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