Win Hide (Extraordinary Professor - Visiting)
- Name: Win Hide
- Role: Visiting Extraordinary Professor
- Professional Status
- Active grant development and research ongoing at UWC
- Visiting Extraordinary Professor of Genomics and Bioinformatics, UWC
- Kerr Fellow, Ludwig Institute for Cancer Research
- Associate Professor, Harvard School of Public Health, Department of Biostatistics
- Contact Details
- Telephone: +27 21 959 3910
- Facsimile: +27 21 959 2512
- Email: winhide(at)sanbi.ac.za
- Skype: winhide
- website&papers mysite
- Lab Members
- Post Doctoral - Nicki Tiffin, Adele Kruger
- PhD - Sumir Panji
- Programmer - Marius Albertyn
Research Area
My work focuses upon the discovery of genes and groups of genes that are involved in disease processes. I apply this approach to the discovery of genes that contribute to resistance from infection, and the gene groups that contribute to the process of development and proliferation of cancers.
Three areas I am working in are (1) The development and delivery of systems to group SNPs to functional genomic features (2) The discovery of regulatory networks of transcripts expressed during the proliferation of lineages from cancer stem cells (3) The training and dissemination of systems for the control of Tsetse fly, the vector for African sleeping sickness
All of these are impacted by work in my laboratory on gene expression and its management in the form of ontologies.
Together with the researchers I am fortunate to work with at SANBI, and our collaborators in South Africa and in several other countries, we are working on defining, characterizing and exploiting high-resolution knowledge of cellular networks involved in cancer and pathogenesis. We achieve this by development and application of systems and tools that allow efficient linkage between interdisciplinary information to result in novel or improved clinical outcomes.
Selected recent Publications
2009
Hofmann O, Caballero OL, Stevenson BJ, Chen YT, Cohen T, Chua R, Maher CA, Panji S, Schaefer U, Kruger A, Lehvaslaiho M, Carninci P, Hayashizaki Y, Jongeneel CV, Simpson AJG, Old LJ, Hide W. Genome-wide analysis of cancer/testis gene expression. Proceedings of the National Academy of Sciences of the United States of America, In Press.
Quantitating the multiplicity of infection with HIV-1 subtype C . M-R Abrahams, JA Anderson, EE Giorgi, C Seoighe, K Mlisana, L-H Ping, GS Athreya, F Treurnicht, B Keele, N Wood, J Gonzalez-Salazar, J Passmore, L Roberts, T Bhattacharya, H. Chu, I Hoffman, S Galvin, C Mapanje, P Kazembe, R Thebus, S Fiscus, W Hide, MS Cohen, S Abdool Karim, BF Haynes, GM Shaw, BH Hahn, BT Korber, R Swanstrom, C Williamson, for the CAPRISA Acute Infection Study Team and the Center for HIV-AIDS Vaccine Immunology Consortium. Journal of Virology. In press.
2008
Mathivanan S, Ahmed M, Ahn NG, Alexandre H, Amanchy R, Andrews PC, Bader JS, Balgley MB, Bantscheff M, Bennett KL Björling E, Blagoev B, Bose R, Bahmachari SK, Burlingame AS, Bustelo XR, Cagney G, Cantin GT, Cardasis HL, Celis JE, Chaerkady R, Chu F, Cole PA, Costello CE, Cotter RJ, Crockett D, DeLany JP, De Marzo AM, DeSouza LV, Deutsch EW, Dransfield E, Drewes G, Droit A, Dunn MJ, Elenitoba-Johnson K, Ewing RM, Van Eyk J, Faca V, Falkner J, Fang X Fenselau C, Figeys D, Gagné P, Gelfi C, Gevaert K, Gimble JM, Gnad F, Goel R, Gromov P, Hanash SM, Hancock WS, Harsha HC, Hart G, Hays F, He F, Hebbar P, Helsens K, Hermeking H, Hide WA, Hjernø K, Hochstrasser DF, Hofmann O, Horn DM, Hruban RH, Ibarrola N, James P, Jensen ON, Jensen PH, Jung P, Kandasamy K, Kheterpal I, Kikuno RF, Korf U, Körner R, Kuster B, Kwon MS, Lee HJ, Lee YJ, Lefevre M, Lehvaslaiho M, Lescuyer P, Levander F, Lim MS, Löbke C, Loo JA, Mann M, Martens L, Martinez-Heredia J, McComb M, McRedmond J, Mehrle A, Menon R, Miller CA, Mischak H, Mohan SS, Mohmood R, Molina H, Moran MF, Morgan JD, Moritz R, Morzel M, Muddiman DC, Nalli A, Navarro JD, Neubert TA, Ohara O, Oliva R, Omenn GS, Oyama M, Paik YK, Pennington K, Pepperkok R, Periaswamy B, Petricoin EF, Poirier GG, Prasad TS, Purvine SO, Rahiman BA, Ramachandran P, Ramachandra YL, Rice RH, Rick J, Ronnholm RH, Salonen J, Sanchez JC, Sayd T, Seshi B, Shankari K, Sheng SJ, Shetty V, Shivakumar K, Simpson RJ, Sirdeshmukh R, Siu KW, Smith JC, Smith RD, States DJ, Sugano S, Sullivan M, Superti-Furga G, Takatalo M, Thongboonkerd V, Trinidad JC, Uhlen M, Vandekerckhove J, Vasilescu J, Veenstra TD, Vidal-Taboada JM, Vihinen M, Wait R, Wang X, Wiemann S, Wu B, Xu T, Yates JR, Zhong J, Zhou M, Zhu Y, Zurbig P, Pandey A. Human Proteinpedia enables sharing of human protein data. Nature Biotechnology. 2008 Feb;26(2):164-7
Hazelhurst S, Hide W, Liptak Z, Nogueira R, Starfield R. An overview of the wcd EST Clustering Tool. Bioinformatics. 2008 Jul 1;24(13):1542-6. Epub 2008 May 14
Douglas Howe, Maria Costanzo, Petra Fey, Takashi Gojobori, Linda Hannick, Winston Hide, David P. Hill, Renate Kania, Mary Schaeffer, Susan St. Pierre, Simon Twigger, Owen White, Seung Yon Rhee. The Future of Biocuration. Nature. 2008 Sep 4;455(7209):47-50.
Gautier Koscielny, Vincent Le Texier, Chellappa Gopalakrishnan, Vasudev Kumanduri, Jean-Jack Riethoven, Francesco Nardone, Eleanor Stanley, Christine Fallsehr, Oliver Hofmann, Meelis Kull, Eoghan Harrington, Stéphanie Boué, Eduardo Eyras, Mireya Plass, Fabrice Lopez, William Ritchie, Virginie Moucadel, Takeshi Ara, Heike Pospisil, Alexander Herrmann, Jens G. Reich, Roderic Guigó, Peer Bork, Magnus von Knebel Doeberitz, Jaak Vilo, Winston Hide, Rolf Apweiler, Thangavel Alphonse Thanaraj, Daniel Gautheret. ASTD: the Alternative Splicing and Transcript Diversity Database. Genomics. 2008 Dec 3. [Epub ahead of print]
Mandeep Kaur, Sebastian Schmeier, Cameron R MacPherson, Oliver Hofmann, Winston Hide, Stephen Taylor, Nick Willcox, Vladimir B Bajic. Prioritizing genes with potential relevance to Myasthenia Gravis. BMC Genomics. 2008 Oct 13;9(1):481.
2007
Kruger A, Hofmann O, Carninci P, Hayashizaki Y, Hide W. Simplified ontologies allowing comparison of developmental mammalian gene expression. Genome Biology, 2007. 8(10): R229.Lombard Z, Tiffin N, Hofmann O, Bajic VB, Hide W, Ramsay M. Computational selection and prioritization of candidate genes for Fetal Alcohol Syndrome. BMC Genomics, 2007. 8(1): 389.
Seoighe C, Ketwaroo F, Pillay V, Scheffler K, Wood N, Duffet R, Zvelebil M, Martinson N, McIntyre J, Morris L, Hide, W.. A Model of Directional Selection Applied to the Evolution of Drug Resistance in HIV-1. Mol Biol Evol. doi: 10.1093/molbev/msm021 . 2007. 24(4): 1025-1031
Schwegmann A, Guler R, Cutler AJ, Arendse B, Horsnell WGC, Flemming A, Kottmann AH, Ryan G, Hide, W., Leitges M, Seoighe C, Brombacher F. Protein kinase C-delta is essential for optimal macrophage-mediated phagosomal containment of Listeria monocytogenes. Proceedings of the National Academy of Sciences of the United States of America, 2007. 104(41): 16251-16256.
Yamasaki C, Murakami K, Fujii Y, Sato Y, Harada E, Takeda J, Taniya T, Sakate R, Kikugawa S, Shimada M, Tanino M, Koyanagi KO, Barrero RA, Gough C, Chun HW, Habara T, Hanaoka H, Hayakawa Y, Hilton PB, Kaneko Y, Kanno M, Kawahara Y, Kawamura T, Matsuya A, Nagata N, Nishikata K, Noda AO, Nurimoto S, Saichi N, Sakai H, Sanbonmatsu R, Shiba R, Suzuki M, Takabayashi K, Takahashi A, Tamura T, Tanaka M, Tanaka S, Todokoro F, Yamaguchi K, Yamamoto N, Okido T, Mashima J, Hashizume A, Jin L, Lee KB, Lin YC, Nozaki A, Sakai K, Tada M, Miyazaki S, Makino T, Ohyanagi H, Osato N, Tanaka N, Suzuki Y, Ikeo K, Saitou N, Sugawara H, O’Donovan C, Kulikova T, Whitfield E, Halligan B, Shimoyama M, Twigger S, Yura K, Kimura K, Yasuda T, Nishikawa T, Akiyama Y, Motono C, Mukai Y, Nagasaki H, Suwa M, Horton P, Kikuno R, Ohara O, Lancet D, Eveno E, Graudens E, Imbeaud S, Debily MA, Hayashizaki Y, Amid C, Han M, Osanger A, Endo T, Thomas MA, Hirakawa M, Makalowski W, Nakao M, Kim NS, Yoo HS, De Souza SJ, Bonaldo M, Niimura Y, Kuryshev V, Schupp I, Wiemann S, Bellgard M, Shionyu M, Jia L, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Zhang Q, Go M, Minoshima S, Ohtsubo M, Hanada K, Tonellato P, Isogai T, Zhang J, Lenhard B, Kim S, Chen Z, Hinz U, Estreicher A, Nakai K, Makalowska I, Hide, W., Tiffin N, Wilming L, Chakraborty R, Soares M, Chiusano ML, Suzuki Y, Auffray C, Yamaguchi-Kabata Y, Itoh T, Hishiki T, Fukuchi S, Nishikawa K, Sugano S, Nomura N, Tateno Y, Imanishi T, and Gojobori The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Research, 2007. 10.1093/nar/gkm999 Database issue.
Kruger A, Hofmann O, Carninci P, Hayashizaki Y, Hide, W.. Simplified ontologies allowing comparison of developmental mammalian gene expression. Genome Biology, 2007. 8(10): R229.
Lombard Z, Tiffin N, Hofmann O, Bajic VB, Hide, W., Ramsay M. Computational selection and prioritization of candidate genes for Fetal Alcohol Syndrome. BMC Genomics, 2007. 8(1): 389.
2006
Computational disease gene identification: a concert of methods prioritises type 2 diabetes and obesity candidate genes.
Nicola Tiffin, Euan Adie, Frances Turner , Han G. Brunner, Marc A. van Driel , Martin Oti , Nuria Lopez-Bigas , Christos Ouzounis , Carolina Perez-Iratxeta , Miguel A. Andrade-Navarro , Adebowale Adeyemo , Mary Elizabeth Patti, Winston Hide.
Nucl. Acids Res. 2006 34: 3067-3081; doi:10.1093/nar/gkl381
Mice and Men: Their Promoter Properties.
Vladimir B. Bajic, Sin Lam Tan, Alan Christoffels, Christian Scho¨nbach, Leonard Lipovich, Liang Yang, Oliver Hofmann, Adele Kruger, Hide, W., Chikatoshi Kai, Jun Kawai, David A. Hume, Piero Carninci, Yoshihide Hayashizaki.
PLOS Genetics, April 2006. Volume 2 , Issue 4.
The LIFEdb database in 2006
Alexander Mehrle, Heiko Rosenfelder, Ingo Schupp, Coral del Val, Dorit Arlt, Florian Hahne, Stephanie Bechtel, Jeremy Simpson, Oliver Hofmann, Hide, W., Karl-Heinz Glatting1, Wolfgang Huber, Rainer Pepperkok, Annemarie Poustka and Stefan Wiemann.
Nucleic Acids Research 2006 34 (Database Issue):D415-D418; doi:10.1093/nar/gkj139
2005
The Transcriptional Landscape of the Mammalian Genome.
The FANTOM Consortium.
Science. September 2, 2005 ;309(5740):1559-63.
The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platforms.
Tanino M, Debily MA, Tamura T, Hishiki T, Ogasawara O, Murakawa K, Kawamoto S, Itoh K, Watanabe S, de Souza SJ, Imbeaud S, Graudens E, Eveno E, Hilton P, Sudo Y, Kelso J, Ikeo K, Imanishi T, Gojobori T, Auffray C, Hide, W., Okubo K.
Nucleic Acids Research. 2005 Jan 1;33 Database Issue:D567-72
A case for Glossina genome project.
Serap Aksoy, Matt Berriman, Neil Hall, Masahira Hattori, Hide, W., Michael J. Lehane.
Trends in Parasitology, Volume 21, Issue 3 , March 2005, Pages 107-111 2005
Integration of Text- and Data Mining Using Ontologies Successfully Selects Disease Gene Candidates.
N. Tiffin, J. Kelso, A. Powell, H. Pan, V. Bajic, Hide, W..
Nucleic Acids Research, 2005 33(5): 1544-1552.
2004
Integrative Annotation of 21,037 Human Genes Validated by Full-length cDNA Clones.
Imanishi T, Itoh T, Suzuki Y, O’Donovan C, Fukuchi S, et al.
Public Library of Science Biology 2004 2(6): 1-21
FRAGS: estimation of coding sequence substitution rates from fragmentary data.
Estienne C Swart, Winston Hide and Cathal Seoighe. BMC Bioinformatics 2004 5: 8
2003
Integrative analysis of Intraerythrocytic differentially expressed transcripts yields novel insights into the biology of Plasmodium falciparum. Isokpehi RD and Hide, W.A.. Malaria Journal 2003 2: 38
New Methods for finding disease-susceptibility genes: impact and potential. Mark I McCarthy, Damian Smedley and Winston Hide. Genome Biology 2003 4: 119
Transcriptome Analysis of Mouse Stem Cells and Early Embryos.
Alexei A Sharov, Yulan Piao, Ryo Matoba, Dawood B Dudekula, Yong Qian, Vincent VanBuren, Geppino Falco, Patrick R Martin, Carole A Stagg, Uwem C Bassey, Yuxia Wang, Mark G Carter, Toshio Hamatani, Kazuhiro Aiba, Hidenori Akutsu, Lioudmila Sharova, Tetsuya S Tanaka, Wendy L Kimber, Toshiyuki Yoshikawa, Saied A Jaradat, Serafino Pantano, Ramaiah Nagaraja, Kenneth R Boheler, Dennis Taub, Richard J Hodes, Dan L Longo, David Schlessinger, Jonathan Keller, Emily Klotz, Garnett Kelsoe, Akihiro Umezawa, Angelo L Vecovi, Janet Rossant, Tilo Kunath, Brigid LM Hogan, Anna Curci, Michele D Urso, Janet Kelso, Winston Hide and Minoru SH Ko.
Public Library of Science Biology 2003 1(3):410-419.
eVOC: A Controlled Vocabulary for Unifying Gene Expression Data.
Kelso J, Visagie J, Theiler G, Christoffels A, Bardien S, Smedley D, Otgaar D, Greyling G, Jongeneel CV, McCarthy MI, Hide T, Hide, W.. Genome Research 2003. 13(6): 1220-1230.
The S-star Trial Bioinformatics Course. An online Learning Success.
Yun Ping Lim, Jan-Olov Hoog, Phyllis Gardner, Shoba Ranganathan, Siv Andersson, Subramanian Subbiah, Tin Wee Tan, Winston Hide and Anthony S. Weiss.
Biochemistry and Molecular Biology Education 2003. 31(1): 20-23.
The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags. Brentani H, Caballero OL, Camargo AA, da Silva AM, da Silva WA Jr, Dias Neto E, Grivet M, Gruber A, Moreira Guimaraes PE, Hide, W., Iseli C, Jongeneel CV, Kelso J, Nagai MA, Ojopi EP, Osorio EC, Reis EM, Riggins GJ, Simpson AJ, de Souza S, Stevenson BJ, Strausberg RL, Tajara EH, Verjovski-Almeida S, Acencio ML, Bengtson MH, Bettoni F, Bodmer WF, Briones MR, Camargo LP, Cavenee W, Cerutti JM, Coelho Andrade LE, Costa dos Santos PC, Ramos Costa MC, da Silva IT, Estecio MR, Sa Ferreira K, Furnari FB, Faria M Jr, Galante PA, Guimaraes GS, Holanda AJ, Kimura ET, Leerkes MR, Lu X, Maciel RM, Martins EA, Massirer KB, Melo AS, Mestriner CA, Miracca EC, Miranda LL, Nobrega FG, Oliveira PS, Paquola AC, Pandolfi JR, Campos Pardini MI, Passetti F, Quackenbush J, Schnabel B, Sogayar MC, Souza JE, Valentini SR, Zaiats AC, Amaral EJ, Arnaldi LA, de Araujo AG, de Bessa SA, Bicknell DC, Ribeiro de Camaro ME, Carraro DM, Carrer H, Carvalho AF, Colin C, Costa F, Curcio C, Guerreiro da Silva ID, Pereira da Silva N, Dellamano M, El-Dorry H, Espreafico EM, Scattone Ferreira AJ, Ayres Ferreira C, Fortes MA, Gama AH, Giannella-Neto D, Giannella ML, Giorgi RR, Goldman GH, Goldman MH, Hackel C, Ho PL, Kimura EM, Kowalski LP, Krieger JE, Leite LC, Lopes A, Luna AM, Mackay A, Mari SK, Marques AA, Martins WK, Montagnini A, Mourao Neto M, Nascimento AL, Neville AM, Nobrega MP, O’Hare MJ, Otsuka AY, Ruas de Melo AI, Paco-Larson ML, Guimaraes Pereira G, Pereira da Silva N, Pesquero JB, Pessoa JG, Rahal P, Rainho CA, Rodrigues V, Rogatto SR, Romano CM, Romeiro JG, Rossi BM, Rusticci M, Guerra de Sa R, Sant’ Anna SC, Sarmazo ML, Silva TC, Soares FA, Sonati Mde F, de Freitas Sousa J, Queiroz D, Valente V, Vettore AL, Villanova FE, Zago MA, Zalcberg H;
Proceedings of the National Academy of Science. 2003 100(23): 13418-23.
2002
Assembly, verification, and initial annotation of the NIA mouse 7.4K cDNA clone set.
Vincent VanBuren, Yulan Piao, Dawood B. Dudekula, Yong Qian, Mark G. Carter, Patrick R. Martin, Carole A. Stagg, Uwem C. Bassey, Kazuhiro Aiba, Toshio Hamatani, George J. Kargul, Amber G. Luo, Janet Kelso, Winston Hide, and Minoru S.H. Ko.
Genome Research 2002. 12(12): 1999-2003
Vertical HIV transmission in South Africa: translating research into policy and practice.
Salim Abdool Karim, Quarraisha Abdool Karim, Miriam Adhikari, Sharon Cassol, Matthew Chersich, Peter Cooper, Ashraf Coovadia, Hoosen Coovadia, Mark Cotton, Anna Coutsoudis, Win Hide, Greg Hussey, Gary Maartens, Shabir Madhi, Des Martin, John M Pettifor, Nigel Rollins, Gayle Sherman, Stanley Thula, Michael Urban, Sithembiso Velaphi, Carolyn Williamson.
The Lancet. March 23, 2002 359: 992-993.
Positive Selection Scanning Reveals Decoupling of Ensymatic Activities of Carbamoyl Phosphate Synthetase in H. pylori. Wagied Davids, Junaid Gamieldien, David A Liberles and Winston Hide.
Journal of Molecular Evolution. 2002 54: 458-464.
Assessment of the Parallelisation approach of d2-cluster for High-Performance Sequence Clustering. John E. Carpenter, Alan Christoffels Yael Weinbach, Winston Hide.
Journal of Computational Chemistry. 2002 23(7): 755-757.
Eukaryotic genes in Mycobacterium tuberculosis could have a role in pathogenesis and immunomodulation. Junaid Gamieldien, Andrey Ptitsyn, Winston Hide.
Trends in Genetics 2002 18(1): 5-8.
Physical and transcriptional map of the critical region for keratolytic winter erythema (KWE) on chromosome 8p22-p23 between D8S550 and D8S1759. Appel S, Filter M, Reis A, Hennies HC, Bergheim A, Ogilvie E, Arndt S, Simmons A, Lovett M, Hide, W., Ramsay M, Reichwald K, Zimmermann W, Rosenthal A.
European Journal of Human Genetics. 2002, 10(1): 17-25.
Parallelisation of d2-cluster.John Carpenter, Alan Christoffels and Winston Hide.
Journal of Computational Chemistry 2002 23(7).