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Papers

2012

  • Fisher R, van Zyl GU, Travers SA, Kosakovsky Pond SL, Engelbrech S, Murrell B, Scheffler K, Smith D. Deep sequencing reveals minor protease resistance mutations in patients failing a protease inhibitor regimen. J Virol. 2012 Jun;86(11):6231-7. Epub 2012 Mar 28.
  • Adam Dawe, Aleksandar Radovanovic, Mandeep Kaur, Sunil Sagar, Sundarararajan Seshadri, Ulf Schaefer, Allan Kamau, Alan Christoffels and Vladimir Bajic. DESTAF: A Database of Text-Mined Associations for Reproductive Toxins Potentially Affecting Human Fertility. Reproductive Toxicology 33 (2012) 99–105
  • Ishla Seager, Michael D. Leeson, Amelia C. Crampin,Dominic Mulawa,Neil French,Judith R. Glynn, Simon A.A. Travers, and Grace P. McCormack. HIV Type 1 Mutational Patterns in HIV Type 1 Subtype C-Infected Long-Term Survivors in Karonga District Malawi: Further Analysis and Correction. Aids Research and Human Retroviruses, Volume 28, Number 3, 2012. DOI: 10.1089/aid.2011.0168
  • Okpechi I, Swanepoel CR, Tiffin N, Duffield M, Rayner B. Clinicopathological insights into lupus nephritis in South Africans: A study of 251 patients. Lupus 2012, March 26, 2012.
  • M.V. Akinyi, C. Dandara, J. Gamieldien, J.M. Heckmann. Association of transforming growth factor beta-1 (TGFB1) regulatory region polymorphisms with myasthenia gravis-related ophthalmoparesis. Journal of Neuroimmunology 246 (2012) 96–99 doi:10.1016/j.jneuroim.2012.03.002

2011

  • Vladimir Shulaev, Daniel J Sargent, Ross N Crowhurst, Todd C Mockler, Otto Folkerts, Arthur L Delcher, Pankaj Jaiswal, Keithanne Mockaotis, Aaron Liston, Shrinivasrao P Mane, Paul Burns, Thomas M Davis, Janet P Slovin, Nahla Bassil, Roger P Hellens, Clive Evans, Tim Harkins, Chinnappa Kodira, Brian Desany, Oswald R Crastam Roderick V Jensen, Andrew C Allan, Todd P Michael, Joao Carlos Setubal, Jean-Marc Celton, D Jasper G Rees, Kelly P Williams, Sarah H Holt, Juan Jairo Ruiz Rojas, Mithu Chatterjee, Bo Liu, Herman Silva, Lee Meisel, Avital Adato, Sergei A Filichkin, Michela Troggio, Roberto Viola, Tia-Lynn Ashman, Hao Wang, Palitha Dharmawardhana, Justin Elser, Rajani Raja, Henry D Priet, Douglas W Bruant Jr, Samuel E Fox, Scott A Givan, Larry J Wilhelm, Sushma Naithani, Alan Christoffels et al. The genome of woodland strawberry (Fragaria vesca). Nature Genetics. 2011. 43: 109-116. Doi:10.1038/ng.740
  • Samuel Kwofie, Ulf Schaefer, Vijayaraghava Sundararajan, Vladimir Bajic, Alan Christoffels. HCVpro: Hepatitis C virus protein interaction database (2011). Infection, Genetics and Evolution.
  • Vijay B Bansode, Simon A A Travers, Amelia C Crampin, Bagrey Ngwira, Neil French, Judith R Glynn and Grace P McCormack (2011) Reverse Transcriptase drug resistance mutations in HIV-1 Subtype C infected patients on ART in Karonga District, Malawi. AIDS Research and Therapy 8(38) doi:10.1186/1742-6405-8-38
  • Redmond N. E., Raleigh J, van Soest R.W.M., Kelly M., Travers S.A.A., Bradshaw B., Vartia S., McCormack G.P. (2011) Molecular Systematics of the Order Haplosclerida (Phylum Porifera) Employing Ribosomal (28S rRNA) and Mitochondrial (mtCOI, NAD1) Gene Sequence Data. Plos One. 6(9) e24344
  • Samuel K Kwofie, Aleksandar Radovanovic, Vijayaraghava S Sundararajan, Monique Maqungo, Alan Christoffels and Vladimir B Bajic. Dragon Exploratory System on Hepatitis C Virus (DESHCV). Infection, Genetics and Evolution. 2011. 11(4):734-9
  • Sarah Mwangi, Edwin Murungi, Mario Jonas and Alan Christoffels. Evolutionary Genomics of Glossina morsitans immune-related Serine proteases and Serine Protease inhibitors. Infection, Genetics and Evolution. 2011. 11(4): 740-745.
  • Seager I, Leeson MD, Crampin A, Mulawa D, French D, Glynn J, Travers S.A.A., McCormack GP. HIV-1 mutational patterns in HIV-1 subtype C infected long-term survivors in Karonga District Malawi: correction and further analysis. AIDS Research and Human Retroviruses, June 2011
  • Vijayaraghava Seshadri Sundararajan, Musa Nur Gabere, Ashley Pretorius, Saleem Adam, Alan Christoffels, Minna Lehvaslaiho, John A. C. Archer and Vladimir B. Bajic. DAMPD: a manually curated antimicrobial peptide database. Nucleic Acids Research, 2011 (1-5). doi:10.1093/nar/gkr1063
  • Niamh E. Redmond, Jean Raleigh, Rob W. M. van Soest, Michelle Kelly, Simon A. A. Travers, Brian Bradshaw, Salla Vartia, Kelly M. Stephens, Grace P. McCormack. Phylogenetic Relationships of the Marine Haplosclerida (Phylum Porifera) Employing Ribosomal (28S rRNA) and Mitochondrial (cox1, nad1) Gene Sequence Data. PLoS ONE. 2011. 6(9): e24344
  • Semegni JY, Wamalwa M, Gaujoux R, Harkins GW, Gray A, Martin DP. NASP: a parallel program for identifying evolutionarily conserved nucleic acid secondary structures from nucleotide sequence alignments. Bioinformatics. 2011 Sep 1;27(17):2443-5. Epub 2011 Jul 14.
  • Monjane AL, Harkins GW, Martin DP, Lemey P, Lefeuvre P, Shepherd DN, Oluwafemi S, Simuyandi M, Zinga I, Komba EK, Lakoutene DP, Mandakombo N, Mboukoulida J, Semballa S, Tagne A, Tiendrébéogo F, Erdmann JB, van Antwerpen T, Owor BE, Flett B, Ramusi M, Windram OP, Syed R, Lett JM, Briddon RW, Markham PG, Rybicki EP, Varsani A. Reconstructing the history of maize streak virus strain a dispersal to reveal diversification hot spots and its origin in southern Africa. Journal of Virology. 2011 Sep;85(18):9623-36. Epub 2011 Jun 29.
  • Lefeuvre P, Harkins GW, Lett JM, Briddon RW, Chase MW, Moury B, Martin DP. Evolutionary time-scale of the begomoviruses: evidence from integrated sequences in the Nicotiana genome. PLoS One. 2011;6(5):e19193. Epub 2011 May 16.

2010

  • Meehan CJ, Hedge JA, Robertson DL, McCormack GP, Travers S. Emergence, dominance and possible decline of CXCR4 chemokine receptor usage during the course of HIV infection. J Med Virol. 82 (12): 2004-12.
  • Bansode V, Drebert ZJ, Travers SA, Banda E, Molesworth A, Crampin A, Ngwira B, French N, Glynn JR, McCormack GP. Drug resistance mutations in drug-naïve HIV type 1 subtype C-infected individuals from rural Malawi. AIDS Res Hum Retroviruses.
  • Tiffin N, Meintjes A, Ramesa R, Bajic VB, Rayner B. Computational Analysis of Candidate disease Genes and Variants for Salt-sensitive Hypertension in Indigenous Southern Africans. PloS One.2010 September 20;5(9):e12989
  • Okpechi I, Rayner BL, van der Merwe L, Mayosi BM, Adebowale A, Tiffin N, Ramesar R. Genetic variation at selected SNPs in the Leptin gene and association of Alleles with markers of kidney kidney disease in a Xhosa population of South Africa. PloS One 2010 Feb 5;5(2):e9086
  • Samuel K Kwofie, Aleksandar Radovanovic, Vijayaraghava S Sundararajan, Monique Maqungo, Alan Christoffels and Vladimir B Bajic. Hepatitis C Virus discovery database (HCVdd): Dragon Exploratory System on Hepatitis C Virus (DESHCV) 2010. Infection, Genetics and Evolution.
  • Sarah Mwangi, Edwin Murungi, Mario Jonas and Alan Christoffels (2010) Evolutionary Genomics of Glossina morsitans immune-related Serine proteases and Serine Protease inhibitors. Infection, Genetics and Evolution
  • Vladimir Shulaev, Daniel J Sargent, Ross N Crowhurst, Todd C Mockler, Otto Folkerts, Arthur L Delcher, Pankaj Jaiswal, Keithanne Mockaotis, Aaron Liston, Shrinivasrao P Mane, Paul Burns, Thomas M Davis, Janet P Slovin, Nahla Bassil, Roger P Hellens, Clive Evans, Tim Harkins, Chinnappa Kodira, Brian Desany, Oswald R Crastam Roderick V Jensen, Andrew C Allan, Todd P Michael, Joao Carlos Setubal, Jean-Marc Celton, D Jasper G Rees, Kelly P Williams, Sarah H Holt, Juan Jairo Ruiz Rojas, Mithu Chatterjee, Bo Liu, Herman Silva, Lee Meisel, Avital Adato, Sergei A Filichkin, Michela Troggio, Roberto Viola, Tia-Lynn Ashman, Hao Wang, Palitha Dharmawardhana, Justin Elser, Rajani Raja, Henry D Priet, Douglas W Bruant Jr, Samuel E Fox, Scott A Givan, Larry J Wilhelm, Sushma Naithani, Alan Christoffels et al (2010) The genome of woodland strawberry (Fragaria vesca). Nature Genetics. Doi:10.1038/ng.740
  • Jean-Marc Celton, Alan Christoffels, Daniel J Sargent, Xiangming X and David J.G Rees (2010) Genome-wide SNP identification by high-throughput sequencing and selective mapping allows sequence assembly positioning using a framework genetic linkage map. BMC Biology. 8:155-8
  • Monique Maqungo, Mandeep Kaur, Samuel K. Kwofie, Aleksandar Radovanovic, Ulf Schaefer, Sebastian Schmeier, Ekow Oppon, Alan Christoffels and Vladimir B. Bajic (2010). DDPC: Dragon Database of Genes associated with Prostate Cancer. Nucleic Acids Research; doi: 10.1093/nar/gkq849.
  • Rocca-Serra P, Brandizi M, Maguire E, Sklyar N, Taylor C, Begley K, Field D, Harris S, Hide W, Hofmann O, Neumann S, Sterk P, Tong W, Sansone SA. ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level. Bioinformatics. 26(18): 2354-6
  • Voight BF, Scott LJ, Steinthorsdottir V, Morris AP, Dina C, Welch RP, Zeggini E, Huth C, Aulchenko YS, Thorleifsson G, McCulloch LJ, Ferreira T, Grallert H, Amin N, Wu G, Willer CJ, Raychaudhuri S, McCarroll SA, Langenberg C, Hofmann OM, Dupuis J, Qi L, Segrè AV, van Hoek M, Navarro P, Ardlie K, Balkau B, Benediktsson R, Bennett AJ, Blagieva R, Boerwinkle E, Bonnycastle LL, Bengtsson Boström K, Bravenboer B, Bumpstead S, Burtt NP, Charpentier G, Chines PS, Cornelis M, Couper DJ, Crawford G, Doney AS, Elliott KS, Elliott AL, Erdos MR, Fox CS, Franklin CS, Ganser M, Gieger C, Grarup N, Green T, Griffin S, Groves CJ, Guiducci C, Hadjadj S, Hassanali N, Herder C, Isomaa B, Jackson AU, Johnson PR, Jørgensen T, Kao WH, Klopp N, Kong A, Kraft P, Kuusisto J, Lauritzen T, Li M, Lieverse A, Lindgren CM, Lyssenko V, Marre M, Meitinger T, Midthjell K, Morken MA, Narisu N, Nilsson P, Owen KR, Payne F, Perry JR, Petersen AK, Platou C, Proença C, Prokopenko I, Rathmann W, Rayner NW, Robertson NR, Rocheleau G, Roden M, Sampson MJ, Saxena R, Shields BM, Shrader P, Sigurdsson G, Sparsø T, Strassburger K, Stringham HM, Sun Q, Swift AJ, Thorand B, Tichet J, Tuomi T, van Dam RM, van Haeften TW, van Herpt T, van Vliet-Ostaptchouk JV, Walters GB, Weedon MN, Wijmenga C, Witteman J, Bergman RN, Cauchi S, Collins FS, Gloyn AL, Gyllensten U, Hansen T, Hide WA, Hitman GA, Hofman A, Hunter DJ, Hveem K, Laakso M, Mohlke KL, Morris AD, Palmer CN, Pramstaller PP, Rudan I, Sijbrands E, Stein LD, Tuomilehto J, Uitterlinden A, Walker M, Wareham NJ, Watanabe RM, Abecasis GR, Boehm BO, Campbell H, Daly MJ, Hattersley AT, Hu FB, Meigs JB, Pankow JS, Pedersen O, Wichmann HE, Barroso I, Florez JC, Frayling TM, Groop L, Sladek R, Thorsteinsdottir U, Wilson JF, Illig T, Froguel P, van Duijn CM, Stefansson K, Altshuler D, Boehnke M, McCarthy MI; MAGIC investigators; GIANT Consortium. Twelve Type 2 diabetes susceptibility loci identified through large-scale association analysis. Nature Genetics. 42 (7): 579-89.
  • Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB, Tan K, Akalin A, Schmeier S, Kanamori-Katayama M, Bertin N, Carninci P, Daub CO, Forrest AR, Gough J, Grimmond S, Han JH, Hashimoto T, Hide W, Hofmann O, Kamburov A, Kaur M, Kawaji H, Kubosaki A, Lassmann T, van Nimwegen E, MacPherson CR, Ogawa C, Radovanovic A, Schwartz A, Teasdale RD, Tegnér J, Lenhard B, Teichmann SA, Arakawa T, Ninomiya N, Murakami K, Tagami M, Fukuda S, Imamura K, Kai C, Ishihara R, Kitazume Y, Kawai J, Hume DA, Ideker T, Hayashizaki Y. An atlas of combinatorial transcriptional regulation in mouse and man. Cell. 140 (5): 744-52
  • Gichora NN, Fatumo SA, Ngara MV, Chelbat N, Ramdayal K, Opap KB, Siwo GH, Adebiyi MO, El Gonnouni A, Zofou D, Maurady AA, Adebiyi EF, de Villiers EP, Masiga DK, Bizzaro JW, Suravajhala P, Ommeh SC, Hide W. Ten simple rules for organizing a virtual conference—anywhere. PLoS Comput Biol. 6(2):e1000650.
  • Lefeuvre P, Martin DP, Harkins GW, Lemey P, Gray AJA, Meredith S, Lakay F, Monjane A, Lett J, Varsani A, Heydarnejad J. The Spread of Tomato Yellow Leaf Curl Virus from the Middle East to the World. PLoS pathogens 6(10):e1001164

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; 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; 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 3rd Asia-Pacific Bioinformatics Conference (APBC05), Imperial College Press, 379, 2005

2004

2003

2002

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

  • 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

1997

1994

1992

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).

2012

Fisher R, van Zyl GU, Travers SA, Kosakovsky Pond SL, Engelbrech S, Murrell B, Scheffler K, Smith D. Deep sequencing reveals minor protease resistance mutations in patients failing a protease inhibitor regimen. J Virol. 2012 Jun;86(11):6231-7. Epub 2012 Mar 28. Adam Dawe, Aleksandar Radovanovic, Mandeep Kaur, Sunil Sagar, Sundarararajan Seshadri, Ulf Schaefer, Allan Kamau, Alan …

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2011

Vladimir Shulaev, Daniel J Sargent, Ross N Crowhurst, Todd C Mockler, Otto Folkerts, Arthur L Delcher, Pankaj Jaiswal, Keithanne Mockaotis, Aaron Liston, Shrinivasrao P Mane, Paul Burns, Thomas M Davis, Janet P Slovin, Nahla Bassil, Roger P Hellens, Clive Evans, Tim Harkins, Chinnappa Kodira, Brian Desany, Oswald R Crastam Roderick V Jensen, Andrew C Allan, …

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2010

Meehan CJ, Hedge JA, Robertson DL, McCormack GP, Travers S. Emergence, dominance and possible decline of CXCR4 chemokine receptor usage during the course of HIV infection. J Med Virol. 82 (12): 2004-12. Bansode V, Drebert ZJ, Travers SA, Banda E, Molesworth A, Crampin A, Ngwira B, French N, Glynn JR, McCormack GP. Drug resistance mutations …

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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, …

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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 …

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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 …

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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 …

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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 …

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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, …

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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 …

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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. …

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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 …

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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 …

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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 …

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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 …

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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 …

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Pre-1997

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 …

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