gene recognition(2002) 2003 | 2002 | 2001 | 2000 | 1999 | 1998 | 1997 | 1996 | 1995 | 1994 |
1993 | 1992 | 1991 | 1990 | 1989 | 1988 | 1987 |
1986 | 1985 | 1984 | 1983 | 1982 | 1981 | 1980 | pre-1980

+ 2002

  1. VB Bajic, A Chong, SH Seah, V Brusic (2002), "Intelligent system for vertebrate promoter recognition", IEEE Intelligent Systems, 17(4):64-70.
    [ PDF]

  2. VB Bajic, SH Seah, A Chong, G Zhang, JLY Koh, V Brusic (2002),
    "Dragon promoter finder: recognition of vertebrate RNA polymerase II promoters", Bioinformatics, 18(1):198-199.
    [PDF]

  3. VB Bajic, S Tang, H Han, V Brusic, AG Hatzigeorgiou (2002), "Artificial neural networks based systems for recognition of genomic signals and regions: a review", Informatica, 26:389-400.

  4. MV Baytaluk, MS Gelfand, AA Mironov (2002),
    "Exact mapping of prokaryotic gene starts",
    Briefings in Bioinformatics, 3(2):181-194.

  5. Stephanie Bocs, Antoine Danchin, Claudine Medigue (2002),
    "Re-annotation of genome microbial CoDing-sequences: finding new genes and inaccurately annotated genes",
    BMC Bioinformatics, 3:5.
    [ abstract]

  6. MR Brent (2002),
    "Predicting full-length transcripts",
    Trends in Biotechnology, 20(7):273-275.

  7. Brona Brejova, Tomas Vinar (2002),
    "A better method for length distribution modeling in HMMs and its application to gene finding",
    in Combinatorial Pattern Matching, 13th Annual Symposium (CPM), 2373 volume of Lecture Notes in Computer Science, eds. A Apostolico, M Takeda, pp.190-202 (Springer).

  8. D Brett, H Pospisil, J Valcarcel, J Reich, P Bork (2002),
    "Alternative splicing and genome complexity",
    Nature Genetics, 30(1):29-30.

  9. P Carpena, P Bernaola-Galván, R Román-Roldán, JL Oliver (2002),
    "A simple and species-independent coding measure",
    Gene, 300(1-2):97-104.

  10. A Chong, G Zhang, VB Bajic (2002),
    "Information and sequence extraction around the 5'-end and translation initiation site of human genes",
    In Silico Biology, 2:0041.
    [ html ]

  11. F Clark, TA Thanaraj (2002),
    "Categorization and characterization of transcript-confirmed constitutively and alternatively spliced introns and exons from human",
    Human Molecular Genetics, 11(4):451-464.
    [ abstract]

  12. T Clark, S Lee, LR Scott, SM Wang (2002),
    "Computational analysis of gene identification with SAGE",
    Journal of Computational Biology, 9(3):513-526.

  13. Darrell Conklin, Inge Jonassen, Rein Aasland, William R. Taylor (2002),
    "Association of nucleotide patterns with gene function classes: application to human 3' untranslated sequences",
    Bioinformatics, 18:182-189.

  14. W Fairbrother, RF Yeh, PA Sharp, CB Burge (2002),
    "Predictive identification of exonic splicing enhancers in human genes",
    Science, 297:1007-1013.

  15. Ulrich Gerland, J. David Moroz, Terence Hwa (2002),
    "Physical constraints and functional characteristics of transcription factor-DNA interaction",
    Proceedings of National Academy of Sciences, 99:12015-12020.

  16. Matthias Frisch, Kornelie Frech, Andreas Klingenhoff, Kerstin Cartharius, Ines Liebich, Thomas Werner (2002),
    "In Silico prediction of scaffold/matrix attachment regions in large genomic sequences",
    Genome Research, 12:349-354.

  17. Alexandre Gattiker, Elisabeth Gasteiger, Amos Bairoch (2002),
    "ScanProsite: a reference implementation of a PROSITE scanning tool",
    Applied Bioinformatics Journal, 1(2):51-52.

  18. Marc S Halfon, Yonatan Grad, George M Church, Alan M Michelson (2002),
    "Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model",
    Genome Research, 12:1019-1028.

  19. Paul M Harrison, Hedi Hegyi, Suganthi Balasubramanian, Nicholas M Luscombe, Paul Bertone, Nathaniel Echols, Ted Johnson, Mark Gerstein (2002),
    "Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22 ",
    Genome Research, 12:272-280.

  20. Artemis G. Hatzigeorgiou (2002),
    "Translation initiation start prediction in human cDNAs with high accuracy ",
    Bioinformatics, 18:343-350.

  21. Jorng-Tzong Horng, Hsien-Da Huang, Shir-Ly Huang, Ueng-Cheng Yang and Yu-Chang Chang (2002),
    "Mining putative regulatory elements in gene promoter regions of Saccharomyces cerevisiae",
    In Silico Biology, 2:0026.

  22. Biju Issac, Harpreet Singh, Harpreet Kaur, GPS Raghava (2002),
    "Locating probable genes using Fourier transform approach",
    Bioinformatics, 18:196-197.

  23. U Keich, PA Pevzner (2002), "Finding motifs in the twilight zone", Proceedings of the Sixth Internaltional Conference on Computational Biology, pp.195-204.

  24. OV Kel-Margoulis, TG Ivanova, E Wingender, AE Kel (2002),
    "Automatic annotation of genomic regulatory sequences by searching for composite clusters",
    PSB02, 7:187-198.

  25. OV Kel-Margoulis, AE Kel, I Reuter, IV Deineko, E Wingender (2002),
    "TRANSCompel: a database on composite regulatory elements in eukaryotic genes",
    Nucleic Acids Res.earch, 30(1):332-334.

  26. Hiromi Kochiwa, Ryosuke Suzuki, Takanori Washio, Rintaro Saito, The RIKEN Genome Exploration Research Group Phase II Team, Hidemasa Bono, Piero Carninci, Yasushi Okazaki, Rika Miki, Yoshihide Hayashizaki, and Masaru Tomita (2002),
    "Inferring alternative splicing patterns in mouse from a full-length cDNA library and microarray data",
    Genome Research, 12:1286-1293.

  27. MJ Korenberg, ED Lipson, JR Green, JE Solomon (2002),
    "Parallel cascade recognition of exon and intron DNA sequences",
    Annals of Biomedical Engineering, 30(1):129-140.

  28. Boris Lenhard and Wyeth W. Wasserman (2002),
    "TFBS: Computational framework for transcription factor binding site analysis",
    Bioinformatics, 18:1135-1136.

  29. XS Liu, DL Brutlag, JS Liu (2002),
    "An algorithm for finding protein DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments",
    Nature Biotechnology, 20(8):835-839.

  30. Ann E Loraine and Gregg A Helt (2002),
    "Visualizing the genome: techniques for presenting human genome data and annotations",
    BMC Bioinformatics, 3:19.

  31. Václav Mach (2002),
    "PRESTA: associating promoter sequences with information on gene expression",
    Genome Biology, 3(9):research0050.1 - 0050.7

  32. V Makarov (2002),
    "Computer programs for eukaryotic gene prediction",
    Briefings in Bioinformatics, 3(2):195-199.

  33. Catherine Mathe, Marie-France Sagot, Thomas Schiex, Pierre Rouze (2002), "Current methods of gene prediction, their strengths and weaknesses", Nucleic Acids Research, 30:4103-4117.

  34. Xavier Messeguer, Ruth Escudero, Domènec Farré, Oscar Núñez, Javier Martínez, M.Mar Albà (2002),
    "PROMO: detection of known transcription regulatory elements using species-tailored searches",
    Bioinformatics, 18:333-334.

  35. Barmak Modrek, Christopher Lee (2002),
    "A genomic view of alternative splicing",
    Nature Genetics, 30(1):13-19.

  36. Burkhard Morgenstern, Oliver Rinner, Saïd Abdeddaïm, Dirk Haase, Klaus F. X. Mayer, Andreas W. M. Dress, and Hans-Werner Mewes (2002),
    "Exon discovery by genomic sequence alignment",
    Bioinformatics, 18:777-787.

  37. Anton Nekrutenko, Kateryna D Makova, Wen-Hsiung Li (2002),
    "The KA/KS ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study",
    Genome Research, 12:198-202.

  38. Guy Oshiro, Lisa M Wodicka, Michael P Washburn, John R Yates III, David J Lockhart, Elizabeth A Winzeler (2002),
    "Parallel identification of new genes in Saccharomyces cerevisiae",
    Genome Research, 12:1210-1220.

  39. Y Ozawa, S Hanaoka, R Saito, T Washio, S Nakano, A Shinagawa, M Itoh, K Shibata, P Carninci, H Konno, J Kawai, Y Hayashizaki, M Tomita (2002),
    "Comprehensive sequence analysis of translation termination sites in various eukaryotes",
    Gene, 300(1-2):79-87.
    [PDF ]

  40. L Pachter, M Alexandersson, S Cawley (2002),
    "Application of generalized pair Hidden Markov Models to alignments and gene finding problems",
    Journal of Computational Biology, 9(2):389-400.

  41. RA Padgett, CB Burge (2002),
    "Splice Sites",
    In Encyclopedia of the Human Genome (Nature Press), in press.

  42. DA Papatsenko, VJ Makeev, AP Lifanov, M Regnier, AG Nazina, C Desplan (2002),
    "Extraction of functional binding sites from unique regulatory regions: the Drosophila early developmental enhancers",
    Genome Research, 12(3):470-81.

  43. Donald J Patterson, Ken Yasuhara, Walter L Ruzzo (2002),
    "Pre-mRNA secondary structure prediction aids splice site prediction",
    PSB02, 7:223-234.

  44. Vladimir Pavlovic, Ashutosh Garg, Simon Kasif (2002),
    "A Bayesian framework for combining gene predictions",
    Bioinformatics, 18:19-27.

  45. Loïc Ponger and Dominique Mouchiroud (2002),
    "CpGProD: identifying CpG islands associated with transcription start sites in large genomic mammalian sequences",
    Bioinformatics, 18:631-633.

  46. Nikolaus Rajewsky, Nicholas D Socci, Martin Zapotocky, Eric D Siggia (2002),
    "The evolution of DNA regulatory regions for proteo-gamma bacteria by interspecies comparisons",
    Genome Research, 12:298-308.

  47. Sanja Rogic, BF Francis Ouellette, Alan K Mackworth (2002),
    "Improving gene recognition accuracy by combining predictions from two gene-finding programs",
    Bioinformatics, 18:1034-1045.

  48. Rotem Sorek, Gil Ast, Dan Graur (2002),
    "Alu-containing exons are alternatively spliced",
    Genome Research, 12:1060-1067.

  49. LZ Strichman-Almashanu, RS Lee, PO Onyango, E Perlman, F Flam, MB Frieman, AP Feinberg (2002), "A genome-wide screen for normally methylated human CpG islands that can identify novel imprinted genes",
    Genome Research, 12(4):543-554.

  50. G Thijs, K Marchal, M Lescot, S Rombauts, D de Moor, P Rouze, Y Moreau (2002),
    "A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes",
    Journal of Computational Biology, 9(2):447-?.

  51. Eugenii E Vityaev, Yury L Orlov, Oleg V Vishnevsky, Mikhail A Pozdnyakov, Nikolay A Kolchanov (2002),
    "Computer system 'Gene Discovery' for promoter structure analysis ",
    In Silico Biology, 2:0024.

  52. Y Wang, CT Zhang, P Dong (2002),
    "Recognizing shorter coding regions of human genes based on the statistics of stop codons",
    Biopolymers, 63:207-216.
    [ PDF ]

  53. Thomas Werner (2002),
    "Finding and decrypting of promoters contributes to the elucidation of gene function",
    In Silico Biology, 2:0023.

  54. Zhenyu Xuan, W Richard McCombie, Michael Q Zhang (2002),
    "GFScan: A gene family search tool at genomic DNA level",
    Genome Research, 12:1142-1149.

  55. Edouard Yeramian, Serge Bonnefoy, Gordon Langsley (2002),
    "Physics-based gene identification: proof of concept for Plasmodium falciparum
    Bioinformatics, 18:190-193.

  56. CT Zhang, J Wang, R Zhang (2002),
    "Using a Euclid distance discriminant method to find protein coding genes in the yeast genome",
    Computer & Chemistry, 26:195-206.

  57. CT Zhang, R Zhang (2002),
    "Evaluation of gene-finding algorithms by a content-balancing accuracy index",
    Journal of Biomolecular Structure and Dynamics, 19:1045-1052.
    [ PDF]

  58. J Zhang, XF Shi (2002),
    "Tentative study of the coding sequences without 3-base periodicity" (in Chinese),
    Progress in Biochemistry and Biophysics, 29(2):267-272.

  59. MQ Zhang (2002),
    "Computational methods for promoter recognition",
    in Current Topics in Computational Molecular Biology, eds. T Jiang, Y Xu, MQ Zhang (MIT Press).

  60. Yu Zheng, Joseph D Szustakowski, Lance Fortnow, Richard J Roberts, Simon Kasif (2002),
    "Computational identification of operons in microbial genomes",
    Genome Research, 12:1221-1230.

  61. Wei Zhu, Volker Brendel (2002),
    "Gene structure identification with MyGV using cDNA evidence and protein homologs to improve ab initio predictions",
    Bioinformatics, 18:761-762.