BIBLIOGRAPHY

Brazas MD, Blackford S & Attwood TK (2017)

"Training: Plug gap in essential bioinformatic skills."

Nature

544

Finn RD, Attwood TK, Babbitt PC, Bateman A, Bork P, Bridge AJ, Chang HY, Doszt?nyi Z, El-Gebali S, Fraser M, Gough J, Haft D, Holliday GL, Huang H, Huang X, Letunic I, Lopez R, Lu S, Marchler-Bauer A, Mi H, Mistry J, Natale DA, Necci M, Nuka G, Orengo CA, Park Y, Pesseat S, Piovesan D, Potter SC, Rawlings ND, Redaschi N, Richardson L, Rivoire C, Sangrador-Vegas A, Sigrist C, Sillitoe I, Smithers B, Squizzato S, Sutton G, Thanki N, Thomas PD, Tosatto SC, Wu CH, Xenarios I, Yeh LS, Young SY & Mitchell AL (2017)
"InterPro in 2017 - beyond protein family and domain annotations."
Nucleic Acids Res., 45(D1), D190-199. doi:10.1093/nar/gkw1107.

Horro C, Cook M, Attwood TK, Brazas MD, Hancock JM, Palagi PM, Corpas M & Jimenez RC (2017)
"BioCIDER: a Contextualisation InDEx for biological Resource discovery."
Bioinformatics, doi:10.1093/bioinformatics/btx213

Brazas MD, Brooksbank C, Jimenez RC, Blackford S, Palagi PM, De Las Rivas J, Ouellette BFF, Kumuthini J, Korpelainen E, Lewitter F, van Gelder CWG, Mulder N, Corpas M, Schneider MV, Tan TW, Clements D, Davies A & Attwood TK. (2017)
"A global perspective on bioinformatics training needs."
BioRXiv, 098996. doi:https://doi.org/10.1101/098996

Schneider MV, Attwood TK, Corpas M, Charleston M, Dayalan S, Gaudet P, Kumuthini J, Morgan S, Palagi PM & Rustici G. (2017)
"GOBLET Standards Committee: best practices and standards in bioinformatics and biocuration. [version 1; not peer reviewed]"
F1000Research, 6, 327(poster). doi:10.7490/f1000research.1113789.1

Larcombe L, Hendricusdottir R, Attwood TK, Bacall F, Beard N, Bellis LJ, Dunn WB, Hancock JM, Nenadic A, Orengo C, Overduin B, Sansone S-A, Thurston M, Viant MR, Winder CL, Goble CA, Ponting CP & Rustici G. (2017)
"ELIXIR-UK role in bioinformatics training at the national level and across ELIXIR. [version 1; referees: 3 approved, 1 approved with reservations]."
F1000Research, 6, 952. doi:10.12688/f1000research.11837.1

Attwood TK, Brazas MD, van Gelder CWG & McGrath A. (2017)
"Five years of GOBLET: to unite, inspire and equip bioinformatics trainers worldwide. [version 1; not peer reviewed]"
F1000Research, 6(ISCB Comm J), 1304(poster). doi:10.7490/f1000research.1114553.1

Tyagi S, Schneider MV, Morgan S, Charleston M, Palagi P, Kumuthini J, Rustici G & Attwood TK. (2017)
"GOBLET Standards Committee: our activities and forward vision. [version 1; not peer reviewed]"
F1000Research, 6(ISCB Comm J), 1305(poster). doi: 10.7490/f1000research.1114554.1

Attwood TK, Blackford S, Brazas MD, Davies A, Schneider MV. (2017)
"A global perspective on evolving bioinformatics and data-science training needs."
Briefings in Bioinformatics, doi: 10.1093/bib/bbx100

Morgan S, Palagi PM, Fernandes P, Korperlainen E, Dimec J, Marek D, Larcombe L, Rustici G, Attwood TK & Via A. (2017)
"The ELIXIR-EXCELERATE Train-the-Trainer pilot programme: empower researchers to deliver high-quality training. [version 1; referees: awaiting peer review]"
F1000Research, 6, 1557. doi:10.12688/f1000research.12332.1

Attwood TK, Pettifer SR & Thorne D (2016)

John Wiley and Sons.

van Gelder C, Morgan S, Via A, Hendricusdottir R, Korpelainen E, Ponting C, Attwood T & Palagi P. (2016)
"Report on the training needs identified across the ELIXIR community."
Zenodo, https://zenodo.org/record/61411#.WX-j0hiZPI0.

Attwood TK, Leskosek BL, Dimec J, Morgan S, Mulder N, van Gelder CWG & Palagi PM. (2016)
"Defining a lingua franca for the ELIXIR/GOBLET e-learning ecosystem."
Zenodo, https://zenodo.org/record/166378#.WYHLCBiZPUK.

Attwood TK, Bongcam-Rudloff E, Fernandes P, Korpelainen E, Lewitter F, Rustici G, Schneider MV, van Gelder CWG & Palagi PM. (2016)
"Train-the-Trainer: GOBLET's initiative to increase the provision of bioinformatics training in NGS. [version 1; not peer reviewed]"
F1000Research, 5(ISCB Comm J), 1683(poster). doi: 10.7490/f1000research.1112581.1

Beard N, Attwood T & Nenadic A. (2016)
"TeSS - Training Portal. [version 1; not peer reviewed]"
F1000Research, 5(ISCB Comm J), 1762(poster). doi:10.7490/f1000research.1112652.1

Mulder N, Attwood TK, Black P, Blatter M-C, Fernandes P, Palagi PM, Rustici G, Schneider MV & van Gelder CWG. (2016)
"GOBLET's Bioinformatics Learning, Education & Training Activities. [version 1; not peer reviewed]"
F1000Research, 5(ISCB Comm J), 1944(poster). doi:10.7490/f1000research.1112737.1

Attwood TK, Black P, Blatter M-C, Brooksbank C, Fernandes P, Mulder N, Palagi PM, Rustici G, Schneider MV & van Gelder CWG. (2016)
"GOBLET's Bioinformatics Learning, Education & Training Activities. [version 1; not peer reviewed]"
F1000Research, 5, 2152(poster). doi:10.7490/f1000research.1112990.1

Nenadic A, Beard N, Thurston M, Sansone S-A, Goble CA & Attwood TK. (2016)
"TeSS - Training Portal. [version 1; not peer reviewed]"
F1000Research, 5(ELIXIR), 326(poster). doi:10.7490/f1000research.1111409.1

Hancock JM, Attwood TK, Hendricusdottir R, Larcombe L, Nenadic A, Ponting CP, Rustici G, Sansone S-A & Goble CA. (2016)
"ELIXIR UK. [version 1; not peer reviewed]"
F1000Research, 5(ELIXIR), 346(poster). doi:10.7490/f1000research.1111425.1

Hendricusdottir R, Palagi PM, van Gelder CWG, Larcombe L, Korpelainen E, Leskosek B, Attwood TK, Morgan SL, Peterson H, Upton A, Vannerum K, Via A, Kafetzopoulos D, Reczko M, Dominguez del Angel V, Spiwok V, Linial M, Unger R, Husum Bak-Jensen H, Nygard S, Fernandes P, Light S, Rustici G, Repo S, Smith A, Ponting C & Blomberg N. (2016)
"The ELIXIR training platform: highlights and overview. [version 1; not peer reviewed]"
F1000Research, 5(ELIXIR), 525(poster). doi:10.7490/f1000research.1111595.1

Beard N, Cook M, Nenadic A, Jimenez R, Attwood T, Morrison N, van Gelder CWG, Coppens F, Leskosek B, Ison J, McQuilton P, Gonzalez-Beltran A, Sansone S-A, De Bo, C, Botzki A, Van Horn JD, Ambite J-L, Lerman K, Tracktenberg R, Horro C, Preste R, Janko C, Johnson C, Dallakian P & Pergl R. (2016)
"Bioschemas: structured data for life science using schema.org. [version 1; not peer reviewed]"
F1000Research, 5(ELIXIR), 2296(poster). doi:10.7490/f1000research.1113119.1

Atwood TK, Bongcam-Rudloff E, Brazas ME, Corpas M, Gaudet P, Lewitter F, Mulder N, Palagi PM, Schneider MV & van Gelder CW; GOBLET Consortium (2015)

"GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training."

PLoS Comput.Biol.

Attwood TK, Bongcam-Rudloff E, Brazas ME, Corpas M, Gaudet P, Lewitter F, Mulder N, Palagi PM, Schneider MV & van Gelder CW; GOBLET Consortium (2015)
"Correction: GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training."
PLoS Comput.Biol., 11(5):e1004281. DOI:10.1371/journal.pcbi.1004281

Mitchell A, Chang HY, Daugherty L, Fraser M, Hunter S, Lopez R, McAnulla C, McMenamin C, Nuka G, Pesseat S, Sangrador-Vegas A, Scheremetjew M, Rato C, Yong SY, Bateman A, Punta M, Attwood TK, Sigrist CJ, Redaschi N, Rivoire C, Xenarios I, Kahn D, Guyot D, Bork P, Letunic I, Gough J, Oates M, Haft D, Huang H, Natale DA, Wu CH, Orengo C, Sillitoe I, Mi H, Thomas PD & Finn RD (2015)
"The InterPro protein families database: the classification resource after 15 years."
Nucleic Acids Res., 43, D213-21. DOI:10.1093/nar/gku1243

Corpas M, Jimenez RC, Bongcam-Rudloff E, Budd A, Brazas MD, Fernandes PL, Gaeta B, van Gelder C, Korpelainen E, Lewitter F, McGrath A, MacLean D, Palagi PM, Rother K, Taylor J, Via A, Watson M, Schneider MV & Attwood TK (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

Aleksic J, Alexa A, Attwood TK, Chue Hong N, Dahlo M, Davey R, Dinkel H, Forstner KU, Grigorov I, Heriche JK, Lahti L, MacLean D, Markie ML, Molloy J, Schneider MV, Scott C, Smith-Unna R & Vieira BM; as part of the AllBio: Open Science & Reproducibility Best Practice Workshop (2015)
"An open science peer review oath."
F1000Research, 3, 271. doi:10.12688/f1000research.5686.2. eCollection 2014

Ellis LBM & Attwood TK (2015)
"Longevity of biological databases."
EMBnet.journal, 21, e803.

The GOBLET Consortium. (2015)
"Meeting the Global Thirst for Bioinformatics Training. [version 1; not peer reviewed]"
F1000Research, 4(ISCB Comm J), 328. doi:10.7490/f1000research.1110075.1

Beard N, Nenadic A, Attwood T, Goble C, Thurston M, Sansone S-A. (2015)
"ELIXIR-UK TeSS Training Portal. [version 1; not peer reviewed]"
F1000Research, 4(ISCB Comm J), 518(poster). doi:10.7490/f1000research.1110257.1

Overman, R.C., Debreczeni, J.E., Truman, C.M., McAlister, M.S. & Attwood, T.K. (2014)

Protein Sci.

Concise Encyclopaedia of Bioinformatics and Computational Biology, 2nd Edition. (2014)
Bioinformatics Subject Editor. John Wiley and Sons, ISBN 978-0-470-97871-9.
J.M.Hancock & M.J.Zvelebil, Eds.

GOBLET Consortium. Attwood TK, Blackford S, Brazas MD, Brooksbank C, Budd A, Corpas M, Davies A, Fatumo S, Fernandes PL, Gaudet P, Hayer J, Jimenez R, Korpelainen E, Kumuthini J, Maclean D, McGrath A, Orengo C, Palagi PM, Ponting C, Sansone S, Schneider MV, Sch?nbach C, Taylor J, van Gelder CWG & Vriend G.(2014)
"GOBLET: achievements and goals a year on"
EMBnet.journal, 20:e751. http://dx.doi.org/10.14806/ej.20.0.751

Schneider MV, Brazas MD, Lewitter F, Attwood TK & The GOBLET Consortium. (2014)
"Bioinformatics training: a global survey of training needs."
ISMB 2014, Boston, poster D4. https://www.iscb.org/cms_addon/conferences/ismb2014/posterlist.php?cat=D

Overman RC, Green I, Truman CM, Read J, Embrey K, McAlister MS & Attwood TK (2013)

"Stability and solubility engineering of the EphB4 receptor tyrosine kinase catalytic domain."

Protein Eng. Des. Sel.

Overman, R.C., Debreczeni, J.E., Truman, C.M., McAlister, M.S. & Attwood, T.K. (2013)
"Biochemical and biophysical characterization of four EphB kinase domains reveals contrasting thermodynamic, kinetic and inhibition profiles."
Biosci. Rep., 33(3). pii: e00040. DOI:10.1042/BSR20130028.

Via, A., Blicher, T., Bongcam-Rudloff, E., Brazas, M.D., Brooksbank, C., Budd, A., De Las Rivas, J., Dreyer, J., Fernandes, P.L., van Gelder, C., Jacob, J., Jimenez, R.C., Loveland, J., Moran, F., Mulder, N., Nyronen, T., Rother, K., Schneider, M.V. & Attwood, T.K. (2013)
"Best Practices in Bioinformatics Training for Life Scientists."
Briefings in Bioinformatics, 14(5), 528-537. DOI: 10.1093/bib/bbt043

Jimenez, R.C., Albar, J.P., Bhak, J., Blatter, M.C., Blicher, T., Brazas, M.D., Brooksbank, C., Budd, A., De Las Rivas,J., Dreyer, J., van Driel, M.A., Dunn, M.J., Fernandes, P.L., van Gelder, C.W., Hermjakob, H., Ioannidis, V., Judge, D.P., Kahlem, P., Korpelainen, E., Kraus, H.J., Loveland, J., Mayer, C., McDowall, J., Moran, F., Mulder, N., Nyronen, T., Rother, K., Salazar, G.R., Schneider, R., Via, A., Villaveces, J.M., Yu, P., Schneider, M.V., Attwood, T.K. & Corpas, M. (2013)
"iAnn: An Event Sharing Platform for the Life Sciences."
Bioinformatics, 29(15), 1919-1921. DOI:10.1093/bioinformatics/btt306

GOBLET Consortium. Attwood TK, Appel R, Blackford S, Blatter M-C, Bongcam-Rudloff E, Brazas MD, Brooksbank C, Collado-Vides J, Corpas M, Cossey S, De Las Rivas J, Falquet L, Fernandes PL, Gaeta B, Gaudet P, Helmer-Citterich M, Heringa J, Howard JC, Hutchinson P, Jimenez R, Kok R, Kumuthini J, Lewitter F, Lovell D, Maclean D, Ouellette F, Mulder N, Palagi PM, Peitsch MC, Ranganathan S, Robinson-Rechavi M, Rost B, Schneider MV, Schneider R, Sch?nbach C, Trelles O, van Gelder CWG, van Kampen B, Via A & Vriend G.(2013)
"The Global Organisation for Bioinformatics Learning, Education & Training (GOBLET)."
EMBnet.journal, 19(1), 10-13. http://dx.doi.org/10.14806/ej.19.1.606

Luo J, Nijveen H, Attwood T, Judge D, Pongor S, Landsman D, Bishop M. (2013)
"Obituary: in memory of Jack Leunissen."
Brief Bioinform., 14(3), 261-262. DOI:10.1093/bib/bbt036

The GOBLET Consortium. (2013)
"Bioinformatics training & education: towards global sustainable solutions."
ISMB/ECCB 2013, Berlin, poster D11. https://www.iscb.org/cms_addon/conferences/ismbeccb2013/posterlist.php?cat=D

Pettifer, S., Attwood, T., Marsh, J & Thorne, D. (2012)

Open source software in life science research: practical solutions to common challenges in the pharmaceutical industry and beyond

Schneider, M.V., Walter, P., Blatter, M.C., Watson, J., Brazas, M.D., Rother, K., Budd, A., Via, A., van Gelder, C.W.G., Jacob, J., Fernandes, P., Nyronen, T., De Las Rivas, J., Blicher, T., Loveland, J., McDowall, J., Jones, P., Vaughan, B., Lopez, R., Attwood, T.K. & Brooksbank, C. (2012)
"Bioinformatics Training Network (BTN): A community resource for bioinformatics trainers."
Briefings in Bioinformatics, 13(3), 383-389.

Attwood, T.K., Coletta, A., Muirhead, G., Pavlopoulou, A., Philippou, P.B., Popov, I., Roma-Mateo, C., Theodosiou, A. & Mitchell, A. (2012)
"The PRINTS database: a fine-grained protein sequence annotation and analysis resource - its status in 2012."
Database, 10.1093/database/base019.

Hunter, S., Jones, P., Mitchell, A., Apweiler, R., Attwood, T.K., Bateman, A., Bernard, T., Binns, D., Bork, P., Burge, S., de Castro, E., Coggil, P., Corbett, M., Das, U., Daugherty, L., Duquenne, L., Finn, R.D., Fraser, M., Gough, J., Haft, D., Hulo, N., Kahn, D., Kelly, E., Letunic, I., Lonsdale, D., Lopez, R., Madera, M., Maslen, J., McAnulla, C., McDowall, J., McMenamin, C., Mi, H., Mutowo-Muellenet, P., Mulder, N., Natale, D., Orengo, C., Pesseat, S., Punta, M., Quinn, A.F., Rivoire, C., Sangrador-Vegas, A., Selengut, J.D., Sigrist, C.J.A., Scheremetjew, M., Tate, J., Thimmajanarthanan, M., Thomas, P.D., Wu, C.H., Yeats, C. & Yong, S.Y. (2012)
"InterPro in 2011: new developments in the family and domain prediction database."
Nucleic Acids Res., 40, D306-12.

Vroling, B., Thorne, D., McDermott, P., Joosten, H.J., Attwood, T.K., Pettifer, S. & Vriend, G. (2012)
"NuclearDB: information system for nuclear receptors."
Nucleic Acids Res., 40, D377-380.

Burge, S., Attwood, T.K., Bateman, A., Berardinin, T.Z., Cherry, J.M., O'Donovan, C., Xenarios, I. & Gaudet, P. (2012)
"Biocurators and biocuration: surveying the 21st century challenges."
Database, 10.1093/database/bar059.

Mischak, H., Ioannidis, J.P.A., Argiles, A., Attwood, T.K., Bongcam-Rudloff, E., Broenstrup, M., Charonis, A., Chrousos, G.P., Delles, C., Dominiczak, A., Dylag, T., Ehrich, J., Egido, J., Jankowski, J., Johnson, R.W., Julien, B., Lankisch, T., Leung, H., Maahs, D., Magni, F., Manns, M.P., Manolis, E., Mayer, G., Navis, G., Novak, J., Ortiz, A., Persson, F., Peter, K., Riese, H.H.,Rossing, P., Sattar, N., Spasovski, G., Thongboonkerd, V., Vanholder, R., Schanstra, J.P. & Vlahou, A. (2012)
"Implementation of proteomic biomarkers: making it work"
European Journal of Clinical Investigation, 10.1111/j.1365-2362.2012.02674.x.

Pettifer S, Velterop J, Attwood T, Harland L, Marsh J, Thorne D & Tunbridge A (2012)
"Reuniting data and narrative in scientific articles."
Insights, 25(3), 288-293. DOI:http://doi.org/10.1629/2048-7754.25.3.288

Schneider MV, Attwood TK, Via A & Brooksbank C. (2012)
"Bioinformatics training for life scientists: guidelines for best practice. Deliberable report D2.05 of FP7 project, SLING (grant agreement number 226073), submitted to the European Commission February 2012"
Zenodo, https://doi.org/10.5281/zenodo.31087.

Attwood, T.K., Gisel, A., Eriksson, N-E. & Bongcam-Rudloff, E. (2011)

"Concepts, historical milestones and the central place of bioinformatics in modern biology: a European perspective."

Bioinformatics - Trends and Methodologies

Mitchell, A.L., Selimas, I. & Attwood, T.K. (2011)
"MINOTAUR - a Web-based annotator assistant tool."
International Journal of Systems Biology & Biomedical Technologies, 1(1), 1-10.DOI:10.4018/ijsbbt.2012010101, ISSN: 2160-9586.

Via, A., De Las Rivas, J., Attwood, T.K., Landsman, D., Brazas, M.D., Leunissen, J.A.M., Tramontano, A. & Schneider, M.V. (2011)
"10 simple rules for developing a short bioinformatics training courses."
PLoS Computational Biology, 7(10), e1002245. DOI:10.1371/journal.pcbi.1002245.

Vroling, B., Thorne, D., McDermott, P., Attwood, T.K. & Pettifer, S.R. (2011)
"Integrating GPCR-specific information with full text articles."
BMC Bioinformatics, 12(1), 362.

Pettifer, S.R., McDermott, P., Marsh, J., Thorne, D. & Attwood, T.K. (2011)
"Ceci n'est pas un hamburger."
Learned Publishing, 24(3), 207-220.

Gaudet, P., Bairoch, A., Field, D., Sansone, S_A., Taylor, C., Attwood, T.K., Bateman, A., Blake, J.A., Bult, C.J., Cherry, J.M., Chisholm, R.L., Cochrane, G.,Cook, C.E., Eppig, J.T., Galperin, M.Y., Gentleman, R., Goble, C.A., Gojobori, T., Hancock, J.M., Howe, D.G., Imanishi, T., Kelso, J., Landsman, D., Lewis, S.E., Mizrachi, I.K.,Orchard, S., Ouellette, B.F.F, Ranganathan, S., Richardson, L., Rocca-Serra, P., Schofield, P.N., Smedley, D., Southan, C., Tan, T.W., Tatusova, T., Whetzel, P.L., White, O. & Yamasaki, C. on behalf of the BioDBCore working group. (2011)
"Towards BioDBcore: a community-defined information specification for biological databases."
Nucleic Acids Res., 39, D7-10.

Gaudet, P., Bairoch, A., Field, D., Sansone, S_A., Taylor, C., Attwood, T.K., Bateman, A., Blake, J.A., Bult, C.J., Cherry, J.M., Chisholm, R.L., Cochrane, G.,Cook, C.E., Eppig, J.T., Galperin, M.Y., Gentleman, R., Goble, C.A., Gojobori, T., Hancock, J.M., Howe, D.G., Imanishi, T., Kelso, J., Landsman, D., Lewis, S.E., Mizrachi, I.K.,Orchard, S., Ouellette, B.F.F, Ranganathan, S., Richardson, L., Rocca-Serra, P., Schofield, P.N., Smedley, D., Southan, C., Tan, T.W., Tatusova, T., Whetzel, P.L., White, O. & Yamasaki, C. on behalf of the BioDBCore working group. (2010)
"Towards BioDBcore: a community-defined information specification for biological databases."
Database, 10.1093/database/baq027.

Clark, T., Ciccarese, P., Attwood, T.K., de Waard, A. & Pettifer, S.R. (2011)
"A Round-Trip to the Annotation Store: Open, Transferable Semantic Annotation of Biomedical Publications."
Beyond the PDF, Workshop, January 19-21, 2011, University of California San Diego.

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

Mischak, H., Allmaier, G., Apweiler, R., Attwood, T.K., Baumann, M., Benigni, A., Bennett, S.E., Bischoff, R., Bongcam-Rudloff, E., Capasso, G., Coon, J.J., D'Haese, P., Dominiczak, A.F., Dakna, M., Dihazi, H., Ehrich, J.H., Fernandez-Llama, P., Fliser, D., Frokiaer, J., Garin, J., Girolami, M., Hancock, W.S., Haubitz, M., Hochstrasser, D., Holman, R., Ioannidis, J.P.A., Jankowski, J., Julian, B.A., Klein, J.B., Kolch, W., Luider, T., Massy, Z., Mattes, W.B., Molina, F., Monsarrat, B., Novak, J., Peter, K., Rossing, P., S�nchez-Carbayo, M., Schanstra, J.P., Semmes, O.J., Spasovski, G., Theodorescu, D., Thongboonkerd, V., Vanholder, R., Veenstra, T., Weissinger, E., Yamamoto, T. & Vlahou, A. (2010)
"Recommendations for biomarker identification & classifier qualification in clinical proteomics."
Science Translational Medicine, 2(46).

Pettifer, S., Ison, J., Kalas, M., Thorne, D., McDermott, P., Jonassen, I., Liaquat, A., Fernandez, 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 Res., 38, Suppl. W683-8. PMID 20462862.

Hekkelman, M.L., te Beek, T.A.H., Pettifer, S., Thorne, D., Attwood, T.K. & Vriend, G. (2010)
"WIWS: a protein structure bioinformatics Web service collection."
Nucleic Acids Res., 38, Suppl.W7, 19-23. PMID 20501602.

Coletta, A., Pinney, J.W., Weiss Solis, D.Y., Marsh, J., Pettifer, S.R. & Attwood, T.K. (2010)
"Low-complexity regions within protein sequences have position-dependent roles."
BMC Syst. Biol., 4(1), 43.

Maria Victoria Schneider, James Watson, Teresa Attwood, Kristian Rother, Aidan Budd, Jennifer McDowall, Allegra Via, Pedro Fernandes, Tommy Nyronen, Thomas Blicher, Phil Jones, Marie-Claude Blatter, Javier De Las Rivas, David Phillip Judge,Wouter van der Gool & Cath Brooksbank (2010)
"Bioinformatics training: a review of challenges, actions and support requirements."
Briefings in Bioinformatics, 11(16), 544-551. doi:10.1093/bib/bbq021.

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

Attwood, T.K., Kell, D.B., McDermott, P., Marsh, J., Pettifer, S.R. & Thorne, D. (2009)
"Knowledge lost in literature and data landslide: calling international rescue!"
The Biochemist, December 2009, pp.23-38.

Pettifer, S., Thorne, D., McDermott, P., Marsh, J., Villeger, A., Kell, D.B. & Attwood, T.K. (2009)
"Visualising biological data: a semantic approach to tool and database integration."
BMC Bioinformatics, 10, S18.

Pettifer, S., Thorne, D., McDermott, P., Attwood, T., Baran, J., Bryne, J.C., Hupponen, T., Mowbray, D. & Vriend, G. (2009)
"An active registry for bioinformatics Web services."
Bioinformatics, 25, 2090-2091.

Hunter, S., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., Bork, P., Das, U., Daugherty, L., Duquenne, L., Finn, R., Gough, J., Haft, D., Hulo, N., Kahn, D., Kelly, E., Laugraud, A., Letunic, I., Lonsdale, D., Lopez, R., Madera, M., Maslen, J., McAnulla, C., McDowall, J., Mistry, J., Mitchell, A., Mulder, N., Natale, D., Orengo, C., Quinn, A.F., Selengut, J.D., Sigrist, C.J.A., Thimma, M., Thomas, P.D., Valentin, F., Wilson, D., Wu, C.H. & Yeats, C. (2009)
"InterPro: the integrative protein signature database."
Nucleic Acids Res., 37, D211-5. doi:10.1093/nar/gkn785

Mabey Gilsenan, J., Atherton, G., Bartholomew, J., Giles, P.F., Attwood, T.K., Denning, D.W. & Bowyer, P. (2009)
"Aspergillus Genomes and The Aspergillus Cloud."
Nucleic Acids Research, 37, D509-14. doi:10.1093/nar/gkn876.

Vlahou, A., Allmaier, G., Attwood, T.K., Bongcam-Rudloff, E., Charonis, A., Frokiaer, J., Mischak, H., Schanstra, J.P. & Spasovski, G. (2009)
"2nd Combined Working Group and Management Committee Meeting of Urine and Kidney Proteomics COST Action 29-30 March 2009, Nafplio, Greece."
Proteomics Clin.Appl., 3(9), 1017-1022.

Attwood, T.K., Kell, D.B., McDermott, P., Marsh, J., Pettifer, S.R. & Thorne, D. (2009)
"Utopia Documents and The Semantic Biochemical Journal experiment."
EMBnet.journal, 15(4), 3-6.

Attwood, T.K. (2009)
"UMBER - University of Manchester Bioinformatics Education & Research."
EMBnet.journal, 15(4), 41-42.

Attwood, T.K., Selimas, I., Buis, R., Altenburg, R., Herzog, R., Ledent, V., Ghita, V., Fernandes, P., Marques, I. & Brugman, M. (2009)
"EMBER - A European Multimedia Bioinformatics Educational Resource."
In Bioscience Education, Collected Papers, 1-8, Ed. S.Maw, pp.167-178. ISBN-13:978-0-9548751-5-2

Park, H., Huxley-Jones, J., Boot-Handford, R.P., Bishop, P.N., Attwood, T.K & Bella, J. (2008)

BMC Genomics

Stockinger, H., Attwood, T.K., Chohan, S.N., Cote, R., Cudre-Mauroux, P., Falquet, L., Fernandes, P., Finn, R.D., Hupponen, T., Korpelainen, E., Labarga, A., Laugraud, A., Lima, T., Pafilis, E., Pagni, M., Pettifer, S., Phan, I. & Rahman, N. (2008)
"Experience using Web services for biological sequence analysis."
Briefings in Bioinformatics, 9(6), 493-505. doi:10.1093/bib/bbn029.

Vlahou, A., Schanstra, J., Frokiaer, J., El Nahas, M., Spasovski, G., Mischak, H., Domon, B., Allmaier, G., Bongham-Rudloff, E. & Attwood, T.K. (2008)
"Establishment of a European Network for Urine and Kidney Proteomics."
Journal of Proteomics, 71(4), 490-492. PMID 18620085.

Higgs, P. & Attwood, T.K. (2008)
"Bioinformatyka i ewolucja molekularna (Bioinformatics and Molecular Evolution)"
Translated by Murzin, K., Liguzinski, P. & Kurdziel, M.
Blackwell Science Ltd., ISBN 978-83-01-15494-3

Pettifer, S., Thorne, D., McDermott, P., Attwood, T., Baran, J., Bryne, J.C., Hupponen, T. & Vriend, G. (2008)
"The EMBRACE registry."
EMBnet News, 14(4), 58-62.

Mulder, N.J., Apweiler, R., Attwood, T.K., Bairoch, A., Binns, D., Bork, P., Cerutti, L., Copley, R., Courcelle, E., Das, U., Daugherty, L., Dibley, M., Finn, R., Fleischmann, W., Haft, D., Hulo, N., Hunter, S., Kanapin, A., Kejariwal, A., Labarga, A., Langendijk-Genevauz, P.S., Lonsdale, D., Lopez, Letunic, I., R., Madera, M., Maslen, J., McAnulla, C., McDowall, J., Mistry, J., Mitchell, A., Nikolskaya, A.N., Orchard, S., Orengo, C., Petryszak, R., Selengut, J.D., Sigrist, C.J.A., Thomas, P.D., Valentin, F., Wilson, D., Wu, C.H. & Yeats, C. (2007)

Nucleic Acids Res.

Kim, J-H., Mitchell, A.L., Attwood, T.K. & Hilario, M. (2007)
"Learning to extract relations for protein annotation."
Bioinformatics, 23(13), i256-i263. DOI:10.1093/bioinformatics/btm168

Nordle, A.K.L., Rios, P., Gaulton, A., Pulido, R., Attwood, T.K. & Tabernero, L. (2007)
"Functional assignment of MAPK phosphatase domains."
PROTEINS: Structure, Function & Bioinformatics, 69(1), 19-31.

Roma-Mateo, C., Rios, P., Tabernero, L., Attwood, T.K. & Pulido, R. (2007)
"A novel phosphatase family, structurally related to dual-specificity phosphatases, that displays unique amino acid sequence and substrate specificity."
Journal of Molecular Biology, 374(4), 899-909. PMID: 17976645.

Attwood, T.K., Parry-Smith, D.J. & Phukan, S. (2007)
"Introduction to bioinformatics."
Pearson Education, South Asia.
ISBN 81-7758-641-6

Corpas, C., Sinnott, J., Thorne, D., Pettifer, S. & Attwood, T.K. (2007)
"PFF - an integrated database of residues and fragments critical for protein folding."
BMC Systems Biology, 1(Suppl 1), P48 doi:10.1186/1752-0509-1-S1-P48.

Park, H., Huxley-Jones, J., Attwood, T.K. & Bella, J. (2007)
"LRRCE: a cysteine capping motif unique to small leucine-rich repeat proteins and proteoglycans of the extracellular matrix.."
BMC Systems Biology, 1(Suppl 1), P55 doi:10.1186/1752-0509-1-S1-P55.

Attwood, T.K. (2007)
"Genetic databases."
In Encyclopaedia of the Life Sciences, John Wiley & Sons, Ltd. DOI:10.1002/9780470015902.a0005312.pub2.

Pettifer, S., Attwood, T.K., McDermott, P., Sinnott, J. & Thorne, D. (2007)
"UTOPIA: User-friendly Tools for OPerating Informatics Applications."
EMBnet News, 13(2), 19-24.

Pettifer, S.R., Attwood, T.K., Thorne, D., Sinnott, J., Li, P., McDermott, P., Oinn, P., Alper, P., Goble, C.A., Wolstencroft, K. (2007)
"myGrid and UTOPIA: an integrated approach to enacting and visualising in silico experiments in the Life Sciences."
International Workshop on Data Integration in the Life Sciences 2007 (DILS2007), 27-29 June 2007, Philadelphia, USA.

Moulton, G., Selimas, I. & Attwood, T.K. (2007)
"EMBER - A European Multimedia Bioinformatics Educational Resource."
International Technology, Education and Development Conference (INTED-2007), 7-9 March 2007, Valencia, Spain.

Moulton, G., Selimas, I. & Attwood, T.K. (2007)
"EMBER - An evolving bioinformatics e-learning resource."
Bioinformatics 2007: Workshop on Collaborative Bioinformatics, Joint Meeting of Red Iberoamericana de Bioinformatica and EMBnet, 11-13 June 2007, Malaga, Spain.

Pettifer, S. & Attwood, T.K. (2007)
"Progress with UTOPIA."
Bioinformatics 2007: Workshop on Collaborative Bioinformatics, Joint Meeting of Red Iberoamericana de Bioinformatica and EMBnet, 11-13 June 2007, Malaga, Spain.

Attwood, T.K., Mitchell, A., Gaulton, A., Moulton, G. & Tabernero, L.(2006)

Encyclopaedia of Genetics, Genomics, Proteomics and Bioinformatics

Taylor, P.D., Toseland, C.P., Attwood, T.K. & Flower, D.R. (2006)
"Combining algorithms to predict Bacterial protein sub-cellular location: Parallel versus Concurrent implementations."
Bioinformation, 1(8), 285-289.

Taylor, P.D., Toseland, C.P., Attwood, T.K. & Flower, D.R. (2006)
"Toward bacterial protein sub-cellular location prediction: single-class discrimminant models for all Gram- and Gram+ compartments."
Bioinformation, 1(8), 276-280.

Taylor, P.D., Attwood, T.K. & Flower, D.R. (2006)
"Multi-class subcellular location prediction for bacterial proteins."
Bioinformation, 1(7), 260-264.

Taylor, P.D., Toseland, C.P., Attwood, T.K. & Flower, D.R. (2006)
"Alpha-helical transmembrane proteins: enhanced prediction using a Bayesian approach."
Bioinformation, 1(6), 234-236.

Taylor, P.D., Toseland, C.P., Attwood, T.K. & Flower, D.R. (2006)
"Beta-Barrel transmembrane proteins: enhanced prediction using a Bayesian approach."
Bioinformation, 1(6), 231-233.

Taylor, P.D., Toseland, C.P., Attwood, T.K. & Flower, D.R. (2006)
"A Predictor of Membrane Class: Discriminating alpha-helical and beta-barrel membrane proteins from non-membranous proteins."
Bioinformation, 1(6), 208-213.

Taylor, P.D., Toseland, C.P., Attwood, T.K. & Flower, D.R. (2006)
"TATPred: a Bayesian method for the identification of twin arginine translocation pathway signal sequences."
Bioinformation, 1(5), 184-187.

Taylor, P.D., Toseland, C.P., Attwood, T.K. & Flower, D.R. (2006)
"LIPPRED: A web server for accurate prediction of lipoprotein signal sequences and cleavage sites."
Bioinformation, 1(5), 176-179.

Oxford Dictionary of Biochemistry and Molecular Biology, Second Edition. (2006)
Bioinformatics Editor. Oxford University Press.
R.Cammack, Ed. in Chief.

McDermott, P., Sinnott, J., Thorne, D., Pettifer, S. & Attwood, T.K. (2006)
"An Architecture for Visualisation and Interactive Analysis of Proteins."
In Proceedings of 4th Int. Conference on Coordinated and Multiple Views in Exploratory Visualization (CMV06).

Mitchell, AL, Selimas, I. & Attwood, T.K. (2006)
"Challenges for protein family annotation."
In The 17th European Conference on Machine Learning & the 10th European Conference on Principles & Practice of Knowledge Discovery in Databases(ECML/PKDD-2006), September 18-22, Berlin, Germany.

Attwood, T.K. (2006)
"Seeking functional clues in GPCR seaquences and structures: cautionary tales for bioinformatics."
In The Hellenic Crystallographic Association 3rd Conference, September 22-24, Patras, Greece.

Attwood, T.K. & Bussey, L. (2006)
"A close shave."
MSL, 547, 111-116.

Attwood, T.K. & Bussey, L. (2006)
"Proof of the pudding."
DL, 182-183.

Mitchell, A.L., Divoli, A., Kim, J-H., Hilario, M., Selimas, I. & Attwood T.K. (2005)

Bioinformatics,

Divoli, A. & Attwood, T.K. (2005)
"BioIE: extracting informative sentences from the biomedical literature."
Bioinformatics, 21(9), 2138-9.

Mulder, N.J., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., Bradley, P., Bork, P., Bucher, P., Cerutti, L., Copley, R., Courcelle, E., Das, U., Durbin, R., Fleischmann, W., Gough, J., Haft, D., Harte, N., Hulo, N., Kahn, D., Kanapin, A., Krestyaninova, M., Lonsdale, D., Lopez, R., Letunic, I., Madera, M., Maslen, J., McDowall, J., Mitchell, A., Nikolskaya, A.N., Orchard, S., Pagni, M., Ponting, C.P., Quevillon, E., Selengut, J., Sigrist, C.J., Silventoinen, V., Studholme, D.J., Vaughan, R. & Wu, C.H. (2005)
"InterPro, progress and status in 2005."
Nucleic Acids Res., 33, D201-5.

Farhan R., Aplin J.D., Attwood T.K., et al. (2005)
" Retrieving reproductive biology literature using natural language processing."
Placenta, 26(8-9), A22.

Attwood, T.K., Selimas, I., Buis, R., Altenburg, R., Herzog, R., Ledent, V., Ghita, V., Fernandes, P., Marques, I. & Brugman, M. (2005)
"EMBER - A European Multimedia Bioinformatics Educational Resource."
Bee-J, 6-4.

Divoli, A. & Attwood, T.K. (2005)
"Protein family databases: text-mining & annotation. "
ISMB 2005: 13th Int. Conference on Intelligent Systems for Molecular Biology, BioLINK SIG workshop. Detroit, USA.

Divoli, A. & Attwood, T.K. (2005)
"Text-mining challenges for protein family database annotation. "
ISMB 2005: 13th Int. Conference on Intelligent Systems for Molecular Biology. Detroit, USA.

Corpas, M., Thorne, D., Sinnott, J., Pettifer, S. & Attwood, T.K. (2005)
"An integrated approach to structural & functional motif prediction."
In Exploring Protein Structure, September 2005, Haifa.

Gilsenan, J.E., Anderson, M., Attwood, T.K., Oliver, S.G., Paton, N.W., Robson, G.D. & Denning, D.W. (2005)
"Viewing annotated Aspergillus genomes on the Central Aspergillus Data REpository (CADRE) Website."
23rd Fungal Genetics Conference, Pacific Grove, USA.

Divoli, A., Winter, R., Pettifer, S. & Attwood, T.K. (2005)
"BioQSpace: An interactive visualisation tool for clustering MEDLINE abstracts. "
1st Int. Student Symposium in Computational Biology, at ECCB, Madrid, 2005. Best Presentation Award.

Higgs, P. & Attwood, T.K. (2005)
"Bioinformatics and Molecular Evolution."
Blackwell publishing, ISBN 1 4051 0683 2

Mulder, N.J.,Attwood, T.K., Bairoch, A., Apweiler, R., Bateman, A., Barker, W.C., Binns, D., Bradley, P., Das, U., Fleischmann, W., Harte, N., Hulo, N., Kanapin, A., Krestyaninova, M., Langendijk-Genevaux, P.S., Le Saux, V., Lonsdale, D., Lopez, R., Maslen, J., McDowall, J., Mitchell, A., Natale, D.A., Nikolskaya, A.N., Orchard, S., Quevillon, E., Sigrist, C.J., Studholme, D.J. & Wu, C.H. (2005)
"Bioinformatics tools for large-scale functional classification of proteins - the InterPro database."
Trends in Bioinformatics Research, Yan, P.V. Ed., Nova Science Publishers, Hauppauge, NY, USA, pp.59-94. ISBN: 1-59454-739-4(S).

Pettifer, S.R., Sinnott, J. & Attwood, T.K. (2005)
"Integrated approaches for bioinformatics data analysis and visualisation - challenges, opportunities and new solutions."
In Data Analysis and Visualisation in Genomics and Proteomics, pp.137-152. John Wiley & Sons. ISBN 0-470-09439-7

Flower D.R. & Attwood T.K. (2004)

Semin.Cell Dev.Biol.,

15(6)

Maudling N. & Attwood T.K. (2004)
"FAN: fingerprint analysis of nucleotide sequences."
Nucleic Acids Res., 32, W620-3.

Mabey, J.E., Anderson, M.J., Giles, P.F., Miller, C.J., Attwood, T.K., Paton, N.W.,
Bornberg-Bauer, E., Robson, G.D., Oliver, S.G. & Denning, D.W. (2004)
"CADRE: the Central Aspergillus Data REpository."
Nucleic Acids Research, 32, D401-405.

Pettifer, S.R., Sinott, J.R. & Attwood, T.K. (2004)
"UTOPIA - User-friendly Tools for OPerating Informatics Applications."
Comparative and Functional Genomics, 5, CFG359.

Dictionary of Bioinformatics and Computational Biology. (2004)
Bioinformatics Subject Editor. John Wiley and Sons, ISBN 978-0-471-43622-5.
J.Hancock & M.Zvelebil, Eds.

Farhan, R., Attwood, T.K., McGee-Wood, M., Aplin, J. & Sibley, C. (2004)
"Information Retrieval and Natural Language Processing Techniques Applied to Reproductive Biology."
Proceedings of the 7th Annual Colloquium for the UK SIG for Computational Linguistics,
M.Lee (Ed.), Birmingham 6-7th January, pp.56-61.
ISBN 07044 24533

Ghita, V., Ledent, V., Herzog, R., Attwood, T.K., Selimas, I. & Brugman, M. (2004)
"EMBER - a new tutorial for sequence analysis and biocomputing."
BBC04: Belgian Bioinformatics Conference, Bruxelles, April 23.

Hilario, M., Mitchell, A.L., Kim, J-H., Bradley, P. & Attwood, T.K. (2004)
"Classifying Protein Fingerprints."
In Proceedings of the 8th European Conference on Principles and Practice of Knowledge Discovery in Databases (PKDD-04 Best Paper award), Pisa, Italy.

Divoli, A., Mitchell, A.L., Bradley, P. & Attwood, T.K. (2004)
"METIS: Multiple Extraction Techniques for Informative Sentences."
ISMB/ECCB 2004: 12th Int. Conference on Intelligent Systems for Molecular Biology. Glasgow, UK.

Walker, N., Attwood, T.K. & Sharrocks, A.D. (2004)
"A rule based system for the identification of transcription factor binding sites in S.cerevisiae.
In Genome Informatics, Joint Cold Spring Harbour/Wellcome Trust Conference, Hinxton, UK.

Walker, N., Attwood, T.K. & Sharrocks, A.D. (2004)
"Use of an integrated rule system for identification of the transcription factor binding sites for MCM1 and FKH2 in S.cerevisiae. "
In Proceedings of the 4th Int. Confernce on Bioinformatics of Genome Regulation & Structure, vol.1, pp212. Novosibirsk, Russia, July 25-30.

Attwood, T.K., Bradley, P., Daelemans, W., Dehaspe, L., Durant, F., Hilario, M., Kim, J-H.,
Mitchell, A.L., Petrak, J., Pillet, V., Seewald, A.K., Van Belleghem, K., Veuthey, A-L. & Zehnder, M. (2004)
"BioMinT: a database curator's assistant for biomedical text processing. "
ISMB 2004: Special Interest Biolink Group Workshop, Glasgow, UK.

Attwood, T.K., Bradley, P., Gaulton, A., Maudling, N., Mitchell, A.L. & Moulton, G. (2004)
"The PRINTS protein fingerprint database: functional and evolutionary applications."
In Encyclopaedia of Genetics, Genomics, Proteomics and Bioinformatics, M.Dunn, L.Jorde, P.Little & A.Subramaniam (Eds.). John Wiley & Sons.

Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., Bradley, P., Bordoli, L., Bucher, P.,
Courcelle, E., Das, U., Durbin, R., Flegel, V., Fleischmann, W., Griffiths-Jones, S., Haft, D., Harte, N.,
Hulo, N., Kahn, D., Kanapin, A., Krestyaninova, M., Lonsdale, D., Lopez, R., Maslen, J., McDowall, J.,
Mulder, N., Nikolskaya, A.N., Orchard, S., Quevillon, E., Servant, F., Sigrist, C.J.A.,
Silventoinen, V., Studholme, D.J. & Wu, C.H.(2004)
"InterPro - prediction of protein families, domains and functional sites"
In Focus on Genome Research, Nova Science Publishers, New York, C.Williams (Ed.), pp.169-205. ISBN 1-59033-960-6.

Pettifer, S.R., Sinott, J.R. & Attwood, T.K. (2004)
"CINEMA - A UTOPIAn sequence editor."
CCP11 Newsletter, 10.

Sinnott, J.R., Pettifer, S.R. & Attwood, T.K. (2004)
"Introduction to the CINEMA5 sequence alignment editor. "
EMBNet News, 10(3).

Attwood, TK, Selimas, I, Buis, R, Altenburg, R, Herzog, R, Ledent, V, Ghita, V, Fernandes, P,
Marques, I & Brugman, M (2004)
"EMBER - A European Bioinformatics Educational Resource."
LTSN Bioscience Bulletin, 13, 8-9.

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

Mulder, N.J., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D.,
Biswas, M., Bradley, P., Bork, P., Bucher, P., Copley, R.R., Courcelle, E.,
Das, U., Durbin, R., Falquet, L., Fleischmann, W., Griffith-Jones, S., Haft, D.,
Harte, N., Hermjakob, H., Hulo, N., Kahn, D., Kanapin, A., Krestyaninova, M.,
Lopez, R., Letunic, I., Lonsdale, D., Silventoinen, V., Orchard, S., Pagni, M.,
Peyruc, D., Ponting, C.P., Servant, F., Sigrist, C.J.A., Vaughan, R. & Zdobnov, E. (2003)
"The InterPro Database - 2003 brings increased coverage and new features."
Nucleic Acids Research, 31(1), 315-318.

Mitchell, A.L., Reich, J.R. & Attwood, T.K. (2003)
"PRECIS - Protein Reports Engineered from Concise Information in SWISS-PROT."
Bioinformatics, 19, 1664-1671.

Miller, C.J. & Attwood, T.K. (2003)
"Bioinformatics goes back to the future."
Nature Reviews Molecular Cell Biology, 4(2), 157-162.

Attwood, T.K. (2003)
"Genetic databases."
In Encyclopaedia of the Human Genome, Nature Publishing Group.

Gaulton, A. & Attwood, T.K. (2003)
"Bioinformatic approaches for analysing GPCRs."
Current opinions in pharmacology, 3(2), 114-120.

Moulton, G., Attwood, T.K., Parry-Smith, D.J. & Packer, J. (2003)
"Phylogenomic analysis and evolution of the potassium channel gene family."
Receptors and Channels, 9(6), 363-377.

Gaulton, A. & Attwood, T.K. (2003)
"Motif3D - relating sequence motifs to structure."
Nucleic Acids Research, 31, 3333-3336.

Taylor, P, Attwood, T.K. & Flower, D.R. (2003)
"BPROMPT - a consensus server for membrane protein prediction."
Nucleic Acids Research, 31, 3698-3700.

Attwood, T.K. (2003)
"What is Bioinformatics?"
Biological Sciences Review, 15(3), 13-15.

Attwood, T.K. (2003)
"Bioinformatics - what use is it?"
Biological Sciences Review, 15(4), 2-5.

Attwood, T.K. (2003)
"Focus on UMBER - University of Manchester Bioinformatics, Education & Research."
EMBnet News, 9(1), 3-8.

Attwood, T.K., Blythe, M., Flower, D.R., Gaulton, A., Mabey, J.E., Maudling, N.,
McGregor, L., Mitchell, A., Moulton, G., Paine, K. & Scordis, P. (2002)

"PRINTS and PRINTS-S shed light on protein ancestry."

Nucleic Acids Research

Attwood, T.K., Croning, M.D.R. & Gaulton, A. (2002)
"Deriving structural and functional insights from a ligand-based hierarchical classification of G protein-coupled receptors."
Protein Engineering, 15(1), 7-12.

Attwood, T.K. & Miller, C.J. (2002)
"Progress in bioinformatics and the importance of being earnest"
In Biotechnology Annual Review, 8, 1-55.

Attwood, T.K. (2002)
"The PRINTS database: a resource for identification of protein families."
Briefings in Bioinformatics, 3(3), 252-263.

The InterPro Consortium: Mulder, N.J., Apweiler, R., Attwood,T.K., Bairoch, A., Bateman, A., Binns, D.,
Biswas, M., Bradley, P., Bucher, P., Copley, R., Durbin, R., Falquet, L., Fleischmann, W., Gouzy, J.,
Griffith-Jones, S., Haft, D., Hermjakob, H., Hulo, N., Jonassen, I., Kahn, D., Kanapin, A.,
Krestyaninova, M., Lopez, R., Pagni, M., Ponting, C., Servant, F. & Sigrist, C.J.A.(2002)
"InterPro - An integrated documentation resource for protein families, domains and functional sites."
Briefings in Bioinformatics, 3(3), 225-245.

Attwood, T.K. & Flower, D.R. (2002)
"Trawling the genome for G protein-coupled receptors: the importance of integrating bioinformatic approaches."
In Drug Design - Cutting Edge Approaches, 60-71.

Lord, P.W., Selley, J.N. & Attwood, T.K. (2002)
"CINEMA-MX: a modular multiple alignment editor."
Bioinformatics, 18(10), 1402-1403.

Attwood, T.K. (2002)
"Bioinformatics: gene-protein-structure-function."
In Proceedings of the 18th Annual Meeting of the European Society of Human Reproduction and Embryology.

Attwood, T.K. (2002)
"Bugging cancer with COBALT."
Trends in Biotechnology, 20(3), 95.

Attwood, T.K. (2002)
"Metals in prion disease."
Trends in Biotechnology, 20(6), 235.

Attwood, T.K. (2002)
"Rhodopsin sheds light on neurodegenerative disease."
Trends in Biotechnology, 20(10), 415.

Attwood, T.K. on behalf of the EMBER consortium (2002)
"EMBER - A European Multimedia Bioinformatics Educational Resource."
EMBnet.news, 8(1), 15-19.

Attwood, T.K. (2001)

"A compendium of specific motifs for diagnosing GPCR subtypes."

Trends in Pharmacological Sciences,

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, T.M., Servant, F., Sigrist, C.J.A. & Zdobnov, E. (2001)
"The InterPro database, an integrated documentation resource for protein families,
domains and functional sites."
Nucleic Acids Research, 29(1), 37-40.

Selley, J.N. & Attwood, T.K. (2001)
"EASY - an Expert Analysis SYstem for interpreting database search outputs."
Bioinformatics, 17(1), 105-106.

Attwood, T.K. & Miller, C.J. (2001)
"Which craft is best in bioinformatics?"
Computers and Chemistry, 25(4), 329-339.

Ellis, L.B.M. & Attwood, T.K. (2001)
"Molecular biology databases: today and tomorrow."
Drug Discovery Today, 6, 509-513.

Reich, J.R., Mitchell, A., Goble, C.A. & Attwood, T.K. (2001)
"Toward more intelligent annotation tools: a prototype."
IEEE Intelligent Systems, 16(6), 42-51.

Miller, C.J. & Attwood, T.K. (2001)
"PSST...The probabilistic sequence search tool."
IEEE Int. Symposium on Bioinformatics and Bioengineering, pp.33-40.Washington DC, November 2001. IEEE press, ISBN 0-7695-1423-5.

Lord, P., Reich, J.R., Mitchell, A., Stevens, R., Attwood, T.K. & Goble, C. (2001)
"PRECIS: An automated pipeline for producing concise reports about proteins."
IEEE Int. Symposium on Bioinformatics and Bioengineering, pp.57-64. Washington DC, November 2001. IEEE press, ISBN 0-7695-1423-5.

Attwood, T.K. (2001)
"A new dimension to the vCJD epidemic: multiple QTL."
Trends in Genetics, 17(8), 439.

Attwood, T.K. (2001)
"A new dimension to the vCJD epidemic."
Trends in Biotechnology, 19(8), 283.

Attwood, T.K. (2001)
"Looking slim: peripherin/rds and photoreceptor cell morphology."
Trends in Biotechnology, 19(2), 40.

Attwood, T.K. (2001)
"Mobile, metamorphosing academic databases - capturing IP on the move."
Workshop on Managing IPR in a knowledge-based economy - Bioinformatics
and the influence of public policy, Brussels, Belgium, 11-12 September.

S.Crespi, T.K.Attwood, M.Bates, L.Bendekgey, B.Callan, G.Cameron, A.De Clercq, J.Franklin, B.Gannon,
B.Hammer Jensen, J.A.M.Leunissen, T.Mueller-Gerger, A.Kamperman Sanders, R.Tschannen, P.V.U.van Grevenstein (2001)
"Managing IPR in a knowledge-based economy - bioinformatics and the influence of public policy."
Report for the European Commission Research Directorate General, based on a Workshop held in Brussels, Belgium, 11-12 September.

Attwood, T.K. (2001)
"Pattern Databases."
Proceedings of the Joint Annual Meeting of Osterreichische Gesellschaft fur Biochemie und Molekularbiologie, Osterreichische
Gesellschaft fur Genetik und Gentechnik, Osterreichische Gesellschaft fur Biotechnologie, 27.

Attwood, T.K. (2001)
"A European Multimedia Bioinformatics Educational Resource (EMBER)."
LTSN Bioscience Bulletin, 4, 9.

Mabey, J.E. & Attwood, T.K. (2001)
"EMBER: a European Multimedia Bioinformatics Educational Resource."
CAL-laborate. A collaborative publication on the use of Computer Aided
Learning for tertiary level physical sciences, 6, 13-16.

Attwood, T.K. (2000)

"The Babel of Bioinformatics."

Science

290

Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Birney, E., Biswas, M.,
Bucher, P., Cerutti, L., Croning, M.D.R., Durbin, R., Fleischmann, W.,
Hermjakob, H., Hulo, N., Kahn, D., Kanapin, A., Karavidopoulou, Y., Lopez,
R., Marx, B. Mulder, N.J. Oinn, T.M., Sigrist, C.J.A. & Zdobnov, E. (2000)
"InterPro - An integrated documentation resource for protein families,
domains and functional sites."
Bioinformatics, 16(12), 1145-1150.

Attwood, T.K. (2000)
"Bridging the gap with ORF ESTs."
Trends in Biotechnology, 18(9), 363.

Attwood, T.K., Croning, M.D.R., Flower, D.R., Lewis, A.P., Mabey, J.E.,
Scordis, P., Selley, J. & Wright, W. (2000)
"PRINTS-S: the database formerly known as PRINTS."
Nucleic Acids Research, 28(1), 225-227.

Attwood, T.K. (2000)
"The quest to deduce protein function from sequence: the role of pattern databases."
International Journal of Biochemistry and Cell Biology, 32(2), 139-155.

Attwood, T.K. (2000)
"The role of pattern databases in sequence analysis."
Briefings in Bioinformatics, 1, 45-59.

Vaughan, S., Attwood, T.K., Navarro, M., Scott, V., McKean, P. & Gull, K. (2000)
"New tubulins in protozoal parasites."
Current Biology, 10(7), R258-259.

Vaughan, S., Attwood, T.K., Navarro, M., Scott, V., McKean, P. & Gull, K. (2000)
"Tubulins in parasite protozoa."
Biochem.Soc.Transactions, 28(5), A218.

Apweiler R., Attwood, T.K., Bairoch A., Bateman, A., Birney, E., Bucher P.,
Codani, J-J., Corpet, F., Croning, M.D.R., Durbin, R., Etzold, T.,
Fleischmann, W., Gouzy, J., Hermjakob, H., Jonassen, I., Kahn, D.,
Kanapin, A., Schneider, R., Servant, F. & Zdobnov, E. (2000)
"InterPro - An integrated documentation resource for protein families,
domains and functional sites."
CCP11 Newsletter, 10.

Attwood, T.K. (2000)
"Focus on UMBER - University of Manchester Bioinformatics, Education and Research."
EMBnet News, 7(1).

Attwood, T.K. (2000)
"An interactive practical at the interface of Web-based and conventional publishing."
CAL-laborate. A collaborative publication on the use of Computer Aided Learning for tertiary level physical sciences, 4, 1-6.

Attwood, T.K. & Parry-Smith, D.J. (1999)

"Introduction to bioinformatics."

Addison Wesley Longman

Attwood, T.K., Flower, D.R., Lewis, A.P., Mabey, J.E., Morgan, S.R., Scordis, P.,
Selley, J. & Wright, W. (1999)
"PRINTS prepares for the new millennium."
Nucleic Acids Research, 27(1), 220-225.

Scordis, P., Flower, D.R. & Attwood, T.K. (1999)
"FingerPRINTScan: Intelligent searching of the PRINTS motif database."
Bioinformatics, 15(10), 799-806.

Wright, W., Scordis, P. & Attwood, T.K. (1999)
"BLAST PRINTS - An alternative perspective on sequence similarity."
Bioinformatics, 15(6), 523-524.

Attwood, T.K., Croning, M.D.R., Mabey, J.E., Scordis, P., Selley, J. & Wright, W. (1999)
"PRINTS evolves into a streamlined PRINTS-S."
CCP11 Newsletter, 9, 5-8.

Attwood, T.K. (1999)
"An interactive bioinformatics practical on the World Wide Web."
In Laboratory Work in Science Education: an Evaluation with Case studies, (Ed.L.Jervis), pp.42-45. SEED Publications, University of Plymouth.

Attwood, T.K. (1999)
"Introduction to bioinformatics: an interactive practical on the WWW."
Life Sciences Educational Computing, 10(2), 12.

Attwood, T.K. (1999)
"An interactive practical at the interface of Web-based and conventional publishing."
CAL-laborate. A collaborative publication on the use of Computer AidedLearning for tertiary level physical sciences, 3, 1-6.

Attwood, T.K., Beck, M.E., Flower, D.R., Scordis, P. & Selley, J. (1998)

"The PRINTS protein fingerprint database in its fifth year."

Nucleic Acids Research

Attwood, T.K. (1998)
"The pedigree of PRINTS - who owns the database?"
Proceedings of Building and Owning Biotechnology Databases, a workshop held in Purmerend, The Netherlands, 22-23 September.

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), GC57-63.

Henikoff, S., Greene, E.A., Pietrokovski, S., Attwood, T.K., Bork, P. & Hood, L. (1997)

"Gene families: the taxonomy of protein paralogs and chimeras."

Science

278

Greene, E.A., Pietrokovski, S., Henikoff, S., Bork, P., Attwood, T.K., Hood, L. & Bairoch, A. (1997)
"Building gene families."
Science, 278, 615-626.

Attwood, T.K., Beck, M.E., Bleasby, A.J., Degtyarenko, K., Michie, A.D. & Parry-Smith, D.J. (1997)
"Novel developments with the PRINTS protein fingerprint database."
Nucleic Acids Research, 25(1), 212-216.

Attwood, T.K. (1997)
"Exploring the language of bioinformatics."
In Oxford Dictionary of Biochemistry and Molecular Biology, Oxford University
Press, Ed. H.Stanbury, pp 715-723.

Attwood, T.K., Avison, H., Beck, M.E., Bewley, M., Bleasby, A.J., Brewster, F.,
Cooper, P., Degtyarenko, K., Flower, D.R., Geddes, A.J., Kelly, M., Lott, S., Measures, K.M., Parry-Smith, D.J., Perkins, D.N., Scordis, P., Scott, D. & Worledge, C. (1997)
"The PRINTS database of protein fingerprints: a novel information resource for computational molecular biology."
Journal of Chemical Information and Computer Science, 37, 417-424.

Attwood, T.K. (1997)
"BioActivity: An Interactive Bioinformatics Practical on the WWW."
Life Sciences Educational Computing, 8(3), 10-13.

Attwood, T.K., Payne, A.W.R., Michie, A.D. & Parry-Smith, D.J. (1997)
"A Colour INteractive Editor for Multiple Alignments - CINEMA."
EMBnet News, 3(3).

Attwood, T.K. (1997)
"University College London joins EMBnet."
EMBnet News, 4(3).

Attwood, T.K. (1997)
"Collaboration in Bioinformatics on the WWW."
Structural Biology in Europe, 5.

Attwood, T.K. (1997)
"Databases from Universities - PRINTS, a research tool that has grown into a resource."
Proceedings of Financing Biotechnology Databases, a workshop held in Purmerend, The Netherlands, 29-30 May.

Attwood, T.K., Beck, M.E., Bleasby, A.J., Degtyarenko, K. & Parry-Smith, D.J. (1996)

"Progress with the PRINTS protein fingerprint database."

Nucleic Acids Research

Attwood, T.K & Parry-Smith, D.J. (1996)
"Diagnosis of Complex Patterns in Protein Sequences."
In Visualizing Biological Information , Ed. Clifford Pickover, pp145-157.

Michie, A.D., Jones, M.L. & Attwood, T.K. (1996)
"DbBrowser: integrated access to databases worldwide."
TiBS, 21(5), 191.

Perkins, D.N. & Attwood, T.K. (1996)
"XFINGER - A tool for searching and visualising protein fingerprints and patterns."
CABIOS, 12(2), 89-94.

Flower, D.R., Sansom, C.E., Beck, M.E., Attwood, T.K. (1995)

TiBS

Perkins, D.N. & Attwood, T.K. (1995)
"VISTAS - A package for VIsualising STructures And Sequences of proteins."
J.Mol.Graph., 13, 73-75.

Bleasby, A.J., Akrigg, D. & Attwood, T.K. (1994)

Nucleic Acids Research

Attwood, T.K. & Beck, M.E. (1994)
"PRINTS - A protein motif fingerprint database."
Protein Engineering, 7(7), 841-848.

Attwood, T.K., Beck, M.E., Bleasby, A.J. & Parry-Smith, D.J. (1994)
"PRINTS - A database of protein motif fingerprints."
Nucleic Acids Research, 22(17), 3590-3596.

Attwood, T.K. & Findlay, J.B.C. (1994)
"Fingerprinting G-protein-coupled receptors."
Protein Engineering, 7(2), 195-203.

Findlay, J.B.C., Akrigg, D., Attwood, T.K., Beck, M.E., Bleasby, A.J., North, A.C.T.,
Parry-Smith, D.J. & Perkins, D.N. (1994)
"Protein sequence analysis, storage and retrieval."
J.Prot.Chem., 13, 462-463.

Attwood, T.K. & Findlay, J.B.C. (1993)

Protein Engineering

Flower, D.R., North, A.C.T. & Attwood, T.K. (1993)
"Structure and sequence relationships in the lipocalins and related proteins."
Protein Science, 2, 753-761.

Findlay, J.B.C., Donnelly, D., Bhogal, N., Hurrell, C. & Attwood, T.K. (1993)
"Structure of G-protein-linked receptors."
Biochem.Soc.Trans., 21, 869-873.

Boguski, M.S., Bairoch, A., Attwood, T.K. & Michaels, G.S. (1992)

Nature

358

Parry-Smith, D.J. & Attwood, T.K. (1992)
"ADSP - A new package for computational sequence analysis."
CABIOS, 8(5), 451-459.

Akrigg, D.A., Attwood, T.K., Bleasby, A.J., Findlay, J.B.C., North, A.C.T.,
Parry-Smith, D.J., Perkins, D.N. & Wootton, J.C. (1992)
"SERPENT - An information storage and analysis resource for protein sequences."
CABIOS, 8(3), 295-296.

Parry-Smith, D.J. & Attwood, T.K. (1991)

CABIOS

Flower, D.R., North, A.C.T. & Attwood, T.K. (1991)
"Mouse oncogene protein 24p3 is a member of the lipocalin protein family."
BBRC, 180, 69-74.

Attwood, T.K., Eliopoulos, E.E. & Findlay, J.B.C. (1991)
"Multiple sequence alignment of protein families showing low sequence homology: a methodological approach using database pattern-matching discriminators for G-protein-linked receptors."
Gene, 98(2), 153-159.

North, A.C.T. & Attwood, T.K. (1991)
"Protein Structure."
Carolina Biology Readers, 34, Ed. J.J.Head.

Findlay, J.B.C., Eliopoulos, E.E. & Attwood, T.K. (1990)

Biochem.Soc.Symp.

Fritjof C.F.Korber, Pierre J.Rizkallah, Teresa K.Attwood, John C.Wootton, Michael J.McPherson,
Anthony C.T.North, Alexander J.Geddes, I.Sarath B.Abeysinghe, Patrick J.Baker, Jonathan L.Dean,
Paul C.Engel, Timothy J.Stillman and David W.Rice(1993)
"Crystallisation of the NADP(+)-dependent Glutamate Dehydrogenase from Escherichia coli."
J.Mol.Biol., 234, 1270-1273.

Attwood, T.K., Lydon, J.E., Hall, C. and Tiddy, G.J.T.Tiddy (1990)

Liquid Crystals

Attwood, T.K and Sellen, D.B. (1990)
"An X-ray diffraction study of agarose gel as a function of concentration."
Biopolymers, 29, 1325-1328.

Attwood, T.K., Nelmes, B.J. and Sellen, D.B. (1988)

Biopolymers

Attwood, T.K., Lydon, J.E. and Jones, F. (1986)

Liquid Crystals

Attwood, T.K. and Lydon, J.E. (1986)
"A new model for the molecular arrangements in chromonic mesophases."
Mol.Cryst.Liq.Cryst., 4(1), 9-14.

Attwood, T.K. and Lydon, J.E. (1984)

Mol.Cryst.Liq.Cryst.,

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