Newcastle University

Roles and Responsibilities

I am a Research Associate and PhD student at Newcastle University. I am a member of the Centre for Integrated Systems Biology of Ageing and Nutrition (CISBAN), as well as part of the School for Computing Science.

Qualifications

I received my undergraduate degree in Biology and Ancient Mediterranean Civilizations from Rice University and a Master's degree in Bioinformatics from the University of York.

Previous Positions

Before working at Newcastle University, I spent 6 1/2 years as part of the UniProt team at the European Bioinformatics Institute.

Informal Interests

You can also find me on my blog or on FriendFeed and Twitter. While all of these deal primarily with my research areas, they are my personal accounts, and do not necessarily reflect the position or opinions of Newcastle University.

Research Interests

My work focuses on data integration, ontologies and data standards, specifically in the area of systems biology.

Current Work

Semantic data integration to provide novel annotation for quantitative biological models is the main area of my research.
Other current projects include Saint, SyMBA, and MFO. I am also a developer of the OBI ontology and FuGE toolkits.

Projects

• Model Format OWL (MFO): Integration of constraints facilitates validation of biological models
  Project Leader(s): Allyson Lister, Prof. Anil Wipat
• Saint – A lightweight integration environment for model annotation
  Project Leader(s): Allyson Lister, Morgan Taschuk, Anil Wipat
• SyMBA: Storing experimental knowledge in a FuGE-compliant archive
  Project Leader(s): Anil Wipat

• Lister AL, Datta RS, Hofmann O, Krause R, Kuhn M, Roth B, Schneider R. Live Coverage of Scientific Conferences Using Web Technologies. PLoS Computational Biology 2010, 6(1), e1000563.
• Lister AL, Pocock M, Taschuk M, Wipat A. Saint: A Lightweight Integration Environment for Model Annotation. Bioinformatics 2009, 25(22), 3026-3027.
• Lister AL, Lord P, Pocock M, Wipat A. Annotation of SBML Models Through Rule-Based Semantic Integration. In: 12th Annual Bio-Ontologies Meeting colocated with ISMB. 2009, Stockholm, Sweden: Intelligent Systems for Molecular Biology.
• Jones AR, Lister AL, Hermida L, Wilkinson P, Eisenacher M, Belhajjame K, Gibson F, Lord P, Pocock M, Rosenfelder H, Santoyo-Lopez J, Wipat A, Paton NW. Modeling and Managing Experimental Data Using FuGE. OMICS: A Journal of Integrative Biology 2009, 13(3), 239-251.
• Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen M, Angiuoli S, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, Cochrane G, Cole J, Dawyndt P, De Vos P, Depamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glöckner F, Goldstein P, Guralnick R, Haft D, Hancock D, Hermjakob H, Hertz-Fowler C, Hugenholtz P, Joint I, Kagan L, Kane M, Kennedy J, Kowalchuk G, Kottmann R, Kolker E, Kravitz S, Kyrpides N, Leebens-Mack J, Lewis S, Li K, Lister AL, Lord P, Maltsev N, Markowitz V, Martiny J, Methe B, Mizrachi I, Moxon R, Nelson K, Parkhill J, Proctor L, White O, Sansone S, Spiers A, Stevens R, Swift P, Taylor C, Tateno Y, Tett A, Turner S, Ussery D, Vaughan B, Ward N, Whetzel T, San Gil I, Wilson G, Wipat A. The minimum information about a genome sequence (MIGS) specification. Nature Biotechnology 2008, 26(5), 541-547.
• Brinkman R, Bug B, Causton H, Clancy K, Cocos C, Courtot M, Derom D, Deutsch E, Fan L, Field D, Fostel J, Fragaso G, Gibson F, Gray T, Greenbaum J, Grenom P, Grethe J, He Y, Heiskanen M, Hernandez-Boussard T, Lord P, Lister AL, Malone J, Manduchi E, Montecchi L, Morrison N, Mungall C, Parkinson H, Peters B, Pocock M, Rocca-Serra P, Rubin D, Ruttenberg A, Sansone S-A, Scheuermann R, Schober D, Smith B, Soldatova LN, Stenzhorn H, Stoeckert C, Taylor C, Vita R, Westbrook J, White J, Whetzel PL, Wiemann S, Zheng J. Modeling biomedical experimental processes with OBI. In: 12th Annual Bio-Ontologies Meeting, ISMB/ECCB 2009. 2009, Stockholm, Sweden: Intelligent Systems for Molecular Biology.
• Lister AL, Datta RS, Hofmann O, Krause R, Kuhn M, Roth B, Schneider R. Live Coverage of Intelligent Systems for Molecular Biology/European Conference on Computational Biology (ISMB/ECCB) 2009. PLoS Computational Biology 2010, 6(1), e1000640.
• Lister AL, Charoensawan V, De S, James K, Chandra JSC, Huppert J. Interfacing systems biology and synthetic biology. Genome Biology 2009, 10(309), 3.
• Lister AL, Pocock M, Wipat A. Saint: a lightweight SBML annotation integration environment. In: BioSysBio.2009,Cambridge
• Sansone S, Rocca-Serra P, Brandizi M, Brazma A, Field D, Fostel J, Garrow A, Gilbert J, Goodsaid F, Hardy N, Jones P, Lister AL, Miller M, Morrison N, Rayner T, Sklyar N, Taylor C, Tong W, Warner G, Wiemann S. The first RSBI (ISA-TAB) workshop: "Can a simple format work for complex studies?". OMICS: A Journal of Integrative Biology 2008,12 2 143-149.
• Courtot M, Bug B, Gibson F, Lister AL, Malone J, Schober D, Brinkman R, Ruttenberg A. The OWL of Biomedical Investigations. In: OWLED. 2008, Karlsruhe, Germany: W3C Web Ontology Language Workshops.
• Field D, Glöckner F, Garrity G, Gray T, Sterk P, Cochrane G, Vaughan R, Kolker E, Kottmann R, Kyrpides N, Angiuoli S, Dawyndt P, Guralnick R, Goldstein P, Hall N, Hirschman L, Kravitz S, Lister AL, Markowitz V, Thomson N, Whetzel T. Meeting report: The fourth Genomic Standards Consortium (GSC) workshop. In: The Fourth Genomic Standards Consortium (GSC) Workshop. 2008, National Institute for Environmental eScience (NIEeS), Cambridge: Mary Ann Liebert, Inc. Publishers.
• Lister AL, Pocock M, Wipat A. Integration of constraints documented in SBML, SBO, and the SBML Manual facilitates validation of biological models. Journal of Integrative Bioinformatics 2007, 4(3), 80.
• Field D, Garrity G, Gray T, Selengut J, Sterk P, Thomson N, Tatusova T, Cochrane G, Glöckner F, Kottmann R, Lister AL, Tateno Y, Vaughan R. eGenomics: Cataloguing our complete genome collection III. Comparative and Functional Genomics 2007, 2007(47304), 7.
• Lister AL, Jones AR, Pocock M, Shaw O, Wipat A. Implementing the FuGE Object Model: a Systems Biology Data Portal and Integrator. Newcastle upon Tyne: School of Computing Science, University of Newcastle upon Tyne, 2007. School of Computing Science Technical Report Series 1016.
• Lister A L, Pocock M, Wipat A. Integration of constraints documented in SBML, SBO, and the SBML Manual facilitates validation of biological models. Newcastle upon Tyne: School of Computing Science, University of Newcastle upon Tyne, 2007. School of Computing Science Technical Report Series 1043.
• Williams AL, Kersey PJ, Pruess M, Apweiler R. Biological Databases: Infrastructure, Content, and Integration. In: Azuaje F; Dopazo J, ed. Data Analysis and Visualization in Genomics and Proteomics. Hoboken, New Jersey: John Wiley & Sons, 2005, pp. 11-28.
• Kersey PJ, Duarte J, Williams AL, Karavidopoulou Y, Birney E, Apweiler R. The International Protein Index: An integrated database for proteomics experiments. Proteomics 2004, 4(7), 1985-1988.
• Courtot M, Juty N, Knupfer C, Waltemath D, Zhukova A, Drager A, Dumontier M, Finney A, Golebiewski M, Hastings J, Hoops S, Keating S, Kell DB, Kerrien S, Lawson J, Lister A, Lu J, Machne R, Mendes P, Pocock M, Rodriguez N, Villeger A, Wilkinson DJ, Wimalaratne S, Laibe C, Hucka M, LeNovere N. Controlled vocabularies and semantics in systems biology. Molecular Systems Biology 2011, 7, 543.
• Courtot M, Juty N, Knupfer C, Waltemath D, Zhukova A, Drager A, Dumontier M, Finney A, Golebiewski M, Hastings J, Hoops S, Keating S, Kell DB, Kerrien S, Lawson J, Lister A, Lu J, Machne R, Mendes P, Pocock M, Rodriguez N, Villeger A, Wilkinson DJ, Wimalaratne S, Laibe C, Hucka M, Le Novere N. Controlled vocabularies and semantics in systems biology. Molecular Systems Biology 2011, 7, 543.
• Courtot M, Gibson F, Lister AL, Malone J, Schober D, Brinkman RR, Ruttenberg A. MIREOT: The minimum information to reference an external ontology term. Applied Ontology 2011, 6(1), 23-33.
• Addinall SG, Holstein EM, Lawless C, Yu M, Chapman K, Banks AP, Ngo HP, Maringele L, Taschuk M, Young A, Ciesiolka A, Lister AL, Wipat A, Wilkinson DJ, Lydall D. Quantitative Fitness Analysis Shows That NMD Proteins and Many Other Protein Complexes Suppress or Enhance Distinct Telomere Cap Defects. PLoS Genetics 2011, 7(4), e1001362.