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Papers

2009

• Dalai SC, de Oliveira T, Harkins GW, Kassaye SG, Lint J, Manasa J, Johnston E, Katzenstein D, Evolution and molecular epidemiology of subtype C HIV-1 in Zimbabwe, AIDS. 2009 Nov 27;23(18):2523-32

• 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

• Sagar S, Kaur M, Dawe A, Seshadri SV, Christoffels A, Schaefer U,  Radovanovic A, Bajic VB, DDESC: Dragon Database for Exploration of Sodium Channels in Human, BMC Genomics, 9:622, 2008 (IF=4.18)

• Thompson CL, Pathak S, Jeromin A, Ng L, MacPherson C, Mortrud M, Cusick A, Riley Z, Sunkin SM, Bernard A, Puchalski R, Gage FH, Jones AR, Bajic VB, Hawrylycz MJ, Lein ES. Genomic Anatomy of the Hippocampus, Neuron, 60(6):1010-1021, 2008 (IF=13.4)

• Meier S, Gehring C, MacPherson CR, Kaur M, Maqungo M, Reuben S, Muyanga S, Shih MD, Wei FJ, Wanchana S, Mauleon R, Radovanovic A, Bruskiewich R, Tanaka T, Mohanty B, Itoh T, Wing R, Gojobori T, Sasaki T, Swarup S, Hsing YI, Bajic VB, The promoter signatures in rice LEA genes can be used to build a co-expressing LEA gene network, RICE, 2008, 1(2): 177

• Rajini Sreenivasan, Minnie Cai, Richard Bartfai, Xingang Wang, Alan Christoffels and Laszlo Orban (2008). Transcriptomic analyses reveal novel genes with sexually dimorphic expression in the zebrafish gonad and brain. PloSONE 3(3) e1791.

• 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]

• Kaur M, Schmeier S, MacPherson CR, Hofmann O, Hide WA, Taylor S, Willcox N, Bajic VB, Prioritizing genes of potential relevance to diseases affected by sex hormones: An example of Myasthenia Gravis, BMC Genomics, 2008, 13;9(1):481. [Epub ahead of print] (IF=4.18)

• Kaur M, Radovanovic A, Essack M, Schaefer U, Maqungo M, Kibler T, Schmeier S, Christoffels A, Narasimhan K, Choolani M, Bajic VB, Database for exploration of functional context of genes implicated in ovarian cancer, Nucleic Acids Research, 2008 Sep 12. [Epub ahead of print] (IF=6.954)

• Meier S, Bastian R, Donaldson L, Murray S, Bajic VB, Gehring C, Co-expression and Promoter Content Analyses Assign a Role in Biotic and Abiotic Stress Responses to Plant Natriuretic Peptides, BMC Plant Biology, 2008 Feb 29;8:24 (IF=3.44)

2007

• 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.

• Hannah MF, Bajic VB, Klein SL, Sex differences in the recognition of and innate antiviral responses to Seoul virus in Norway rats, Brain, Behavior, and Immunity, 2008 May;22(4):503-16. Epub 2007 Nov 28. (IF=3.757)

• Christoffels, A (2007). Dealing with duplicated geomes in teleosts. In: Acquaculture Genome technologies. 511-524. Editor: Zhanjiang Liu. Blackwell Publishers, UK. ISBN 9780813802039.

• Bartfai R., Wang X, Sreenivasan R, Cai M, Srinivasan H, Hossain MS, Komen J, Christoffels A and Orban L. (2007) Cyprinid gonad differentiation: A comparative genomics study. Aquaculture. 272: S244-S245. Elsevier Science, Netherlands. ISSN 0044-8486.

• 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:R229.

2006

• Bajic VB, Brent MR, Brown RH, Frankish A, Harrow J, Ohler U, Solovyev VV, Tan SL.: Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment. Genome Biol. 2006;7 Suppl 1:S3.1-13. Epub 2006 Aug 7. Review.

• Guigo R, Flicek P, Abril JF, Reymond A, Lagarde J, Denoeud F, Antonarakis S, Ashburner M, Bajic VB, Birney E, Castelo R, Eyras E, Ucla C, Gingeras TR, Harrow J, Hubbard T, Lewis SE, Reese MG: EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biol. 2006;7 Suppl 1:S2.1-31. Epub 2006 Aug 7. Review.

• Nilsson R, Bajic VB, Suzuki H, di Bernardo D, Bjorkegren J, Katayama S, Reid JF, Sweet MJ, Gariboldi M, Carninci P, Hayashizaki Y, Hume DA, Tegner J, Ravasi T.: Transcriptional network dynamics in macrophage activation. Genomics. 2006 Aug;88(2):133-42. Epub 2006 May 12.

• A Christoffels, R Bartfai, H Srinivasan, H Komen and L Orban (2006). Comparative genomics in cyprinids: Common carp ESTs help the annotation of the zebrafish genome. BMC Bioinformatics 7 Suppl 5:S2.

• A Christoffels, Sydney Brenner and Byrappa Venkatesh (2006). Tetraodon genome analysis provides further evidence for whole-genome duplication in the ray-finned fish lineage. Comparative Biochemistry and Physiology Part D. 13-19.

• Bajic VB, Tan SL, Christoffels A, Schonbach C, Lipovich L, Yang L, Hofmann O, Kruger A, Hide W, Kai C, Kawai J, Hume DA, Carninci P, Hayashizaki Y.: Mice and men: their promoter properties. PLoS Genet. 2006 Apr;2(4):e54. Epub 2006 Apr 28.

• Tiffin N, Adie E, Turner F, Brunner HG, van Driel MA, Oti M, Lopez-Bigas N, Ouzounis C, Perez-Iratxeta C, Andrade-Navarro MA, Adeyemo A, Patti ME, Semple CA, Hide W, Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes. Nucleic Acids Res. 2006 Jun 6;34(10):3067-81. Print 2006.

• Mehrle A, Rosenfelder H, Schupp I, del Val C, Arlt D, Hahne F, Bechtel S, Simpson J, Hofmann O, Hide W, Glatting KH, Huber W, Pepperkok R, Poustka A, Wiemann S.: The LIFEdb database in 2006. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D415-8.

• Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, Forrest AR, Zavolan M, Davis MJ, Wilming LG, Aidinis V, Allen JE, Ambesi-Impiombato A, Apweiler R, Aturaliya RN, Bailey TL, Bansal M, Baxter L, Beisel KW, Bersano T, Bono H, Chalk AM, Chiu KP, Choudhary V, Christoffels A, Clutterbuck DR, Crowe ML, Dalla E, Dalrymple BP, de Bono B, Della Gatta G, di Bernardo D, Down T, Engstrom P, Fagiolini M, Faulkner G, Fletcher CF, Fukushima T, Furuno M, Futaki S, Gariboldi M, Georgii-Hemming P, Gingeras TR, Gojobori T, Green RE, Gustincich S, Harbers M, Hayashi Y, Hensch TK, Hirokawa N, Hill D, Huminiecki L, Iacono M, Ikeo K, Iwama A, Ishikawa T, Jakt M, Kanapin A, Katoh M, Kawasawa Y, Kelso J, Kitamura H, Kitano H, Kollias G, Krishnan SP, Kruger A, Kummerfeld SK, Kurochkin IV, Lareau LF, Lazarevic D, Lipovich L, Liu J, Liuni S, McWilliam S, Madan Babu M, Madera M, Marchionni L, Matsuda H, Matsuzawa S, Miki H, Mignone F, Miyake S, Morris K, Mottagui-Tabar S, Mulder N, Nakano N, Nakauchi H, Ng P, Nilsson R, Nishiguchi S, Nishikawa S, Nori F, Ohara O, Okazaki Y, Orlando V, Pang KC, Pavan WJ, Pavesi G, Pesole G, Petrovsky N, Piazza S, Reed J, Reid JF, Ring BZ, Ringwald M, Rost B, Ruan Y, Salzberg SL, Sandelin A, Schneider C, Schonbach C, Sekiguchi K, Semple CA, Seno S, Sessa L, Sheng Y, Shibata Y, Shimada H, Shimada K, Silva D, Sinclair B, Sperling S, Stupka E, Sugiura K, Sultana R, Takenaka Y, Taki K, Tammoja K, Tan SL, Tang S, Taylor MS, Tegner J, Teichmann SA, Ueda HR, van Nimwegen E, Verardo R, Wei CL, Yagi K, Yamanishi H, Zabarovsky E, Zhu S, Zimmer A, Hide W, Bult C, Grimmond SM, Teasdale RD, Liu ET, Brusic V, Quackenbush J, Wahlestedt C, Mattick JS, Hume DA, Kai C, Sasaki D, Tomaru Y, Fukuda S, Kanamori-Katayama M, Suzuki M, Aoki J, Arakawa T, Iida J, Imamura K, Itoh M, Kato T, Kawaji H, Kawagashira N, Kawashima T, Kojima M, Kondo S, Konno H, Nakano K, Ninomiya N, Nishio T, Okada M, Plessy C, Shibata K, Shiraki T, Suzuki S, Tagami M, Waki K, Watahiki A, Okamura-Oho Y, Suzuki H, Kawai J, Hayashizaki Y; FANTOM Consortium; RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group).: The transcriptional landscape of the mammalian genome. Science. 2005 Sep 2;309(5740):1559-63. Erratum in: Science. 2006 Mar 24;311(5768):1713.

2005

• Ptitsyn A, Hide W, CLU: a new algorithm for EST clustering, BMC Bioinformatics, 2005 Jul 15;6 Suppl 2:S3.
• Tiffin N, Kelso JF, Powell AR, Pan H, Bajic VB, Hide WA, Integration of text- and data-mining using ontologies successfully selects disease gene candidates, Nucleic Acids Res, 2005, Mar 14;33(5):1544-52. Print 2005.
• Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, Forrest AR, Zavolan M, Davis MJ, Wilming LG, Aidinis V, Allen JE, Ambesi-Impiombato A, Apweiler R, Aturaliya RN, Bailey TL, Bansal M, Baxter L, Beisel KW, Bersano T, Bono H, Chalk AM, Chiu KP, Choudhary V, Christoffels A, Clutterbuck DR, Crowe ML, Dalla E, Dalrymple BP, de Bono B, Della Gatta G, di Bernardo D, Down T, Engstrom P, Fagiolini M, Faulkner G, Fletcher CF, Fukushima T, Furuno M, Futaki S, Gariboldi M, Georgii-Hemming P, Gingeras TR, Gojobori T, Green RE, Gustincich S, Harbers M, Hayashi Y, Hensch TK, Hirokawa N, Hill D, Huminiecki L, Iacono M, Ikeo K, Iwama A, Ishikawa T, Jakt M, Kanapin A, Katoh M, Kawasawa Y, Kelso J, Kitamura H, Kitano H, Kollias G, Krishnan SP, Kruger A, Kummerfeld SK, Kurochkin IV, Lareau LF, Lazarevic D, Lipovich L, Liu J, Liuni S, McWilliam S, Madan Babu M, Madera M, Marchionni L, Matsuda H, Matsuzawa S, Miki H, Mignone F, Miyake S, Morris K, Mottagui-Tabar S, Mulder N, Nakano N, Nakauchi H, Ng P, Nilsson R, Nishiguchi S, Nishikawa S, Nori F, Ohara O, Okazaki Y, Orlando V, Pang KC, Pavan WJ, Pavesi G, Pesole G, Petrovsky N, Piazza S, Reed J, Reid JF, Ring BZ, Ringwald M, Rost B, Ruan Y, Salzberg SL, Sandelin A, Schneider C, Schonbach C, Sekiguchi K, Semple CA, Seno S, Sessa L, Sheng Y, Shibata Y, Shimada H, Shimada K, Silva D, Sinclair B, Sperling S, Stupka E, Sugiura K, Sultana R, Takenaka Y, Taki K, Tammoja K, Tan SL, Tang S, Taylor MS, Tegner J, Teichmann SA, Ueda HR, van Nimwegen E, Verardo R, Wei CL, Yagi K, Yamanishi H, Zabarovsky E, Zhu S, Zimmer A, Hide W, Bult C, Grimmond SM, Teasdale RD, Liu ET, Brusic V, Quackenbush J, Wahlestedt C, Mattick JS, Hume DA, Kai C, Sasaki D, Tomaru Y, Fukuda S, Kanamori-Katayama M, Suzuki M, Aoki J, Arakawa T, Iida J, Imamura K, Itoh M, Kato T, Kawaji H, Kawagashira N, Kawashima T, Kojima M, Kondo S, Konno H, Nakano K, Ninomiya N, Nishio T, Okada M, Plessy C, Shibata K, Shiraki T, Suzuki S, Tagami M, Waki K, Watahiki A, Okamura-Oho Y, Suzuki H, Kawai J, Hayashizaki Y; FANTOM Consortium; RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group), The transcriptional landscape of the mammalian genome, Science, 309: 1559-1563, 02 Sept. 2005
• Nicki Tiffin, Janet F. Kelso, Alan R. Powell, Hong Pan, Vladimir B. Bajic and Winston A. Hide, Integration of text- and data-mining using ontologies successfully selects disease gene candidates, Nucleic Acids Research, 2005 33(5):1544-1552
• Winston Hide, EST Clustering: A short tutorial, 2005
• A case for Glossina genome project. Serap Aksoy, Matt Berriman, Neil Hall, Masahira Hattori, Winston Hide, Michael J. Lehane. Trends in Parasitology 2005
• 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 1(33): Database Issue 567-572
• VB Bajic, M Veronika, PS Veladandi, A Meka, M-W Heng, K Rajaraman, H Pan, S Swarup, DPBE: A Text-mining Tool for Integrating Associations between Genetic and Biochemical Entities with Genome Annotation and Biochemical Terms Lists, Plant Physiology, 138 (4), 1914-1925, 2005
• R Chowdhary, R. Ayesha Ali, W Albig, D Doenecke and VB Bajic, Promoter modeling: The case study of mammalian histone promoters, Bioinformatics, Mar 15; [Epub ahead of print], 21(11):2623-2628, 2005
• N Tiffin, JF Kelso, AR Powell, H Pan, VB Bajic, WA Hide, Integration of Text- and Data-Mining Using Ontologies Successfully Selects Disease Gene Candidates, Nucleic Acids Research, 33(5):1544-1552, 2005
• B Mohanty, SPT Krishnan, S Swarup, VB Bajic, Detection and Preliminary Analysis of Motifs in Promoters of Anaerobically Induced Genes of Different Plant Species, Ann Bot-London, Jul 18; [Epub ahead of print], 96(4):669-81, 2005
• L Yang, E Huang, VB Bajic, Some implementation issues of heuristic methods for motif extraction from DNA sequences, Int.J.Comp.Syst.Signals, 6(2):3-12, 2005
• VB Bajic, TW Tan (Eds.), Information Processing and Living Systems, World Scientific, 800 pages, 2005
• H Pan, L Zuo, K Rajaraman, Z Zhang, V Choudhary, B Mohanty, SL Tan, S.P.T. Krishnan, PS Veladandi, A Meka, WK Choy, S Swarup, VB Bajic, Extracting information for meaningful function inference through text-mining, Chapter in Discovering Biomolecular Mechanism with Computational Biology (F Eisenhaber, Ed.), Landes Bioscience, 2005
• VB Bajic, T Werner, Promoter Prediction, Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, Part 4. Bioinformatics, 4.2. Gene Finding and Gene Structure, John Wiley & Sons, Ltd., DOI: 7:2881-2886, 2005
• TW Tan, KH Choo, JC Tong, MT Tammi, VB Bajic, Biological Databases and Web Services: Metrics for Quality, Chapter 16 in Information Processing and Living Systems, World Scientific, 771-777, 2005
• K Rajaraman, L Zuo, V Choudhary, Z Zhang, VB Bajic, H Pan, T-S Sim, S Swarup, Overview of text-mining in life sciences, Chapter 9 in Information Processing and Living Systems, World Scientific, 687-694, 2005
• E Huang, L Yang, R Chowdhary, A Kassim, VB Bajic, An algorithm for ab initio DNA motif detection, Chapter 4 in Information Processing and Living Systems, World Scientific, 611-614, 2005
• SL Tan, V Choudhary, A Christoffels, B Venkatesh, VB Bajic, Comparison of core promoters in Fugu rubripes and human (Keynote lecture), (Eds. Y-P P Chen and L Wong) in Proc. of the 3^rd Asia-Pacific Bioinformatics Conference (APBC05), Imperial College Press, 379, 2005

2004

• Response to Hertz-Fowler and Berriman: Continuing tsetse and Trypanosoma genome sequencing projects. Davila AM, Majiwa PA, Grisard EC, Aksoy S, Hide W. Trends in Parasitology 2004 20(7): 309-310
• Positive selection scanning of parasite DNA sequences. Hide WA, Isokpehi RD. Parasite Genomics Protocols, Methods in Melicualr Biology Series Ed. Sara E. Melville. New Jersey: Humana Press, 2004 127-150
• Integrative Annotation of 21,037 Human Genes Validated by Full-length cDNA Clones. Imanishi et al. PLoS Biology 2004 2(6): 1-21
• FRAGS: estimation of coding sequence substitution rates from fragmentary data. Estienne C Swart, Winston A Hide and Cathal Seoighe. BMC Bioinformatics 2004 5: 8
• Incidence of HIV-1 Dual Infection and its Association with Increased Viral Load Set Point in a Cohort of HIV-1 Subtype C-infected Female Sex Workers. Grobler J, Gray CM, Rademeyer C, Seoighe C, Ramjee G, Karim SA, Morris L, Williamson C. Journal of Infectious Diseases 2004 190: 1355-1359
• Opportunities in Africa for training in genome science. Daniel K Masiga and Raphael D Isokpehi. African Journal of Biotechnology 2004 3(2): 117
• A plant natriuretic peptide-like gene in the bacterial pathogen Xanthomonas axonopodis may induce hyper-hydration in the plant host: a hypothesis of molecular mimicry. Nembaware V, Seoighe C, Sayed M, Gehring, C. BMC Evolutionary Biology 2004 4(1): 10
• Computational method for discovery of estrogen responsive genes, S Tang, SL Tan, SK Ramadoss, AP Kumar, M-H.E Tang, VB Bajic, Nucleic Acids Research, 32(21):6212-6217, 2004
• N Kothandaraman, VB Bajic, A Loganath, S Koh, J Ng, M Choolani, K Razvi, Early detection of epithelial ovarian cancer using a proteomics-based protein-profiling approach combined with a novel selection strategy, Ann. Acad. Med. Singap. 33(5):S59-S60, 2004
• VB Bajic, SL Tan, Y Suzuki, S Sugano, Promoter prediction analysis on the whole human genome, Nature Biotechnology, 22(11):1467-73, 2004
• C-Y Lin, A Ström, VB Vega, SL Kong, AL Yeo, JS Thomsen, WC Chan, B Doray, DK Bangarusamy, A Ramasamy, LA Vergara, S Tang, A Chong, VB Bajic, L D Miller, J-Å Gustafsson, ET Liu, Estrogen receptor a target gene and response element discovery in breast tumor cells, Genome Biology, 5:R66 doi:10.1186/gb-2004-5-9-r66 (2004)
• A Chong, G Zhang, VB Bajic, ICE (Information for the Coordinates of Exons): A Human Splice Sites Database, Genomics, 84(4): 762-766, 2004
• V Brusic, VB Bajic, N Petrovsky, Computational methods for prediction of T-cell epitopes. Methods 34(4):436-43, 2004
• Pan H, Zuo L, Choudhary V, Zhang Z, Leow SH, Chong FT, Huang Y, Ong VW, Mohanty B, Tan SL, Krishnan SP, Bajic VB. Dragon TF Association Miner: a system for exploring transcription factor associations through text-mining. Nucleic Acids Research, Jul 1;32: W230-W234, 2004
• S Tang, H Han, VB Bajic, ERGDB: Estrogen Responsive Genes Database, Nucleic Acids Research, 32: D533-D536, 2004
• M Brahmachary, SPT Krishnan, JLY Koh, AM Khan, SH Seah, TW Tan, V Brusic, VB Bajic, ANTIMIC: A database of antimicrobial sequences, Nucleic Acids Research, 32: D586-D589, 2004
• VB Bajic, V Choudhary, CK Hock, Content analysis of the core promoter region of human genes, In Silico Biology, 4:109-125, 2004
• Bajic VB, Bajic IV, How Neural Networks Find Promoters Using Recognition of Micro-Structural Promoter Components (32 pages), Chapter in Practical Bioinformatician (L. Wong, Ed.), 91-122, World Scientific Publishing Co., New Jersey, 2004
• Wang H, Li X, Bajic VB, Neural-Statistical Model of TATA-box Motifs in Eukaryotes (34 pages), Chapter in Practical Bioinformatician (L. Wong, Ed.), 123-156, World Scientific Publishing Co. , New Jersey, 2004
• Bajic VB, Chong A., Tuning the Dragon Promoter Finder system for human promoter recognition (10 pages), Chapter in Practical Bioinformatician (L. Wong, Ed.), 157-166, World Scientific Publishing Co., New Jersey, 2004

2003

• Integrative analysis of intraerythrocytic differentially expressed transcripts yields novel insights into the biology of Plasmodium falciparum. Isokpehi RD and Hide WA. Malaria Journal 2003 2: 38
• New Methods for finding disease-susceptability genes: impact and potential. Mark I McCarthy, Damian Smedley and Winston Hide. Genome Biology 2003 4: 119
• Application of eVOC: controlled vocabularies for unifying gene expression data. Winston Hide, Damian Smedley, Mark McCarthy and Janet Kelso. Comptes Rendus Biologies 2003 326(10-11): 1089-1096.
• 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. PLoS Biology 2003 1(3):410-419.
• eVOC: A Controlled Vocabulary for Unifying Gene Expression Data. Janet Kelso, Johann Visagie, Gregory Theiler, Alan Christoffels, Soraya Bardien, Damian Smedley, Darren Otgaar, Gary Greyling, C Victor Jongeneel, Mark I McCarthy, Tania Hide and Winston Hide. Genome Research. 2003 13:1222-1230.
• 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.
• Genome Databases. Win Hide. Encyclopedia of the Human Genome. 2003 3:1-9. London: Nature Publishing Group.
• 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.
• Turning the clock back on ancient genome duplication. Seoighe C. Current Opinion Genetics and Development. 2003 Dec; 13(6): 636-43.
• Significantly Different Patterns of Amino Acid Replacement After Gene Duplication as Compared to After Speciation.Molecular Biology and Evolution. 2003 20(4): 484-490. Cathal Seoighe, Catriona R Johnston, and Denis C Shields
• 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. PLoS Biology 2003.
• Arcobacter butzleri strains from poultry abattoir effluent in Nigeria. Amisu, K.O., Coker, A.O., On, S.L.W., Isokpehi, R.D. East African Medical Journal 2003 80(4): 218-222.
• Bioinformatics and drug target selection for malaria control. Isokpehi RD. Tropical Journal of Pharmaceutical Research 2003 2(1): 123-24.
• VB Bajic, V Brusic, Computational detection of vertebrate polymerase II promoters, Methods in Enzymology, 370: 237-50, 2003
• Yu Kun, Lee Chee How, Tan Puay Hoon, Vladimir B Bajic, Tan Sin Lam, Amit Aggarwal, Hong Ga Sze, Wee Siew Bok, Wong Chow Yin, and Patrick Tan, Classifying the Estrogen Receptor Status of Breast Cancers by Expression Profiles Reveals a Poor Prognosis Subpopulation Exhibiting High Expression of the ERBB2 Receptor, Human Molecular Genetics, 12(24): 3245-3258, 2003
• Bajic VB, Seah SH, Dragon Gene Start Finder: An Advanced System for Finding Approximate Locations of the Start of Gene Transcriptional Units, Genome Research, 13:1923-1929, 2003
• A Chong, G Zhang, VB Bajic, FIE2: A program for the extraction of genomic DNA sequences around the start and translation initiation site of human genes, Nucleic Acids Research, 31(13): 3546-3553, 2003
• Bajic VB, Seah SH, Dragon Gene Start Finder identifies approximate locations of the 5′ ends of genes, Nucleic Acids Research, 31(13):3560-3563, 2003
• Bajic VB, Tan SL, Chong A, Tang S, Ström A, Gustafsson J-Å, Lin C-Y, Liu E, Dragon ERE Finder ver.2: A Tool for Accurate Detection and Analysis of Estrogen Response Elements in Vertebrate Genomes, Nucleic Acids Research, 31(13):3605-3607, 2003
• K Narasimhan, C Basheer, VB Bajic, S Swarup, Enhancement of plant-microbe interactions using a rhizosphere metabolomics-driven approach and its application in the removal of polychlorinated biphenyls, Plant Physiology, 2003 May;132(1):146-53
• CN Bezuidenhout, GJ O’Leary, A Singels, VB Bajic, A process-based model to simulate changes in tiller density and light interception of sugarcane crops, Agricultural Systems, 76(2):589-599, 2003
• VB Bajic, SH Seah, A Chong, SPT Krishnan, JLY Koh, V Brusic, Computer model for recognition of functional transcription start sites in polymerase II promoters of vertebrates, Journal of Molecular Graphics & Modeling, 21(5):323-332, 2003
• VB Bajic, V Brusic, J Li, SK Ng, L Wong (2003) From Informatics to Bioinformatics (Keynote lecture), Proc. of the 1st Asia Pacific Bioinformatics Conference (APBC’2003), pp.3-14, Feb. 4-7, Adelaide, Australia (primary author Limsoon Wong)

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 A. 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. January 2002, 10(1): 17-25.
• Impact of the presence of paralogs on sequence divergence in a set of mouse-human orthologs. Nembaware V, Crum K, Kelso J, Seoighe C. Genome Research. 2002 12(9): 1370-1376.
• Expansin-like molecules: Novel functions derived from common domains. Ludidi NN, Heazlewood JL, Seoighe C, Irving HR and Gehring CA. Journal of Molecular Evolution. 2002 54(5): 587-594
• PATH: a task for the inference of phylogenies. Coral del Val, Peter Ernst, Rudiger Brauning, Karl-Heinz Glatting and Sandor Suhai. Bioinformatics. 2002 18(4): 646-647.
• Artificial neural networks based systems for recognition of genomic signals and regions: A review, VB Bajic, S Tang, H Han, V Brusic, AG Hatzigeorgiou, Informatica: An International Journal of Computing and Informatics, 26:389-400, 2002.
• S Human, VB Bajic, Contribution to skin cancer prevention in South Africa: Modeling the UV index utilizing imprecise data, Austrian J. Statistics, 31(2&3):169-175, 2002
• VB Bajic, A Chong, SH Seah, V Brusic, Intelligent System for Vertebrate Promoter Recognition, IEEE Intelligent Systems Magazine, July/August, 17(4):64-70, 2002
• A Chong, G Zhang, VB Bajic, Information and sequence extraction around the 5′-end and translation initiation site of human genes, In Silico Biology, 2(4):461-465, 2002
• V Brusic, N Petrovsky, G Zhang, VB Bajic, Prediction of promiscuous peptides that bind HLA class I molecules, Immunology and Cell Biology, Jun; 80(3):280-285, June 2002
• D Sha, VB Bajic, On-line Hybrid Learning Algorithm for MLP in Identification Problems, Computers & Electrical Engineering, An International Journal (Elsevier), 28(6):587-598, 2002
• DH Sha, VB Bajic, HY Yang, New model and sliding mode control of hydraulic elevator velocity tracking system, Simulation Modeling Practice & Theory (Elsevier), 9(6-8):365-385, May 15 2002
• Bajic VB, Seah SH, Chong A, Zhang G, Koh JLY, Brusic V, Dragon Promoter Finder: recognition of vertebrate RNA polymerase II promoters, Bioinformatics, 18(1):198-199, 2002
• N Petrovsky, SK Tam, V Brusic, VB Bajic, Use of artificial neural networks in improving renal transplantation outcomes, Graft, 4:6-13, 2002
• Bajic VB, Tang S., Han H., Brusic V. (2002) Recognition of genomic signals and regions by artificial neural networks: an overview (Invited paper), Proceedings of the 5th International Multi-Conference: Information Society IS’2002, pp.28-34, 14-18 October, Ljubljana, Slovenia
• VB Bajic, Which transcription regulatory patterns are most represented in human promoters?, (Keynote lecture), Bioinformatics and Genomics: Methods, Data, and Predictions Workshop (BGMDP2002), part of the Post-Genome Knowledge Discovery, IMS & LIT, Singapore, 24-26 June 2002
• VB Bajic, C-Y Lin, Estrogen Response Element: A Challenge of Computational Recognition (Invited lecture), Language of the DNA, Workshop, IMS, Singapore, 18 February, 2002.
• VB Bajic, Mathematical methods used in promoter recognition systems (Invited tutorial), Post Genome Knowledge Discovery, part 1, Workshop, Singapore, 15 January, 2002.

2001

• Molecular evolution of Mycobacterium tuberculosis: Phylogenetic reconstruction of clonal expansion. R. M. Warren, M. Richardson, S. L. Sampson, G. D. van der Spuy, W. Bourn, J. H. Hauman, H. Heersma, W. Hide, N. Beyers, P. D. van Helden. Tuberculosis. 2001 81(4): 291-302.
• Conserved domains of Subtype C Nef from South African HIV type 1-infected Individuals include Cytotoxic T Lymphocyte Epitope-rich regions. Tumelo Mashishi, Shayne Loubser, Winston Hide, Gillian Hunt, Lynn Morris, Gita Ramjee, Salim Abdool-Karim, Carolyn Williamson, Clive M Gray. AIDS Research and Human Retroviruses 2001 17(17): 1681-1687
• Profiling the malaria genome: a gene survey of three species of malaria parasite with comparison to other apicomplexan species. Jane M.-R. Carlton, Ralhston Muller, Charles A. Yowell, Michelle R. Fluegge, Kenneth A. Sturrock, Jonathan R. Pritt, Esmeralda Vargas-Serrato, Mary R. Galisnki, Hohn W, Barnwell, Nicoa Mulder, Alexander Kanapin, Simon E. Cawley, Winston A. Hide, John B. Dame. Molecular & Biochemical Parasitology 2001 118: 201-210.
• The ESAT-6 gene cluster of Mycobacterium tuberculosis and other high G+C gram-positive bacteria. Nico C. Gey van Pittius, Junaid Gamieldien, Winston Hide, Gordon D. Brown, Roland J. Siezen, and Albert D. Beyers.Genome Biology 2001 2(10).
• Exscript: An ‘Ex’-centric approach to the description of transcript diversity. Winston Hide. Editorial. Bioinformatics. 2001 17(6): 485-6.
• A platform for genomics in South Africa. Win Hide, Valerie Mizrahi, B Venkatesh, Sydney Brenner, Andrew Simpson, Greg Blatch, Himla Soodyall, Katherine Denby, Mike Wingfield, Brenda Wingfield, Paul van Helden, Raj Ramesar, Rosemary Dorrington, Janet Kelso, Ekow Oppon, Elizabeth Goyvaerts, Michele Ramsay, Etienne de Villiers, Carel van Heerden, Basil Allsopp, Cathal Seoighe. South African Medical Journal. 2001 91(12): 1006-1007.
• National Strategy Document for Biotechnology. Frikkie Botha, Winston Hide, Mohammed Jeenah, Nozibusiso Madolo, John Mogabe, Mbudzeni Sibara, Jennifer Thomson, David Walwyn, Brenda Wingfield. May-June 2001.
• STACKdb: Sequence Tag Alignment and Consensus Knowledgebase. Alan Christoffels, Antoine van Gelder, Gary Greyling, Robert Miller, Tania Hide and Winston Hide. Nucleic Acids Research 2001 29(1): 234-238.
• The contribution of exon-skipping events on Chromosome 22 to Protein Coding Diversity. Winston A.Hide, Vladimir N. Babenko, Peter A. van Heusden, Cathal Seoighe, and Janet F. Kelso. Genome Research. 2001 11: 1848-1853.
• The National Genome Initiative. Win Hide, Valerie Mizrahi, B. Venkatesh, Sydney Brenner, Andrew Simpson, Greg Blatch, Himla Soodyall, Katherine Denby, Mike Wingfield, Brenda Wingfield, Paul van Helden, Raj Ramesar, Rosemary Dorrington, Janet Kelso, Ekow Oppon, Elizabeth Goyvaerts, Michele Ramsay, Etienne de Villiers, Carel van Heerden, Basil Allsopp and Cathal Seoighe. January 2001.
• Adaptive control of a pressure tank system with saturation nonlinearities, Z Ma , A Jutan, VB Bajic, Journal of Applied Computer Science, 9(1):61-83, 2001

2000

• Malaria and the Developing Worlds of Genome Bioinformatics. W Hide, Science Scope, 1 May 2000.
• Prevalence of small inversions in yeast gene order volution. Seoighe C, Federspiel N, Jones T, Hansen N, Bivolarovic V, Surzycki R, Tamse R, Komp C, Huizar L, Davis RW, Scherer S, Tait E, Shaw DJ, Harris D, Murphy L, Oliver K, Taylor K, Rajandream MA, Barrell BG, Wolfe KH. Proceedings of the National Acadamy of Science of the United States of America. 19 Dec 2000. 97(26): 14433-14437.
• High Frequency of Inversions during Eukaryote Gene Order Evolution in Comparative Genomics. McLysaght, A., Seoighe, C. and Wolfe, KH. Eds. D. Sankoff and J.H. Nadeau. 2000. Kluyver Academic Publishers pp 47-58.
• A Career in Bioinformatics. J Kelso. SA Society of Biochemists and Molecular Biologists. January 2000; 3 (2).
• P Tabakov, VB Bajic, Genetic Algorithms and extraction of rules for detection of short DNA motifs, International Journal of Computers, Systems and Signals, (Special issue: Knowledge discovery from structured and unstructured data), 1(1):106-117, 2000.
• Z Ma, A Jutan, VB Bajic, Nonlinear self-tuning controller for plants with Hammerstein type model and application to a pressure tank system, International Journal of Computers, Systems and Signals, (Special issue: Computer-based control systems), 1(2):221-230, 2000.
• Z Ma, A Jutan, VB Bajic, Adaptive control of a nonlinear pressure tank using gray box modelling with neural networks, Journal of Applied Computer Science, 8(2):45-63, 2000
• X Li, VB Bajic, D. Sha, X Wang, Neural network control with fuzzy-logic compensation, Journal of Applied Computer Science, (Special issue: Selected Applications of Artificial Intelligence), 8(2):121-127, 2000.
• VB Bajic, Stability problems of fuzzy-descriptor systems, Facta Universitatis, Series: Mechanics, Automatic Control and Robotics, Invited paper, 2(10):1403-1413, 2000.
• VB Bajic, D. Sha, X Li, AI-based discrete sliding-mode control for real-time implementation, International Journal of Computers, Systems and Signals (Special issue: Computer-based control systems), 1(2):196-213, 2000.
• D Sha, VB Bajic, X Li, X Wang, Real-time experiments with discrete sliding-mode control enhanced by AI components, Journal of Applied Computer Science (Special issue: Selected Applications of Artificial Intelligence), 8(2): 99-117, 2000.
• VB Bajic, Comparing the success of different prediction software in sequence analysis: A review, Briefings in Bioinformatics, 1(3):214-228, 2000.
• S. Human, VB Bajic, Modelling Ultraviolet Irradiance in South Africa, Radiation Protection Dosimetry, 91(1-3):181-183, 2000.
• D Sha, VB Bajic, Robust Discrete Adaptive I/O Based Sliding Mode Controller, International Journal of Systems Science, 31(12):1601-1614, 2000
• KJ Duffy, VB Bajic, BR Page, Analysis and Dynamics of an Elephant-Tree Ecosystem having Abundant and Rare Tree Species, Systems Analysis Modelling Simulations, 38:663-676, 2000
• VB Bajic, Neural network clustering of DNA data for improved PWM determination, Journal of Applied Computer Science, 8(1):49-61, 2000.
• Z Ma, VB Bajic, Adaptive Controller for a Class of Systems with Saturation Nonlinearity, Systems Analysis Modelling Simulation, 37(1):1-14, 2000.
• VB Bajic, IV Bajic, Neural network system for promoter recognition (20 pages), Chapter 14 in Future Directions for Intelligent Systems and Information Science (Nik Kasabov, Ed.), 288-305, Physica-Verlag, New York, 2000.

1999

• D2_cluster: A Validated Method for Clustering EST and Full-length cDNA Sequences. J. Burke, D. Davison, and W. Hide. Genome Research 1999 9(11): 1135-1142.
• RFLP analysis of M. tuberculosis demonstrates strain-dependent evolution. Warren RM, Richardson M, Sampson S, Bourn W, Van der Spuy G, Hide W, Heersma H, Beyers N, Van Helden PD. 30th IUATLD World Conference on Lung Health, Madrid, Spain. 1999. The International Journal of Tuberculosis and Lung Disease. 9 (3): S38.Genome Project.
  W Hide.
  Pesquesa (Brazilian Newsletter). November 1999. –>
• A comprehensive approach to clustering of expressed human gene sequence: The Sequence Tag Alignment and Consensus Knowledgebase. R.T. Miller, A. G. Christoffels, C. Gopalakrishnan, J. A. Burke, A. A. Ptitsyn, T. R. Broveak and W. A. Hide. Genome Research 1999 9(11): 1143-1155.
• STACK_PACK and STACK (Sequence tag alignment and consensus knowledgebase). A novel, comprehensive, hierachical EST clustering and consensus generation and analysis system providing unique insight into the human genome. Christoffels A, Miller R and Hide W. American Journal of Human Genetics. 1999 65(4): 477 Suppl S.
• Mutations in a novel retina-specific gene cause autosomal dominant retinitis pigmentosa. Lori S. Sullivan, John R. Heckenlively, Sara J. Bowne, Jian Zuo, Winston A. Hide, Andreas Gal, Michael Denton, Chris F. Inglehearn, Susan H. Blanton, Stephen P. Daiger. Nature Genetics 1999 22(3):255-259.
• Yeast genome evolution in the post genome era. Seoighe, C. and Wolfe, KH. Current Opinion in Microbiology, Review. Oct 1999. 2(5):548-554.
• Updated map of duplicated regions in the yeast genome. Seoighe, C. and Wolfe, KH. Gene. 30 Sep 1999 238(1): 253-61.
• G+C content along and among Saccharomyces cerevisiae chromosomes. Bradnam KR, Seoighe C, Sharp PM and Wolfe KH. Molecular Biology and Evolution. 1999. 16(5): 666-675.
• A comprehensive approach to clustering of expressed human gene sequence: The Sequence Tag Alignment and Consensus Knowledgebase. R. T. Miller, A. G. Christoffels, C. Gopalakrishnan, J. A. Burke, A. A. Ptitsyn, T. R. Broveak and W. A. Hide. Genome Research 1999 9(11): 1143-1155.
• D Sha, VB Bajic, Adaptive on-line ANN learning algorithm and application to identification of non-linear systems, Informatica: An International Journal of Computing and Informatics, 23(4):251-259, 1999.
• D Sha, VB Bajic, On-line adaptive learning rate BP algorithm for MLP and application to an identification problem, Journal of Applied Computer Science, 7(2):67-82, 1999.
• KJ Duffy, BR Page, JH Swart, VB Bajic, Realistic Parameter Assessment for a Well Known Elephant-Tree Ecosystem Model Reveals that Limit Cycles are Unlikely, Ecological Modelling, 121:115-125, 1999
• Z Ma, VB Bajic, DWC Ho, Neural Network based Adaptive Internal Model Control for Nonlinear Plants, Journal of Applied Computer Science, 7(1):63-78, 1999.
• VB Bajic, D Sha, Eds, Development and Practice of Artificial Intelligence Techniques, ISBN 0-620-24836-X, IAAMSAD, Durban, South Africa, 1999
• VB Bajic, IV Bajic, Neural networks in promoter recognition, in Development and Practice of Artificial Intelligence Techniques (V B Bajic, D Sha, Editors), pp. 20-24, IAAMSAD, South Africa, 1999 - (also Plenary lecture at the International Conference on Artificial Intelligence - ICAI’99, 24-26 September 1999).

1998

• Assessment of utility of ESTs for nucleotide diversity using available assembled alignments from dbEST, STACK 2.0 and STACK-INDEX. Karlak, B.R. and Hide, W.A. Genome Informatics 1998 9: 266-268. Satoru Miyano and Toshihisa Takagi Eds. Universal Academy Press Inc. Tokyo, Japan. ISBN 0919-9454.
• A Genome-Level Search for Bacterial Genes on Which Positive Selection May Operate: A Means for Identifying Possible Virulence Factors? Junaid Gamieldien and Winston Hide. Genome Informatics 1998 9: 269-270.
• A Statistical Model for Prokaryotic Promoter Prediction. Joseph C. Oppon and Winston A. Hide. Genome Informatics 1998 9: 271-273.
• Data services and software for identifying genes and mutations causing retinal degeneration. Daiger S.P., Rossiter B.F., Greenberg J., Christoffels A., Hide W. Investigative Ophthalmology & Visual Science 1998 39: S295.
• Alternative Gene Form Discovery and Candidate Gene Selection from gene indexing projects. Burke, J., Wang, H., Hide, W. and Davison D. Genome Research 1998 8(3): 276-290.
• Extent of genomic rearrangement after genome duplication in yeast. Seoighe C and Wolfe KH. Proceedings of the National Acadamy of Science of the United States of America. 14 Apr 1998. 95(8), 4447-4452.
• Evolution of gene order and chromosome number in Saccharomyces, Kluyveromyces and related fungi. Keogh RS, Seoighe C and Wolfe KH. Yeast. 30 March 1998. 14(5): 443-457.
• A Tn7-like Transposon is present in the glmUS region of the Obligately Chemoautolithotrophic Bacterium Theobacillus ferrooxidans. Joseph C. Oppon, Robert R. Sarnovsky, Nancy L. Craig and Douglas E Rawlings. Journal of Bacteriology. 1998 180(11):3007-12.

1997

• Promoting HIV vaccine research and development in Southern Africa. Van der Ryst E, Gray C, Williamson C, Morris L, Abdool Karim Q, Hide W, Esparza J.South African Medical Journal 1997 87(8): 1015-1016.
• A novel approach towards a comprehensive consensus representation of the expressed human genome. Hide W., Burke, J., Christoffels, A., Miller, R.Genome Informatics 1997 pp187-196. Satoru Miyano and Toshihisa Takagi Eds. Universal Academy Press Inc. Tokyo, Japan. ISSN 0919-9454.
• Data services and computational tools for identification of genes and mutations causing retinal degeneration. Daiger S, Rossiter B, Greenberg et al. American Journal of Human Genetics. 1997 61(4):2396 Suppl S.
• A novel approach towards a comprehensive consensus representation of the expressed human genome. Hide W., Burke, J., Christoffels, A., Miller, R. Genome Informatics 1997 pp187-196. Satoru Miyano and Toshihisa Takagi Eds. Universal Academy Press Inc. Tokyo, Japan. ISSN 0919-9454.

1994

• Biological evaluation of d² . An algorithm for high-performance sequence comparison. Hide, W.A. Burke, J. Davison, D. Journal of Computational Biology 1994 1(3): 199-215.

1992

• Isolation of a gene required for programmed initiation in development of Aspergillus nidulans. Adams, T.H., W.A Hide, L.Y. Yager, V.A. Valadez and B.N. Lee. Molecular and Cellular Biology 1992 12(9): 3827-33.
• The molecular taxonomy and evolution of the guinea pig. Li, W-H., A. Zharkikh , W.A. Hide, D. Ma and D. GraurJournal of Heredity 1992 83: 174-181.
• A common missense mutation (Asp250->Asn) in the lipoprotein lipase gene in two unrelated families with familial lipoprotein lipase deficiency. Ishimura-Oka, K. C. F. Semenkovich, F. Faustinella, I. Goldberg, N. Schacter, P. D.Thompson, L. C. Smith, T. Coleman, W. A. Hide, W. V. Brown, K. Oka and L. Chan.Journal of Lipid Research 1992 33(5): 745-54. Abstract.
• A review of the structural, functional and evolutionary relationships of the lipase gene super-family. Hide, W.A., L.Chan and W-H. Li.Journal of Lipid Research 1992 33(2): 167-78.
• The biochemical phylogeny of guinea pigs and gundis, and the paraphyly of the order Rodentia. Graur, D. A Zharkikh, W. Hide, and W-H. Li.Comparative Biochemistry and Physiology 1992 101(4): 495-8.
• Origin of rodents and guinea pigs. W-H. Li, W. Hide and D. Graur.Nature 1992 359(6393): 277.

1991

• Is the guinea pig a rodent? Graur, D., W. Hide and W-H. Li. Nature 1991 351(6328): 649-652.
• Structure and evolution of the apolipoprotein and lipase gene families. Chan, L., W.A. Hide, Y-W Yang and W-H Li. Cellular and Molecular Biology of Atherosclerosis. 1991 A.M. Gotto Jr. Ed. Springer-Verlag (London).