Terri Attwood

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Terri Attwood
AttwoodTerri.jpeg
Born
Teresa K. Attwood

(1959-11-20) 20 November 1959 (age 64) [1]
Alma mater University of Leeds
Known for
Awards Royal Society University Research Fellowship 1993–2002 [2]
Scientific career
Fields Bioinformatics
Protein fingerprinting
Institutions
Thesis Chromonic mesophases  (1984)
Doctoral advisor John E. Lydon [3]
Doctoral students
Website

Teresa K. Attwood (born 20 November 1959) is a professor of Bioinformatics in the Department of Computer Science and School of Biological Sciences at the University of Manchester and a visiting fellow at the European Bioinformatics Institute (EMBL-EBI). [5] 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. [2]

Contents

Education

Attwood gained her Bachelor of Science in Biophysics from the University of Leeds in 1982. [6] She was awarded a PhD, also in Biophysics, two years later, in 1984 [3] under the supervision of John E. Lydon [7] studying chromonic mesophases.

Research and career

Attwood undertook postdoctoral research at Leeds until 1993, when she moved to University College London [8] for five years before moving to the University of Manchester in 1999. Her research [9] [10] 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 [11] [12] [13] 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, [14] [15] with Pfam, ProDom and Swiss-Prot/TrEMBL as consortium partners in 1997. [16]

Attwood has led major projects including the BioMinT FP5 [17] text-mining consortium, the EMBER [18] bioinformatics education consortium (including EBI and Swiss Institute of Bioinformatics as partners), and the EPSRC PARADIGM Platform. [19] She is the Manchester principal investigator on projects SeqAhead (Next-generation sequencing data analysis network) [20] and AllBio (bioinformatics infrastructure for unicellular, animal and plant sciences), [21] and was also Manchester PI on EMBRACE [22] and EuroKUP (kidney and urine proteomics). [23] Attwood was a member of ELIXIR's Bioinformatics Training Strategy Committee (Work Package 11) [24] 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. [25] [26]

As well as being a biocurator [16] [27] she has co-developed tools to align and visualise protein sequences and structures, including Ambrosia and CINEMA. [28] [29] The group are building re-usable software components to create useful bioinformatics applications through UTOPIA (Bioinformatics tools), [30] [31] and are developing new approaches for automatic annotation and text mining, like PRECIS, [32] METIS, [33] BioIE, [34] and semantic approaches to data integration, [35] such as the Semantic Biochemical Journal [36] 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, [37] the Biotechnology and Biological Sciences Research Council, the Wellcome Trust, the Royal Society, the European Union and industry. [6]

Teaching

Attwood teaches on undergraduate and postgraduate courses and has been doctoral advisor or co-supervisor to several PhD students (e.g., Manuel Corpas). Attwood has co-authored several book chapters and three popular bioinformatics textbooks: Introduction to Bioinformatics [38] and Bioinformatics and Molecular Evolution. [39] Attwood is a co-author of the bioinformatics textbook Bioinformatics Challenges at the Interface of Biology and Computer Science: Mind the Gap [40] with Steve Pettifer and Dave Thorne.

Academic service

Attwood serves on the editorial board of the Biochemical Journal , [41] Database: The Journal of Biological Databases and Curation , [42] Molecular and Cellular Proteomics,[ citation needed ] the Journal of Molecular Graphics and Modelling and the EMBnet.journal.[ citation needed ]

Awards and honours

Attwood held a Royal Society University Research Fellowship (URF) from 1993 to 2002. [2]

Related Research Articles

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<span class="mw-page-title-main">Amos Bairoch</span>

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In molecular biology, the PRINTS database is a collection of so-called "fingerprints": it provides both a detailed annotation resource for protein families, and a diagnostic tool for newly determined sequences. A fingerprint is a group of conserved motifs taken from a multiple sequence alignment - together, the motifs form a characteristic signature for the aligned protein family. The motifs themselves are not necessarily contiguous in sequence, but may come together in 3D space to define molecular binding sites or interaction surfaces. The particular diagnostic strength of fingerprints lies in their ability to distinguish sequence differences at the clan, superfamily, family and subfamily levels. This allows fine-grained functional diagnoses of uncharacterised sequences, allowing, for example, discrimination between family members on the basis of the ligands they bind or the proteins with which they interact, and highlighting potential oligomerisation or allosteric sites.

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References

  1. ↑ Teresa Attwood at Library of Congress
  2. 1 2 3 Anon (2016). "Teresa Attwood Professor of Bioinformatics". manchester.ac.uk. Manchester. Archived from the original on 24 December 2016.
  3. 1 2 Attwood, Teresa K. (1984). Chromonic mesophases (PhD thesis). University of Leeds. OCLC   59334329.
  4. ↑ Corpas, Manuel (2007). Folding patterns in protein sequences (PhD thesis). University of Manchester. doi:10.6084/m9.figshare.964811.v1.
  5. ↑ 57193816586 Attwood, Teresa's publications indexed by the Scopus bibliographic database. (subscription required)
  6. 1 2 Terri Attwood's ORCID   0000-0003-2409-4235
  7. ↑ Attwood, T. K.; Lydon, J. E. (1984). "Lyotropic Mesophase Formation by Anti-Asthmatic Drugs". Molecular Crystals and Liquid Crystals. 108 (3–4): 349. Bibcode:1984MCLC..108..349A. doi:10.1080/00268948408078686.
  8. ↑ "Teresa K Attwood". biochem.ucl.ac.uk/bsm/dbbrowser.
  9. ↑ Terri K. Attwood at DBLP Bibliography Server OOjs UI icon edit-ltr-progressive.svg
  10. ↑ Terri Attwood publications indexed by Google Scholar OOjs UI icon edit-ltr-progressive.svg
  11. ↑ 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.
  12. ↑ 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.
  13. ↑ 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.
  14. ↑ 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.
  15. ↑ 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.
  16. 1 2 http://www.biocurator.org/elec/candidates2011/Attwood.pdf Attwood biography from biocurator.org
  17. ↑ "BioMinT: Biological Text Mining EU FP5 Quality of Life Project". Archived from the original on 19 June 2012.
  18. ↑ "EMBER - European Multimedia Bioinformatics Educational Resource". www.bioinf.man.ac.uk.
  19. ↑ "Platform grant: PARADIGM - Platform for Annotation, Robust Analysis, Data Integration & Genome Management" . Retrieved 25 July 2012.
  20. ↑ "COST Action: NGS-Data Analysis Network" . Retrieved 25 July 2012.
  21. ↑ "start – AllBio". Archived from the original on 29 December 2012.
  22. ↑ 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.
  23. ↑ "European Kidney and Urine Proteomics | Eurokup" . Retrieved 25 July 2012.
  24. ↑ "Welcome to ELIXIR" . Retrieved 26 July 2012.
  25. ↑ "Committees | GOBLET". www.mygoblet.org. 16 November 2014. Retrieved 24 August 2016.
  26. ↑ Corpas, M.; Jimenez, R. C.; Bongcam-Rudloff, E.; Budd, A.; Brazas, M. D.; Fernandes, P. L.; van Gelder, C.; Korpelainen, E.; Lewitter, F.; McGrath, A.; MacLean, D.; Palagi, P.; Rother, K.; Taylor, J.; Via, A.; Watson, M.; Schneider, M. V.; Attwood, T. K. (2015). "The GOBLET training portal: a global repository of bioinformatics training materials, courses and trainers". Bioinformatics. 31 (1): 140–142. doi:10.1093/bioinformatics/btu601. PMC   4271145 . PMID   25189782.
  27. ↑ 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.
  28. ↑ 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.
  29. ↑ 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.
  30. ↑ 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.
  31. ↑ 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.
  32. ↑ Mitchell, A. L.; Reich, J. R.; Attwood, T. K. (2003). "PRECIS: Protein reports engineered from concise information in SWISS-PROT". Bioinformatics. 19 (13): 1664–1671. doi: 10.1093/bioinformatics/btg204 . PMID   12967963.
  33. ↑ 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.
  34. ↑ 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.
  35. ↑ 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 (Suppl 6): S19. doi: 10.1186/1471-2105-10-S6-S19 . PMC   2697642 . PMID   19534744.
  36. ↑ 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.
  37. ↑ Anon. "Grants awarded to Terri Attwood by the EPSRC". epsrc.ac.uk. Swindon. Retrieved 25 July 2012.
  38. ↑ Parry-Smith, David J.; Attwood, Teresa K. (1999). Introduction to bioinformatics. New York: Longman. ISBN   978-0-582-32788-7.
  39. ↑ Attwood, Teresa K.; Higgs, Paul (2005). Bioinformatics And Molecular Evolution. Cambridge, Massachusetts: Blackwell Publishers. ISBN   978-1-4051-0683-2.
  40. ↑ 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.
  41. ↑ "Biochemical Journal Editorial Board". Archived from the original on 20 February 1999. Retrieved 25 July 2012.
  42. ↑ "Oxford Journals | Life Sciences | Database | Editorial board" . Retrieved 25 July 2012.
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