Terri Attwood

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Terri Attwood
AttwoodTerri.jpeg
Portrait of Terri Attwood by Linda Bussey
Born Teresa K. Attwood
(1959-11-20) November 20, 1959 (age 57)[1]
Fields Bioinformatics
Protein fingerprinting
Institutions
Alma mater University of Leeds
Thesis Chromonic mesophases (1984)
Doctoral advisor John E. Lydon[2]
Doctoral students
Known for
Notable awards Royal Society University Research Fellowship 1993-2002[16]
Website

Teresa K. Attwood is a Professor of Bioinformatics in the School of Computer Science and School of Biological Sciences at the University of Manchester and a visiting fellow at the European Bioinformatics Institute (EMBL-EBI).[17] She held a Royal Society University Research Fellowship at University College London (UCL) from 1993 to 1999 and at the University of Manchester from 1999 to 2002.[16]

Education[edit]

Attwood gained her Bachelor of Science in Biophysics from the University of Leeds in 1982.[18] She was awarded a PhD, also in Biophysics, two years later, in 1984[2] under the supervision of John E. Lydon[19] studying chromonic mesophases.

Research and career[edit]

Attwood undertook postdoctoral research at Leeds until 1993, when she moved to University College London[20] for five years before moving to the University of Manchester in 1999. Her research[21][22] concerns protein sequence alignment and protein analysis.

Inspired by the creation of PROSITE, Attwood developed a method of protein fingerprinting and used this to establish the PRINTS[23][24][25] database. With Amos Bairoch she sought to unify work on protein family classification and annotation, eventually jointly securing a European Union grant with Rolf Apweiler to establish InterPro,[26][27] with Pfam, ProDom and Swiss-Prot/TrEMBL as consortium partners in 1997.[28]

Attwood has led major projects including the BioMinT FP5[29] text-mining consortium, the EMBER[30] bioinformatics education consortium (including EBI and Swiss Institute of Bioinformatics as partners), and the EPSRC PARADIGM Platform.[31] She is the Manchester principal investigator on projects SeqAhead (Next-generation sequencing data analysis network)[32] and AllBio (bioinformatics infrastructure for unicellular, animal and plant sciences),[33] and was also Manchester PI on EMBRACE[34] and EuroKUP (kidney and urine proteomics).[35] Attwood was a member of ELIXIR’s Bioinformatics Training Strategy Committee (Work Package 11)[36] during ELIXIR's preparatory phase. She is currently Chair of the EMBnet Global Bioinformatics Network, she was a member of the Executive Committees of the International Society for Biocuration, and the Bioinformatics Training Network, and was recently elected to the Board of Directors of the International Society for Computational Biology. In 2012, she spearheaded the establishment of a GOBLET (Global Organisation for Bioinformatics Learning, Education and Training), with the major bioinformatics, computational biology and biocuration societies, networks and organisations as partners. As of 2016, Attwood is the Chair of the GOBLET Executive Board.[37]

As well as being a biocurator[28][38] she has co-developed tools to align and visualise protein sequences and structures, including Ambrosia and CINEMA.[39][40] The group are building re-usable software components to create useful bioinformatics applications through UTOPIA (Bioinformatics tools),[41][42] and are developing new approaches for automatic annotation and text mining, like PRECIS,[43] METIS,[44] BioIE,[45] and semantic approaches to data integration,[46] such as the Semantic Biochemical Journal[47] published by Portland Press. The UTOPIA tools underpin both the Semantic Biochemical Journal and a collaborative project with Pfizer and AstraZeneca to develop a 21st-century interface to biomedical literature and data management.

Attwood's research has received funding from the Engineering and Physical Sciences Research Council,[48] the Biotechnology and Biological Sciences Research Council, the Wellcome Trust, the Royal Society, the European Union and industry.[18]

Teaching[edit]

Attwood teaches on undergraduate and postgraduate courses and has been doctoral advisor or co-supervisor to several successful PhD students.[3][12][4][5][6][7][8][9][10][11][13][14][15] Attwood has co-authored several book chapters and three popular bioinformatics textbooks: Introduction to Bioinformatics[49] and Bioinformatics and Molecular Evolution.[50] Attwood is a co-author of the bioinformatics textbook Bioinformatics Challenges at the Interface of Biology and Computer Science: Mind the Gap[51] with Steve Pettifer and Dave Thorne.

Academic service[edit]

Attwood serves on the editorial board of the Biochemical Journal,[52] Database: The Journal of Biological Databases and Curation,[53] Molecular and Cellular Proteomics,[citation needed] the Journal of Molecular Graphics and Modelling and the EMBnet.journal.[citation needed]

Awards and honours[edit]

Attwood held a Royal Society University Research Fellowship (URF) from 1993 to 2002.[16]

References[edit]

  1. ^ Teresa Attwood at Library of Congress Authorities
  2. ^ a b Attwood, Teresa K. (1984). Chromonic mesophases (PhD thesis). University of Leeds. OCLC 59334329. 
  3. ^ a b Corpas, Manuel (2006). Folding patterns in protein sequences. librarysearch.manchester.ac.uk (PhD thesis). University of Manchester. OCLC 930689045. 
  4. ^ a b Coletta, Alain Nava (2009). Characterisation of low-complexity regions in protein sequences. librarysearch.manchester.ac.uk (PhD thesis). University of Manchester. OCLC 643625913. 
  5. ^ a b Divoli, Anna (2006). Biomedical text mining approaches: applications in protein family annotation. librarysearch.manchester.ac.uk (PhD thesis). University of Manchester. OCLC 930686752. 
  6. ^ a b Farhan, Reyhood (2008). Improving information retrieval for the biomedical sciences: a case study on mouse knockout literature. librarysearch.manchester.ac.uk (PhD thesis). University of Manchester. OCLC 643588840. 
  7. ^ a b Gaulton, Anna (2004). G protein-coupled receptors: relating sequence motifs to structure and function. librarysearch.manchester.ac.uk (PhD thesis). University of Manchester. OCLC 643553676. 
  8. ^ a b Kaján, László (2005). Development of computer-based methods for the prediction of protein structure and function (PhD thesis). Open University. OCLC 399699435. 
  9. ^ a b Mabey, Jane Elizabeth (2001). Improving functional diagnosis of protein families. librarysearch.manchester.ac.uk (PhD thesis). University of Manchester. OCLC 642667012. 
  10. ^ a b Maudling, Neil (2005). Analysing nucleotide sequence data with the PRINTS protein "pattern" database. librarysearch.manchester.ac.uk (PhD thesis). University of Manchester. OCLC 643539398. 
  11. ^ a b Moulton, Georgina (2005). Improving methods for functional analysis: a phylogenomic approach. librarysearch.manchester.ac.uk (PhD thesis). University of Manchester. OCLC 930686710. 
  12. ^ a b Overman, Ross (2013). Thesis restricted indefinitely. librarysearch.manchester.ac.uk (PhD thesis). University of Manchester. 
  13. ^ a b Taylor, Paul David (2004). Computational prediction of bacterial protein subcellular location and characterisation of transmembrance protein topology. librarysearch.manchester.ac.uk (PhD thesis). University of Manchester. OCLC 643479278. 
  14. ^ a b Walker, Nic (2007). Computational Identification of Regulatory Sequence in Genomes (PhD thesis). University of Manchester. 
  15. ^ a b Wright, William (2001). Perspectives on protein family database management and pattern recognition (PhD thesis). University of Manchester. 
  16. ^ a b c Anon (2016). "Teresa Attwood Professor of Bioinformatics". manchester.ac.uk. Manchester. Archived from the original on 2016-12-24. 
  17. ^ Attwood, Teresa's publications indexed by the Scopus bibliographic database, a service provided by Elsevier. (subscription required)
  18. ^ a b Terri Attwood's Entry at ORCID
  19. ^ Attwood, T. K.; Lydon, J. E. (1984). "Lyotropic Mesophase Formation by Anti-Asthmatic Drugs". Molecular Crystals and Liquid Crystals. 108 (3–4): 349. doi:10.1080/00268948408078686. 
  20. ^ "Teresa K Attwood". biochem.ucl.ac.uk/bsm/dbbrowser. 
  21. ^ Terri K. Attwood at DBLP Bibliography Server
  22. ^ Terri Attwood publications indexed by Google Scholar
  23. ^ Attwood, T. K.; Coletta, A.; Muirhead, G.; Pavlopoulou, A.; Philippou, P. B.; Popov, I.; Romá-Mateo, C.; Theodosiou, A.; Mitchell, A. L. (2012). "The PRINTS database: A fine-grained protein sequence annotation and analysis resource--its status in 2012". Database. 2012: bas019. PMC 3326521Freely accessible. PMID 22508994. doi:10.1093/database/bas019. 
  24. ^ Attwood, T. K.; Croning, M. D.; Flower, D. R.; Lewis, A. P.; Mabey, J. E.; Scordis, P.; Selley, J. N.; Wright, W. (2000). "PRINTS-S: The database formerly known as PRINTS". Nucleic Acids Research. 28 (1): 225–227. PMC 102408Freely accessible. PMID 10592232. doi:10.1093/nar/28.1.225. 
  25. ^ Attwood, T. K.; Bradley, P.; Flower, D. R.; Gaulton, A.; Maudling, N.; Mitchell, A. L.; Moulton, G.; Nordle, A.; Paine, K.; Taylor, P.; Uddin, A.; Zygouri, C. (2003). "PRINTS and its automatic supplement, prePRINTS". Nucleic Acids Research. 31 (1): 400–402. PMC 165477Freely accessible. PMID 12520033. doi:10.1093/nar/gkg030. 
  26. ^ Apweiler, R.; Attwood, T. K.; Bairoch, A.; Bateman, A.; Birney, E.; Biswas, M.; Bucher, P.; Cerutti, L.; Corpet, F.; Croning, M. D.; Durbin, R.; Falquet, L.; Fleischmann, W.; Gouzy, J.; Hermjakob, H.; Hulo, N.; Jonassen, I.; Kahn, D.; Kanapin, A.; Karavidopoulou, Y.; Lopez, R.; Marx, B.; Mulder, N. J.; Oinn, T. M.; Pagni, M.; Servant, F.; Sigrist, C. J.; Zdobnov, E. M. (2001). "The InterPro database, an integrated documentation resource for protein families, domains and functional sites". Nucleic Acids Research. 29 (1): 37–40. PMC 29841Freely accessible. PMID 11125043. doi:10.1093/nar/29.1.37. 
  27. ^ Apweiler, R.; Attwood, T. K.; Bairoch, A.; Bateman, A.; Birney, E.; Biswas, M.; Bucher, P.; Cerutti, L.; Corpet, F.; Croning, M. D. R.; Durbin, R.; Falquet, L.; Fleischmann, W.; Gouzy, J.; Hermjakob, H.; Hulo, N.; Jonassen, I.; Kahn, D.; Kanapin, A.; Karavidopoulou, Y.; Lopez, R.; Marx, B.; Mulder, N. J.; Oinn, T. M.; Pagni, M.; Servant, F.; Sigrist, C. J. A.; Zdobnov, E. M.; Interpro, C. (2000). "InterPro--an integrated documentation resource for protein families, domains and functional sites". Bioinformatics. 16 (12): 1145–1150. PMID 11159333. doi:10.1093/bioinformatics/16.12.1145. 
  28. ^ a b http://www.biocurator.org/elec/candidates2011/Attwood.pdf Attwood biography from biocurator.org
  29. ^ "BioMinT: Biological Text Mining EU FP5 Quality of Life Project". Archived from the original on 2012-07-25. 
  30. ^ EMBER - European Multimedia Bioinformatics Educational Resource
  31. ^ "Platform grant: PARADIGM - Platform for Annotation, Robust Analysis, Data Integration & Genome Management". Retrieved 2012-07-25. 
  32. ^ "COST Action: NGS-Data Analysis Network". Retrieved 2012-07-25. 
  33. ^ "start – AllBio". Archived from the original on 2012-07-25. 
  34. ^ Pettifer, S.; Ison, J.; Kalas, M.; Thorne, D.; McDermott, P.; Jonassen, I.; Liaquat, A.; Fernández, J. M.; Rodriguez, J. M.; Partners, I. -; Pisano, D. G.; Blanchet, C.; Uludag, M.; Rice, P.; Bartaseviciute, E.; Rapacki, K.; Hekkelman, M.; Sand, O.; Stockinger, H.; Clegg, A. B.; Bongcam-Rudloff, E.; Salzemann, J.; Breton, V.; Attwood, T. K.; Cameron, G.; Vriend, G. (2010). "The EMBRACE web service collection". Nucleic Acids Research. 38 (Web Server issue): W683–W688. PMC 2896104Freely accessible. PMID 20462862. doi:10.1093/nar/gkq297. 
  35. ^ "European Kidney and Urine Proteomics | Eurokup". Retrieved 2012-07-25. 
  36. ^ "Welcome to ELIXIR". Retrieved 2012-07-26. 
  37. ^ "Committees | GOBLET". www.mygoblet.org. Retrieved 24 August 2016. 
  38. ^ Burge, S.; Attwood, T. K.; Bateman, A.; Berardini, T. Z.; Cherry, M.; O'Donovan, C.; Xenarios, L.; Gaudet, P. (2012). "Biocurators and Biocuration: Surveying the 21st century challenges". Database. 2012: bar059. PMC 3308150Freely accessible. PMID 22434828. doi:10.1093/database/bar059. 
  39. ^ Lord, P. W.; Selley, J. N.; Attwood, T. K. (2002). "CINEMA-MX: A modular multiple alignment editor". Bioinformatics. 18 (10): 1402–1403. PMID 12376388. doi:10.1093/bioinformatics/18.10.1402. 
  40. ^ Parry-Smith, D. J.; Payne, A. W. R.; Michie, A. D.; Attwood, T. K. (1998). "CINEMA—a novel Colour INteractive Editor for Multiple Alignments". Gene. 221 (1): GC57–GC63. PMID 9852962. doi:10.1016/S0378-1119(97)00650-1. 
  41. ^ Attwood, T. K.; Kell, D. B.; McDermott, P.; Marsh, J.; Pettifer, S. R.; Thorne, D. (2010). "Utopia documents: Linking scholarly literature with research data". Bioinformatics. 26 (18): i568–i574. PMC 2935404Freely accessible. PMID 20823323. doi:10.1093/bioinformatics/btq383. 
  42. ^ Pettifer, S. R.; Sinnott, J. R.; Attwood, T. K. (2004). "UTOPIA—User-Friendly Tools for Operating Informatics Applications". Comparative and Functional Genomics. 5 (1): 56–60. PMC 2447318Freely accessible. PMID 18629035. doi:10.1002/cfg.359. 
  43. ^ Mitchell, A. L.; Reich, J. R.; Attwood, T. K. (2003). "PRECIS: Protein reports engineered from concise information in SWISS-PROT". Bioinformatics (Oxford, England). 19 (13): 1664–1671. PMID 12967963. doi:10.1093/bioinformatics/btg204. 
  44. ^ Mitchell, A. L.; Divoli, A.; Kim, J. -H.; Hilario, M.; Selimas, I.; Attwood, T. K. (2005). "METIS: Multiple extraction techniques for informative sentences". Bioinformatics. 21 (22): 4196–4197. PMID 16159915. doi:10.1093/bioinformatics/bti675. 
  45. ^ Divoli, A.; Attwood, T. K. (2005). "BioIE: Extracting informative sentences from the biomedical literature". Bioinformatics. 21 (9): 2138–2139. PMID 15691860. doi:10.1093/bioinformatics/bti296. 
  46. ^ Pettifer, S.; Thorne, D.; McDermott, P.; Marsh, J.; Villéger, A.; Kell, D. B.; Attwood, T. K. (2009). "Visualising biological data: A semantic approach to tool and database integration". BMC Bioinformatics. 10: S19. PMC 2697642Freely accessible. PMID 19534744. doi:10.1186/1471-2105-10-S6-S19. 
  47. ^ Attwood, T. K.; Kell, D. B.; McDermott, P.; Marsh, J.; Pettifer, S. R.; Thorne, D. (2009). "Calling International Rescue: Knowledge lost in literature and data landslide!". Biochemical Journal. 424 (3): 317–333. PMC 2805925Freely accessible. PMID 19929850. doi:10.1042/BJ20091474. 
  48. ^ Anon. "Grants awarded to Terri Attwood by the EPSRC". epsrc.ac.uk. Swindon. Retrieved 2012-07-25. 
  49. ^ Parry-Smith, David J.; Attwood, Teresa K. (1999). Introduction to bioinformatics. New York: Longman. ISBN 0-582-32788-1. 
  50. ^ Attwood, Teresa K.; Higgs, Paul (2005). Bioinformatics And Molecular Evolution. Cambridge, MA: Blackwell Publishers. ISBN 1-4051-0683-2. 
  51. ^ Attwood, Teresa K.; Pettifer, Stephen Robert; Thorne, David (2016). Bioinformatics Challenges at the Interface of Biology and Computer Science: Mind the Gap. Chichester, West Sussex ; Hoboken, New Jersey: Wiley-Blackwell. p. 424. ISBN 9780470035481. OCLC 951190363. 
  52. ^ "Biochemical Journal Editorial Board". Retrieved 2012-07-25. 
  53. ^ "Oxford Journals | Life Sciences | Database | Editorial board". Retrieved 2012-07-25.