Dr. Jennifer Hallinan

Lecturer in Computing Science

I am a researcher in the School of Computing Science at Newcastle University in the United Kingdom. I have a backgroud in both molecular biology and computing science, and am interested in the interface between the two.

I am particularly interested in the use of computational intelligence techniques to design synthetic genetic circuits. Our team has laboratory space in the Centre for Bacterial Cell Biology, where our designs can be implemented in our favourite organism, Bacillus subtilis.

Research Interests

  • Systems and synthetic biology
  • Computational intelligence and machine learning
  • Molecular biology of Bacillus subtilis

Publications

  • [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] 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] 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] 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}
    }
  • 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}
    }
  • 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}
    }
  • 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] 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] 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}
    }
  • [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] 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] 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}
    }
  • [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}
    }
  • [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] 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}
    }