缅北禁地

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Staff Profile

Professor Anil Wipat

Professor of Integrative Bioinformatics

  • Telephone: +44 191 208 8213 or 208 3212
  • Address: School of Computing
    Urban Sciences Building
    缅北禁地
    1 Science Square
    Science Central
    缅北禁地 upon Tyne
    NE4 5TG

Background

I am a Professor of Bioinformatics at the  at 缅北禁地.

I co-direct 缅北禁地's .



Research

My research forms part of the larger research effort of the the 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 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 ). 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  and the EPSRC funded . We have recently established a high-throughput automation lab where we are developing methods for the rapid exploration of the functional properties of enzymes.


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 ).


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.

Teaching
  • I was degree programme director (from 2005-2019) and founder of our successful , , and for which I contribute on a number of modules.
Publications

  • Articles

    • Sadegh S, Skelton J, Anastasi E, Maier A, Adamowicz K, Moller A, Kriege NM, Kronberg J, Haller T, Kacprowski T, Wipat A, Baumbach J, Blumenthal DB. . Nature Communications 2023, 14(1), 1662.
    • Huang Y, Sinha N, Wipat A, Bacardit J. . Synthetic and Systems Biotechnology 2023, 8(1), 97-106.
    • Ling W-L, Yeo JY, Ng Y-L, Wipat A, Gan SK-E. . Antibodies 2022, 11(1), 14.
    • Yang B, Misirli G, Wipat A, Hallinan J. . BioSystems 2022, 219, 104730.
    • James K, Alsobhe A, Cockell SJ, Wipat A, Pocock M. . BMC Bioinformatics 2022, 23, 302.
    • Mori K, Fukui K, Amatsu R, Ishikawa S, Verrone V, Wipat A, Meijer WJJ, Yoshida K-I. . Microbial Cell Factories 2022, 21(1), 34.
    • Crowther M, Wipat A, Goni-Moreno A. . ACS Synthetic Biology 2022, 11(9), 3058-3066.
    • Mlslrll G, Yang B, James K, Wipat A. . ACS Synthetic Biology 2021, 10(12), 3304-3315.
    • Konur S, Mierla L, Fellermann H, Ladroue C, Brown B, Wipat A, Twycross J, Dun BP, Kalvala S, Gheorghe M, Krasnogor N. . ACS Synthetic Biology 2021, 10(8), 1931-1945.
    • Huang Y, Smith W, Harwood C, Wipat A, Bacardit J. . Sensors 2021, 21(7), 2436.
    • Mori K, Verrone V, Amatsu R, Fukui K, Meijer WJJ, Ishikawa S, Wipat A, Yoshida K-I. . Microorganisms 2021, 9(9), 1931.
    • McLaughlin JA, Beal J, Misirli G, Grunberg R, Bartley BA, Scott-Brown J, Vaidyanathan P, Fontanarrosa P, Oberortner E, Wipat A, Gorochowski TE, Myers CJ. . Frontiers in Bioengineering and Biotechnology 2020, 8, 1009.
    • Ling WL, Ng YL, Wipat A, Lane DP, Gan SKE. . Journal of Immunological Methods 2020, 476, 112683.
    • 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. . GigaScience 2020, 9(5).
    • Baig H, Fontanarrosa P, Kulkarni V, McLaughlin J, Vaidyanathan P, Bartley B, Bhatia S, Bhakta S, Bissell M, Clancy K, Cox RS, Moreno AG, Gorochowski T, Grunberg R, Luna A, Madsen C, Misirli G, Nguyen T, Le Novere N, Palchick Z, Pocock M, Roehner N, Sauro H, Scott-Brown J, Sexton JT, Stan G-B, Tabor JJ, Vilar MV, Voigt CA, Wipat A, Zong D, Zundel Z, Beal J, Myers C. . Journal of Integrative Bioinformatics 2020, 17(2-3), 20200014.
    • Baig H, Fontanarrosa P, Kulkarni V, McLaughlin JA, Vaidyanathan P, Bartley B, Beal J, Crowther M, Gorochowski TE, Grunberg R, Misirli G, Scott-Brown J, Oberortner E, Wipat A, Myers CJ. . Journal of Integrative Bioinformatics 2020, 17(2-3), 20200017.
    • Elbatreek MH, Sadegh S, Anastasi E, Guney E, Nogales C, Kacprowski T, Hassan AA, Teubner A, Huang P-H, Hsu C-Y, Schiffers PMH, Janssen GM, Kleikers PWM, Wipat A, Baumbach J, De Mey JGR, Schmidt HHHW. . PLoS Biology 2020, 18(11), e3000885.
    • Jana S, Charlton SGV, Eland LE, Burgess JG, Wipat A, Curtis TP, Chen J. . npj Biofilms and Microbiomes 2020, 6, 19.
    • Wu LJ, Lee S, Park S, Eland LE, Wipat A, Holden S, Errington J. . Nature Communications 2020, 11(1), 4149.
    • Ling W-L, Su CT-T, Lua W-H, Poh J-J, Ng Y-L, Wipat A, Gan SK-E. . Frontiers in Immunology 2020, 11, 604318.
    • Lahme S, Callbeck CM, Eland LE, Wipat A, Enning D, Head IM, Hubert CRJ. . Environmental Microbiology 2020, 22(5), 1784-1800.
    • Brown B, Bartley B, Beal J, Bird JE, Goni-Moreno A, McLaughlin JA, Misirli G, Roehner N, Skelton DJ, Poh CL, Ofiteru ID, James K, Wipat A. . ACS Synthetic Biology 2020, 9(9), 2410-2417.
    • Mısırlı G, Taylor R, Goñi-Moreno A, McLaughlin JA, Myers C, Gennari JH, Lord P, Wipat A. . ACS Synthetic Biology 2019, 8(7), 1498-1514.
    • McLaughlin JA, Myers CJ, Zundel Z, Wilkinson N, Atallah C, Wipat A. . ACS Synthetic Biology 2019, 8(1), 191-193.
    • Charlton S, White M, Jana S, Eland L, Jayathilake P, Burgess J, Chen J, Wipat A, Curtis T. . Journal of Bacteriology 2019, 201(18), e00101-19.
    • 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. . Briefings in Bioinformatics 2019, 20(2), 540-550.
    • Hallinan JS, Wipat A, Kitney R, Woods S, Taylor K, Goñi-Moreno A. . Engineering Biology 2019, 3(2), 25-31.
    • 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. . ACS Synthetic Biology 2019, 8(8), 1818-1825.
    • McLaughlin JA, Myers CJ, Zundel Z, Misirli G, Zhang M, Ofiteru ID, Goni-Moreno A, Wipat A. . ACS Synthetic Biology 2018, 7(2), 682-688.
    • Lawry BM, Johnson CL, Flanagan K, Spoors JA, McNeil CJ, Wipat A, Keegan N. . Analytical Chemistry 2018, 90(22), 13475-13482.
    • Guyet A, Dade-Robertson M, Wipat A, Casement J, Smith W, Mitrani H, Zhang M. . PLoS ONE 2018, 13(7), e0200660.
    • Dade-Robertson M, Mitrani H, Rodriguez-Corral J, Zhang M, Hernan L, Guyet A, Wipat A. . Bioinspiration & Biomimetics 2018, 13(4), 046004.
    • Houghton D, Stewart CJ, Stamp C, Nelson A, Ajami NJ, Petrosino JF, Wipat A, Trenell MI, Turnbull DM, Greaves LC. . The Journals of Gerontology: Series A, Biological Sciences & Medical Sciences 2018, 73(5), 571-578.
    • Waites W, Mlslrll G, Cavaliere M, Danos V, Wipat A. . ACS Synthetic Biology 2018, 7(12), 2812-2823.
    • Zhang M, McLaughlin JA, Wipat A, Myers CJ. . ACS Synthetic Biology 2017, 6(7), 1150-1160.
    • Houghton D, Stewart CJ, Stamp C, Nelson A, Ajami NJ, Petrosino JF, Wipat A, Trenell MI, Turnbull DM, Greaves LC. . The Journals of Gerontology: Series A 2017, 73(5), 571-578.
    • Cox RS, McLaughlin JA, Grünberg R, Beal J, Wipat A, Sauro HM. . ACS Synthetic Biology 2017, 6(7), 1120-1123.
    • McLaughlin JA, Pocock M, Misirli G, Madsen C, Wipat A. . ACS Synthetic Biology 2016, 5(8), 874-876.
    • Madsen C, McLaughlin JA, Misirli G, Pocock M, Flanagan K, Hallinan J, Wipat A. . ACS Synthetic Biology 2016, 5(6), 487-497.
    • 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. . ACS Synthetic Biology 2016, 5(6), 498-506.
    • Mullen J, Cockell SJ, Tipney H, Woollard PM, Wipat A. . PeerJ 2016, 4, e1558.
    • Zhang Z, Nguyen T, Roehner N, Misirli G, Pocock M, Oberortner E, Samineni M, Zundel Z, Beal J, Clancy K, Wipat A, Myers CJ. . IEEE Life Sciences Letters 2016, 1(4), 34-37.
    • Misirli G, Hallinan J, Pocock M, Lord P, McLaughlin JA, Sauro H, Wipat A. . ACS Synthetic Biology 2016, 5(10), 1086-1097.
    • Misirli G, Cavaliere M, Waites W, Pocock M, Madsen C, Gilfellon O, Honorato-Zimmer R, Zuliani P, Danos V, Wipat A. . Bioinformatics 2016, 32(6), 908-917.
    • Mullen J, Cockell SJ, Woollard P, Wipat A. . PLoS One 2016, 11(5), e0155811.
    • 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. . PLOS Biology 2015, 13(12), e1002310.
    • Roehner N, Oberortner E, Pocock M, Beal J, Clancy K, Madsen C, Misirli G, Wipat A, Sauro H, Myers CJ. . ACS Synthetic Biology 2015, 4(1), 57-71.
    • 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. . International Journal of Epidemiology 2015, 44(4), 1181-1190.
    • 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. . PLoS ONE 2015, 10(12), e0143970.
    • 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. . Nature Biotechnology 2014, 32(6), 545-550.
    • Rusakovica J, Hallinan J, Wipat A, Zuliani P. . Journal of Integrative Bioinformatics 2014, 11(2), 243.
    • 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. . Nature Communications 2014, 5, 4760.
    • Misirli G, Hallinan J, Wipat A. . ACM Journal on Emerging Technologies in Computing Systems 2014, 11(3), 22.
    • Misirli G, Hallinan J, Röttger R, Baumbach J, Wipat A. . Journal of Integrative Bioinformatics 2014, 11(2), 244.
    • Flanagan K, Cockell S, Harwood C, Hallinan J, Nakjang S, Lawry B, Wipat A. . Journal of Integrative Bioinformatics 2014, 11(2), 242.
    • Pohl S, Bhavsar G, Hulme J, Bloor AE, Misirli G, Leckenby MW, Radford DS, Smith W, Wipat A, Williamson ED, Harwood CR, Cranenburgh RM. . Proteomics 2013, 13(22), 3298-3308.
    • Misirli G, Wipat A, Mullen J, James K, Pocock M, Smith W, Allenby N, Hallinan J. . Journal of Integrative Bioinformatics 2013, 10(2), 224.
    • Flanagan K, Nakjang S, Hallinan J, Harwood C, Hirt RP, Pocock MR, Wipat A. . Journal of Integrative Bioinformatics 2012, 9(2), 12.
    • James K, Wipat A, Hallinan J. . Integrative Biology 2012, 4(7), 715-727.
    • Collison M, Hirt RP, Wipat A, Nakjang S, Sanseau P, Brown JR. . Briefings in Bioinformatics 2012, 13(6), 751-768.
    • Weile J, James K, Hallinan J, Cockell SJ, Lord P, Wipat A, Wilkinson DJ. . Bioinformatics 2012, 28(11), 1495-1500.
    • Nakjang S, Ndeh DA, Wipat A, Bolam DN, Hirt RP. . PLoS One 2012, 7(1), 1-18.
    • 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. . Protein Engineering Design and Selection 2011, 24(9), 751-763.
    • 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. . PLoS Genetics 2011, 7(4), e1001362.
    • Misirli G, Hallinan JS, Yu T, Lawson JR, Wimalaratne SM, Cooling MT, Wipat A. . Bioinformatics 2011, 27(7), 973-979.
    • Weatherhead SC, Farr PM, Jamieson D, Hallinan JS, Lloyd JL, Wipat A, Reynolds NJ. . Journal of Investigative Dermatology 2011, 131(9), 1916-1926.
    • Chang H, Lawless C, Addinall SG, Oexle S, Taschuk M, Wipat A, Wilkinson DJ, Lydall D. . G3: Genes, Genomes, Genetics 2011, 1(3), 197-208.
    • Weile J, Pocock M, Cockell SJ, Lord P, Dewar JM, Holstein EM, Wilkinson D, Lydall D, Hallinan J, Wipat A. . Bioinformatics 2011, 27(9), 1299-1306.
    • Kolluru B, Nakjang S, Hirt RP, Wipat A, Ananiadou S. . Journal of Integrative Bioinformatics 2011, 8(2), 184.
    • 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. . Proteomics 2010, 10(17), 3073-3081.
    • Cooling MT, Rouilly V, Misirli G, Lawson J, Yu T, Hallinan J, Wipat A. . Bioinformatics 2010, 26(7), 925-931.
    • 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. . Molecular Systems Biology 2010, 6(1), 347.
    • Cockell SJ, Weile J, Lord P, Wipat C, Andriychenko D, Pocock M, Wilkinson D, Young M, Wipat A. . Journal of Integrative Bioinformatics 2010, 7(3), 116.
    • Lister AL, Pocock M, Taschuk M, Wipat A. . Bioinformatics 2009, 25(22), 3026-3027.
    • 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. . 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. . Nature Biotechnology 2008, 26(5), 541-547.
    • Craddock T, Harwood CR, Hallinan J, Wipat A. . Nature Reviews in Microbiology 2008, 6(12), 948-954.
    • 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. . Genetics 2008, 180(4), 2251-2266.
    • Greenall A, Lei GY, Swan DC, James K, Wang LM, Peters H, Wipat A, Wilkinson DJ, Lydall D. . Genome Biology 2008, 9(10), R146.
    • Steggles LJ, Banks R, Shaw O, Wipat A. . Bioinformatics 2007, 23(3), 336-343.
    • Lister AL, Pocock M, Wipat A. . Journal of Integrative Bioinformatics 2007, 4(3), 80.
    • Sun Y, Wipat A, Pocock M, Lee PA, Flanagan K, Worthington JT. . IEEE Transactions on Information Technology in Biomedicine 2007, 11(4), 435-442.
    • 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. . Concurrency and Computation: Practice and Experience 2006, 18(10), 1067-1100.
    • Allenby NEE, Watts CA, Homuth G, Pragai Z, Wipat A, Ward AC, Harwood CR. . Journal of Bacteriology 2006, 188(14), 5299-5303.
    • Antelmann H, Williams RC, Miethke M, Wipat A, Albrecht D, Harwood CR, Hecker M. . Proteomics 2005, 5(14), 3684-3695.
    • Allenby NEE, O'Connor N, Pragai Z, Ward AC, Wipat A, Harwood CR. . Journal of Bacteriology 2005, 187(23), 8063-8080.
    • Oinn T, Addis M, Ferris J, Marvin D, Senger M, Greenwood M, Carver T, Glover K, Pocock MR, Wipat A, Li P. . Bioinformatics 2004, 20(17), 3045-3054.
    • Shaw OJ, Harwood C, Steggles LJ, Wipat A. . Bioinformatics 2004, 20(18), 3638-3640.
    • Allenby NEE, O'Connor N, Pragai Z, Carter NM, Miethke M, Engelmann S, Hecker M, Wipat A, Ward AC, Harwood CR. . Microbiology 2004, 150(8), 2619-2628.
    • Stevens R, McEntire R, Goble C, Greenwood M, Zhao J, Wipat A, Li P. . Drug Discovery Today: BIOSILICO 2004, 4(2), 140-148.
    • 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. . Proceedings of the National Academy of Sciences 2003, 100(8), 4678-4683.
    • Harwood CR, Wipat A, Pragai Z. . Methods in Microbiology 2002, 33, 337-367.
    • Harwood CR, Crawshaw SG, Wipat A. . Comparative and Functional Genomics 2001, 2(1), 22-24.
    • Wipat A, Brignell SC, Guy BJ, Rose M, Emmerson PT, Harwood CR. . Microbiology 1998, 144(6), 1593-1600.
    • Kunst F, Ogasawara N, Moszer I, Albertini AM, Alloni G, Azevedo V, Bertero MG, Bessieres P, Bolotin A, Borchert S, Borriss R, Boursier L, Brans A, Braun M, Brignell SC, Bron S, Brouillet S, Bruschi CV, Caldwell B, Capuano V, Carter NM, Choi S-K, Codani J-J, Connerton IF, Cummings NJ, Daniel RA, Denizot F, Devine KM, Dusterhoft A, Ehrlich SD, Emmerson PT, Entian KD, Errington J, Fabret C, Ferrari E, Foulger D, Fritz C, Fujita M, Fujita Y, Fuma S, Galizzi A, Galleron N, Ghim S-Y, Glaser P, Goffeau A, Golightly EJ, Grandi G, Guiseppi G, Guy BJ, Haga K, Haiech J, Harwood CR, Henaut A, Hilbert H, Holsappel S, Hosono S, Hullo M-F, Itaya M, Jones L, Joris B, Karamata D, Kasahara Y, Klaerr-Blanchard M, Klein C, Kobayashi Y, Koetter P, Koningstein G, Krogh S, Kumano M, Kurita K, Lapidus A, Lardinois S, Lauber J, Lazarevic V, Lee S-M, Levine A, Liu H, Masuda S, Mauel C, Medigue C, Medina N, Mellado RP, Mizuno M, Moestl D, Nakai S, Noback M, Noone D, O'Reilly M, Ogawa K, Ogiwara A, Oudega B, Park S-H, Parro V, Pohl TM, Portetelle D, Porwollik S, Prescott AM, Presecan E, Pujic P. . Nature 1997, 390(6657), 249-256.
    • Gothel SF, Schmid R, Wipat A, Carter NM, Emmerson PT, Harwood CR, Marahiel MA. . European Journal of Biochemistry 1997, 244(1), 59-65.
    • Fnlmerson P-I, Brignell C, Wipat A, Cartez N, Pragia Z, Guy BJ, Harwood CR. . FASEB Journal 1997, 11(9), A1368-.
    • Wipat A, Carter N, Brignell SC, Guy BJ, Piper K, Sanders J, Emmerson PT, Harwood CR. . Microbiology 1996, 142(11), 3067-3078.
    • Harwood CR, Wipat A. . FEBS Letters 1996, 389(1), 84-87.
    • Gerth U, Wipat A, Harwood CR, Carter N, Emmerson PT, Hecker M. . Gene 1996, 181(1-2), 77-83.
    • Wipat A, Wellington EMH, Saunders VA. . Microbiology 1994, 140(8), 2067-2076.
    • Wipat A, Wellington EMH, Saunders VA. . Applied and Environmental Microbiology 1991, 57(11), 3322-3330.

  • Book Chapters

    • Armstrong R, Ferracina S, Caldwell G, Ieropoulos I, Rimbu G, Adamatzky A, Phillips N, De Lucrezia D, Imhof B, Hanczyc MM, Nogales J, Garcia J. . In: Heisel, F; Hebel, D, ed. Cultivated Building Materials: Industrialized Natural Resources for Architecture and Construction. Berlin, Germany: Birkhauser, 2017, pp.170-177.
    • Eland LE, Wipat A, Lee S, Park S, Wu LJ. . In: Harwood, C, ed. Methods in Microbiology. London, UK: Elsevier, 2016, pp.69-111.
    • Harwood CR, Pohl S, Smith W, Wipat A. . In: Colin Harwood and Anil Wipat, ed. Microbial Synthetic Biology. Oxford: Academic Press, 2013, pp.87-117.
    • Harwood CR, Wipat A, Prágai Z. . In: Wren, B. and Dorrell, N, ed. Functional Microbial Genomics. London: Academic Press, 2003, pp.337-367.
    • Harwood CR, Wipat A. . In: Sussman, M, ed. Molecular Medical Microbiology. San Diego: Academic Press, 2002, pp.321-388.
    • Harwood CR, Wipat A. . In: Ratledge, C. and Kristiansen, B, ed. Basic Biotechnology. Cambridge: Cambridge University Press, 2001, pp.73-118.
    • Bron S, Meima R, van Dijl J-M et al. . In: Demain, A.L. and Davids, J.E, ed. Manual of Industrial Microbiology and Biotechnology. Washington, DC: American Society for Microbiology (ASM) Press, 1999, pp.392-416.
    • Wipat A, Wellington EM, Saunders VA. . 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.
    • Wellington EMH, Cresswell N, Herron PR , Wipat A. . In: Fry, J.C. and Day, M.J, ed. Bacterial Genetics in Natural Environments. London: Chapman and Hall, 1990, pp.216-230.

  • Conference Proceedings (inc. Abstracts)

    • Atallah C, James K, Ou Z, Skelton J, Markham D, Finnigan J, Charnock S, Wipat A. . In: 2022 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). 2022, Ottawa, ON, Canada: IEEE.
    • Dade-Robertson M, Rodriguez-Corral J, Guyet A, Mitrani H, Wipat A, Zhang M. . In: 3rd International Conference Biodigital: Architecture & Genetics. 2017, Barcelona: UIC.
    • Myers CJ, McLaughlin J, Misirli G, Nguyen T, Samineni M, Zhang M, Zundel Z, Wipat A. . In: Synthetic Biology Conference (SEED 2017): Engineering, Evolution, and Design. 2017, Vancouver, British Columbia, Canada: AIChE.
    • Dade-Robertson M, Corral J, Mitrani H, Zhang M, Wipat A, Ramirez-Figueroa C, Hernan L. . In: ACADIA 2016 - Posthuman Frontiers: Data, Designers and Cognitive Machines. 2016, Ann Arbor, Michigan: Association for Computer Aided Design in Architecture.
    • Dade-Robertson M, Rodriguez-Corral J, Guyet A, Mitrani H, Wipat A, Zhang M. . In: Sustainable Smart Manufacturing (S2M). 2016, Lisbon, Portugal: CRC Press LLC.
    • Sutantyo D, Walker C, Debono N, Vargas J, Wipat A, Hallinan JS. . In: CIBCB 2016 - Annual IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology. 2016, IEEE.
    • Skelton DJ, Hallinan JS, Park S, Wipat A. . 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.
    • James K, Ng WF, Wipat A, Hallinan J. . In: 13th International Symposium on Sjögren's Syndrome. 2015, Bergen, Norway: Wiley-Blackwell.
    • 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. . In: The 13th International Symposium on Sjögren's Syndrome. 2015, Bergen, Norway: Wiley-Blackwell.
    • 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. . In: The 13th International Symposium on Sjögren's Syndrome. 2015, Bergen, Norway: Wiley-Blackwell.
    • Hallinan JS, Gilfellon O, Misirli G, Wipat A. . In: IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology. 2014, Honolulu, HI: IEEE.
    • Hallinan JS, Park S, Wipat A. . In: BioInformatics: International Conference on Bioinformatics Models, Methods and Algorithms. 2012, Algarve, Portugal: ScitePress.
    • Weatherhead S, Farr P, Swan D, Jamieson D, Hallinan J, Lloyd J, Wipat A, Reynolds N. . In: 41st Annual Meeting of the European Society for Dermatological Research. 2011, Barcelona, Spain: Nature Publishing Group.
    • Hallinan J, Misirli G, Wipat A. . In: 32nd Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC). 2010, Buenos Aires, Argentina: IEEE.
    • James K, Wipat A, Hallinan J. . In: Data Integration in the Life Sciences: 6th International Workshop (DILS). 2009, Manchester, UK: Springer.
    • Hallinan JS, Pocock MR, Addinall S, Lydall D, Wipat A. . In: CIBCB '09: IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology. 2009, Nashville, TN, USA: IEEE.
    • Lister AL, Lord P, Pocock M, Wipat A. . In: 12th Annual Bio-Ontologies Meeting colocated with ISMB. 2009, Stockholm, Sweden: Intelligent Systems for Molecular Biology.
    • Hallinan JS, Wipat A. . In: IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology. 2008, Idaho, USA: IEEE.
    • Hallinan JS, Wipat A. . In: IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 07). 2007, Honolulu, Hawaii: IEEE.
    • Steggles LJ, Banks R, Wipat A. . In: Computational Methods in Systems Biology: International Conference (CMSB 2006). 2006, Trento, Italy: Springer-Verlag.
    • Craddock T, Lord P, Harwood C, Wipat A. . In: Proceedings of the UK e-Science All Hands Meeting 2006. 2006, Nottingham, UK: National e-Science Centre.
    • Hallinan J, Wipat A. . In: IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). 2006, Toronto, Ontario, Canada: IEEE.
    • Shaw O, Steggles J, Wipat A. . In: Second International Workshop on the Practical Application of Stochastic Modeling (PASM 2005). 2006, 缅北禁地 upon Tyne: Electronic Notes in Theoretical Computer Science: Elsevier BV.
    • Shaw O, Steggles J, Wipat A. . In: 2nd International Workshop on the Practical Application of Stochastic Modeling (PASM 2005). 2005, 缅北禁地 upon Tyne, UK: Electronic Notes in Theoretical Computer Science: Elsevier.
    • Sun Y, Wipat A, Pocock M, Lee PA, Watson P, Flanagan K, Worthington JT. . In: IEEE International Symposium on Cluster Computing and the Grid, CCGrid 2005. 2005, Cardiff, Wales: IEEE.
    • Flanagan K, Stevens R, Pocock M, Lee P, Wipat A. . In: 7th Annual Bio-Ontologies Meeting. 2004, Glasgow, Scotland: Comparative and Functional Genomics.
    • Wipat A, Sun Y, Pocock M, Lee P, Watson P, Flanagan K. . In: UK e-Science All Hands Meeting 2004. 2004, Nottingham UK: EPSRC.
    • Oinn T, Addis M J, Ferris J, Marvin DJ, Greenwood M, Goble C, Wipat A, Li P, Carver T. . In: 13th World Wide Web Conference (WWW2004). 2004, New York, USA: ACM.
    • Li P, Hayward K, Jennings C, Owen K, Oinn T, Stevens R, Pearce S, Wipat A. . In: 2004 UK e-Science All Hands Meeting. 2004, Nottingham, UK: Engineering and Physical Sciences Research Council.
    • Shaw O, Koelmans A, Steggles J, Wipat A. . 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.
    • Stevens R, Glover K, Greenhalgh C, Jennings C, Pearce S, Li P , Wipat A. . In: UK e-Science All Hands Meeting 2003. 2003, Nottingham, UK: Engineering and Physical Sciences Research Council.
    • Addis M, Ferris J, Greenwood M, Li P, Marvin D, Oinn T, Wipat A. . In: UK e-Science All Hands Meeting 2003. 2003, Nottingham, UK: Engineering and Physical Sciences Research Council.
    • Saunders VA, Wellington EMH, Wipat A. . 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.
    • Wellington EMH, Saunders VA, Cresswell N, Wipat A. . In: 7th International Symposium on Biology of Actinomycetes (ISBA 1988). 1988, Tokyo: Japan Scientific Societies Press.

  • Edited Book

    • Harwood CR, Wipat A, ed. . Oxford: Academic Press, 2012.

  • Editorial

    • Myers CJ, Sauro H, Wipat A. . ACM Journal on Emerging Technologies in Computing Systems (JETC) 2014, 11(3), 20.

  • Letters

    • Hoogland C, O'Gorman M, Bogard P, Gibson F, Berth M, Cockell SJ, Ekefjard A, Forsstrom-Olsson O, Kapferer A, Nilsson M, Martinez-Bartolome S, Albar JP, Echevarria-Zomeno S, Martinez-Gomariz M, Joets J, Binz PA, Taylor CF, Dowsey A, Jones AR. . Nature Biotechnology 2010, 28(7), 655-656.
    • 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. . Nature Biotechnology 2008, 26(8), 863-864.

  • Reports

    • Misirli G, Hallinan J, Wipat A. . 缅北禁地 upon Tyne: School of Computing Science, University of 缅北禁地 upon Tyne, 2014. School of Computing Science Technical Report Series 1424.
    • 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. . Massachusetts, USA: MIT Press, 2011. BBF RFC;84.
    • James K, Lycett SJ, Wipat A, Hallinan JS. . 缅北禁地 upon Tyne: School of Computing Science, University of 缅北禁地 upon Tyne, 2011. School of Computing Science Technical Report Series 1302.
    • Misirli G, Hallinan JS, Pocock M, Cockell SJ, Weile J, Wipat A. . 缅北禁地 upon Tyne: School of Computing Science, University of 缅北禁地 upon Tyne, 2011. School of Computing Science Technical Report Series 1237.
    • Lister A L, Pocock M, Wipat A. . 缅北禁地 upon Tyne: School of Computing Science, University of 缅北禁地 upon Tyne, 2007. School of Computing Science Technical Report Series 1043.
    • Lister AL, Jones AR, Pocock M, Shaw O, Wipat A. . 缅北禁地 upon Tyne: School of Computing Science, University of 缅北禁地 upon Tyne, 2007. School of Computing Science Technical Report Series 1016.
    • Steggles LJ, Banks R, Wipat A. . 缅北禁地 upon Tyne: School of Computing Science, University of 缅北禁地 upon Tyne, 2006. School of Computing Science Technical Report Series 962.
    • Gibson F, Wipat A, Pocock M, Morris N. . 缅北禁地 upon Tyne: School of Computing Science, University of 缅北禁地 upon Tyne, 2006. School of Computing Science Technical Report Series 942.
    • Sun Y, Wipat A, Pocock M, Lee P, Flanagan K, Worthington J. . 缅北禁地 upon Tyne: School of Computing Science, University of 缅北禁地 upon Tyne, 2005. School of Computing Science Technical Report Series 931.
    • Shaw OJ, Steggles LJ, Wipat A. . 缅北禁地 upon Tyne: School of Computing Science, University of 缅北禁地 upon Tyne, 2005. School of Computing Science Technical Report Series 909.
    • Shaw O, Koelmans A, Steggles J, Wipat A. . 缅北禁地 upon Tyne: School of Computing Science, University of 缅北禁地 upon Tyne, 2004. School of Computing Science Technical Report Series 827.
    • Sun Y, Wipat A, Pocock M, Lee P, Watson P, Flanagan K, Worthington J. . 缅北禁地 upon Tyne: School of Computing Science, University of 缅北禁地 upon Tyne, 2004. School of Computing Science Technical Report Series 881.

  • Reviews

    • James K, Wipat A, Cockell SJ. . Briefings in Functional Genomics 2022, 21(4), 243-269.
    • Gonzalez-Cabaleiro R, Mitchell AM, Smith W, Wipat A, Ofiteru ID. . Frontiers in Microbiology 2017, 8, 1813.
    • Goni-Moreno A, Wipat A, Krasnogor N. . Biochemical Society Transactions 2017, 45(3), 781-783.
    • 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. . Biochemical Society Transactions 2017, 45(3), 793-803.
    • Hallinan JS, James K, Wipat A. . Advances in Microbial Physiology 2011, 59, 101-133.
    • Passos J, Simillion C, Hallinan J, Wipat A, Von Zglinicki T. . Age 2009, 31(4), 353-363.
    • Wipat A, Harwood CR. . FEMS Microbiology Ecology 1999, 28(1), 1-9.