Terri Attwood

Terri Attwood

Portrait of Terri Attwood by Linda Bussey
Born Teresa K. Attwood
Fields Bioinformatics
Protein fingerprinting
Institutions
Alma mater University of Leeds
Thesis Chromonic mesophases (1984)
Doctoral advisor John E. Lydon[1]
Doctoral students
  • Karl Burgess
  • Manuel Corpas[2]
  • Lisa Li Chun Lee
  • Alain Coletta[3]
  • Anna Divoli[4]
  • Rey Farhan[5]
  • Anna Gaulton[6]
  • László Kaján[7]
  • Jane Mabey[8]
  • Neil Maudling[9]
  • George Moulton[10]
  • Phil Scordis
  • Paul Taylor[11]
  • Nick Walker[12]
  • William Wright[13]
Known for
Notable awards Royal Society University Research Fellow

Website

Teresa (Terri) K. Attwood is a Professor of Bioinformatics in the School of Computer Science and Faculty of Life Sciences at the University of Manchester. She is a former Royal Society University Research Fellow[14] and visiting fellow at the European Bioinformatics Institute (EMBL-EBI).[15]

Education

Attwood gained her Bachelor of Science in Biophysics from the University of Leeds in 1982. She was awarded a PhD, also in Biophysics, two years later, in 1984[1] under the supervision of John E. Lydon[16] studying chromonic mesophases. Attwood undertook postdoctoral research at Leeds until 1993, when she moved to University College London[17] for five years before moving to the University of Manchester in 1999.

Research

Her research[18][19] 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[20][21][22] 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,[23][24] with Pfam, ProDom and Swiss-Prot/TrEMBL as consortium partners in 1997.[25]

Attwood has led major projects including the BioMinT FP5[26] text-mining consortium, the EMBER[27] bioinformatics education consortium (including EBI and Swiss Institute of Bioinformatics as partners), and the EPSRC PARADIGM Platform.[28] She is the Manchester principal investigator on projects SeqAhead (Next-generation sequencing data analysis network)[29] and AllBio (bioinformatics infrastructure for unicellular, animal and plant sciences),[30] and was also Manchester PI on EMBRACE[31] and EuroKUP (kidney and urine proteomics).[32] Attwood was a member of ELIXIR’s Bioinformatics Training Strategy Committee (Work Package 11)[33] 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. She is spearheading the establishment of a Global Organisation for Bioinformatics Learning, Education and Training (GOBLET), with the major bioinformatics, computational biology and biocuration societies, networks and organisations as partners.

As well as being a biocurator[25][34] she has co-developed tools to align and visualise protein sequences and structures, including Ambrosia and CINEMA.[35][36] The group are building re-usable software components to create useful bioinformatics applications through UTOPIA (Bioinformatics tools),[37][38] and are developing new approaches for automatic annotation and text mining, like PRECIS,[39] METIS,[40] BioIE,[41] and semantic approaches to data integration,[42] such as the Semantic Biochemical Journal[43] 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,[44] the Biotechnology and Biological Sciences Research Council, the Wellcome Trust, the European Union and industry.

Teaching

Attwood teaches on undergraduate and postgraduate courses and has been doctoral advisor or co-supervisor to several successful PhD students.[2][3][4][5][6][7][8][9][10][11][12][13] Attwood has co-authored several book chapters and two popular bioinformatics textbooks: Introduction to Bioinformatics[45] and Bioinformatics and Molecular Evolution.[46]

Academic service

Attwood serves on the editorial board of the Biochemical Journal,[47] Database: The Journal of Biological Databases and Curation,[48] Molecular and Cellular Proteomics, the Journal of Molecular Graphics and Modelling and the EMBnet.journal.

References

  1. 1 2 Attwood, Teresa K. (1984). Chromonic mesophases (PhD thesis). University of Leeds.
  2. 1 2 Corpas, Manuel (2006). Folding patterns in protein sequences (PhD thesis). University of Manchester. Archived from the original on March 17, 2014.
  3. 1 2 Coletta, Alain Nava (2009). Characterisation of low-complexity regions in protein sequences (PhD thesis). University of Manchester. Archived from the original on March 17, 2014.
  4. 1 2 Divoli, Anna (2006). Biomedical text mining approaches: applications in protein family annotation (PhD thesis). University of Manchester. Archived from the original on March 17, 2014.
  5. 1 2 Farhan, Reyhood (2008). Improving information retrieval for the biomedical sciences: a case study on mouse knockout literature (PhD thesis). University of Manchester. Archived from the original on March 17, 2014.
  6. 1 2 Gaulton, Anna (2004). G protein-coupled receptors: relating sequence motifs to structure and function (PhD thesis). University of Manchester. Archived from the original on March 17, 2014.
  7. 1 2 Kaján, László (2005). Development of computer-based methods for the prediction of protein structure and function (PhD thesis). Open University.
  8. 1 2 Mabey, Jane Elizabeth (2001). Improving functional diagnosis of protein families (PhD thesis). University of Manchester. Archived from the original on March 17, 2014.
  9. 1 2 Maudling, Neil (2005). Analysing nucleotide sequence data with the PRINTS protein "pattern" database (PhD thesis). University of Manchester. Archived from the original on March 17, 2014.
  10. 1 2 Moulton, Georgina (2005). Improving methods for functional analysis: a phylogenomic approach (PhD thesis). University of Manchester. Archived from the original on March 17, 2014.
  11. 1 2 Taylor, Paul David (2004). Computational prediction of bacterial protein subcellular location and characterisation of transmembrance protein topology (PhD thesis). University of Manchester. Archived from the original on March 17, 2014.
  12. 1 2 Walker, Nick (2007). Computational Identification of Regulatory Sequence in Genomes (PhD thesis). University of Manchester.
  13. 1 2 Wright, William (2001). Perspectives on protein family database management and pattern recognition (PhD thesis). University of Manchester.
  14. ↑ "University Research Fellowship | Royal Society". Retrieved 2012-06-11.
  15. ↑ Terri Attwood's publications indexed by the Scopus bibliographic database, a service provided by Elsevier.
  16. ↑ 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.
  17. ↑ Teresa K Attwood
  18. ↑ Terri Attwood's publications indexed by the DBLP Bibliography Server at the University of Trier
  19. ↑ Terri Attwood's publications indexed by Google Scholar, a service provided by Google
  20. ↑ 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. doi:10.1093/database/bas019. PMC 3326521. PMID 22508994.
  21. ↑ 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. doi:10.1093/nar/28.1.225. PMC 102408. PMID 10592232.
  22. ↑ 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. doi:10.1093/nar/gkg030. PMC 165477. PMID 12520033.
  23. ↑ 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. doi:10.1093/nar/29.1.37. PMC 29841. PMID 11125043.
  24. ↑ 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. doi:10.1093/bioinformatics/16.12.1145. PMID 11159333.
  25. 1 2 http://www.biocurator.org/elec/candidates2011/Attwood.pdf Attwood biography from biocurator.org
  26. ↑ "BioMinT: Biological Text Mining EU FP5 Quality of Life Project". Archived from the original on 2012-07-25.
  27. ↑ EMBER - European Multimedia Bioinformatics Educational Resource
  28. ↑ "Platform grant: PARADIGM - Platform for Annotation, Robust Analysis, Data Integration & Genome Management". Retrieved 2012-07-25.
  29. ↑ "COST Action: NGS-Data Analysis Network". Retrieved 2012-07-25.
  30. ↑ "start – AllBio". Archived from the original on 2012-07-25.
  31. ↑ 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. doi:10.1093/nar/gkq297. PMC 2896104. PMID 20462862.
  32. ↑ "European Kidney and Urine Proteomics | Eurokup". Retrieved 2012-07-25.
  33. ↑ "Welcome to ELIXIR". Retrieved 2012-07-26.
  34. ↑ 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. doi:10.1093/database/bar059. PMC 3308150. PMID 22434828.
  35. ↑ Lord, P. W.; Selley, J. N.; Attwood, T. K. (2002). "CINEMA-MX: A modular multiple alignment editor". Bioinformatics 18 (10): 1402–1403. doi:10.1093/bioinformatics/18.10.1402. PMID 12376388.
  36. ↑ 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. doi:10.1016/S0378-1119(97)00650-1. PMID 9852962.
  37. ↑ 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. doi:10.1093/bioinformatics/btq383. PMC 2935404. PMID 20823323.
  38. ↑ 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. doi:10.1002/cfg.359. PMC 2447318. PMID 18629035.
  39. ↑ 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. doi:10.1093/bioinformatics/btg204. PMID 12967963.
  40. ↑ 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. doi:10.1093/bioinformatics/bti675. PMID 16159915.
  41. ↑ Divoli, A.; Attwood, T. K. (2005). "BioIE: Extracting informative sentences from the biomedical literature". Bioinformatics 21 (9): 2138–2139. doi:10.1093/bioinformatics/bti296. PMID 15691860.
  42. ↑ 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. doi:10.1186/1471-2105-10-S6-S19. PMC 2697642. PMID 19534744.
  43. ↑ 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. doi:10.1042/BJ20091474. PMC 2805925. PMID 19929850.
  44. ↑ "Grants awarded to Terri Attwood by the EPSRC". Retrieved 2012-07-25.
  45. ↑ Parry-Smith, David J.; Attwood, Teresa K. (1999). Introduction to bioinformatics. New York: Longman. ISBN 0-582-32788-1.
  46. ↑ Attwood, Teresa K.; Higgs, Paul (2005). Bioinformatics And Molecular Evolution. Cambridge, MA: Blackwell Publishers. ISBN 1-4051-0683-2.
  47. ↑ "Biochemical Journal Editorial Board". Retrieved 2012-07-25.
  48. ↑ "Oxford Journals | Life Sciences | Database | Editorial board". Retrieved 2012-07-25.
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