhance distinct telomere cap defects,” Plos genet, vol. 7, iss. 4, 2011.
    [Bibtex]
    @ARTICLE{Addinall:2011:PLoS-Genet:21490951,
    author = {Addinall, S G and Holstein, E M and Lawless, C and Yu, M and Chapman,
    K and Banks, A P and Ngo, H P and Maringele, L and Taschuk, M and
    Young, A and Ciesiolka, A and Lister, A L and Wipat, A and Wilkinson,
    D J and Lydall, D},
    title = {Quantitative fitness analysis shows that NMD proteins and many other protein complexes suppress or enhance distinct telomere cap defects},
    journal = {PLoS Genet},
    year = {2011},
    volume = {7},
    number = {4},
    month = {Apr},
    abstract = {To better understand telomere biology in budding yeast, we have performed
    systematic suppressor/enhancer analyses on yeast strains containing
    a point mutation in the essential telomere capping gene CDC13 (cdc13-1)
    or containing a null mutation in the DNA damage response and telomere
    capping gene YKU70 (yku70Delta). We performed Quantitative Fitness
    Analysis (QFA) on thousands of yeast strains containing mutations
    affecting telomere-capping proteins in combination with a library
    of systematic gene deletion mutations. To perform QFA, we typically
    inoculate 384 separate cultures onto solid agar plates and monitor
    growth of each culture by photography over time. The data are fitted
    to a logistic population growth model; and growth parameters, such
    as maximum growth rate and maximum doubling potential, are deduced.
    QFA reveals that as many as 5% of systematic gene deletions, affecting
    numerous functional classes, strongly interact with telomere capping
    defects. We show that, while Cdc13 and Yku70 perform complementary
    roles in telomere capping, their genetic interaction profiles differ
    significantly. At least 19 different classes of functionally or physically
    related proteins can be identified as interacting with cdc13-1, yku70Delta,
    or both. Each specific genetic interaction informs the roles of individual
    gene products in telomere biology. One striking example is with genes
    of the nonsense-mediated RNA decay (NMD) pathway which, when disabled,
    suppress the conditional cdc13-1 mutation but enhance the null yku70Delta
    mutation. We show that the suppressing/enhancing role of the NMD
    pathway at uncapped telomeres is mediated through the levels of Stn1,
    an essential telomere capping protein, which interacts with Cdc13
    and recruitment of telomerase to telomeres. We show that increased
    Stn1 levels affect growth of cells with telomere capping defects
    due to cdc13-1 and yku70Delta. QFA is a sensitive, high-throughput
    method that will also be useful to understand other aspects of microbial
    cell biology.},
    doi = {10.1371/journal.pgen.1001362},
    owner = {n8384838},
    pmid = {21490951},
    timestamp = {2013.05.07},
    url = {http://www.hubmed.org/display.cgi?uids=21490951}
    }
  • [DOI] H. Y. Chang, C. Lawless, S. G. Addinall, S. Oexle, M. Taschuk, A. Wipat, D. J. Wilkinson, and D. Lydall, “Genome-wide analysis to identify pathways affecting telomere-initiated senescence in budding yeast,” G3 (bethesda), vol. 1, iss. 3, pp. 197-208, 2011.
    [Bibtex]
    @ARTICLE{Chang:2011:G3-Bethesda:22384331,
    author = {Chang, H Y and Lawless, C and Addinall, S G and Oexle, S and Taschuk,
    M and Wipat, A and Wilkinson, D J and Lydall, D},
    title = {Genome-wide analysis to identify pathways affecting telomere-initiated senescence in budding yeast},
    journal = {G3 (Bethesda)},
    year = {2011},
    volume = {1},
    pages = {197-208},
    number = {3},
    month = {Aug},
    abstract = {In telomerase-deficient yeast cells, like equivalent mammalian cells,
    telomeres shorten over many generations until a period of senescence/crisis
    is reached. After this, a small fraction of cells can escape senescence,
    principally using recombination-dependent mechanisms. To investigate
    the pathways that affect entry into and recovery from telomere-driven
    senescence, we combined a gene deletion disrupting telomerase (est1Delta)
    with the systematic yeast deletion collection and measured senescence
    characteristics in high-throughput assays. As expected, the vast
    majority of gene deletions showed no strong effects on entry into/exit
    from senescence. However, around 200 gene deletions behaving similarly
    to a rad52Deltaest1Delta archetype (rad52Delta affects homologous
    recombination) accelerated entry into senescence, and such cells
    often could not recover growth. A smaller number of strains similar
    to a rif1Deltaest1Delta archetype (rif1Delta affects proteins that
    bind telomeres) accelerated entry into senescence but also accelerated
    recovery from senescence. Our genome-wide analysis identifies genes
    that affect entry into and/or exit from telomere-initiated senescence
    and will be of interest to those studying telomere biology, replicative
    senescence, cancer, and ageing. Our dataset is complementary to other
    high-throughput studies relevant to telomere biology, genetic stability,
    and DNA damage responses.},
    doi = {10.1534/g3.111.000216},
    owner = {n8384838},
    pmid = {22384331},
    timestamp = {2013.05.07},
    url = {http://www.hubmed.org/display.cgi?uids=22384331}
    }
  • [DOI] L. K. Stadler, T. Hoffmann, D. C. Tomlinson, Q. Song, T. Lee, M. Busby, Y. Nyathi, E. Gendra, C. Tiede, K. Flanagan, S. J. Cockell, A. Wipat, C. Harwood, S. D. Wagner, M. A. Knowles, J. J. Davis, N. Keegan, and P. K. Ferrigno, “Structure-function studies of an engineered scaffold protein derived from stefin a. ii: development and applications of the sqt variant,” Protein eng des sel, vol. 24, iss. 9, pp. 751-763, 2011.
    [Bibtex]
    @ARTICLE{Stadler:2011:Protein-Eng-Des-Sel:21616931,
    author = {Stadler, L K and Hoffmann, T and Tomlinson, D C and Song, Q and Lee,
    T and Busby, M and Nyathi, Y and Gendra, E and Tiede, C and Flanagan,
    K and Cockell, S J and Wipat, A and Harwood, C and Wagner, S D and
    Knowles, M A and Davis, J J and Keegan, N and Ferrigno, P K},
    title = {Structure-function studies of an engineered scaffold protein derived from Stefin A. II: Development and applications of the SQT variant},
    journal = {Protein Eng Des Sel},
    year = {2011},
    volume = {24},
    pages = {751-763},
    number = {9},
    month = {Sep},
    abstract = {Constrained binding peptides (peptide aptamers) may serve as tools
    to explore protein conformations and disrupt protein-protein interactions.
    The quality of the protein scaffold, by which the binding peptide
    is constrained and presented, is of crucial importance. SQT (Stefin
    A Quadruple Mutant-Tracy) is our most recent development in the Stefin
    A-derived scaffold series. Stefin A naturally uses three surfaces
    to interact with its targets. SQT tolerates peptide insertions at
    all three positions. Peptide aptamers in the SQT scaffold can be
    expressed in bacterial, yeast and human cells, and displayed as a
    fusion to truncated pIII on phage. Peptides that bind to CDK2 can
    show improved binding in protein microarrays when presented by the
    SQT scaffold. Yeast two-hybrid libraries have been screened for binders
    to the POZ domain of BCL-6 and to a peptide derived from PBP2', specific
    to methicillin-resistant Staphylococcus aureus. Presentation of the
    Noxa BH3 helix by SQT allows specific interaction with Mcl-1 in human
    cells. Together, our results show that Stefin A-derived scaffolds,
    including SQT, can be used for a variety of applications in cellular
    and molecular biology. We will henceforth refer to Stefin A-derived
    engineered proteins as Scannins.},
    doi = {10.1093/protein/gzr019},
    owner = {n8384838},
    pmid = {21616931},
    timestamp = {2013.05.07},
    url = {http://www.hubmed.org/display.cgi?uids=21616931}
    }
  • [DOI] B. Kolluru, S. Nakjang, R. P. Hirt, A. Wipat, and S. Ananiadou, “Automatic extraction of microorganisms and their habitats from free text using text mining workflows,” J integr bioinform, vol. 8, iss. 2, pp. 184-184, 2011.
    [Bibtex]
    @ARTICLE{Kolluru:2011:J-Integr-Bioinform:21987583,
    author = {Kolluru, B and Nakjang, S and Hirt, R P and Wipat, A and Ananiadou,
    S},
    title = {Automatic extraction of microorganisms and their habitats from free text using text mining workflows},
    journal = {J Integr Bioinform},
    year = {2011},
    volume = {8},
    pages = {184-184},
    number = {2},
    abstract = {In this paper we illustrate the usage of text mining workflows to
    automatically extract instances of microorganisms and their habitats
    from free text; these entries can then be curated and added to different
    databases. To this end, we use a Conditional Random Field (CRF) based
    classifier, as part of the workflows, to extract the mention of microorganisms,
    habitats and the inter-relation between organisms and their habitats.
    Results indicate a good performance for extraction of microorganisms
    and the relation extraction aspects of the task (with a precision
    of over 80%), while habitat recognition is only moderate (a precision
    of about 65%). We also conjecture that pdf-to-text conversion can
    be quite noisy and this implicitly affects any sentence-based relation
    extraction algorithms.},
    doi = {10.2390/biecoll-jib-2011-184},
    owner = {n8384838},
    pmid = {21987583},
    timestamp = {2013.05.07},
    url = {http://www.hubmed.org/display.cgi?uids=21987583}
    }
  • [DOI] J. Weile, M. Pocock, S. J. Cockell, P. Lord, J M. Dewar, E. M. Holstein, D. Wilkinson, D. Lydall, J. Hallinan, and A. Wipat, “Customizable views on semantically integrated networks for systems biology,” Bioinformatics, vol. 27, iss. 9, pp. 1299-1306, 2011.
    [Bibtex]
    @ARTICLE{Weile:2011:Bioinformatics:21414991,
    author = {Weile, J and Pocock, M and Cockell, S J and Lord, P and Dewar, J
    M and Holstein, E M and Wilkinson, D and Lydall, D and Hallinan,
    J and Wipat, A},
    title = {Customizable views on semantically integrated networks for systems biology},
    journal = {Bioinformatics},
    year = {2011},
    volume = {27},
    pages = {1299-1306},
    number = {9},
    month = {May},
    abstract = {The rise of high-throughput technologies in the post-genomic era has
    led to the production of large amounts of biological data. Many of
    these datasets are freely available on the Internet. Making optimal
    use of these data is a significant challenge for bioinformaticians.
    Various strategies for integrating data have been proposed to address
    this challenge. One of the most promising approaches is the development
    of semantically rich integrated datasets. Although well suited to
    computational manipulation, such integrated datasets are typically
    too large and complex for easy visualization and interactive exploration.We
    have created an integrated dataset for Saccharomyces cerevisiae using
    the semantic data integration tool Ondex, and have developed a view-based
    visualization technique that allows for concise graphical representations
    of the integrated data. The technique was implemented in a plug-in
    for Cytoscape, called OndexView. We used OndexView to investigate
    telomere maintenance in S. cerevisiae.The Ondex yeast dataset and
    the OndexView plug-in for Cytoscape are accessible at http://bsu.ncl.ac.uk/ondexview.},
    doi = {10.1093/bioinformatics/btr134},
    owner = {n8384838},
    pmid = {21414991},
    timestamp = {2013.05.08},
    url = {http://www.hubmed.org/display.cgi?uids=21414991}
    }
  • [DOI] G. Misirli, J. S. Hallinan, T. Yu, J. R. Lawson, S. M. Wimalaratne, M. T. Cooling, and A. Wipat, “Model annotation for synthetic biology: automating model to nucleotide sequence conversion,” Bioinformatics, vol. 27, iss. 7, pp. 973-979, 2011.
    [Bibtex]
    @ARTICLE{Misirli:2011:Bioinformatics:21296753,
    author = {Misirli, G and Hallinan, J S and Yu, T and Lawson, J R and Wimalaratne,
    S M and Cooling, M T and Wipat, A},
    title = {Model annotation for synthetic biology: automating model to nucleotide sequence conversion},
    journal = {Bioinformatics},
    year = {2011},
    volume = {27},
    pages = {973-979},
    number = {7},
    month = {Apr},
    abstract = {The need for the automated computational design of genetic circuits
    is becoming increasingly apparent with the advent of ever more complex
    and ambitious synthetic biology projects. Currently, most circuits
    are designed through the assembly of models of individual parts such
    as promoters, ribosome binding sites and coding sequences. These
    low level models are combined to produce a dynamic model of a larger
    device that exhibits a desired behaviour. The larger model then acts
    as a blueprint for physical implementation at the DNA level. However,
    the conversion of models of complex genetic circuits into DNA sequences
    is a non-trivial undertaking due to the complexity of mapping the
    model parts to their physical manifestation. Automating this process
    is further hampered by the lack of computationally tractable information
    in most models.We describe a method for automatically generating
    DNA sequences from dynamic models implemented in CellML and Systems
    Biology Markup Language (SBML). We also identify the metadata needed
    to annotate models to facilitate automated conversion, and propose
    and demonstrate a method for the markup of these models using RDF.
    Our algorithm has been implemented in a software tool called MoSeC.The
    software is available from the authors' web site http://research.ncl.ac.uk/synthetic\_biology/downloads.html.},
    doi = {10.1093/bioinformatics/btr048},
    owner = {n8384838},
    pmid = {21296753},
    timestamp = {2013.05.08},
    url = {http://www.hubmed.org/display.cgi?uids=21296753}
    }
  • [DOI] S. C. Weatherhead, P. M. Farr, D. Jamieson, J. S. Hallinan, J. J. Lloyd, A. Wipat, and N. J. Reynolds, “Keratinocyte apoptosis in epidermal remodeling and clearance of psoriasis induced by uv radiation,” J invest dermatol, vol. 131, iss. 9, pp. 1916-1926, 2011.
    [Bibtex]
    @ARTICLE{Weatherhead:2011:J-Invest-Dermatol:21614017,
    author = {Weatherhead, S C and Farr, P M and Jamieson, D and Hallinan, J S
    and Lloyd, J J and Wipat, A and Reynolds, N J},
    title = {Keratinocyte apoptosis in epidermal remodeling and clearance of psoriasis induced by UV radiation},
    journal = {J Invest Dermatol},
    year = {2011},
    volume = {131},
    pages = {1916-1926},
    number = {9},
    month = {Sep},
    abstract = {Psoriasis is a common chronic skin disorder, but the mechanisms involved
    in the resolution and clearance of plaques remain poorly defined.
    We investigated the mechanism of action of UVB, which is highly effective
    in clearing psoriasis and inducing remission, and tested the hypothesis
    that apoptosis is a key mechanism. To distinguish bystander effects,
    equal erythemal doses of two UVB wavelengths were compared following
    in vivo irradiation of psoriatic plaques; one is clinically effective
    (311 nm) and one has no therapeutic effect on psoriasis (290 nm).
    Only 311 nm UVB induced significant apoptosis in lesional epidermis,
    and most apoptotic cells were keratinocytes. To determine clinical
    relevance, we created a computational model of psoriatic epidermis.
    Modeling predicted apoptosis would occur in both stem and transit-amplifying
    cells to account for plaque clearance; this was confirmed and quantified
    experimentally. The median rate of keratinocyte apoptosis from onset
    to cell death was 20 minutes. These data were fed back into the
    model and demonstrated that the observed level of keratinocyte apoptosis
    was sufficient to explain UVB-induced plaque resolution. Our human
    studies combined with a systems biology approach demonstrate that
    keratinocyte apoptosis is a key mechanism in psoriatic plaques clearance,
    providing the basis for future molecular investigation and therapeutic
    development.},
    doi = {10.1038/jid.2011.134},
    owner = {n8384838},
    pmid = {21614017},
    timestamp = {2013.05.08},
    url = {http://www.hubmed.org/display.cgi?uids=21614017}
    }
  • [DOI] J. S. Hallinan, K. James, and A. Wipat, “Network approaches to the functional analysis of microbial proteins,” Adv microb physiol, vol. 59, pp. 101-133, 2011.
    [Bibtex]
    @ARTICLE{Hallinan:2011:Adv-Microb-Physiol:22114841,
    author = {Hallinan, J S and James, K and Wipat, A},
    title = {Network approaches to the functional analysis of microbial proteins},
    journal = {Adv Microb Physiol},
    year = {2011},
    volume = {59},
    pages = {101-133},
    abstract = {Large amounts of detailed biological data have been generated over
    the past few decades. Much of these data is freely available in over
    1000 online databases; an enticing, but frustrating resource for
    microbiologists interested in a systems-level view of the structure
    and function of microbial cells. The frustration engendered by the
    need to trawl manually through hundreds of databases in order to
    accumulate information about a gene, protein, pathway, or organism
    of interest can be alleviated by the use of computational data integration
    to generated network views of the system of interest. Biological
    networks can be constructed from a single type of data, such as protein-protein
    binding information, or from data generated by multiple experimental
    approaches. In an integrated network, nodes usually represent genes
    or gene products, while edges represent some form of interaction
    between the nodes. Edges between nodes may be weighted to represent
    the probability that the edge exists in vivo. Networks may also be
    enriched with ontological annotations, facilitating both visual browsing
    and computational analysis via web service interfaces. In this review,
    we describe the construction, analysis of both single-data source
    and integrated networks, and their application to the inference of
    protein function in microbes.},
    doi = {10.1016/B978-0-12-387661-4.00005-7},
    owner = {n8384838},
    pmid = {22114841},
    timestamp = {2013.05.09},
    url = {http://www.hubmed.org/display.cgi?uids=22114841}
    }
  • [DOI] D. Waltemath, N. Swainston, A. Lister, F. Bergmann, R. Henkel, S. Hoops, M. Hucka, N. Juty, S. Keating, C. Knuepfer, F. Krause, C. Laibe, W. Liebermeister, C. Lloyd, G. Misirli, M. Schulz, M. Taschuk, and N. Le Novère, “SBML level 3 package proposal: annotation,” Nature precedings, iss. 713, 2011.
    [Bibtex]
    @ARTICLE{citeulike:9274960,
    author = {Waltemath, Dagmar and Swainston, Neil and Lister, Allyson and Bergmann,
    Frank and Henkel, Ron and Hoops, Stefan and Hucka, Michael and Juty,
    Nick and Keating, Sarah and Knuepfer, Christian and Krause, Falko
    and Laibe, Camille and Liebermeister, Wolfram and Lloyd, Catherine
    and Misirli, Goksel and Schulz, Marvin and Taschuk, Morgan and Le
    Nov\`{e}re, Nicolas},
    title = {{SBML} Level 3 Package Proposal: Annotation},
    journal = {Nature Precedings},
    year = {2011},
    number = {713},
    month = jan,
    abstract = {The annotation of Systems Biology Markup Language ({SBML}) models
    with semantic terms has been supported for a number of years. The
    prevalence of such annotated models is growing, with repositories
    such as Biomodels.net and an increasing number of software tools
    supporting and encouraging their use and {development.With} the increasing
    use of semantic annotations in the context of systems biology modeling
    has come the realization that the current Core {SBML} specification
    defining their use contains limitations that reduce the scope of
    metadata that can be captured in such {models.SBML} Level 3 provides
    the facility to propose and develop optional extensions to the Core
    specification. One such extension is described here, with an initial
    proposal of an Annotation {package.This} proposal extends the current
    Core annotation specification to provide support for a richer set
    of semantic annotations while adhering more closely to the existing
    specification of Resource Description Framework ({RDF}).},
    citeulike-article-id = {9274960},
    citeulike-linkout-0 = {http://dx.doi.org/10.1038/npre.2011.5610.1},
    citeulike-linkout-1 = {http://precedings.nature.com/documents/5610/version/1},
    day = {31},
    doi = {10.1038/npre.2011.5610.1},
    issn = {1756-0357},
    keywords = {sbml},
    owner = {n8384838},
    posted-at = {2011-05-11 09:17:37},
    priority = {2},
    publisher = {Nature Publishing Group},
    timestamp = {2013.05.09},
    url = {http://dx.doi.org/10.1038/npre.2011.5610.1}
    }
  • [DOI] M. Courtot, N. Juty, C. Knupfer, D. Waltemath, A. Zhukova, A. Drager, M. Dumontier, A. Finney, M. Golebiewski, J. Hastings, S. Hoops, S. Keating, D. B. Kell, S. Kerrien, J. Lawson, A. Lister, J. Lu, R. Machne, P. Mendes, M. Pocock, N. Rodriguez, A. Villeger, D. J. Wilkinson, S. Wimalaratne, C. Laibe, M. Hucka, and N. Le Novere, “Controlled vocabularies and semantics in systems biology,” Molecular systems biology, vol. 7, iss. 1, 2011.
    [Bibtex]
    @ARTICLE{citeulike:9946377,
    author = {Courtot, Melanie and Juty, Nick and Knupfer, Christian and Waltemath,
    Dagmar and Zhukova, Anna and Drager, Andreas and Dumontier, Michel
    and Finney, Andrew and Golebiewski, Martin and Hastings, Janna and
    Hoops, Stefan and Keating, Sarah and Kell, Douglas B. and Kerrien,
    Samuel and Lawson, James and Lister, Allyson and Lu, James and Machne,
    Rainer and Mendes, Pedro and Pocock, Matthew and Rodriguez, Nicolas
    and Villeger, Alice and Wilkinson, Darren J. and Wimalaratne, Sarala
    and Laibe, Camille and Hucka, Michael and Le Novere, Nicolas},
    title = {Controlled vocabularies and semantics in systems biology},
    journal = {Molecular Systems Biology},
    year = {2011},
    volume = {7},
    number = {1},
    month = oct,
    abstract = {The use of computational modeling to describe and analyze biological
    systems is at the heart of systems biology. Model structures, simulation
    descriptions and numerical results can be encoded in structured formats,
    but there is an increasing need to provide an additional semantic
    layer. Semantic information adds meaning to components of structured
    descriptions to help identify and interpret them unambiguously. Ontologies
    are one of the tools frequently used for this purpose. We describe
    here three ontologies created specifically to address the needs of
    the systems biology community. The Systems Biology Ontology ({SBO})
    provides semantic information about the model components. The Kinetic
    Simulation Algorithm Ontology ({KiSAO}) supplies information about
    existing algorithms available for the simulation of systems biology
    models, their characterization and interrelationships. The Terminology
    for the Description of Dynamics ({TEDDY}) categorizes dynamical features
    of the simulation results and general systems behavior. The provision
    of semantic information extends a model's longevity and facilitates
    its reuse. It provides useful insight into the biology of modeled
    processes, and may be used to make informed decisions on subsequent
    simulation experiments.},
    citeulike-article-id = {9946377},
    citeulike-linkout-0 = {http://dx.doi.org/10.1038/msb.2011.77},
    citeulike-linkout-1 = {http://dx.doi.org/10.1038/msb201177},
    citeulike-linkout-2 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3261705/},
    citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/22027554},
    citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=22027554},
    day = {25},
    doi = {10.1038/msb.2011.77},
    issn = {1744-4292},
    keywords = {ontologies, semantics, systems-biology},
    owner = {n8384838},
    pmcid = {PMC3261705},
    pmid = {22027554},
    posted-at = {2011-10-26 09:42:09},
    priority = {0},
    publisher = {Nature Publishing Group},
    timestamp = {2013.05.09},
    url = {http://dx.doi.org/10.1038/msb.2011.77}
    }
  • [DOI] S. Pohl, W. Y. Tu, P. D. Aldridge, C. Gillespie, H. Hahne, U. Mäder, T. D. Read, and C. R. Harwood, “Combined proteomic and transcriptomic analysis of the response of bacillus anthracis to oxidative stress,” Proteomics, vol. 11, iss. 15, pp. 3036-3055, 2011.
    [Bibtex]
    @ARTICLE{Pohl:2011:Proteomics:21726052,
    author = {Pohl, S and Tu, W Y and Aldridge, P D and Gillespie, C and Hahne,
    H and M{\"a}der, U and Read, T D and Harwood, C R},
    title = {Combined proteomic and transcriptomic analysis of the response of Bacillus anthracis to oxidative stress},
    journal = {Proteomics},
    year = {2011},
    volume = {11},
    pages = {3036-3055},
    number = {15},
    month = {Aug},
    abstract = {The endospore-forming Gram-positive pathogen Bacillus anthracis is
    responsible for the usually fatal disease, inhalational anthrax.
    The success of this pathogen is dependent on its ability to subvert
    elements of the innate immune system of its animal hosts. B. anthracis
    spores, which are the main infective agent, are engulfed and germinate
    in patrolling alveolar macrophages. In order for the infection to
    progress, the resulting vegetative cells must resist the antimicrobial
    oxidative burst mounted by the host NADPH oxidase complex. The response
    of B. anthracis to this and other macrophage-related stresses is
    therefore of major importance to the success of this pathogen, and
    consequently we have analysed the superoxide and peroxide stress
    stimulons of B. anthracis strain UM23C1-2 by means of a combined
    transcriptomics and proteomics approach. The results show distinct
    patterns of expression in response to paraquat (endogenous superoxide)
    and hydrogen peroxide stress. While the main response to paraquat
    is the induction of iron uptake pathways, the response to peroxide
    predominantly involves the induction of protection and repair mechanisms.
    Comparisons between the responses of B. anthracis and related soil
    bacterium, B. subtilis, reveal differences that are likely to be
    relevant to their respective habitats.},
    doi = {10.1002/pmic.201100085},
    owner = {n8384838},
    pmid = {21726052},
    timestamp = {2013.05.24},
    url = {http://www.hubmed.org/display.cgi?uids=21726052}
    }
  • [DOI] S. J. Cockell, J. Weile, P. Lord, C. Wipat, D. Andriychenko, M. Pocock, D. Wilkinson, M. Young, and A. Wipat, “An integrated dataset for in silico drug discovery,” J integr bioinform, vol. 7, iss. 3, 2010.
    [Bibtex]
    @ARTICLE{Cockell:2010:J-Integr-Bioinform:20375448,
    author = {Cockell, S J and Weile, J and Lord, P and Wipat, C and Andriychenko,
    D and Pocock, M and Wilkinson, D and Young, M and Wipat, A},
    title = {An integrated dataset for in silico drug discovery},
    journal = {J Integr Bioinform},
    year = {2010},
    volume = {7},
    number = {3},
    abstract = {Drug development is expensive and prone to failure. It is potentially
    much less risky and expensive to reuse a drug developed for one condition
    for treating a second disease, than it is to develop an entirely
    new compound. Systematic approaches to drug repositioning are needed
    to increase throughput and find candidates more reliably. Here we
    address this need with an integrated systems biology dataset, developed
    using the Ondex data integration platform, for the in silico discovery
    of new drug repositioning candidates. We demonstrate that the information
    in this dataset allows known repositioning examples to be discovered.
    We also propose a means of automating the search for new treatment
    indications of existing compounds.},
    doi = {10.2390/biecoll-jib-2010-116},
    owner = {n8384838},
    pmid = {20375448},
    timestamp = {2013.05.07},
    url = {http://www.hubmed.org/display.cgi?uids=20375448}
    }
  • [DOI] A. L. Lister, P. Lord, M. Pocock, and A. Wipat, “Annotation of sbml models through rule-based semantic integration,” J biomed semantics, vol. 1 Suppl 1, 2010.
    [Bibtex]
    @ARTICLE{Lister:2010:J-Biomed-Semantics:20626923,
    author = {Lister, A L and Lord, P and Pocock, M and Wipat, A},
    title = {Annotation of SBML models through rule-based semantic integration},
    journal = {J Biomed Semantics},
    year = {2010},
    volume = {1 Suppl 1},
    abstract = {The creation of accurate quantitative Systems Biology Markup Language
    (SBML) models is a time-intensive, manual process often complicated
    by the many data sources and formats required to annotate even a
    small and well-scoped model. Ideally, the retrieval and integration
    of biological knowledge for model annotation should be performed
    quickly, precisely, and with a minimum of manual effort.Here we present
    rule-based mediation, a method of semantic data integration applied
    to systems biology model annotation. The heterogeneous data sources
    are first syntactically converted into ontologies, which are then
    aligned to a small domain ontology by applying a rule base. We demonstrate
    proof-of-principle of this application of rule-based mediation using
    off-the-shelf semantic web technology through two use cases for SBML
    model annotation. Existing tools and technology provide a framework
    around which the system is built, reducing development time and increasing
    usability.Integrating resources in this way accommodates multiple
    formats with different semantics, and provides richly-modelled biological
    knowledge suitable for annotation of SBML models. This initial work
    establishes the feasibility of rule-based mediation as part of an
    automated SBML model annotation system.Detailed information on the
    project files as well as further information on and comparisons with
    similar projects is available from the project page at http://cisban-silico.cs.ncl.ac.uk/RBM/.},
    doi = {10.1186/2041-1480-1-S1-S3},
    owner = {n8384838},
    pmid = {20626923},
    timestamp = {2013.05.07},
    url = {http://www.hubmed.org/display.cgi?uids=20626923}
    }
  • [DOI] F. Gibson, C. Hoogland, S. Martinez-Bartolomé, J. A. Medina-Aunon, J. P. Albar, G. Babnigg, A. Wipat, H. Hermjakob, J. S. Almeida, R. Stanislaus, N. W. Paton, and A. R. Jones, “The gel electrophoresis markup language (gelml) from the proteomics standards initiative,” Proteomics, vol. 10, iss. 17, pp. 3073-3081, 2010.
    [Bibtex]
    @ARTICLE{Gibson:2010:Proteomics:20677327,
    author = {Gibson, F and Hoogland, C and Martinez-Bartolom{\'e}, S and Medina-Aunon,
    J A and Albar, J P and Babnigg, G and Wipat, A and Hermjakob, H and
    Almeida, J S and Stanislaus, R and Paton, N W and Jones, A R},
    title = {The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative},
    journal = {Proteomics},
    year = {2010},
    volume = {10},
    pages = {3073-3081},
    number = {17},
    month = {Sep},
    abstract = {The Human Proteome Organisation's Proteomics Standards Initiative
    has developed the GelML (gel electrophoresis markup language) data
    exchange format for representing gel electrophoresis experiments
    performed in proteomics investigations. The format closely follows
    the reporting guidelines for gel electrophoresis, which are part
    of the Minimum Information About a Proteomics Experiment (MIAPE)
    set of modules. GelML supports the capture of metadata (such as experimental
    protocols) and data (such as gel images) resulting from gel electrophoresis
    so that laboratories can be compliant with the MIAPE Gel Electrophoresis
    guidelines, while allowing such data sets to be exchanged or downloaded
    from public repositories. The format is sufficiently flexible to
    capture data from a broad range of experimental processes, and complements
    other PSI formats for MS data and the results of protein and peptide
    identifications to capture entire gel-based proteome workflows. GelML
    has resulted from the open standardisation process of PSI consisting
    of both public consultation and anonymous review of the specifications.},
    doi = {10.1002/pmic.201000120},
    owner = {n8384838},
    pmid = {20677327},
    timestamp = {2013.05.07},
    url = {http://www.hubmed.org/display.cgi?uids=20677327}
    }
  • [DOI] G. Fuellen, J. Adjaye, A. de Grey, G. Lepperdinger, J. P. de Magalhães, J. Sühnel, and A. Wipat, “Bioinformatics in aging research: a workshop report,” Rejuvenation res, vol. 13, iss. 6, pp. 763-767, 2010.
    [Bibtex]
    @ARTICLE{Fuellen:2010:Rejuvenation-Res:21204651,
    author = {Fuellen, G and Adjaye, J and de Grey, A and Lepperdinger, G and de
    Magalh{\~a}es, J P and S{\"u}hnel, J and Wipat, A},
    title = {Bioinformatics in aging research: a workshop report},
    journal = {Rejuvenation Res},
    year = {2010},
    volume = {13},
    pages = {763-767},
    number = {6},
    month = {Dec},
    abstract = {Evidence is accumulating that the first genuine antiaging interventions
    (e.g., approved pharmaceutical, nutriceutical, and stem-cell-based
    therapies) will become available within the next decades. Model organism
    data, next-generation sequencing, and further advances call for sophisticated
    large-scale data analysis. To present the state-of-the art and to
    talk about upcoming tasks and challenges in the bioinformatics and
    systems biology of aging-related data, a workshop on Bioinformatics
    in Ageing Research convened leading experts from Europe on May 4-5,
    2010, in Rostock/Warnem\{\"u\}nde. This meeting report summarizes
    talks and gives some outlook into future developments.},
    doi = {10.1089/rej.2010.1125},
    owner = {n8384838},
    pmid = {21204651},
    timestamp = {2013.05.07},
    url = {http://www.hubmed.org/display.cgi?uids=21204651}
    }
  • [DOI] M. T. Cooling, V. Rouilly, G. Misirli, J. Lawson, T. Yu, J. Hallinan, and A. Wipat, “Standard virtual biological parts: a repository of modular modeling components for synthetic biology,” Bioinformatics, vol. 26, iss. 7, pp. 925-931, 2010.
    [Bibtex]
    @ARTICLE{Cooling:2010:Bioinformatics:20160009,
    author = {Cooling, M T and Rouilly, V and Misirli, G and Lawson, J and Yu,
    T and Hallinan, J and Wipat, A},
    title = {Standard virtual biological parts: a repository of modular modeling components for synthetic biology},
    journal = {Bioinformatics},
    year = {2010},
    volume = {26},
    pages = {925-931},
    number = {7},
    month = {Apr},
    abstract = {MOTIVATION: Fabrication of synthetic biological systems is greatly
    enhanced by incorporating engineering design principles and techniques
    such as computer-aided design. To this end, the ongoing standardization
    of biological parts presents an opportunity to develop libraries
    of standard virtual parts in the form of mathematical models that
    can be combined to inform system design. RESULTS: We present an online
    Repository, populated with a collection of standardized models that
    can readily be recombined to model different biological systems using
    the inherent modularity support of the CellML 1.1 model exchange
    format. The applicability of this approach is demonstrated by modeling
    gold-medal winning iGEM machines. Availability and Implementation:
    The Repository is available online as part of http://models.cellml.org.
    We hope to stimulate the worldwide community to reuse and extend
    the models therein, and contribute to the Repository of Standard
    Virtual Parts thus founded. Systems Model architecture information
    for the Systems Model described here, along with an additional example
    and a tutorial, is also available as Supplementary information. The
    example Systems Model from this manuscript can be found at http://models.cellml.org/workspace/bugbuster.
    The Template models used in the example can be found at http://models.cellml.org/workspace/SVP\_Templates200906.},
    doi = {10.1093/bioinformatics/btq063},
    owner = {n8384838},
    pmid = {20160009},
    timestamp = {2013.05.08},
    url = {http://www.hubmed.org/display.cgi?uids=20160009}
    }
  • [DOI] J. F. Passos, G. Nelson, C. Wang, T. Richter, C. Simillion, C. J. Proctor, S. Miwa, S. Olijslagers, J. Hallinan, A. Wipat, G. Saretzki, K. L. Rudolph, T. B. Kirkwood, and T. von Zglinicki, “Feedback between p21 and reactive oxygen production is necessary for cell senescence,” Mol syst biol, vol. 6, pp. 347-347, 2010.
    [Bibtex]
    @ARTICLE{Passos:2010:Mol-Syst-Biol:20160708,
    author = {Passos, J F and Nelson, G and Wang, C and Richter, T and Simillion,
    C and Proctor, C J and Miwa, S and Olijslagers, S and Hallinan, J
    and Wipat, A and Saretzki, G and Rudolph, K L and Kirkwood, T B and
    von Zglinicki, T},
    title = {Feedback between p21 and reactive oxygen production is necessary for cell senescence},
    journal = {Mol Syst Biol},
    year = {2010},
    volume = {6},
    pages = {347-347},
    abstract = {Cellular senescence--the permanent arrest of cycling in normally proliferating
    cells such as fibroblasts--contributes both to age-related loss of
    mammalian tissue homeostasis and acts as a tumour suppressor mechanism.
    The pathways leading to establishment of senescence are proving to
    be more complex than was previously envisaged. Combining in-silico
    interactome analysis and functional target gene inhibition, stochastic
    modelling and live cell microscopy, we show here that there exists
    a dynamic feedback loop that is triggered by a DNA damage response
    (DDR) and, which after a delay of several days, locks the cell into
    an actively maintained state of 'deep' cellular senescence. The essential
    feature of the loop is that long-term activation of the checkpoint
    gene CDKN1A (p21) induces mitochondrial dysfunction and production
    of reactive oxygen species (ROS) through serial signalling through
    GADD45-MAPK14(p38MAPK)-GRB2-TGFBR2-TGFbeta. These ROS in turn replenish
    short-lived DNA damage foci and maintain an ongoing DDR. We show
    that this loop is both necessary and sufficient for the stability
    of growth arrest during the establishment of the senescent phenotype.},
    doi = {10.1038/msb.2010.5},
    owner = {n8384838},
    pmid = {20160708},
    timestamp = {2013.05.08},
    url = {http://www.hubmed.org/display.cgi?uids=20160708}
    }
  • [DOI] J. S. Hallinan, G. Misirli, and A. Wipat, “Evolutionary computation for the design of a stochastic switch for synthetic genetic circuits,” Conf proc ieee eng med biol soc, vol. 2010, pp. 768-774, 2010.
    [Bibtex]
    @ARTICLE{Hallinan:2010:Conf-Proc-IEEE-Eng-Med-Biol-Soc:21095906,
    author = {Hallinan, J S and Misirli, G and Wipat, A},
    title = {Evolutionary computation for the design of a stochastic switch for synthetic genetic circuits},
    journal = {Conf Proc IEEE Eng Med Biol Soc},
    year = {2010},
    volume = {2010},
    pages = {768-774},
    abstract = {Biological systems are inherently stochastic, a fact which is often
    ignored when simulating genetic circuits. Synthetic biology aims
    to design genetic circuits de novo, and cannot therefore afford to
    ignore the effects of stochastic behavior. Since computational design
    tools will be essential for large-scale synthetic biology, it is
    important to develop an understanding of the role of stochasticity
    in molecular biology, and incorporate this understanding into computational
    tools for genetic circuit design. We report upon an investigation
    into the combination of evolutionary algorithms and stochastic simulation
    for genetic circuit design, to design regulatory systems based on
    the Bacillus subtilis sin operon.},
    doi = {10.1109/IEMBS.2010.5626353},
    owner = {n8384838},
    pmid = {21095906},
    timestamp = {2013.05.08},
    url = {http://www.hubmed.org/display.cgi?uids=21095906}
    }
  • A. L. Lister, “Semantic integration in the life sciences,” Ontogenesis, 2010.
    [Bibtex]
    @ARTICLE{citeulike:9635823,
    author = {Lister, Allyson L.},
    title = {Semantic Integration in the Life Sciences},
    journal = {Ontogenesis},
    year = {2010},
    month = jan,
    abstract = {There are a number of limitations in data integration: data sets are
    often noisy, incomplete, of varying levels of granularity and highly
    changeable. Every time one of the underlying databases changes, the
    integrated database needs to be updated, and if there are any format
    changes, the parsers that convert to the unified format need to be
    modified as well. This �� {character}database churn�� {character}
    was identified by Stein to be a major limiting factor in establishing
    a successful data warehouse (Stein 2003).
    Ruttenberg et al. see the Semantic Web, of which both {OWL} and {RDF}
    are components, as having the potential to aid translational and
    systems biology research; indeed, any life science field where there
    are large amounts of data in distributed, disparate formats should
    benefit from Semantic Web technologies (Ruttenberg et al. 2007).},
    citeulike-article-id = {9635823},
    citeulike-linkout-0 = {http://ontogenesis.knowledgeblog.org/126},
    day = {21},
    owner = {n8384838},
    posted-at = {2011-08-09 10:52:38},
    priority = {0},
    timestamp = {2013.05.09},
    url = {http://ontogenesis.knowledgeblog.org/126}
    }
  • [DOI] A. L. Lister, P. Lord, M. Pocock, and A. Wipat, “Annotation of SBML models through rule-based semantic integration.,” Journal of biomedical semantics, vol. 1 Suppl 1, iss. Suppl 1, p. S3+, 2010.
    [Bibtex]
    @ARTICLE{citeulike:7351534,
    author = {Lister, Allyson L. and Lord, Phillip and Pocock, Matthew and Wipat,
    Anil},
    title = {Annotation of {SBML} models through rule-based semantic integration.},
    journal = {Journal of biomedical semantics},
    year = {2010},
    volume = {1 Suppl 1},
    pages = {S3+},
    number = {Suppl 1},
    abstract = {{ABSTRACT} : {BACKGROUND} : The creation of accurate quantitative
    Systems Biology Markup Language ({SBML}) models is a time-intensive,
    manual process often complicated by the many data sources and formats
    required to annotate even a small and well-scoped model. Ideally,
    the retrieval and integration of biological knowledge for model annotation
    should be performed quickly, precisely, and with a minimum of manual
    effort. {RESULTS} : Here we present rule-based mediation, a method
    of semantic data integration applied to systems biology model annotation.
    The heterogeneous data sources are first syntactically converted
    into ontologies, which are then aligned to a small domain ontology
    by applying a rule base. We demonstrate proof-of-principle of this
    application of rule-based mediation using off-the-shelf semantic
    web technology through two use cases for {SBML} model annotation.
    Existing tools and technology provide a framework around which the
    system is built, reducing development time and increasing usability.
    {CONCLUSIONS} : Integrating resources in this way accommodates multiple
    formats with different semantics, and provides richly-modelled biological
    knowledge suitable for annotation of {SBML} models. This initial
    work establishes the feasibility of rule-based mediation as part
    of an automated {SBML} model annotation system. {AVAILABILITY} :
    Detailed information on the project files as well as further information
    on and comparisons with similar projects is available from the project
    page at {http://cisban-silico.cs.ncl.ac.uk/RBM}/.},
    citeulike-article-id = {7351534},
    citeulike-linkout-0 = {http://dx.doi.org/10.1186/2041-1480-1-s1-s3},
    citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/20626923},
    citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=20626923},
    doi = {10.1186/2041-1480-1-s1-s3},
    issn = {2041-1480},
    keywords = {ontologies, owl, semantic-data-integration, systems-biology},
    owner = {n8384838},
    pmid = {20626923},
    posted-at = {2010-07-21 13:53:43},
    priority = {0},
    timestamp = {2013.05.09},
    url = {http://dx.doi.org/10.1186/2041-1480-1-s1-s3}
    }
  • [DOI] A. L. Lister, R. S. Datta, O. Hofmann, R. Krause, M. Kuhn, B. Roth, and R. Schneider, “Live coverage of scientific conferences using web technologies,” Plos comput biol, vol. 6, iss. 1, p. e1000563+, 2010.
    [Bibtex]
    @ARTICLE{Lister2010LiveGeneral,
    author = {Lister, Allyson L. and Datta, Ruchira S. and Hofmann, Oliver and
    Krause, Roland and Kuhn, Michael and Roth, Bettina and Schneider,
    Reinhard},
    title = {Live Coverage of Scientific Conferences Using Web Technologies},
    journal = {PLoS Comput Biol},
    year = {2010},
    volume = {6},
    pages = {e1000563+},
    number = {1},
    month = jan,
    citeulike-article-id = {6603301},
    citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pcbi.1000563},
    citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/20126525},
    citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=20126525},
    day = {29},
    doi = {10.1371/journal.pcbi.1000563},
    issn = {1553-7358},
    keywords = {conferences, eccb, friendfeed, ismb, live\_coverage, social-networking,
    web\_technologies},
    owner = {n8384838},
    pmid = {20126525},
    posted-at = {2010-01-29 14:50:32},
    priority = {0},
    publisher = {Public Library of Science},
    timestamp = {2013.05.09},
    url = {http://dx.doi.org/10.1371/journal.pcbi.1000563}
    }
  • [DOI] A. L. Lister, R. S. Datta, O. Hofmann, R. Krause, M. Kuhn, B. Roth, and R. Schneider, “Live coverage of intelligent systems for molecular Biology/European conference on computational biology (ISMB/ECCB) 2009.,” Plos computational biology, vol. 6, iss. 1, p. e1000640+, 2010.
    [Bibtex]
    @ARTICLE{citeulike:6603290,
    author = {Lister, Allyson L. and Datta, Ruchira S. and Hofmann, Oliver and
    Krause, Roland and Kuhn, Michael and Roth, Bettina and Schneider,
    Reinhard},
    title = {Live Coverage of Intelligent Systems for Molecular {Biology/European} Conference on computational biology ({ISMB}/{ECCB}) 2009.},
    journal = {PLoS computational biology},
    year = {2010},
    volume = {6},
    pages = {e1000640+},
    number = {1},
    month = jan,
    citeulike-article-id = {6603290},
    citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pcbi.1000640},
    citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/20126524},
    citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=20126524},
    day = {29},
    doi = {10.1371/journal.pcbi.1000640},
    issn = {1553-7358},
    keywords = {conference-reports, conferences, eccb, friendfeed, ismb, live\_coverage,
    social-networking},
    owner = {n8384838},
    pmid = {20126524},
    posted-at = {2010-01-29 14:44:12},
    priority = {0},
    publisher = {Public Library of Science},
    timestamp = {2013.05.09},
    url = {http://dx.doi.org/10.1371/journal.pcbi.1000640}
    }
  • [DOI] A. R. Jones and A. L. Lister, “Managing experimental data using FuGE.,” Methods in molecular biology (clifton, n.j.), vol. 604, pp. 333-343, 2010.
    [Bibtex]
    @ARTICLE{citeulike:6527866,
    author = {Jones, Andrew R. and Lister, Allyson L.},
    title = {Managing experimental data using {FuGE}.},
    journal = {Methods in molecular biology (Clifton, N.J.)},
    year = {2010},
    volume = {604},
    pages = {333--343},
    abstract = {Data management and sharing in omics science is highly challenging
    due to the constant evolution of experimental techniques, the range
    of instrument types and software used for analysis, and the high
    volumes of data produced. The Functional Genomics Experiment ({FuGE})
    Model was created to provide a model for capturing descriptions of
    sample processing, experimental protocols and multidimensional data
    for any kind of omics experiment. {FuGE} has two modes of action:
    (a) as a storage architecture for experimental workflows and (b)
    as a framework for building new technology-specific data {standards.FuGE}
    is an object model that is converted into an {XML} implementation
    for data exchange. Software toolkits have been developed for data
    handling and for bridging between {XML} data files and relational
    database implementations. {FuGE} has been adopted by the Proteomics
    Standards Initiative ({PSI}, http://www.psidev.info ) for building
    several new data formats, and it is being used in a variety of other
    experimental contexts, thus allowing data to be integrated across
    a range of experimental types to support Systems Biology approaches.
    This chapter provides a practical guide for laboratories or groups
    wishing to manage their data, and for developers wishing to create
    new data formats using {FuGE}.},
    address = {Totowa, NJ},
    booktitle = {Proteome Bioinformatics },
    chapter = {23},
    citeulike-article-id = {6527866},
    citeulike-linkout-0 = {http://dx.doi.org/10.1007/978-1-60761-444-9\_23},
    citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/20013382},
    citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=20013382},
    citeulike-linkout-3 = {http://www.springerlink.com/content/r72434t642777862},
    doi = {10.1007/978-1-60761-444-9\_23},
    isbn = {978-1-60761-443-2},
    issn = {1940-6029},
    keywords = {data-exchange, data-integration, fuge},
    owner = {n8384838},
    pmid = {20013382},
    posted-at = {2010-01-12 09:40:02},
    priority = {0},
    publisher = {Humana Press},
    timestamp = {2013.05.09},
    url = {http://dx.doi.org/10.1007/978-1-60761-444-9\_23}
    }
  • [DOI] S. Pohl and C. R. Harwood, “Heterologous protein secretion by bacillus species from the cradle to the grave,” Adv appl microbiol, vol. 73, pp. 1-25, 2010.
    [Bibtex]
    @ARTICLE{Pohl:2010:Adv-Appl-Microbiol:20800757,
    author = {Pohl, S and Harwood, C R},
    title = {Heterologous protein secretion by bacillus species from the cradle to the grave},
    journal = {Adv Appl Microbiol},
    year = {2010},
    volume = {73},
    pages = {1-25},
    abstract = {The Gram-positive bacterium Bacillus subtilis and some of its close
    relatives are widely used for the industrial production of enzymes
    for the detergents, food, and beverage industries. The choice of
    these organisms is based almost exclusively on the high capacity
    of their secretion systems that are, under the right conditions,
    able to secrete proteins at grams per liter concentrations. In contrast,
    there are relatively few examples of Bacillus species being used
    for the cytoplasmic production of proteins. The range of proteins
    that are capable of high-level production and secretion is limited
    by a combination of characteristics of both the target protein and
    the host bacterium. The secretion pathway includes checkpoints that
    are designed to validate the authenticity of pathway substrates.
    Although many of these checkpoints are known, only some can be overcome
    by reengineering the host. As a result, the yield of heterologous
    protein production is extremely variable. In this review, we consider
    the Bacillus protein secretion pathway from the synthesis of the
    target protein (cradle) to its emergence at the outer surface of
    the complex cell wall (grave), and discuss the roles of the various
    checkpoints both with respect to the target protein and their role
    on cell homeostasis.},
    doi = {10.1016/S0065-2164(10)73001-X},
    owner = {n8384838},
    pmid = {20800757},
    timestamp = {2013.05.24},
    url = {http://www.hubmed.org/display.cgi?uids=20800757}
    }
  • [DOI] A. L. Lister, M. Pocock, M. Taschuk, and A. Wipat, “Saint: a lightweight integration environment for model annotation,” Bioinformatics, vol. 25, iss. 22, pp. 3026-3027, 2009.
    [Bibtex]
    @ARTICLE{Lister:2009:Bioinformatics:19734151,
    author = {Lister, A L and Pocock, M and Taschuk, M and Wipat, A},
    title = {Saint: a lightweight integration environment for model annotation},
    journal = {Bioinformatics},
    year = {2009},
    volume = {25},
    pages = {3026-3027},
    number = {22},
    month = {Nov},
    abstract = {Saint is a web application which provides a lightweight annotation
    integration environment for quantitative biological models. The system
    enables modellers to rapidly mark up models with biological information
    derived from a range of data sources. Availability and Implementation:
    Saint is freely available for use on the web at http://www.cisban.ac.uk/saint.
    The web application is implemented in Google Web Toolkit and Tomcat,
    with all major browsers supported. The Java source code is freely
    available for download at http://saint-annotate.sourceforge.net.
    The Saint web server requires an installation of libSBML and has
    been tested on Linux (32-bit Ubuntu 8.10 and 9.04).},
    doi = {10.1093/bioinformatics/btp523},
    owner = {n8384838},
    pmid = {19734151},
    timestamp = {2013.05.07},
    url = {http://www.hubmed.org/display.cgi?uids=19734151}
    }
  • [DOI] J. F. Passos, C. Simillion, J. Hallinan, A. Wipat, and T. von Zglinicki, “Cellular senescence: unravelling complexity,” Age (dordr), vol. 31, iss. 4, pp. 353-363, 2009.
    [Bibtex]
    @ARTICLE{Passos:2009:Age-Dordr:19618294,
    author = {Passos, J F and Simillion, C and Hallinan, J and Wipat, A and von
    Zglinicki, T},
    title = {Cellular senescence: unravelling complexity},
    journal = {Age (Dordr)},
    year = {2009},
    volume = {31},
    pages = {353-363},
    number = {4},
    month = {Dec},
    abstract = {Cellular senescence might be a tumour suppressing mechanism as well
    as a contributor to age-related loss of tissue function. It has been
    characterised classically as the result of the loss of DNA sequences
    called telomeres at the end of chromosomes. However, recent studies
    have revealed that senescence is in fact an intricate process, involving
    the sequential activation of multiple cellular processes, which have
    proven necessary for the establishment and maintenance of the phenotype.
    Here, we review some of these processes, namely, the role of mitochondrial
    function and reactive oxygen species, senescence-associated secreted
    proteins and chromatin remodelling. Finally, we illustrate the use
    of systems biology to address the mechanistic, functional and biochemical
    complexity of senescence.},
    doi = {10.1007/s11357-009-9108-1},
    owner = {n8384838},
    pmid = {19618294},
    timestamp = {2013.05.08},
    url = {http://www.hubmed.org/display.cgi?uids=19618294}
    }
  • [DOI] Y. Jin and J. Hallinan, “Evolving gene regulatory networks,” Biosystems, vol. 98, iss. 3, 2009.
    [Bibtex]
    @ARTICLE{Jin:2009:Biosystems:19917456,
    author = {Jin, Y and Hallinan, J},
    title = {Evolving gene regulatory networks},
    journal = {Biosystems},
    year = {2009},
    volume = {98},
    number = {3},
    month = {Dec},
    doi = {10.1016/S0303-2647(09)00181-6},
    owner = {n8384838},
    pmid = {19917456},
    timestamp = {2013.05.08},
    url = {http://www.hubmed.org/display.cgi?uids=19917456}
    }
  • [DOI] A. Lister, V. Charoensawan, S. De, K. James, S C. Janga, and J. Huppert, “Interfacing systems biology and synthetic biology,” Genome biol, vol. 10, iss. 6, pp. 309-309, 2009.
    [Bibtex]
    @ARTICLE{Lister:2009:Genome-Biol:19591648,
    author = {Lister, A and Charoensawan, V and De, S and James, K and Janga, S
    C and Huppert, J},
    title = {Interfacing systems biology and synthetic biology},
    journal = {Genome Biol},
    year = {2009},
    volume = {10},
    pages = {309-309},
    number = {6},
    abstract = {A report of BioSysBio 2009, the IET conference on Synthetic Biology,
    Systems Biology and Bioinformatics, Cambridge, UK, 23-25 March 2009.},
    doi = {10.1186/gb-2009-10-6-309},
    owner = {n8384838},
    pmid = {19591648},
    timestamp = {2013.05.09},
    url = {http://www.hubmed.org/display.cgi?uids=19591648}
    }
  • [DOI] K. James, A. Wipat, and J. Hallinan, “Integration of full-coverage probabilistic functional networks with relevance to specific biological processes,” Data integration in the life sciences, pp. 31-46, 2009.
    [Bibtex]
    @ARTICLE{James2009,
    author = {James, K and Wipat, A and Hallinan, J},
    title = {Integration of full-coverage probabilistic functional networks with relevance to specific biological processes},
    journal = {Data Integration in the Life Sciences},
    year = {2009},
    pages = {31--46},
    abstract = {Probabilistic functional integrated networks are powerful tools with
    which to draw inferences from high-throughput data. However, network
    analyses are generally not tailored to specific biological functions
    or processes. This problem may be overcome by extracting process-specific
    sub-networks, but this approach discards useful information and is
    of limited use in poorly annotated areas of the network. Here we
    describe an extension to existing integration methods which exploits
    dataset biases in order to emphasise interactions relevant to specific
    processes, without loss of data. We apply the method to high-throughput
    data for the yeast Saccharomyces cerevisiae, using Gene Ontology
    annotations for ageing and telomere maintenance as test processes.
    The resulting networks perform significantly better than unbiased
    networks for assigning function to unknown genes, and for clustering
    to identify important sets of interactions. We conclude that this
    integration method can be used to enhance network analysis with respect
    to specific processes of biological interest.},
    citeulike-article-id = {6129326},
    citeulike-linkout-0 = {http://dx.doi.org/10.1007/978-3-642-02879-3_4},
    citeulike-linkout-1 = {http://www.springerlink.com/content/9mm86h61x56m866r},
    doi = {10.1007/978-3-642-02879-3_4},
    keywords = {biological\_processes, coverage\_analysis, data\_integration, dataset\_bias,
    networks},
    owner = {n8384838},
    posted-at = {2009-11-17 11:09:24},
    priority = {2},
    timestamp = {2009.12.11},
    url = {http://dx.doi.org/10.1007/978-3-642-02879-3_4}
    }
  • [DOI] A. R. Jones, A. L. Lister, L. Hermida, P. Wilkinson, M. Eisenacher, K. Belhajjame, F. Gibson, P. Lord, M. Pocock, H. Rosenfelder, J. Santoyo-Lopez, A. Wipat, and N. W. Paton, “Modeling and managing experimental data using FuGE.,” Omics : a journal of integrative biology, vol. 13, iss. 3, pp. 239-251, 2009.
    [Bibtex]
    @ARTICLE{citeulike:4540763,
    author = {Jones, Andrew R. and Lister, Allyson L. and Hermida, Leandro and
    Wilkinson, Peter and Eisenacher, Martin and Belhajjame, Khalid and
    Gibson, Frank and Lord, Phil and Pocock, Matthew and Rosenfelder,
    Heiko and Santoyo-Lopez, Javier and Wipat, Anil and Paton, Norman
    W. W.},
    title = {Modeling and managing experimental data using {FuGE}.},
    journal = {Omics : a journal of integrative biology},
    year = {2009},
    volume = {13},
    pages = {239--251},
    number = {3},
    month = jun,
    abstract = {The Functional Genomics Experiment data model ({FuGE}) has been developed
    to increase the consistency and efficiency of experimental data modeling
    in the life sciences, and it has been adopted by a number of high-profile
    standardization organizations. {FuGE} can be used: (1) directly,
    whereby generic modeling constructs are used to represent concepts
    from specific experimental activities; or (2) as a framework within
    which method-specific models can be developed. {FuGE} is both rich
    and flexible, providing a considerable number of modeling constructs,
    which can be used in a range of different ways. However, such richness
    and flexibility also mean that modelers and application developers
    have choices to make when applying {FuGE} in a given context. This
    paper captures emerging best practice in the use of {FuGE} in the
    light of the experience of several groups by: (1) proposing guidelines
    for the use and extension of the {FuGE} data model; (2) presenting
    design patterns that reflect recurring requirements in experimental
    data modeling; and (3) describing a community software tool kit ({STK})
    that supports application development using {FuGE}. We anticipate
    that these guidelines will encourage consistent usage of {FuGE},
    and as such, will contribute to the development of convergent data
    standards in omics research.},
    citeulike-article-id = {4540763},
    citeulike-linkout-0 = {http://dx.doi.org/10.1089/omi.2008.0080},
    citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19441879},
    citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19441879},
    day = {14},
    doi = {10.1089/omi.2008.0080},
    issn = {1557-8100},
    keywords = {data-integration, data-standards, fuge, xml},
    owner = {n8384838},
    pmid = {19441879},
    posted-at = {2009-05-18 17:16:34},
    priority = {0},
    timestamp = {2013.05.09},
    url = {http://dx.doi.org/10.1089/omi.2008.0080}
    }
  • A. L. Lister, M. Pocock, and A. Wipat, “Saint: a lightweight SBML annotation integration environment,” in Biosysbio 2009, 2009.
    [Bibtex]
    @INPROCEEDINGS{lister2009SaintBSB,
    author = {Lister, A. L. and Pocock, M. and Wipat, A.},
    title = {Saint: a lightweight {SBML} annotation integration environment},
    booktitle = {BioSysBio 2009},
    year = {2009},
    month = mar,
    organization = {IET},
    citeulike-article-id = {4282062},
    keywords = {data-integration, model-annotation, modelling},
    owner = {n8384838},
    posted-at = {2009-04-07 10:53:14},
    priority = {0},
    timestamp = {2013.05.09}
    }
  • M. Courtot, F. Gibson, A. L. Lister, J. Malone, D. Schober, R. R. Brinkman, and A. Ruttenberg, “MIREOT: the minimum information to reference an external ontology term,” in International conference on biomedical ontology, 2009, pp. 87-90.
    [Bibtex]
    @INPROCEEDINGS{citeulike:6336875,
    author = {Courtot, M\'{e}lanie and Gibson, Frank and Lister, Allyson L. and
    Malone, James and Schober, Daniel and Brinkman, Ryan R. and Ruttenberg,
    Alan},
    title = {{MIREOT}: the Minimum Information to Reference an External Ontology Term},
    booktitle = {International Conference on Biomedical Ontology},
    year = {2009},
    editor = {Smith, Barry},
    pages = {87--90},
    month = jul,
    organization = {University at Buffalo College of Arts and Sciences, National Center
    for Ontological Research, National Center for Biomedical Ontology},
    abstract = {While the Web Ontology Language ({OWL}) provides a mechanism to import
    ontologies, this mechanism is not always suitable. First, given the
    current state of editing tools and the issues they have working with
    large ontologies, direct {OWL} imports have sometimes proven impractical
    for day-to-day development. Second, ontologies chosen for integration
    may be under active development and not aligned with the chosen design
    principles. Importing heterogeneous ontologies in their entirety
    may lead to inconsistencies or unintended inferences. In this paper
    we propose a set of guidelines for importing required terms from
    an external resource into a target ontology. We describe the guidelines,
    their implementation, present some examples of application, and outline
    future work and extensions.},
    citeulike-article-id = {6336875},
    citeulike-linkout-0 = {http://purl.obolibrary.org/obo/obi/repository/trunk/docs/papers/MIREOT\_ICBO2009/ICBOCameraReady.pdf},
    keywords = {mireot, obi, ontologies},
    location = {Buffalo, New York},
    owner = {n8384838},
    posted-at = {2009-12-08 10:42:55},
    priority = {0},
    timestamp = {2013.05.09},
    url = {http://purl.obolibrary.org/obo/obi/repository/trunk/docs/papers/MIREOT\_ICBO2009/ICBOCameraReady.pdf}
    }
  • A. L. Lister, P. Lord, M. Pocock, and A. Wipat, “Annotation of SBML models through Rule-Based semantic integration,” in The 12th annual bio-ontologies meeting, ismb 2009, 2009, p. 49+.
    [Bibtex]
    @INPROCEEDINGS{citeulike:5158322,
    author = {Lister, Allyson L. and Lord, Phillip and Pocock, Matthew and Wipat,
    Anil},
    title = {Annotation of {SBML} Models Through {Rule-Based} Semantic Integration},
    booktitle = {The 12th Annual Bio-Ontologies Meeting, ISMB 2009},
    year = {2009},
    editor = {Lord, Phillip and Sansone, Susanna-Assunta and Shah, Nigam and Stephens,
    Susie and Soldatova, Larisa},
    pages = {49+},
    month = jun,
    abstract = {Motivation: The creation of accurate quantitative Systems Biology
    Markup Language ({SBML}) models is a time-intensive, manual process
    often complicated by the many data sources and formats required to
    annotate even a small and well-scoped model. Ideally, the retrieval
    and integration of biological knowledge for model annotation should
    be performed quickly, precisely, and with a minimum of manual effort.
    Here, we present a method using off-the-shelf semantic web technology
    which enables this process: the heterogeneous data sources are first
    syntactically converted into ontologies; these are then aligned to
    a small domain ontology by applying a rule base. Integrating resources
    in this way can accommodate multiple formats with different semantics;
    it provides richly modelled biological knowledge suitable for annotation
    of {SBML} models. Results: We demonstrate proof-of-principle for
    this rule-based mediation with two use cases for {SBML} model annotation.
    This was implemented with existing tools, decreasing development
    time and increasing reusability. This initial work establishes the
    feasibility of this approach as part of an automated {SBML} model
    annotation system. Availability: Detailed information including download
    and mapping of the ontologies as well as integration results is available
    from {http://www.cisban.ac.uk/RBM}},
    citeulike-article-id = {5158322},
    citeulike-linkout-0 = {http://precedings.nature.com/documents/3286/version/1},
    day = {28},
    keywords = {data-integration, model-annotation, ontologies, ontology-mapping,
    owl, rule-based-mediation, sbml, semantics, sqwrl, swrl},
    owner = {n8384838},
    posted-at = {2009-07-15 13:14:59},
    priority = {0},
    timestamp = {2013.05.09},
    url = {http://precedings.nature.com/documents/3286/version/1}
    }
  • [DOI] D. Field, G. Garrity, T. Gray, N. Morrison, J. Selengut, P. Sterk, T. Tatusova, N. Thomson, M. J. Allen, S. V. Angiuoli, M. Ashburner, N. Axelrod, S. Baldauf, S. Ballard, J. Boore, G. Cochrane, J. Cole, P. Dawyndt, P. De Vos, C. DePamphilis, R. Edwards, N. Faruque, R. Feldman, J. Gilbert, P. Gilna, F. O. Glöckner, P. Goldstein, R. Guralnick, D. Haft, D. Hancock, H. Hermjakob, C. Hertz-Fowler, P. Hugenholtz, I. Joint, L. Kagan, M. Kane, J. Kennedy, G. Kowalchuk, R. Kottmann, E. Kolker, S. Kravitz, N. Kyrpides, J. Leebens-Mack, S. E. Lewis, K. Li, A. L. Lister, P. Lord, N. Maltsev, V. Markowitz, J. Martiny, B. Methe, I. Mizrachi, R. Moxon, K. Nelson, J. Parkhill, L. Proctor, O. White, S. A. Sansone, A. Spiers, R. Stevens, P. Swift, C. Taylor, Y. Tateno, A. Tett, S. Turner, D. Ussery, B. Vaughan, N. Ward, T. Whetzel, I. San Gil, G. Wilson, and A. Wipat, “The minimum information about a genome sequence (migs) specification,” Nat biotechnol, vol. 26, iss. 5, pp. 541-547, 2008.
    [Bibtex]
    @ARTICLE{Field:2008:Nat-Biotechnol:18464787,
    author = {Field, D and Garrity, G and Gray, T and Morrison, N and Selengut,
    J and Sterk, P and Tatusova, T and Thomson, N and Allen, M J and
    Angiuoli, S V and Ashburner, M and Axelrod, N and Baldauf, S and
    Ballard, S and Boore, J and Cochrane, G and Cole, J and Dawyndt,
    P and De Vos, P and DePamphilis, C and Edwards, R and Faruque, N
    and Feldman, R and Gilbert, J and Gilna, P and Gl{\"o}ckner, F O
    and Goldstein, P and Guralnick, R and Haft, D and Hancock, D and
    Hermjakob, H and Hertz-Fowler, C and Hugenholtz, P and Joint, I and
    Kagan, L and Kane, M and Kennedy, J and Kowalchuk, G and Kottmann,
    R and Kolker, E and Kravitz, S and Kyrpides, N and Leebens-Mack,
    J and Lewis, S E and Li, K and Lister, A L and Lord, P and Maltsev,
    N and Markowitz, V and Martiny, J and Methe, B and Mizrachi, I and
    Moxon, R and Nelson, K and Parkhill, J and Proctor, L and White,
    O and Sansone, S A and Spiers, A and Stevens, R and Swift, P and
    Taylor, C and Tateno, Y and Tett, A and Turner, S and Ussery, D and
    Vaughan, B and Ward, N and Whetzel, T and San Gil, I and Wilson,
    G and Wipat, A},
    title = {The minimum information about a genome sequence (MIGS) specification},
    journal = {Nat Biotechnol},
    year = {2008},
    volume = {26},
    pages = {541-547},
    number = {5},
    month = {May},
    abstract = {With the quantity of genomic data increasing at an exponential rate,
    it is imperative that these data be captured electronically, in a
    standard format. Standardization activities must proceed within the
    auspices of open-access and international working bodies. To tackle
    the issues surrounding the development of better descriptions of
    genomic investigations, we have formed the Genomic Standards Consortium
    (GSC). Here, we introduce the minimum information about a genome
    sequence (MIGS) specification with the intent of promoting participation
    in its development and discussing the resources that will be required
    to develop improved mechanisms of metadata capture and exchange.
    As part of its wider goals, the GSC also supports improving the 'transparency'
    of the information contained in existing genomic databases.},
    doi = {10.1038/nbt1360},
    owner = {n8384838},
    pmid = {18464787},
    timestamp = {2013.05.07},
    url = {http://www.hubmed.org/display.cgi?uids=18464787}
    }
  • [DOI] F. Gibson, L. Anderson, G. Babnigg, M. Baker, M. Berth, P. A. Binz, A. Borthwick, P. Cash, B. W. Day, D. B. Friedman, D. Garland, H. B. Gutstein, C. Hoogland, N A. Jones, A. Khan, J. Klose, A. I. Lamond, P. F. Lemkin, K. S. Lilley, J. Minden, N. J. Morris, N. W. Paton, M. R. Pisano, J. E. Prime, T. Rabilloud, D. A. Stead, C. F. Taylor, H. Voshol, A. Wipat, and A. R. Jones, “Guidelines for reporting the use of gel electrophoresis in proteomics,” Nat biotechnol, vol. 26, iss. 8, pp. 863-864, 2008.
    [Bibtex]
    @ARTICLE{Gibson:2008:Nat-Biotechnol:18688234,
    author = {Gibson, F and Anderson, L and Babnigg, G and Baker, M and Berth,
    M and Binz, P A and Borthwick, A and Cash, P and Day, B W and Friedman,
    D B and Garland, D and Gutstein, H B and Hoogland, C and Jones, N
    A and Khan, A and Klose, J and Lamond, A I and Lemkin, P F and Lilley,
    K S and Minden, J and Morris, N J and Paton, N W and Pisano, M R
    and Prime, J E and Rabilloud, T and Stead, D A and Taylor, C F and
    Voshol, H and Wipat, A and Jones, A R},
    title = {Guidelines for reporting the use of gel electrophoresis in proteomics},
    journal = {Nat Biotechnol},
    year = {2008},
    volume = {26},
    pages = {863-864},
    number = {8},
    month = {Aug},
    doi = {10.1038/nbt0808-863},
    owner = {n8384838},
    pmid = {18688234},
    timestamp = {2013.05.07},
    url = {http://www.hubmed.org/display.cgi?uids=18688234}
    }
  • [DOI] T. Craddock, C. R. Harwood, J. Hallinan, and A. Wipat, “E-science: relieving bottlenecks in large-scale genome analyses,” Nat rev microbiol, vol. 6, iss. 12, pp. 948-954, 2008.
    [Bibtex]
    @ARTICLE{Craddock:2008:Nat-Rev-Microbiol:19008893,
    author = {Craddock, T and Harwood, C R and Hallinan, J and Wipat, A},
    title = {e-Science: relieving bottlenecks in large-scale genome analyses},
    journal = {Nat Rev Microbiol},
    year = {2008},
    volume = {6},
    pages = {948-954},
    number = {12},
    month = {Dec},
    abstract = {The development of affordable, high-throughput sequencing technology
    has led to a flood of publicly available bacterial genome-sequence
    data. The availability of multiple genome sequences presents both
    an opportunity and a challenge for microbiologists, and new computational
    approaches are needed to extract the knowledge that is required to
    address specific biological problems and to analyse genomic data.
    The field of e-Science is maturing, and Grid-based technologies can
    help address this challenge.},
    doi = {10.1038/nrmicro2031},
    owner = {n8384838},
    pmid = {19008893},
    timestamp = {2013.05.08},
    url = {http://www.hubmed.org/display.cgi?uids=19008893}
    }
  • F. S. A. . C. S. Park N. Draskovci and T. Perera, “Dentate neurogenesis contributes to association of old memory to new memory with subtle but distinct differences,” in Society of biological psychiatry 2008 proceedings, washington d.c., united states, 2008.
    [Bibtex]
    @INPROCEEDINGS{SPark08,
    author = {S. Park, N. Draskovci, A. Fenton, C. Sexton and T. Perera},
    title = {Dentate neurogenesis contributes to association of old memory to
    new memory with subtle but distinct differences},
    booktitle = {Society of Biological Psychiatry 2008 Proceedings, Washington D.C.,
    United States},
    year = {2008},
    owner = {n8384838},
    timestamp = {2013.05.08}
    }
  • T. Perera, S. Park, and Y. Nemirovskaya, “Cognitive role of neurogenesis in depression and antidepressant treatment,” The neuroscientist, 2008.
    [Bibtex]
    @ARTICLE{Perera:2008p3278,
    author = {T Perera and S Park and Y Nemirovskaya},
    title = {Cognitive role of neurogenesis in depression and antidepressant treatment},
    journal = {The Neuroscientist},
    year = {2008},
    month = {Jan},
    abstract = {Abstract The discovery of newborn neurons in the adult brain has generated
    enormous interest over the past decade. Although this process is
    well documented in the hippocampus and olfactory bulb, the possibility
    of neuron formation in other brain regions is under ... },
    date-added = {2012-11-06 17:29:40 +0000},
    date-modified = {2012-11-06 17:29:40 +0000},
    local-url = {file://localhost/Users/spark/Dropbox/workspace1/Papers/The%20Neuroscientist%202008%20Perera.pdf},
    owner = {n8384838},
    pmid = {1710139881058451349related:lb-3PimjuxcJ},
    rating = {0},
    timestamp = {2013.05.08},
    uri = {papers://85714800-3608-429D-85A0-7D00B06F5DFE/Paper/p3278},
    url = {http://nro.sagepub.com/content/14/4/326.short}
    }
  • [DOI] A. Greenall, G. Lei, D. C. Swan, K. James, L. Wang, H. Peters, A. Wipat, D. J. Wilkinson, and D. Lydall, “A genome wide analysis of the response to uncapped telomeres in budding yeast reveals a novel role for the nad+ biosynthetic gene bna2 in chromosome end protection,” Genome biol, vol. 9, iss. 10, 2008.
    [Bibtex]
    @ARTICLE{Greenall:2008:Genome-Biol:18828915,
    author = {Greenall, A and Lei, G and Swan, D C and James, K and Wang, L and
    Peters, H and Wipat, A and Wilkinson, D J and Lydall, D},
    title = {A genome wide analysis of the response to uncapped telomeres in budding yeast reveals a novel role for the NAD+ biosynthetic gene BNA2 in chromosome end protection},
    journal = {Genome Biol},
    year = {2008},
    volume = {9},
    number = {10},
    abstract = {Telomeres prevent the ends of eukaryotic chromosomes from being recognized
    as damaged DNA and protect against cancer and ageing. When telomere
    structure is perturbed, a co-ordinated series of events promote arrest
    of the cell cycle so that cells carrying damaged telomeres do not
    divide. In order to better understand the eukaryotic response to
    telomere damage, budding yeast strains harboring a temperature sensitive
    allele of an essential telomere capping gene (cdc13-1) were subjected
    to a transcriptomic study.The genome-wide response to uncapped telomeres
    in yeast cdc13-1 strains, which have telomere capping defects at
    temperatures above approximately 27 degrees C, was determined. Telomere
    uncapping in cdc13-1 strains is associated with the differential
    expression of over 600 transcripts. Transcripts affecting responses
    to DNA damage and diverse environmental stresses were statistically
    over-represented. BNA2, required for the biosynthesis of NAD+, is
    highly and significantly up-regulated upon telomere uncapping in
    cdc13-1 strains. We find that deletion of BNA2 and NPT1, which is
    also involved in NAD+ synthesis, suppresses the temperature sensitivity
    of cdc13-1 strains, indicating that NAD+ metabolism may be linked
    to telomere end protection.Our data support the hypothesis that the
    response to telomere uncapping is related to, but distinct from,
    the response to non-telomeric double-strand breaks. The induction
    of environmental stress responses may be a conserved feature of the
    eukaryotic response to telomere damage. BNA2, which is involved in
    NAD+ synthesis, plays previously unidentified roles in the cellular
    response to telomere uncapping.},
    doi = {10.1186/gb-2008-9-10-r146},
    owner = {n8384838},
    pmid = {18828915},
    timestamp = {2013.05.09},
    url = {http://www.hubmed.org/display.cgi?uids=18828915}
    }
  • [DOI] S. G. Addinall, M. Downey, M. Yu, M. K. Zubko, J. Dewar, A. Leake, J. Hallinan, O. Shaw, K. James, D. J. Wilkinson, A. Wipat, D. Durocher, and D. Lydall, “A genomewide suppressor and enhancer analysis of cdc13-1 reveals varied cellular processes influencing telomere capping in saccharomyces cerevisiae,” Genetics, vol. 180, iss. 4, pp. 2251-2266, 2008.
    [Bibtex]
    @ARTICLE{Addinall:2008:Genetics:18845848,
    author = {Addinall, S G and Downey, M and Yu, M and Zubko, M K and Dewar, J
    and Leake, A and Hallinan, J and Shaw, O and James, K and Wilkinson,
    D J and Wipat, A and Durocher, D and Lydall, D},
    title = {A genomewide suppressor and enhancer analysis of cdc13-1 reveals varied cellular processes influencing telomere capping in Saccharomyces cerevisiae},
    journal = {Genetics},
    year = {2008},
    volume = {180},
    pages = {2251-2266},
    number = {4},
    month = {Dec},
    abstract = {In Saccharomyces cerevisiae, Cdc13 binds telomeric DNA to recruit
    telomerase and to "cap" chromosome ends. In temperature-sensitive
    cdc13-1 mutants telomeric DNA is degraded and cell-cycle progression
    is inhibited. To identify novel proteins and pathways that cap telomeres,
    or that respond to uncapped telomeres, we combined cdc13-1 with the
    yeast gene deletion collection and used high-throughput spot-test
    assays to measure growth. We identified 369 gene deletions, in eight
    different phenotypic classes, that reproducibly demonstrated subtle
    genetic interactions with the cdc13-1 mutation. As expected, we identified
    DNA damage checkpoint, nonsense-mediated decay and telomerase components
    in our screen. However, we also identified genes affecting casein
    kinase II activity, cell polarity, mRNA degradation, mitochondrial
    function, phosphate transport, iron transport, protein degradation,
    and other functions. We also identified a number of genes of previously
    unknown function that we term RTC, for restriction of telomere capping,
    or MTC, for maintenance of telomere capping. It seems likely that
    many of the newly identified pathways/processes that affect growth
    of budding yeast cdc13-1 mutants will play evolutionarily conserved
    roles at telomeres. The high-throughput spot-testing approach that
    we describe is generally applicable and could aid in understanding
    other aspects of eukaryotic cell biology.},
    doi = {10.1534/genetics.108.092577},
    owner = {n8384838},
    pmid = {18845848},
    timestamp = {2013.05.09},
    url = {http://www.hubmed.org/display.cgi?uids=18845848}
    }
  • M. Courtot, W. Bug, F. Gibson, A. L. Lister, J. Malone, D. Schober, R. Brinkman, and A. Ruttenberg, “The OWL of biomedical investigations,” in Owled 2008, 2008.
    [Bibtex]
    @INPROCEEDINGS{citeulike:3457924,
    author = {Courtot, M\'{e}lanie and Bug, William and Gibson, Frank and Lister,
    Allyson L. and Malone, James and Schober, Daniel and Brinkman, Ryan
    R. and Ruttenberg, Alan},
    title = {The {OWL} of Biomedical Investigations},
    booktitle = {OWLED 2008},
    year = {2008},
    month = oct,
    abstract = {The Ontology for Biomedical Investigations ({OBI}), written in {OWL}
    {DL}, is being developed by a large consortium seeking to provide
    a cross-domain,shared framework for representing investigations in
    the biological andbiomedical sciences. In this paper we report our
    experiences and describe ourdevelopment process as it pertains to
    {OWL}, which includes a number ofelements that might inform tool
    developers as well as suggestgeneral development patterns. Finally,
    we review where improvements to {OWLand} {OWL} related tools might
    be beneficial.},
    citeulike-article-id = {3457924},
    citeulike-linkout-0 = {http://www.webont.org/owled/2008/papers/owled2008eu\_submission\_38.pdf},
    keywords = {methodologies, obi, ontologies, owl},
    owner = {n8384838},
    posted-at = {2008-12-05 14:27:07},
    priority = {0},
    timestamp = {2013.05.09},
    url = {http://www.webont.org/owled/2008/papers/owled2008eu\_submission\_38.pdf}
    }
  • [DOI] S. Sansone, P. Rocca-Serra, M. Brandizi, A. Brazma, D. Field, J. Fostel, A. G. Garrow, J. Gilbert, F. Goodsaid, N. Hardy, P. Jones, A. Lister, M. Miller, N. Morrison, T. Rayner, N. Sklyar, C. Taylor, W. Tong, G. Warner, and S. Wiemann, “The first RSBI (ISA-TAB) workshop: “can a simple format work for complex studies”,” Omics: a journal of integrative biology, vol. 12, iss. 2, pp. 143-149, 2008.
    [Bibtex]
    @ARTICLE{citeulike:3153404,
    author = {Sansone, Susanna-Assunta and Rocca-Serra, Philippe and Brandizi,
    Marco and Brazma, Alvis and Field, Dawn and Fostel, Jennifer and
    Garrow, Andrew G. and Gilbert, Jack and Goodsaid, Federico and Hardy,
    Nigel and Jones, Phil and Lister, Allyson and Miller, Michael and
    Morrison, Norman and Rayner, Tim and Sklyar, Nataliya and Taylor,
    Chris and Tong, Weida and Warner, Guy and Wiemann, Stefan},
    title = {The First {RSBI} ({ISA}-{TAB}) Workshop: "Can a Simple Format Work for Complex Studies"},
    journal = {OMICS: A Journal of Integrative Biology},
    year = {2008},
    volume = {12},
    pages = {143--149},
    number = {2},
    month = jun,
    abstract = {Abstract This article summarizes the motivation for, and the proceedings
    of, the first {ISA}-{TAB} workshop held December 6-8, 2007, at the
    {EBI}, Cambridge, {UK}. This exploratory workshop, organized by members
    of the Microarray Gene Expression Data ({MGED}) Society's Reporting
    Structure for Biological Investigations ({RSBI}) working group, brought
    together a group of developers of a range of collaborative systems
    to discuss the use of a common format to address the pressing need
    of reporting and communicating data and metadata from biological,
    biomedical, and environmental studies employing combinations of genomics,
    transcriptomics, proteomics, and metabolomics technologies along
    with more conventional methodologies. The expertise of the participants
    comprised database development, data management, and hands-on experience
    in the development of data communication standards. The workshop's
    outcomes are set to help formalize the proposed Investigation, Study,
    Assay ({ISA})-{TAB} tab-delimited format for representing and communicating
    experimental metadata. This article is part of the special issue
    of {OMICS} on the activities of the Genomics Standards Consortium
    ({GSC}).},
    citeulike-article-id = {3153404},
    citeulike-linkout-0 = {http://dx.doi.org/10.1089/omi.2008.0019},
    citeulike-linkout-1 = {http://online.liebertpub.com/doi/abs/10.1089/omi.2008.0019},
    citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/18447634},
    citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=18447634},
    doi = {10.1089/omi.2008.0019},
    issn = {1536-2310},
    keywords = {data-standards, fuge, isa-tab},
    owner = {n8384838},
    pmid = {18447634},
    posted-at = {2008-10-15 16:17:15},
    priority = {0},
    timestamp = {2013.05.09},
    url = {http://dx.doi.org/10.1089/omi.2008.0019}
    }
  • P. Rocca-Serra, S. Sansone, A. Jones, A. Lister, F. Gibson, R. Brinkman, J. Spindlen, and M. Miller, XSL transformations for FuGE and FuGE extension documents for HTML and tab-delimited rendering, 2008.
    [Bibtex]
    @MISC{citeulike:10114355,
    author = {Rocca-Serra, Philippe and Sansone, Susanna and Jones, Andy and Lister,
    Allyson and Gibson, Frank and Brinkman, Ryan and Spindlen, Josef
    and Miller, Michael},
    title = {{XSL} transformations for {FuGE} and {FuGE} extension documents for {HTML} and tab-delimited rendering},
    howpublished = {\url{http://isatab.sourceforge.net/docs/FUGE-and-XSL-transformations-R1.doc}},
    month = jun,
    year = {2008},
    citeulike-article-id = {10114355},
    owner = {n8384838},
    posted-at = {2011-12-10 21:50:02},
    priority = {0},
    timestamp = {2013.05.09}
    }
  • Y. Sun, A. Wipat, M. Pocock, P. A. Lee, K. Flanagan, and J. T. Worthington, “Exploring microbial genome sequences to identify protein families on the grid,” Ieee trans inf technol biomed, vol. 11, iss. 4, pp. 435-442, 2007.
    [Bibtex]
    @ARTICLE{Sun:2007:IEEE-Trans-Inf-Technol-Biomed:17674626,
    author = {Sun, Y and Wipat, A and Pocock, M and Lee, P A and Flanagan, K and
    Worthington, J T},
    title = {Exploring microbial genome sequences to identify protein families on the grid},
    journal = {IEEE Trans Inf Technol Biomed},
    year = {2007},
    volume = {11},
    pages = {435-442},
    number = {4},
    month = {Jul},
    abstract = {The analysis of microbial genome sequences can identify protein families
    that provide potential drug targets for new antibiotics. With the
    rapid accumulation of newly sequenced genomes, this analysis has
    become a computationally intensive and data-intensive problem. This
    paper describes the development of a Web-service-enabled, component-based,
    architecture to support the large-scale comparative analysis of complete
    microbial genome sequences and the subsequent identification of orthologues
    and protein families (Microbase). The system is coordinated through
    the use of Web-service-based notifications and integrates distributed
    computing resources together with genomic databases to realize all-against-all
    comparisons for a large volume of genome sequences and to present
    the data in a computationally amenable format through a Web service
    interface. We demonstrate the use of the system in searching for
    orthologues and candidate protein families, which ultimately could
    lead to the identification of potential therapeutic targets.},
    owner = {n8384838},
    pmid = {17674626},
    timestamp = {2013.05.07},
    url = {http://www.hubmed.org/display.cgi?uids=17674626}
    }
  • [DOI] L. J. Steggles, R. Banks, O. Shaw, and A. Wipat, “Qualitatively modelling and analysing genetic regulatory networks: a petri net approach,” Bioinformatics, vol. 23, iss. 3, pp. 336-343, 2007.
    [Bibtex]
    @ARTICLE{Steggles:2007:Bioinformatics:17121774,
    author = {Steggles, L J and Banks, R and Shaw, O and Wipat, A},
    title = {Qualitatively modelling and analysing genetic regulatory networks: a Petri net approach},
    journal = {Bioinformatics},
    year = {2007},
    volume = {23},
    pages = {336-343},
    number = {3},
    month = {Feb},
    abstract = {New developments in post-genomic technology now provide researchers
    with the data necessary to study regulatory processes in a holistic
    fashion at multiple levels of biological organization. One of the
    major challenges for the biologist is to integrate and interpret
    these vast data resources to gain a greater understanding of the
    structure and function of the molecular processes that mediate adaptive
    and cell cycle driven changes in gene expression. In order to achieve
    this biologists require new tools and techniques to allow pathway
    related data to be modelled and analysed as network structures, providing
    valuable insights which can then be validated and investigated in
    the laboratory.We propose a new technique for constructing and analysing
    qualitative models of genetic regulatory networks based on the Petri
    net formalism. We take as our starting point the Boolean network
    approach of treating genes as binary switches and develop a new Petri
    net model which uses logic minimization to automate the construction
    of compact qualitative models. Our approach addresses the shortcomings
    of Boolean networks by providing access to the wide range of existing
    Petri net analysis techniques and by using non-determinism to cope
    with incomplete and inconsistent data. The ideas we present are illustrated
    by a case study in which the genetic regulatory network controlling
    sporulation in the bacterium Bacillus subtilis is modelled and analysed.The
    Petri net model construction tool and the data files for the B. subtilis
    sporulation case study are available at http://bioinf.ncl.ac.uk/gnapn.},
    doi = {10.1093/bioinformatics/btl596},
    owner = {n8384838},
    pmid = {17121774},
    timestamp = {2013.05.07},
    url = {http://www.hubmed.org/display.cgi?uids=17121774}
    }
  • A. L. Lister, A. R. Jones, M. Pocock, O. Shaw, and A. Wipat, “CS-TR number 1016: implementing the FuGE object model: a systems biology data portal and integrator,” Newcastle University 2007.
    [Bibtex]
    @TECHREPORT{citeulike:9846489,
    author = {Lister, A. L. and Jones, A. R. and Pocock, M. and Shaw, O. and Wipat,
    A.},
    title = {{CS}-{TR} Number 1016: Implementing the {FuGE} Object Model: a Systems Biology Data Portal and Integrator},
    institution = {Newcastle University},
    year = {2007},
    month = apr,
    citeulike-article-id = {9846489},
    citeulike-linkout-0 = {http://www.cs.ncl.ac.uk/publications/trs/papers/1016.pdf},
    owner = {n8384838},
    posted-at = {2011-10-03 10:07:40},
    priority = {2},
    publisher = {School of Computing Science},
    timestamp = {2013.05.09},
    url = {http://www.cs.ncl.ac.uk/publications/trs/papers/1016.pdf}
    }
  • A. L. Lister, M. Pocock, and A. Wipat, “Integration of constraints documented in SBML, SBO, and the SBML manual facilitates validation of biological models,” Journal of integrative bioinformatics, vol. 4, iss. 3, p. 80+, 2007.
    [Bibtex]
    @ARTICLE{citeulike:3049915,
    author = {Lister, A. L. and Pocock, M. and Wipat, A.},
    title = {Integration of constraints documented in {SBML}, {SBO}, and the {SBML}
    Manual facilitates validation of biological models},
    journal = {Journal of Integrative Bioinformatics},
    year = {2007},
    volume = {4},
    pages = {80+},
    number = {3},
    abstract = {The creation of quantitative, simulatable, Systems Biology Markup
    Language ({SBML}) models that accurately simulate the system under
    study is a time-intensive manual process that requires careful checking.
    Currently, the rules and constraints of model creation, curation,
    and annotation are distributed over at least three separate documents:
    the {SBML} schema document ({XSD}), the Systems Biology Ontology
    ({SBO}), and the ?Structures and Facilities for Model Definition?
    document. The latter document contains the richest set of constraints
    on models, and yet it is not amenable to computational processing.
    We have developed a Web Ontology Language ({OWL}) knowledge base
    that integrates these three structure documents, and that contains
    a representative sample of the information contained within them.
    This Model Format {OWL} ({MFO}) performs both structural and constraint
    integration and can be reasoned over and validated. {SBML} Models
    are represented as individuals of {OWL} classes, resulting in a single
    computationally amenable resource for model checking. Knowledge that
    was only accessible to humans is now explicitly and directly available
    for computational approaches. The integration of all structural knowledge
    for {SBML} models into a single resource creates a new style of model
    development and checking.},
    citeulike-article-id = {3049915},
    citeulike-linkout-0 = {http://journal.imbio.de/index.php?subid=7\&\#38;paper\_id=80},
    keywords = {data-integration, mfo, model-annotation, model-format-ontology, ontologies,
    sbml, sbo, semantic-data-integration},
    owner = {n8384838},
    posted-at = {2008-10-15 16:44:14},
    priority = {0},
    timestamp = {2013.05.09},
    url = {http://journal.imbio.de/index.php?subid=7\&\#38;paper\_id=80}
    }
  • [DOI] D. Field, G. Garrity, T. Gray, J. Selengut, P. Sterk, N. Thomson, T. Tatusova, G. Cochrane, F. O. Glöckner, R. Kottmann, A. Lister, Y. Tateno, and R. Vaughan, “eGenomics: cataloguing our complete genome collection III,” Comparative and functional genomics, vol. 2007, 2007.
    [Bibtex]
    @ARTICLE{citeulike:4538088,
    author = {Field, Dawn and Garrity, George and Gray, Tanya and Selengut, Jeremy
    and Sterk, Peter and Thomson, Nick and Tatusova, Tatiana and Cochrane,
    Guy and Gl\"{o}ckner, Frank O. and Kottmann, Renzo and Lister, Allyson
    L. and Tateno, Yoshio and Vaughan, Robert},
    title = {{eGenomics}: Cataloguing Our Complete Genome Collection {III}},
    journal = {Comparative and Functional Genomics},
    year = {2007},
    volume = {2007},
    abstract = {This meeting report summarizes the proceedings of the �� {character}
    {eGenomics}: Cataloguing our Complete Genome Collection {III}�� {character}
    workshop held September 11–13, 2006, at the National Institute
    for Environmental {eScience} ({NIEeS}), Cambridge, United Kingdom.
    This 3rd workshop of the Genomic Standards Consortium was divided
    into two parts. The first half of the three-day workshop was dedicated
    to reviewing the genomic diversity of our current and future genome
    and metagenome collection, and exploring linkages to a series of
    existing projects through formal presentations. The second half was
    dedicated to strategic discussions. Outcomes of the workshop include
    a revised �� {character} Minimum Information about a Genome Sequence��
    {character} ({MIGS}) specification (v1.1), consensus on a variety
    of features to be added to the Genome Catalogue ({GCat}), agreement
    by several researchers to adopt {MIGS} for imminent genome publications,
    and an agreement by the {EBI} and {NCBI} to input their genome collections
    into {GCat} for the purpose of quantifying the amount of optional
    data already available (e.g., for geographic location coordinates)
    and working towards a single, global list of all public genomes and
    metagenomes.},
    citeulike-article-id = {4538088},
    citeulike-linkout-0 = {http://dx.doi.org/10.1155/2007/47304},
    citeulike-linkout-1 = {http://www.hindawi.com/GetArticle.aspx?doi=10.1155/2007/47304},
    doi = {10.1155/2007/47304},
    keywords = {curation, data-standards, standards},
    owner = {n8384838},
    posted-at = {2009-05-18 12:50:20},
    priority = {0},
    publisher = {Hindawi},
    timestamp = {2013.05.09},
    url = {http://www.hindawi.com/GetArticle.aspx?doi=10.1155/2007/47304}
    }
  • [DOI] N. E. Allenby, C. A. Watts, G. Homuth, Z. Prágai, A. Wipat, A. C. Ward, and C. R. Harwood, “Phosphate starvation induces the sporulation killing factor of bacillus subtilis,” J bacteriol, vol. 188, iss. 14, pp. 5299-5303, 2006.
    [Bibtex]
    @ARTICLE{Allenby:2006:J-Bacteriol:16816204,
    author = {Allenby, N E and Watts, C A and Homuth, G and Pr{\'a}gai, Z and Wipat,
    A and Ward, A C and Harwood, C R},
    title = {Phosphate starvation induces the sporulation killing factor of Bacillus subtilis},
    journal = {J Bacteriol},
    year = {2006},
    volume = {188},
    pages = {5299-5303},
    number = {14},
    month = {Jul},
    abstract = {Bacillus subtilis produces and exports a peptide sporulation killing
    factor (SkfA) that induces lysis of sibling cells. skfA is part of
    the skf operon (skfA-H), which is responsible for immunity to SkfA,
    as well as for production and export of SkfA. Here we report that
    transcription of skfA is markedly induced when cells of B. subtilis
    are subjected to phosphate starvation. The role of PhoP in regulation
    of the skf operon was confirmed by in vitro gel shift assays, which
    showed that this operon is a new member of the PhoP regulon. A putative
    stem-loop structure in the skfA-skfB intergenic region is proposed
    to act as a stabilizer of an skfA-specific transcript.},
    doi = {10.1128/JB.00084-06},
    owner = {n8384838},
    pmid = {16816204},
    timestamp = {2013.05.07},
    url = {http://www.hubmed.org/display.cgi?uids=16816204}
    }
  • [DOI] H. Antelmann, R. C. Williams, M. Miethke, A. Wipat, D. Albrecht, C. R. Harwood, and M. Hecker, “The extracellular and cytoplasmic proteomes of the non-virulent bacillus anthracis strain um23c1-2,” Proteomics, vol. 5, iss. 14, pp. 3684-3695, 2005.
    [Bibtex]
    @ARTICLE{Antelmann:2005:Proteomics:16121336,
    author = {Antelmann, H and Williams, R C and Miethke, M and Wipat, A and Albrecht,
    D and Harwood, C R and Hecker, M},
    title = {The extracellular and cytoplasmic proteomes of the non-virulent Bacillus anthracis strain UM23C1-2},
    journal = {Proteomics},
    year = {2005},
    volume = {5},
    pages = {3684-3695},
    number = {14},
    month = {Sep},
    abstract = {The recently published genome sequence of Bacillus anthracis Ames
    has facilitated the prediction of proteins associated with the virulence
    of this bacterium. The aim of this study was to define reference
    maps for the extracellular and cytoplasmic proteomes of the avirulent
    B. anthracis strain UM23C1-2 that are useful for physiological studies
    and the development of improved vaccines. Using 2-DE and subsequent
    MALDI-TOF-TOF MS, 64 proteins were identified in the extracellular
    proteome, only 29 of which were predicted to be exported into the
    culture medium. The latter included chitinases, proteases, nucleotidases,
    sulfatases, phosphatases and proteins of unknown function. Of the
    remaining proteins in the culture medium, 18 were predicted to be
    associated with the cell wall or anchored on the trans side of the
    cytoplasmic membrane while 17 other proteins lacked identifiable
    export signals and were predicted to be cytoplasmic proteins. Among
    the S-layer proteins, Sap and Eag account for 10% of the total extracellular
    proteome. Many of the proteins are predicted to contribute to the
    virulence and antigenic signature of B. anthracis. We have also studied
    the composition of the cytoplasmic proteome, identifying 300 distinct
    proteins. The most abundant cytoplasmic proteins are primarily those
    involved in glycolysis, amino acid metabolism, protein translation,
    protein folding and stress adaptation. The presence of a variety
    of proteases, peptidases, peptide binding proteins, as well as enzymes
    required for the metabolism of amino acids, suggests that B. anthracis
    is adapted to life in a protein-rich environment rather than the
    soil. We therefore speculate that proteases and peptidases could
    be useful targets for the development of improved vaccines. In addition,
    both of these B. anthracis compartment-specific proteomes can be
    used as reference maps to monitor changes in the production of secreted
    and cytosolic proteins that occur, for example, during growth in
    macrophages.},
    doi = {10.1002/pmic.200401218},
    owner = {n8384838},
    pmid = {16121336},
    timestamp = {2013.05.07},
    url = {http://www.hubmed.org/display.cgi?uids=16121336}
    }
  • [DOI] N. E. Allenby, N. O’Connor, Z. Prágai, A. C. Ward, A. Wipat, and C. R. Harwood, “Genome-wide transcriptional analysis of the phosphate starvation stimulon of bacillus subtilis,” J bacteriol, vol. 187, iss. 23, pp. 8063-8080, 2005.
    [Bibtex]
    @ARTICLE{Allenby:2005:J-Bacteriol:16291680,
    author = {Allenby, N E and O'Connor, N and Pr{\'a}gai, Z and Ward, A C and
    Wipat, A and Harwood, C R},
    title = {Genome-wide transcriptional analysis of the phosphate starvation stimulon of Bacillus subtilis},
    journal = {J Bacteriol},
    year = {2005},
    volume = {187},
    pages = {8063-8080},
    number = {23},
    month = {Dec},
    abstract = {Bacillus subtilis responds to phosphate starvation stress by inducing
    the PhoP and SigB regulons. While the PhoP regulon provides a specific
    response to phosphate starvation stress, maximizing the acquisition
    of phosphate (P(i)) from the environment and reducing the cellular
    requirement for this essential nutrient, the SigB regulon provides
    nonspecific resistance to stress by protecting essential cellular
    components, such as DNA and membranes. We have characterized the
    phosphate starvation stress response of B. subtilis at a genome-wide
    level using DNA macroarrays. A combination of outlier and cluster
    analyses identified putative new members of the PhoP regulon, namely,
    yfkN (2',3' cyclic nucleotide 2'-phosphodiesterase), yurI (RNase),
    yjdB (unknown), and vpr (extracellular serine protease). YurI is
    thought to be responsible for the nonspecific degradation of RNA,
    while the activity of YfkN on various nucleotide phosphates suggests
    that it could act on substrates liberated by YurI, which produces
    3' or 5' phosphoribonucleotides. The putative new PhoP regulon members
    are either known or predicted to be secreted and are likely to be
    important for the recovery of inorganic phosphate from a variety
    of organic sources of phosphate in the environment.},
    doi = {10.1128/JB.187.23.8063-8080.2005},
    owner = {n8384838},
    pmid = {16291680},
    timestamp = {2013.05.07},
    url = {http://www.hubmed.org/display.cgi?uids=16291680}
    }
  • [DOI] S. Katayama, Y. Tomaru, T. Kasukawa, K. Waki, M. Nakanishi, M. Nakamura, H. Nishida, C. C. Yap, M. Suzuki, J. Kawai, H. Suzuki, P. Carninci, Y. Hayashizaki, C. Wells, M. Frith, T. Ravasi, K. C. Pang, J. Hallinan, J. Mattick, D. A. Hume, L. Lipovich, S. Batalov, P. G. Engström, Y. Mizuno, M. A. Faghihi, A. Sandelin, A. M. Chalk, S. Mottagui-Tabar, Z. Liang, B. Lenhard, C. Wahlestedt, RIKEN Genome Exploration Research Group, {. S. (. N. P. C. Group)}, and FANTOM Consortium, “Antisense transcription in the mammalian transcriptome,” Science, vol. 309, iss. 5740, pp. 1564-1566, 2005.
    [Bibtex]
    @ARTICLE{Katayama:2005:Science:16141073,
    author = {Katayama, S and Tomaru, Y and Kasukawa, T and Waki, K and Nakanishi,
    M and Nakamura, M and Nishida, H and Yap, C C and Suzuki, M and Kawai,
    J and Suzuki, H and Carninci, P and Hayashizaki, Y and Wells, C and
    Frith, M and Ravasi, T and Pang, K C and Hallinan, J and Mattick,
    J and Hume, D A and Lipovich, L and Batalov, S and Engstr{\"o}m,
    P G and Mizuno, Y and Faghihi, M A and Sandelin, A and Chalk, A M
    and Mottagui-Tabar, S and Liang, Z and Lenhard, B and Wahlestedt,
    C and {RIKEN Genome Exploration Research Group} and {Genome Science
    Group (Genome Network Project Core Group)} and {FANTOM Consortium}},
    title = {Antisense transcription in the mammalian transcriptome},
    journal = {Science},
    year = {2005},
    volume = {309},
    pages = {1564-1566},
    number = {5740},
    month = {Sep},
    abstract = {Antisense transcription (transcription from the opposite strand to
    a protein-coding or sense strand) has been ascribed roles in gene
    regulation involving degradation of the corresponding sense transcripts
    (RNA interference), as well as gene silencing at the chromatin level.
    Global transcriptome analysis provides evidence that a large proportion
    of the genome can produce transcripts from both strands, and that
    antisense transcripts commonly link neighboring "genes" in complex
    loci into chains of linked transcriptional units. Expression profiling
    reveals frequent concordant regulation of sense/antisense pairs.
    We present experimental evidence that perturbation of an antisense
    RNA can alter the expression of sense messenger RNAs, suggesting
    that antisense transcription contributes to control of transcriptional
    outputs in mammals.},
    doi = {10.1126/science.1112009},
    owner = {n8384838},
    pmid = {16141073},
    timestamp = {2013.05.08},
    url = {http://www.hubmed.org/display.cgi?uids=16141073}
    }
  • [DOI] K. Flanagan, R. Stevens, M. Pocock, P. Lee, and A. Wipat, “Ontology for genome comparison and genomic rearrangements,” Comp funct genomics, vol. 5, iss. 6-7, pp. 537-544, 2004.
    [Bibtex]
    @ARTICLE{Flanagan:2004:Comp-Funct-Genomics:18629137,
    author = {Flanagan, K and Stevens, R and Pocock, M and Lee, P and Wipat, A},
    title = {Ontology for genome comparison and genomic rearrangements},
    journal = {Comp Funct Genomics},
    year = {2004},
    volume = {5},
    pages = {537-544},
    number = {6-7},
    abstract = {We present an ontology for describing genomes, genome comparisons,
    their evolution and biological function. This ontology will support
    the development of novel genome comparison algorithms and aid the
    community in discussing genomic evolution. It provides a framework
    for communication about comparative genomics, and a basis upon which
    further automated analysis can be built. The nomenclature defined
    by the ontology will foster clearer communication between biologists,
    and also standardize terms used by data publishers in the results
    of analysis programs. The overriding aim of this ontology is the
    facilitation of consistent annotation of genomes through computational
    methods, rather than human annotators. To this end, the ontology
    includes definitions that support computer analysis and automated
    transfer of annotations between genomes, rather than relying upon
    human mediation.},
    doi = {10.1002/cfg.436},
    owner = {n8384838},
    pmid = {18629137},
    timestamp = {2013.05.07},
    url = {http://www.hubmed.org/display.cgi?uids=18629137}
    }
  • [DOI] N. E. Allenby, N. O’Connor, Z. Prágai, N. M. Carter, M. Miethke, S. Engelmann, M. Hecker, A. Wipat, A. C. Ward, and C. R. Harwood, “Post-transcriptional regulation of the bacillus subtilis pst operon encoding a phosphate-specific abc transporter,” Microbiology, vol. 150, iss. Pt 8, pp. 2619-2628, 2004.
    [Bibtex]
    @ARTICLE{Allenby:2004:Microbiology:15289558,
    author = {Allenby, N E and O'Connor, N and Pr{\'a}gai, Z and Carter, N M and
    Miethke, M and Engelmann, S and Hecker, M and Wipat, A and Ward,
    A C and Harwood, C R},
    title = {Post-transcriptional regulation of the Bacillus subtilis pst operon encoding a phosphate-specific ABC transporter},
    journal = {Microbiology},
    year = {2004},
    volume = {150},
    pages = {2619-2628},
    number = {Pt 8},
    month = {Aug},
    abstract = {During phosphate starvation, Bacillus subtilis regulates genes in
    the PhoP regulon to reduce the cell's requirement for this essential
    substrate and to facilitate the recovery of inorganic phosphate from
    organic sources such as teichoic and nucleic acids. Among the proteins
    that are highly induced under these conditions is PstS, the phosphate-binding
    lipoprotein component of a high-affinity ABC-type phosphate transporter.
    PstS is encoded by the first gene in the pst operon, the other four
    members of which encode the integral membrane and cytoplasmic components
    of the transporter. The transcription of the pst operon was analysed
    using a combination of methods, including transcriptional reporter
    gene technology, Northern blotting and DNA arrays. It is shown that
    the primary transcript of the pst operon is processed differentially
    to maintain higher concentrations of PstS relative to other components
    of the transporter. The comparative studies have revealed limitations
    in the use of reporter gene technology for analysing the transcription
    of operons in which the messenger RNA transcript is differentially
    processed.},
    doi = {10.1099/mic.0.27126-0},
    owner = {n8384838},
    pmid = {15289558},
    timestamp = {2013.05.07},
    url = {http://www.hubmed.org/display.cgi?uids=15289558}
    }
  • [DOI] T. Oinn, M. Addis, J. Ferris, D. Marvin, M. Senger, M. Greenwood, T. Carver, K. Glover, M. R. Pocock, A. Wipat, and P. Li, “Taverna: a tool for the composition and enactment of bioinformatics workflows,” Bioinformatics, vol. 20, iss. 17, pp. 3045-3054, 2004.
    [Bibtex]
    @ARTICLE{Oinn:2004:Bioinformatics:15201187,
    author = {Oinn, T and Addis, M and Ferris, J and Marvin, D and Senger, M and
    Greenwood, M and Carver, T and Glover, K and Pocock, M R and Wipat,
    A and Li, P},
    title = {Taverna: a tool for the composition and enactment of bioinformatics workflows},
    journal = {Bioinformatics},
    year = {2004},
    volume = {20},
    pages = {3045-3054},
    number = {17},
    month = {Nov},
    abstract = {MOTIVATION: In silico experiments in bioinformatics involve the co-ordinated
    use of computational tools and information repositories. A growing
    number of these resources are being made available with programmatic
    access in the form of Web services. Bioinformatics scientists will
    need to orchestrate these Web services in workflows as part of their
    analyses. RESULTS: The Taverna project has developed a tool for the
    composition and enactment of bioinformatics workflows for the life
    sciences community. The tool includes a workbench application which
    provides a graphical user interface for the composition of workflows.
    These workflows are written in a new language called the simple conceptual
    unified flow language (Scufl), where by each step within a workflow
    represents one atomic task. Two examples are used to illustrate the
    ease by which in silico experiments can be represented as Scufl workflows
    using the workbench application.},
    doi = {10.1093/bioinformatics/bth361},
    owner = {n8384838},
    pmid = {15201187},
    timestamp = {2013.05.07},
    url = {http://www.hubmed.org/display.cgi?uids=15201187}
    }
  • [DOI] J. Hallinan, “Gene duplication and hierarchical modularity in intracellular interaction networks,” Biosystems, vol. 74, iss. 1-3, pp. 51-62, 2004.
    [Bibtex]
    @ARTICLE{Hallinan:2004:Biosystems:15125992,
    author = {Hallinan, J},
    title = {Gene duplication and hierarchical modularity in intracellular interaction networks},
    journal = {Biosystems},
    year = {2004},
    volume = {74},
    pages = {51-62},
    number = {1-3},
    month = {Apr-Jun},
    abstract = {Networks of interactions evolve in many different domains. They tend
    to have topological characteristics in common, possibly due to common
    factors in the way the networks grow and develop. It has been recently
    suggested that one such common characteristic is the presence of
    a hierarchically modular organization. In this paper, we describe
    a new algorithm for the detection and quantification of hierarchical
    modularity, and demonstrate that the yeast protein-protein interaction
    network does have a hierarchically modular organization. We further
    show that such organization is evident in artificial networks produced
    by computational evolution using a gene duplication operator, but
    not in those developing via preferential attachment of new nodes
    to highly connected existing nodes.},
    doi = {10.1016/j.biosystems.2004.02.004},
    owner = {n8384838},
    pmid = {15125992},
    timestamp = {2013.05.08},
    url = {http://www.hubmed.org/display.cgi?uids=15125992}
    }