Staff Profile
Professor Anil Wipat
Professor of Integrative Bioinformatics
- Email: anil.wipat@ncl.ac.uk
- Telephone: +44 191 208 8213 or 208 3212
- Fax: +44 (0) 191 208 8232
- Address: School of Computing
Urban Sciences Building
Newcastle University
1 Science Square
Science Central
Newcastle upon Tyne
NE4 5TG
I am a Professor of Bioinformatics at the School of Computing at Newcastle University.
I co-direct Newcastle's Interdisciplinary Computing and Complex BioSystems (ICOS) research group.
My research forms part of the larger research effort of the the ICOS research group of which I am the co-founder and co-director.
My individual team researches data integration in bioinformatics at various levels from the local integration of ‘omics’ datasets to form integrated functional networks, through to the integration of remote heterogeneous databases. We apply these data integration strategies to problems in Systems and Synthetic Biology (e.g. the Repotrial Project).
The biological applications of our research are quite diverse ranging from microbiology and metagenomics, through to the mechanisms of human genetic disease and ageing. Traditionally we have a strong interest and background in microbial genomics and functional genomics particularly for Gram-positive microorganisms such as Bacillus and relatives.
We are applying our combined expertise in bioinformatics, data integration, evolutionary computation and microbial genomics to the problem of designing microbial systems, in the area of Synthetic Biology. We are particularly interested in model-driven design for synthetic biology and are exploring how biological data can be used to inform this design process. We also investigating approaches to facilitate an integrative and systems approach to biology, with a particular emphasis on modelling and networks.
Our research in data science and cloud computing technology allows us to tackle problems in biological data analysis, simulation, and integration (see for example Newcastle data NUCoRe). We are interested in how the biological sciences can, in turn, drive developments in computing science. In particular, we are developing technology for data integration, computational modelling and comparative genomics, with an emphasis on the analysis of metagenomic datasets. For example, we are researching new approaches for mining (and designing) the genes encoding industrially useful enzymes from environmental DNA sequences.
The ICOS group maintains wet-lab facilities in collaboration with the Institute for Cell and Molecular Biosciences to allow the implementation of our computational designs of biological systems, with a particular focus on synthetic biology applied to B. subtilis, engineering stress response regulatory networks, portable genetic circuits and the engineering of microbial communities. See for example, the EPSRC funded Portabolomics project and the EPSRC funded Thinking Soils project.
We are also interested in the development and applications of new data standards, and work closely with the community in the development of the major standard in Synthetic Biology, Synthetic Biology Open Language (SBOL). We are currently focussing on data standards for automation and robotics in microbial biotechnology (for example as part of the BioRoboost project, and the ELIXIR Microbial Biotechnology Community).
Opportunities to work in our group arise frequently. We recruit both computational and wet-lab researchers. Please visit the positions available link for details or send a CV to anil.wipat[theusualsymbol]ncl.ac.uk.
We gratefully acknowledge funding from a variety of sources, including the BBSRC, EPSRC, NERC, MRC and the Wellcome Trust.
- I was degree programme director (from 2005-2019) and founder of our successful MSc Bioinformatics, MSc Synthetic Biology, and MSc Neuroinformatics for which I contribute on a number of modules.
- Lahme S, Callbeck CM, Eland LE, Wipat A, Enning D, Head IM, Hubert CRJ. Comparison of sulfide-oxidizing Sulfurimonas strains reveals a new mode of thiosulfate formation in subsurface environments. Environmental Microbiology 2020, 22(5), 1784-1800.
- Jana S, Charlton SGV, Eland LE, Burgess JG, Wipat A, Curtis TP, Chen J. Nonlinear rheological characteristics of single species bacterial biofilms. npj Biofilms and Microbiomes 2020, 6, 19.
- Kenny NJ, McCarthy SA, Dudchenko O, James K, Betteridge E, Corton C, Dolucan J, Mead D, Oliver K, Omer AD, Pelan S, Ryan Y, Sims Y, Skelton J, Smith M, Torrance J, Weisz D, Wipat A, Aiden EL, Howe K, Williams ST. The gene-rich genome of the scallop Pecten maximus. GigaScience 2020, 9(5).
- Beal J, Nguyen T, Gorochowski TE, Goni-Moreno A, Scott-Brown J, McLaughlin JA, Madsen C, Aleritsch B, Bartley B, Bhakta S, Bissell M, Castillo Hair S, Clancy K, Luna A, Le Novere N, Palchick Z, Pocock M, Sauro H, Sexton JT, Tabor JJ, Voigt CA, Zundel Z, Myers C, Wipat A. Communicating Structure and Function in Synthetic Biology Diagrams. ACS Synthetic Biology 2019, 8(8), 1818-1825.
- Hallinan JS, Wipat A, Kitney R, Woods S, Taylor K, Goñi-Moreno A. Future-Proofing Synthetic Biology: Educating the Next Generation. Engineering Biology 2019, 3(2), 25-31.
- Neal ML, Konig M, Nickerson D, Misirli G, Kalbasi R, Drager A, Atalag K, Chelliah V, Cooling MT, Cook DL, Crook S, De Alba M, Friedman SH, Garny A, Gennari JH, Gleeson P, Golebiewski M, Hucka M, Juty N, Myers C, Olivier BG, Sauro HM, Scharm M, Snoep JL, Toure V, Wipat A, Wolkenhauer O, Waltemath D. Harmonizing semantic annotations for computational models in biology. Briefings in Bioinformatics 2019, 20(2), 540-550.
- Charlton S, White M, Jana S, Eland L, Jayathilake P, Burgess J, Chen J, Wipat A, Curtis T. Regulating, Measuring, and Modeling the Viscoelasticity of Bacterial Biofilms. Journal of Bacteriology 2019, 201(18), e00101-19.
- McLaughlin JA, Myers CJ, Zundel Z, Wilkinson N, Atallah C, Wipat A. sboljs: Bringing the Synthetic Biology Open Language to the Web Browser. ACS Synthetic Biology 2019, 8(1), 191-193.
- Mısırlı G, Taylor R, Goñi-Moreno A, McLaughlin JA, Myers C, Gennari JH, Lord P, Wipat A. SBOL-OWL: An Ontological Approach for Formal and Semantic Representation of Synthetic Biology Information. ACS Synthetic Biology 2019, 8(7), 1498-1514.
- Waites W, Mlslrll G, Cavaliere M, Danos V, Wipat A. A Genetic Circuit Compiler: Generating Combinatorial Genetic Circuits with Web Semantics and Inference. ACS Synthetic Biology 2018, 7(12), 2812-2823.
- Houghton D, Stewart CJ, Stamp C, Nelson A, Ajami NJ, Petrosino JF, Wipat A, Trenell MI, Turnbull DM, Greaves LC. Age-related mitochondrial dysfunction influences the mouse intestinal microbiome composition. The Journals of Gerontology: Series A, Biological Sciences & Medical Sciences 2018, 73(5), 571-578.
- Dade-Robertson M, Mitrani H, Rodriguez-Corral J, Zhang M, Hernan L, Guyet A, Wipat A. Design and modelling of an engineered bacteria-based, pressure-sensitive soil. Bioinspiration & Biomimetics 2018, 13(4), 046004.
- Guyet A, Dade-Robertson M, Wipat A, Casement J, Smith W, Mitrani H, Zhang M. Mild hydrostatic pressure triggers oxidative responses in Escherichia coli. PLoS ONE 2018, 13(7), e0200660.
- Lawry BM, Johnson CL, Flanagan K, Spoors JA, McNeil CJ, Wipat A, Keegan N. Species-specific detection of C. difficile using targeted antibody design. Analytical Chemistry 2018, 90(22), 13475-13482.
- McLaughlin JA, Myers CJ, Zundel Z, Misirli G, Zhang M, Ofiteru ID, Goni-Moreno A, Wipat A. SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology. ACS Synthetic Biology 2018, 7(2), 682-688.
- Myers CJ, Beal J, Gorochowski TE, Kuwahara H, Madsen C, McLaughlin JA, Misirli G, Nguyen T, Oberortner E, Samineni M, Wipat A, Zhang M, Zundel Z. A standard-enabled workflow for synthetic biology. Biochemical Society Transactions 2017, 45(3), 793-803.
- Myers CJ, McLaughlin J, Misirli G, Nguyen T, Samineni M, Zhang M, Zundel Z, Wipat A. A synthetic biology workflow using SBOL. In: Synthetic Biology Conference (SEED 2017): Engineering, Evolution, and Design. 2017, Vancouver, British Columbia, Canada: AIChE.
- Cox RS, McLaughlin JA, Grünberg R, Beal J, Wipat A, Sauro HM. A Visual Language for Protein Design. ACS Synthetic Biology 2017, 6(7), 1120-1123.
- Goni-Moreno A, Wipat A, Krasnogor N. CSBB: Synthetic biology research at Newcastle University. Biochemical Society Transactions 2017, 45(3), 781-783.
- Gonzalez-Cabaleiro R, Mitchell AM, Smith W, Wipat A, Ofiteru ID. Heterogeneity in pure microbial systems: Experimental measurements and modeling. Frontiers in Microbiology 2017, 8, 1813.
- Houghton D, Stewart CJ, Stamp C, Nelson A, Ajami NJ, Petrosino JF, Wipat A, Trenell MI, Turnbull DM, Greaves LC. Impact of Age-Related Mitochondrial Dysfunction and Exercise on Intestinal Microbiota Composition. The Journals of Gerontology: Series A 2017, 73(5), 571-578.
- Zhang M, McLaughlin JA, Wipat A, Myers CJ. SBOLDesigner 2: An Intuitive Tool for Structural Genetic Design. ACS Synthetic Biology 2017, 6(7), 1150-1160.
- Dade-Robertson M, Rodriguez-Corral J, Guyet A, Mitrani H, Wipat A, Zhang M. Synthetic Biological Construction: Beyond 'bio-inspired' in the design of new materials and fabrication systems. In: 3rd International Conference Biodigital: Architecture & Genetics. 2017, Barcelona: UIC.
- Mullen J, Cockell SJ, Woollard P, Wipat A. An Integrated Data Driven Approach to Drug Repositioning Using Gene-Disease Associations. PLoS One 2016, 11(5), e0155811.
- Misirli G, Cavaliere M, Waites W, Pocock M, Madsen C, Gilfellon O, Honorato-Zimmer R, Zuliani P, Danos V, Wipat A. Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualisation. Bioinformatics 2016, 32(6), 908-917.
- Skelton DJ, Hallinan JS, Park S, Wipat A. Computational intelligence for metabolic pathway design: Application to the pentose phosphate pathway. In: CIBCB 2016 - Annual IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology. 2016, Chiang Mai, Thailand: Institute of Electrical and Electronics Engineers Inc.
- Misirli G, Hallinan J, Pocock M, Lord P, McLaughlin JA, Sauro H, Wipat A. Data Integration and Mining for Synthetic Biology Design. ACS Synthetic Biology 2016, 5(10), 1086-1097.
- Sutantyo D, Walker C, Debono N, Vargas J, Wipat A, Hallinan JS. Engineering bacterial populations for pattern formation. In: CIBCB 2016 - Annual IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology. 2016, IEEE.
- Zhang Z, Nguyen T, Roehner N, Misirli G, Pocock M, Oberortner E, Samineni M, Zundel Z, Beal J, Clancy K, Wipat A, Myers CJ. libSBOLj 2.0: A Java Library to Support SBOL 2.0. IEEE Life Sciences Letters 2016, 1(4), 34-37.
- Eland LE, Wipat A, Lee S, Park S, Wu LJ. Microfluidics for bacterial imaging. In: Harwood, C, ed. Methods in Microbiology. London, UK: Elsevier, 2016, pp.69-111.
- Mullen J, Cockell SJ, Tipney H, Woollard PM, Wipat A. Mining integrated semantic networks for drug repositioning opportunities. PeerJ 2016, 4, e1558.
- Roehner N, Beal J, Clancy K, Bartley B, Misirli G, Grunberg R, Oberortner E, Pocock M, Bissell M, Madsen C, Nguyen T, Zhang M, Zhang Z, Zundel Z, Densmore D, Gennari JH, Wipat A, Sauro HM, Myers CJ. Sharing Structure and Function in Biological Design with SBOL 2.0. ACS Synthetic Biology 2016, 5(6), 498-506.
- Dade-Robertson M, Rodriguez-Corral J, Guyet A, Mitrani H, Wipat A, Zhang M. Synthetic Biological Construction: Beyond ‘bio-inspired’ in the design of new materials and fabrication systems. In: Sustainable Smart Manufacturing (S2M). 2016, Lisbon, Portugal: CRC Press LLC.
- Madsen C, McLaughlin JA, Misirli G, Pocock M, Flanagan K, Hallinan J, Wipat A. The SBOL Stack: A Platform for Storing, Publishing, and Sharing Synthetic Biology Designs. ACS Synthetic Biology 2016, 5(6), 487-497.
- Dade-Robertson M, Corral J, Mitrani H, Zhang M, Wipat A, Ramirez-Figueroa C, Hernan L. Thinking Soils: A Synthetic Biology approach to material based design computation. In: ACADIA 2016 - Posthuman Frontiers: Data, Designers and Cognitive Machines. 2016, Ann Arbor, Michigan: Association for Computer Aided Design in Architecture.
- McLaughlin JA, Pocock M, Misirli G, Madsen C, Wipat A. VisBOL: Web-Based Tools for Synthetic Biology Design Visualization. ACS Synthetic Biology 2016, 5(8), 874-876.
- James K, Al-Ali S, Tarn J, Cockell SJ, Gillespie CS, Hindmarsh V, Locke J, Mitchell S, Lendrem D, Bowman S, Price E, Pease CT, Emery P, Lanyon P, Hunter JA, Gupta M, Bombardieri M, Sutcliffe N, Pitzalis C, McLaren J, Cooper A, Regan M, Giles I, Isenberg D, Saravanan V, Coady D, Dasgupta B, McHugh N, Young-Min S, Moots R, Gendi N, Akil M, Griffiths B, The UK Primary Sjögren’s Syndrome registry, Wipat A, Newton J, Jones DE, Isaacs J, Hallinan J, Ng W-F. A Transcriptional Signature of Fatigue Derived from Patients with Primary Sjögren’s Syndrome. PLoS ONE 2015, 10(12), e0143970.
- James K, Al-Ali S, Tarn J, Cockell SJ, Gillespie CS, Bowman S, Isaacs J, Jones DE, Newton J, Price E, Wipat A, Hallinan J, Ng WF, UKPSSR. A Transcriptional Signature of Fatigue Derived from Patients with Primary Sjögren's Syndrome. In: The 13th International Symposium on Sjögren's Syndrome. 2015, Bergen, Norway: Wiley-Blackwell.
- Relton CL, Gaunt T, McArdle W, Ho KR, Duggirala A, Shihab H, Woodward G, Lyttleton O, Evans DM, Reik W, Paul YL, Ficz G, Ozanne SE, Wipat A, Flanagan K, Lister A, Heijmans BT, Ring SM, Smith GD. Data Resource Profile: Accessible Resource for Integrated Epigenomic Studies (ARIES). International Journal of Epidemiology 2015, 44(4), 1181-1190.
- James K, Al-Ali S, Tarn J, Cockell SJ, Gillespie CS, Bowman S, Isaacs J, Jones DE, Newton J, Price E, Wipat A, Hallinan J, Ng WF, UKPSSR. Gene Set Enrichment Analysis Across Multiple Expression Studies Reveals a Core Subset of Primary Sjögren's Syndrome-Related Genes. In: The 13th International Symposium on Sjögren's Syndrome. 2015, Bergen, Norway: Wiley-Blackwell.
- James K, Ng WF, Wipat A, Hallinan J. Integrative Network-Based Analysis of the Primary Sjogren's Syndrome Transcriptome between Human and Mouse. In: 13th International Symposium on Sjögren's Syndrome. 2015, Bergen, Norway: Wiley-Blackwell.
- Roehner N, Oberortner E, Pocock M, Beal J, Clancy K, Madsen C, Misirli G, Wipat A, Sauro H, Myers CJ. Proposed Data Model for the Next Version of the Synthetic Biology Open Language. ACS Synthetic Biology 2015, 4(1), 57-71.
- Quinn JY, Cox RS, Adler A, Beal J, Bhatia S, Cai YZ, Chen J, Clancy K, Galdzicki M, Hillson NJ, Le Novere N, Maheshwari AJ, McLaughlin JA, Myers CJ, Umesh P, Pocock M, Rodriguez C, Soldatova L, Stan GBV, Swainston N, Wipat A, Sauro HM. SBOL Visual: A Graphical Language for Genetic Designs. PLOS Biology 2015, 13(12), e1002310.
- Flanagan K, Cockell S, Harwood C, Hallinan J, Nakjang S, Lawry B, Wipat A. A distributed computational search strategy for the identification of diagnostics targets: Application to finding aptamer targets for methicillin-resistant staphylococci. Journal of Integrative Bioinformatics 2014, 11(2), 242.
- Misirli G, Hallinan J, Röttger R, Baumbach J, Wipat A. BacillusRegnet: a transcriptional regulation database and analysis platform for Bacillus species. Journal of Integrative Bioinformatics 2014, 11(2), 244.
- Misirli G, Hallinan J, Wipat A. Composable modular models for synthetic biology. ACM Journal on Emerging Technologies in Computing Systems 2014, 11(3), 22.
- Misirli G, Hallinan J, Wipat A. Composable Modular Models for Synthetic Biology. Newcastle upon Tyne: School of Computing Science, University of Newcastle upon Tyne, 2014. School of Computing Science Technical Report Series 1424.
- Best A, James K, Dalgliesh C, Hong EA, Kheirolahi-Kouhestani M, Curk T, Xu Y, Danilenko M, Hussain R, Keavney B, Wipat A, Klinck R, Cowell IG, Cheong Lee K, Austin C, Venables JP, Chabot B, Santibanez Koref M, Tyson-Capper AJ, Elliott DJ. Human Tra2 proteins jointly control a CHEK1 splicing switch among alternative and constitutive target exons. Nature Communications 2014, 5, 4760.
- Myers CJ, Sauro H, Wipat A. Introduction to the Special Issue on Computational Synthetic Biology. ACM Journal on Emerging Technologies in Computing Systems (JETC) 2014, 11(3), 20.
- Rusakovica J, Hallinan J, Wipat A, Zuliani P. Probabilistic Latent Semantic Analysis Applied to Whole Bacterial Genomes Identifies Common Genomic Features. Journal of Integrative Bioinformatics 2014, 11(2), 243.
- Galdzicki M, Clancy KP, Oberortner E, Pocock M, Quinn JY, Rodriguez CA, Roehner N, Wilson ML, Adam L, Anderson JC, Bartley BA, Beal J, Chandran D, Chen J, Densmore D, Endy D, Grunberg R, Hallinan J, Hillson NJ, Johnson JD, Kuchinsky A, Lux M, Misirli G, Peccoud J, Plahar HA, Sirin E, Stan GB, Villalobos A, Wipat A, Gennari JH, Myers CJ, Sauro HM. The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology. Nature Biotechnology 2014, 32(6), 545-550.
- Hallinan JS, Gilfellon O, Misirli G, Wipat A. Tuning Receiver Characteristics in Bacterial Quorum Communication: An Evolutionary Approach Using Standard Virtual Biological Parts. In: IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology. 2014, Honolulu, HI: IEEE.
- Harwood CR, Pohl S, Smith W, Wipat A. Bacillus subtilis: Model Gram-Positive Synthetic Biology Chassis. In: Colin Harwood and Anil Wipat, ed. Microbial Synthetic Biology. Oxford: Academic Press, 2013, pp.87-117.
- Misirli G, Wipat A, Mullen J, James K, Pocock M, Smith W, Allenby N, Hallinan J. BacillOndex: An Integrated Data Resource for Systems and Synthetic Biology. Journal of Integrative Bioinformatics 2013, 10(2), 224.
- Pohl S, Bhavsar G, Hulme J, Bloor AE, Misirli G, Leckenby MW, Radford DS, Smith W, Wipat A, Williamson ED, Harwood CR, Cranenburgh RM. Proteomic analysis of Bacillus subtilis strains engineered for improved production of heterologous proteins. Proteomics 2013, 13(22), 3298-3308.
- Nakjang S, Ndeh DA, Wipat A, Bolam DN, Hirt RP. A Novel Extracellular Metallopeptidase Domain Shared by Animal Host-Associated Mutualistic and Pathogenic Microbes. PLoS One 2012, 7(1), 1-18.
- Weile J, James K, Hallinan J, Cockell SJ, Lord P, Wipat A, Wilkinson DJ. Bayesian integration of networks without gold standards. Bioinformatics 2012, 28(11), 1495-1500.
- Hallinan JS, Park S, Wipat A. Bridging the Gap Between Design and Reality: A Dual Evolutionary Strategy for the Design of Synthetic Genetic Circuits. In: BioInformatics: International Conference on Bioinformatics Models, Methods and Algorithms. 2012, Algarve, Portugal: ScitePress.
- Collison M, Hirt RP, Wipat A, Nakjang S, Sanseau P, Brown JR. Data mining the human gut microbiota for therapeutic targets. Briefings in Bioinformatics 2012, 13(6), 751-768.
- James K, Wipat A, Hallinan J. Is newer better?-evaluating the effects of data curation on integrated analyses in Saccharomyces cerevisiae. Integrative Biology 2012, 4(7), 715-727.
- Flanagan K, Nakjang S, Hallinan J, Harwood C, Hirt RP, Pocock MR, Wipat A. Microbase2.0: a generic framework for computationally intensive bioinformatics workflows in the cloud. Journal of Integrative Bioinformatics 2012, 9(2), 12.
- Harwood CR, Wipat A, ed. Systems Biology of Bacteria. Oxford: Academic Press, 2012.
- Weatherhead S, Farr P, Swan D, Jamieson D, Hallinan J, Lloyd J, Wipat A, Reynolds N. Apoptosis of keratinocytes is a key mechanism in UVB-induced clearance of psoriasis. In: 41st Annual Meeting of the European Society for Dermatological Research. 2011, Barcelona, Spain: Nature Publishing Group.
- Kolluru B, Nakjang S, Hirt RP, Wipat A, Ananiadou S. Automatic extraction of microorganisms and their habitats from free text using text mining workflows. Journal of Integrative Bioinformatics 2011, 8(2), 184.
- Misirli G, Hallinan JS, Pocock M, Cockell SJ, Weile J, Wipat A. BacillOndex: An Integrated Data Resource for Systems and Synthetic Biology. Newcastle upon Tyne: School of Computing Science, University of Newcastle upon Tyne, 2011. School of Computing Science Technical Report Series 1237.
- Weile J, Pocock M, Cockell SJ, Lord P, Dewar JM, Holstein EM, Wilkinson D, Lydall D, Hallinan J, Wipat A. Customizable views on semantically integrated networks for systems biology. Bioinformatics 2011, 27(9), 1299-1306.
- Chang H, Lawless C, Addinall SG, Oexle S, Taschuk M, Wipat A, Wilkinson DJ, Lydall D. Genome-Wide Analysis to Identify Pathways Affecting Telomere-Initiated Senescence in Budding Yeast. G3: Genes, Genomes, Genetics 2011, 1(3), 197-208.
- Weatherhead SC, Farr PM, Jamieson D, Hallinan JS, Lloyd JL, Wipat A, Reynolds NJ. Keratinocyte Apoptosis in Epidermal Remodeling and Clearance of Psoriasis Induced by UV Radiation. Journal of Investigative Dermatology 2011, 131(9), 1916-1926.
- Misirli G, Hallinan JS, Yu T, Lawson JR, Wimalaratne SM, Cooling MT, Wipat A. Model annotation for synthetic biology: automating model to nucleotide sequence conversion. Bioinformatics 2011, 27(7), 973-979.
- James K, Lycett SJ, Wipat A, Hallinan JS. Multiple Gold Standards Address Bias in Functional Network Integration. Newcastle upon Tyne: School of Computing Science, University of Newcastle upon Tyne, 2011. School of Computing Science Technical Report Series 1302.
- Hallinan JS, James K, Wipat A. Network Approaches to the Functional Analysis of Microbial Proteins. Advances in Microbial Physiology 2011, 59, 101-133.
- 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.
- Stadler LKJ, Hoffmann T, Tomlinson DC, Song Q, Lee T, Busby M, Nyathi Y, Gendra E, Tiede C, Flanagan K, Cockell SJ, Wipat A, Harwood C, Wagner SD, Knowles MA, Davis JJ, Keegan N, KoFerrigno P. Structure-function studies of an engineered scaffold protein derived from Stefin A. II: Development and applications of the SQT variant. Protein Engineering Design and Selection 2011, 24(9), 751-763.
- Galdzicki M, Wilson ML, Rodriguez CA, Adam L, Adler A, Anderson JC, Beal J, Chandran D, Densmore D, Drory OA, Endy D, Gennari JH, Grünberg R, Ham TS, Kuchinsky A, Lux MW, Madsen C, Misirli G, Myers CJ, Peccoud J, Plahar H, Pocock MR, Roehner N, Smith TF, Stan GB, Villalobos A, Wipat A, Sauro HM. Synthetic Biology Open Language (SBOL) Version 1.0.0. Massachusetts, USA: MIT Press, 2011. BBF RFC;84.
- Cockell SJ, Weile J, Lord P, Wipat C, Andriychenko D, Pocock M, Wilkinson D, Young M, Wipat A. An integrated dataset for in silico drug discovery. Journal of Integrative Bioinformatics 2010, 7(3), 116.
- Hallinan J, Misirli G, Wipat A. Evolutionary computation for the design of a stochastic switch for synthetic genetic circuits. In: 32nd Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC). 2010, Buenos Aires, Argentina: IEEE.
- Passos JF, Nelson G, Wang CF, Richter T, Simillion C, Proctor CJ, Miwa S, Olijslagers S, Hallinan J, Wipat A, Saretzki G, Rudolph KL, Kirkwood TBL, von Zglinicki T. Feedback between p21 and reactive oxygen production is necessary for cell senescence. Molecular Systems Biology 2010, 6(1), 347.
- Cooling MT, Rouilly V, Misirli G, Lawson J, Yu T, Hallinan J, Wipat A. Standard virtual biological parts: a repository of modular modeling components for synthetic biology. Bioinformatics 2010, 26(7), 925-931.
- Gibson F, Hoogland C, Martinez-Bartolome S, Medina-Aunon JA, Albar JP, Babnigg G, Wipat A, Hermjakob H, Almeida JS, Stanislaus R, Paton NW, Jones AR. The Gel Electrophoresis Markup Language (GelML) from the Proteomics Standards Initiative. Proteomics 2010, 10(17), 3073-3081.
- 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.
- Passos J, Simillion C, Hallinan J, Wipat A, Von Zglinicki T. Cellular senescence: Unravelling complexity. Age 2009, 31(4), 353-363.
- Hallinan JS, Pocock MR, Addinall S, Lydall D, Wipat A. Clustering incorporating shortest paths identifies relevant modules in functional interaction networks. In: CIBCB '09: IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology. 2009, Nashville, TN, USA: IEEE.
- James K, Wipat A, Hallinan J. Integration of full-coverage probabilistic functional networks with relevance to specific biological processes. In: Data Integration in the Life Sciences: 6th International Workshop (DILS). 2009, Manchester, UK: Springer.
- 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.
- Lister AL, Pocock M, Taschuk M, Wipat A. Saint: A Lightweight Integration Environment for Model Annotation. Bioinformatics 2009, 25(22), 3026-3027.
- Greenall A, Lei GY, Swan DC, James K, Wang LM, Peters H, Wipat A, Wilkinson DJ, Lydall D. 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 Biology 2008, 9(10), R146.
- Addinall SG, Downey M, Yu M, Zubko MK, Dewar J, Leake A, Hallinan J, Shaw O, James K, Wilkinson DJ, Wipat A, Durocher D, Lydall DA. A Genome-wide Suppressor and Enhancer Analysis of cdc13-1 Reveals Varied Cellular Processes Influencing Telomere Capping in Saccharomyces cerevisiae. Genetics 2008, 180(4), 2251-2266.
- Craddock T, Harwood CR, Hallinan J, Wipat A. e-Science: relieving bottlenecks in large-scale genome analyses. Nature Reviews in Microbiology 2008, 6(12), 948-954.
- Gibson F, Anderson L, Babnigg G, Baker M, Berth M, Binz P-A, Borthwick A, Cash P, Day BW, Friedman DB, Garland D, Gutstein HB, Hoogland C, Jones NA, Khan A, Klose J, Lamond AI, Lemkin PF, Lilley KS, Minden J, Morris NJ, Paton NW, Pisano MR, Prime JE, Rabilloud T, Stead DA, Taylor CF, Voshol H, Wipat A, Jones AR. Guidelines for reporting the use of gel electrophoresis in proteomics. Nature Biotechnology 2008, 26(8), 863-864.
- Hallinan JS, Wipat A. Network Motifs in Context: An Exploration of the Evolution of Oscillatory Dynamics in Transcriptional Networks. In: IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology. 2008, Idaho, USA: IEEE.
- 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.
- Sun Y, Wipat A, Pocock M, Lee PA, Flanagan K, Worthington JT. Exploring microbial genome sequences to identify protein families on the grid. IEEE Transactions on Information Technology in Biomedicine 2007, 11(4), 435-442.
- 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 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.
- 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.
- Hallinan JS, Wipat A. Motifs and modules in fractured functional yeast networks. In: IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 07). 2007, Honolulu, Hawaii: IEEE.
- Steggles LJ, Banks R, Shaw O, Wipat A. Qualitatively modelling and analysing genetic regulatory networks: A Petri net approach. Bioinformatics 2007, 23(3), 336-343.
- Shaw O, Steggles J, Wipat A. Automatic Parameterisation of Stochastic Petri Net Models of Biological Networks. In: Second International Workshop on the Practical Application of Stochastic Modeling (PASM 2005). 2006, Newcastle upon Tyne: Electronic Notes in Theoretical Computer Science: Elsevier BV.
- Hallinan J, Wipat A. Clustering and cross-talk in a yeast functional interaction network. In: IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). 2006, Toronto, Ontario, Canada: IEEE.
- Craddock T, Lord P, Harwood C, Wipat A. e-science tools for the genomic scale characterisation of bacterial secreted proteins. In: Proceedings of the UK e-Science All Hands Meeting 2006. 2006, Nottingham, UK: National e-Science Centre.
- Gibson F, Wipat A, Pocock M, Morris N. GELI: a data model for the representation of a gel electrophoresis experiment. Newcastle upon Tyne: School of Computing Science, University of Newcastle upon Tyne, 2006. School of Computing Science Technical Report Series 942.
- Steggles LJ, Banks R, Wipat A. Modelling and analysing genetic networks: From Boolean networks to Petri nets. In: Computational Methods in Systems Biology: International Conference (CMSB 2006). 2006, Trento, Italy: Springer-Verlag.
- Steggles LJ, Banks R, Wipat A. Modelling and Analysing Genetic Networks: From Boolean Networks to Petri Nets. Newcastle upon Tyne: School of Computing Science, University of Newcastle upon Tyne, 2006. School of Computing Science Technical Report Series 962.
- Allenby NEE, Watts CA, Homuth G, Pragai Z, Wipat A, Ward AC, Harwood CR. Phosphate starvation induces the sporulation killing factor of Bacillus subtilis. Journal of Bacteriology 2006, 188(14), 5299-5303.
- Oinn T, Greenwood M, Addis M, Alpdemir MN, Ferris J, Glover K, Goble C, Goderis A, Hull D, Marvin D, Li P, Lord P, Pocock MR, Senger M, Stevens R, Wipat A, Wroe C. Taverna: lessons in creating a workflow environment for the life sciences. Concurrency and Computation: Practice and Experience 2006, 18(10), 1067-1100.
- Sun Y, Wipat A, Pocock M, Lee PA, Watson P, Flanagan K, Worthington JT. A grid-based system for microbial genome comparison and analysis. In: IEEE International Symposium on Cluster Computing and the Grid, CCGrid 2005. 2005, Cardiff, Wales: IEEE.
- Shaw O, Steggles J, Wipat A. Automatic Parameterisation of Stochastic Petri Net Models of Biological Networks. In: 2nd International Workshop on the Practical Application of Stochastic Modeling (PASM 2005). 2005, Newcastle upon Tyne, UK: Electronic Notes in Theoretical Computer Science: Elsevier.
- Shaw OJ, Steggles LJ, Wipat A. Automatic Parameterisation of Stochastic Petri Net Models of Biological Networks. Newcastle upon Tyne: School of Computing Science, University of Newcastle upon Tyne, 2005. School of Computing Science Technical Report Series 909.
- Sun Y, Wipat A, Pocock M, Lee P, Flanagan K, Worthington J. Exploring Microbial Genome Sequences to Identify Protein Families on the Grid. Newcastle upon Tyne: School of Computing Science, University of Newcastle upon Tyne, 2005. School of Computing Science Technical Report Series 931.
- Allenby NEE, O'Connor N, Pragai Z, Ward AC, Wipat A, Harwood CR. Genome-wide transcriptional analysis of the phosphate starvation stimulon of Bacillus subtilis. Journal of Bacteriology 2005, 187(23), 8063-8080.
- Antelmann H, Williams RC, Miethke M, Wipat A, Albrecht D, Harwood CR, Hecker M. The extracellular and cytoplasmic proteomes of the non-virulent Bacillus anthracis strain UM23C1-2. Proteomics 2005, 5(14), 3684-3695.
- Sun Y, Wipat A, Pocock M, Lee P, Watson P, Flanagan K, Worthington J. A Grid-based System for Microbial Genome Comparison and Analysis. Newcastle upon Tyne: School of Computing Science, University of Newcastle upon Tyne, 2004. School of Computing Science Technical Report Series 881.
- Shaw O, Koelmans A, Steggles J, Wipat A. Applying Petri Nets to Systems Biology using XML Technologies. Newcastle upon Tyne: School of Computing Science, University of Newcastle upon Tyne, 2004. School of Computing Science Technical Report Series 827.
- Shaw O, Koelmans A, Steggles J, Wipat A. Applying Petri Nets to Systems Biology using XMLTechnologies. In: Workshop on the Definition, Implementation and Application of a Standard Interchange Format for Petri Nets. Satellite event of ATPN : 25th International Conference on Application and Theory of Petri Nets. 2004, Bologna, Italy.
- Li P, Hayward K, Jennings C, Owen K, Oinn T, Stevens R, Pearce S, Wipat A. Association of variations in I kappa B-epsilon with Graves’ disease using classical and myGrid methodologies. In: 2004 UK e-Science All Hands Meeting. 2004, Nottingham, UK: Engineering and Physical Sciences Research Council.
- Oinn T, Addis M J, Ferris J, Marvin DJ, Greenwood M, Goble C, Wipat A, Li P, Carver T. Delivering Web service coordination capability to users. In: 13th World Wide Web Conference (WWW2004). 2004, New York, USA: ACM.
- Wipat A, Sun Y, Pocock M, Lee P, Watson P, Flanagan K. Developing Grid-based Systems for Microbial Genome. In: UK e-Science All Hands Meeting 2004. 2004, Nottingham UK: EPSRC.
- Stevens R, McEntire R, Goble C, Greenwood M, Zhao J, Wipat A, Li P. myGrid and the drug discovery process. Drug Discovery Today: BIOSILICO 2004, 4(2), 140-148.
- Flanagan K, Stevens R, Pocock M, Lee P, Wipat A. Ontology for genome comparison and genomic rearrangements. In: 7th Annual Bio-Ontologies Meeting. 2004, Glasgow, Scotland: Comparative and Functional Genomics.
- Allenby NEE, O'Connor N, Pragai Z, Carter NM, Miethke M, Engelmann S, Hecker M, Wipat A, Ward AC, Harwood CR. Post-transcriptional regulation of the Bacillus subtilis pst operon encoding a phosphate-specific ABC transporter. Microbiology 2004, 150(8), 2619-2628.
- Shaw OJ, Harwood C, Steggles LJ, Wipat A. SARGE: A tool for creation of putative genetic networks. Bioinformatics 2004, 20(18), 3638-3640.
- Oinn T, Addis M, Ferris J, Marvin D, Senger M, Greenwood M, Carver T, Glover K, Pocock MR, Wipat A, Li P. Taverna: A tool for the composition and enactment of bioinformatics workflows. Bioinformatics 2004, 20(17), 3045-3054.
- Kobayashi K, Ehrlich SD, Albertini A, Amati G, Andersen KK, Arnaud M, Asai K, Ashikaga S, Aymerich S, Bessieres P, Boland F, Brignell SC, Bron S, Bunai K, Chapuis J, Christiansen LC, Danchin A, Debarbouille M, Dervyn E, Deuerling E, Devine K, Devine SK, Dreesen O, Errington J, Fillinger S, Foster SJ, Fujita Y, Galizzi A, Gardan R, Eschevins C, Fukushima T, Haga K, Harwood CR, Hecker M, Hosoya D, Hullo MF, Kakeshita H, Karamata D, Kasahara Y, Kawamura F, Koga K, Koski P, Kuwana R, Imamura D, Ishimaru M, Ishikawa S, Ishio I, Le Coq D, Masson A, Mauel C, Meima R, Mellado RP, Moir A, Moriya S, Nagakawa E, Nanamiya H, Nakai S, Nygaard P, Ogura M, Ohanan T, O'Reilly M, O'Rourke M, Pragai Z, Pooley HM, Rapoport G, Rawlins JP, Rivas LA, Rivolta C, Sadaie A, Sadaie Y, Sarvas M, Sato T, Saxild HH, Scanlan E, Schumann W, Seegers JFML, Sekiguchi J, Sekowska A, Seror SJ, Simon M, Stragier P, Studer R, Takamatsu H, Tanaka T, Takeuchi M, Thomaides HB, Vagner V, Van Dijl JM, Watabe K, Wipat A, Yamamoto H, Yamamoto M, Yamamoto Y, Yamane K, Yata K, Yoshida K, Yoshikawa H, Zuber U, Ogasawara N. Essential Bacillus subtilis genes. Proceedings of the National Academy of Sciences 2003, 100(8), 4678-4683.
- Addis M, Ferris J, Greenwood M, Li P, Marvin D, Oinn T, Wipat A. Experiences with e-Science workflow specification and enactment in bioinformatics. In: UK e-Science All Hands Meeting 2003. 2003, Nottingham, UK: Engineering and Physical Sciences Research Council.
- Harwood CR, Wipat A, Prágai Z. Functional analysis of the Bacillus subtilis genome. In: Wren, B. and Dorrell, N, ed. Functional Microbial Genomics. London: Academic Press, 2003, pp.337-367.
- Harwood CR, Wipat A. Bacterial protein synthesis. In: Sussman, M, ed. Molecular Medical Microbiology. San Diego: Academic Press, 2002, pp.321-388.
- Harwood CR, Wipat A, Pragai Z. Functional analysis of the Bacillus subtilis genome. Methods in Microbiology 2002, 33, 337-367.
- Harwood CR, Crawshaw SG, Wipat A. From genome to function: Systematic analysis of the soil bacterium Bacillus subtilis. Comparative and Functional Genomics 2001, 2(1), 22-24.
- Harwood CR, Wipat A. Genome management and analysis: prokaryotes. In: Ratledge, C. and Kristiansen, B, ed. Basic Biotechnology. Cambridge: Cambridge University Press, 2001, pp.73-118.
- Wipat A, Harwood CR. The Bacillus subtilis genome sequence: The molecular blueprint of a soil bacterium. FEMS Microbiology Ecology 1999, 28(1), 1-9.
- Wipat A, Brignell SC, Guy BJ, Rose M, Emmerson PT, Harwood CR. The yvsA-yvqA (293°-289°) region of the Bacillus subtilis chromosome containing genes involved in metal ion uptake and a putative sigma factor. Microbiology 1998, 144(6), 1593-1600.
- Fnlmerson P-I, Brignell C, Wipat A, Cartez N, Pragia Z, Guy BJ, Harwood CR. A putative DNA repair operon in B. subtilis comprising a gene encoding a DNA repair polymerase, a routs homolog and an unidentified. FASEB Journal 1997, 11(9), A1368-.
- Gothel SF, Schmid R, Wipat A, Carter NM, Emmerson PT, Harwood CR, Marahiel MA. An internal FK506-binding domain is the catalytic core of the prolyl isomerase activity associated with the Bacillus subtilis trigger factor. European Journal of Biochemistry 1997, 244(1), 59-65.
- Gerth U, Wipat A, Harwood CR, Carter N, Emmerson PT, Hecker M. Sequence and transcriptional analysis of clpX, a class-III heat-shock gene of Bacillus subtilis. Gene 1996, 181(1-2), 77-83.
- Harwood CR, Wipat A. Sequencing and functional analysis of the genome of Bacillus subtilis strain 168. FEBS Letters 1996, 389(1), 84-87.
- Wipat A, Carter N, Brignell SC, Guy BJ, Piper K, Sanders J, Emmerson PT, Harwood CR. The dnaB-pheA (256°-240°) region of the Bacillus subtilis chromosome containing genes responsible for stress responses, the utilization of plant cell walls and primary metabolism. Microbiology 1996, 142(11), 3067-3078.
- Wipat A, Wellington EMH, Saunders VA. Monoclonal antibodies for Streptomyces lividans and their use for immunomagnetic capture of spores from soil. Microbiology 1994, 140(8), 2067-2076.
- Saunders VA, Wellington EMH, Wipat A. Detection of Streptomyces marker plasmids in soil. In: 2nd International Conference on the Release of Genetically-engineered Micro-organisms (REGEM 2): Release of Genetically Modified Microorganisms. 1992, Nottingham, England: Kluwer Academic/Plenum Publishers.
- Wipat A, Wellington EM, Saunders VA. Detection systems for streptomycetes. In: Wellington, E.M.H. and van Elsas, J.D, ed. Genetic Interactions Among Microorganisms in the Natural Environment. Oxford: Pergamon Press, 1992, pp.83-90.
- Wipat A, Wellington EMH, Saunders VA. Streptomyces marker plasmids for monitoring survival and spread of streptomycetes in soil. Applied and Environmental Microbiology 1991, 57(11), 3322-3330.
- Wellington EMH, Cresswell N, Herron PR , Wipat A. Gene transfer between streptomycetes in soil. In: Fry, J.C. and Day, M.J, ed. Bacterial Genetics in Natural Environments. London: Chapman and Hall, 1990, pp.216-230.
- Wellington EMH, Saunders VA, Cresswell N, Wipat A. Plasmid transfer between streptomycetes in soil. In: 7th International Symposium on Biology of Actinomycetes (ISBA 1988). 1988, Tokyo: Japan Scientific Societies Press.