computational gene recognition

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+ 2006

  1. promoter/TF
    Irina Abnizova and Walter R. Gilks (2006), "Studying statistical properties of regulatory DNA sequences, and their use in predicting regulatory regions in the eukaryotic genomes", Briefings in Bioinformatics, 7:48-54.
    [abstract]

  2. alternative-splicing
    Ritesh Agrawal and Gary D. Stormo (2006), "Using mRNAs lengths to accurately predict the alternatively spliced gene products in Caenorhabditis elegans", Bioinformatics, 22:1239-1244.
    [abstract]

  3. JE Allen, SL Salzberg (2006), "A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons", Algorithms for Molecular Biology, 1(1):14.
    [abstract]

  4. JE Allen, WH Majoros, M Pertea, SL Salzberg (2006), "JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions", Genome Biology, 7(Suppl 1):S9.1-13.

  5. Alberto Apostolico, Matteo Comin, Laxmi Parida (2006), "Mining, compressing and classifying with extensible motifs", Algorithms for Molecular Biology, 1:4.
    [abstract]

  6. splicing
    AKMA Baten, BCH Chang, SK Halgamuge, Jason Li (2006), "Splice site identification using probabilistic parameters and SVM classification", BMC Bioinformatics, 7(Suppl 5):S15.

  7. Paul Bertone, Valery Trifonov, Joel S. Rozowsky, Falk Schubert, Olof Emanuelsson, John Karro, Ming-Yang Kao, Michael Snyder, and Mark Gerstein (2006), "Design optimization methods for genomic DNA tiling arrays", Genome Research, 16(2):271-281.
    [abstract]

  8. promoter/TF
    Mathieu Blanchette, Alain R. Bataille, Xiaoyu Chen, Christian Poitras, Josée Laganière, Céline Lefèbvre, Geneviève Deblois, Vincent Giguère, Vincent Ferretti, Dominique Bergeron, Benoit Coulombe, and François Robert (2006), "Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression", Genome Research, 16(5):656-668.
    [abstract]

  9. alternative-splicing
    Paola Bonizzoni, Raffaella Rizzi, and Graziano Pesole (2006), "Computational methods for alternative splicing prediction", Briefings in Functional Genomics and Proteomics, 5:46-51.
    [abstract]

  10. expression
    Mark P. Brynildsen, Linh M. Tran, and James C. Liao (2006) "A Gibbs sampler for the identification of gene expression and network connectivity consistency", Bioinformatics, 22(24):3040-3046.
    [abstract]

  11. Emanuele Bultrini and Elisabetta Pizzi (2006), "A new parameter to study compositional properties of non-coding regions in eukaryotic genomes", Gene, 385:75-82.
    [abstract]

  12. promoter/TF
    Piero Carninci, Albin Sandelin, Boris Lenhard, Shintaro Katayama, Kazuro Shimokawa, Jasmina Ponjavic, Colin A M Semple, Martin S Taylor, Pär G Engström, Martin C Frith, Alistair R R Forrest, Wynand B Alkema, Sin Lam Tan, Charles Plessy, Rimantas Kodzius, Timothy Ravasi, Takeya Kasukawa, Shiro Fukuda, Mutsumi Kanamori-Katayama, Yayoi Kitazume, Hideya Kawaji, Chikatoshi Kai, Mari Nakamura, Hideaki Konno, Kenji Nakano, Salim Mottagui-Tabar, Peter Arner, Alessandra Chesi, Stefano Gustincich, Francesca Persichetti, Harukazu Suzuki, Sean M Grimmond, Christine A Wells, Valerio Orlando, Claes Wahlestedt, Edison T Liu, Matthias Harbers, Jun Kawai, Vladimir B Bajic, David A Hume, Yoshihide Hayashizaki (2006), "Genome-wide analysis of mammalian promoter architecture and evolution", Nature Genetics, 38:626-635.
    [abstract]

  13. promoter/TF
    AM Carvalho, AT Freitas, AL Oliveira, MF Sagot (2006), "An efficient algorithm for the identification of structured motifs in DNA promoter sequences", IEEE/ACM Transactions on Computational Biology and Bioinformatics, 3(2):126-140.

  14. Tiziana Castrignanò, Paolo D'Onorio De Meo, Giorgio Grillo, Sabino Liuni, Flavio Mignone, Ivano Giuseppe Talamo, and Graziano Pesole (2006), "GenoMiner: a tool for genome-wide search of coding and non-coding conserved sequence tags", Bioinformatics, 22(4):497-499.
    [abstract]

  15. promoter/TF
    Li-Wei Chang, Rakesh Nagarajan, Jeffrey A. Magee, Jeffrey Milbrandt, and Gary D. Stormo (2006), "A systematic model to predict transcriptional regulatory mechanisms based on overrepresentation of transcription factor binding profiles", Genome Research, 16(3):405-413.
    [abstract]

  16. promoter/TF
    Yu-Hsiang Chang, Yu-Chao Wang, and Bor-Sen Chen (2006), "Identification of transcription factor cooperativity via stochastic system model", Bioinformatics, 22(18):2276-2282.
    [abstract]

  17. Yiming Cheng, Robert M. Miura, and Bin Tian (2006), "Prediction of mRNA polyadenylation sites by support vector machine", Bioinformatics, 22(19):2320-2325.
    [abstract]

  18. promoter/TF
    Rajesh Chowdhary, Sin Lam Tan, R. Ayesha Ali, Brent Boerlage, Limsoon Wong, and Vladimir B Bajic (2006), "Dragon Promoter Mapper (DPM): a Bayesian framework for modelling promoter structures", Bioinformatics, 22(18):2310-2312.
    [abstract]

  19. splicing
    Alexander E Churbanov, Igor B Rogozin, Jitender S Deogun, Hesham H Ali (2006), "Method of predicting Splice Sites based on signal interactions", Biology Direct, 1:10.
    [abstract ]

  20. promoter/TF
    Sara J. Cooper, Nathan D. Trinklein, Elizabeth D. Anton, Loan Nguyen, and Richard M. Myers (2006), "Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome", Genome Research, 16(1):1-10.
    [abstract]

  21. Lior David, Wolfgang Huber, Marina Granovskaia, Joern Toedling, Curtis J. Palm, Lee Bofkin, Ted Jones, Ronald W. Davis, Lars M. Steinmetz (2006), "A high-resolution map of transcription in the yeast genome", Proceedings of National Academy of Sciences, 103(14):5320-5325.
    [abstract]

  22. expression
    Jiang Du, Joel S. Rozowsky, Jan O. Korbel, Zhengdong D. Zhang, Thomas E. Royce, Martin H. Schultz, Michael Snyder, and Mark Gerstein (2006), "A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge", Bioinformatics, 22(24):3016-3024.
    [abstract]

  23. promoter/TF
    Laura Elnitski, Victor X. Jin, Peggy J. Farnham, and Steven J.M. Jones (2006), "Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques", Genome Research, 16(12):1455-1464.
    [abstract]

  24. annotation
    Christine G. Elsik, Kim C. Worley, Lan Zhang, Natalia V. Milshina, Huaiyang Jiang, Justin T. Reese, Kevin L. Childs, Anand Venkatraman, C. Michael Dickens, George M. Weinstock, and Richard A. Gibbs (2006), "Community annotation: Procedures, protocols, and supporting tools", Genome Research, 16(11):1329-1333.
    [abstract]

  25. alternative-splicing
    Ekaterina O Ermakova, Ramil N Nurtdinov, Mikhail S Gelfand (2006), "Fast rate of evolution in alternatively spliced coding regions of mammalian genes", BMC Genomics, 7:84.
    [abstract]

  26. expression
    Logan Everett, Li-San Wang, and Sridhar Hannenhalli (2006), "Dense subgraph computation via stochastic search: application to detect transcriptional modules", Bioinformatics, 22:e117-e123.
    [abstract]

  27. Liliana Florea (2006), "Bioinformatics of alternative splicing and its regulation", Briefings in Bioinformatics, 7:55-69.
    [abstract]

  28. promoter/TF
    Barrett C. Foat, Alexandre V. Morozov, and Harmen J. Bussemaker (2006), "Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE", Bioinformatics, 22:e141-e149.
    [abstract]

  29. promoter/TF
    Eugene Fratkin, Brian T. Naughton, Douglas L. Brutlag, and Serafim Batzoglou (2006), "MotifCut: regulatory motifs finding with maximum density subgraphs", Bioinformatics, 22:e150-e157.
    [abstract]

  30. MC Frith, TL Bailey, T Kasukawa, F Mignone, SK Kummerfeld, M Madera, S Sunkara, M Furuno, CJ Bult, J Quackenbush, C Kai, J Kawai, P Carninci, Y Hayashizaki, G Pesole, JS Mattick (2007), "Discrimination of non-protein-coding transcripts from protein-coding mRNA", RNA Biology, 3(1):40-48.

  31. Martin C. Frith, Jasmina Ponjavic, David Fredman, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayshizaki, and Albin Sandelin (2006), "Evolutionary turnover of mammalian transcription start sites", Genome Reseach, 16(6):713-722.
    [abstract]

  32. expression
    Simon J. Galbraith, Linh M. Tran, and James C. Liao (2006), "Transcriptome network component analysis with limited microarray data", Bioinformatics, 22(15):1886-1894.
    [abstract]

  33. Steven M. Gallo, Long Li, Zihua Hu, and Marc S. Halfon (2006), "REDfly: a Regulatory Element Database for Drosophila", Bioinformatics, 22(3): 381-383.
    [abstract]

  34. promoter/TF
    Ge Gao, Yingfu Zhong, Anyuan Guo, Qihui Zhu, Wen Tang, Weimou Zheng, Xiaocheng Gu, Liping Wei, and Jingchu Luo (2006), "DRTF: a database of rice transcription factors", Bioinformatics, 22(10):1286-1287.
    [abstract]

  35. promoter/TF
    Miklos Gaszner and Gary Felsenfeld (2006), "Insulators: exploiting transcriptional and epigenetic mechanisms", Nature Reviews Genetics, 7(9):703-713.
    [abstract]

  36. Xijin Ge, Qingfa Wu, Yong-Chul Jung, Jun Chen, and San Ming Wang (2006), "A large quantity of novel human antisense transcripts detected by LongSAGE", Bioinformatics, 22(20):2475-2479.
    [abstract]

  37. promoter/TF
    Naum I Gershenzon, Edward N Trifonov, Ilya P Ioshikhes (2006), "The features of Drosophila core promoters revealed by statistical analysis", BMC Genomics, 7:161.
    [abstract]

  38. JJ Gordon, MW Towsey, JM Hogan, SA Mathews, P Timms (2006), "Improved prediction of bacterial transcription start sites", Bioinformatics, 22(2):142-148.
    [abstract]

  39. Feng-Biao Guo, Chun-Ting Zhang (2006), "ZCURVE_V: a new self-training system for recognizing protein-coding genes in viral and phage genomes", BMC Bioinformatics, 7:9.
    [abstract]

  40. Marc S Halfon (2006), "(Re)modeling the transcriptional enhancer" (news and views), Nature Genetics, 38:1102-1103.
    [PDF]

  41. promoter/TF
    Lawrence S Hon and Ajay N Jain (2006), "A deterministic motif finding algorithm with application to the human genome", Bioinformatics, 22(9):1047-1054.
    [abstract]

  42. annotation
    Fan Hsu, W. James Kent, Hiram Clawson, Robert M. Kuhn, Mark Diekhans, and David Haussler (2006), "The UCSC Known Genes", Bioinformatics, 22(9):1036-1046.
    [abstract]

  43. Wolfgang Huber, Joern Toedling, and Lars M. Steinmetz (2006), "Transcript mapping with high-density oligonucleotide tiling arrays", Bioinformatics, 22(16):1963-1970.
    [abstract]

  44. H Ji, WH Wong (2006), "Computational biology: toward deciphering gene regulatory information in mammalian genomes", Biometrics, 62(3):645-663.

  45. promoter/TF
    similarity
    Victor X Jin, Gregory A Singer, Francisco J Agosto-Perez, Sandya Liyanarachchi, Ramana V Davuluri (2006), "Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairs", BMC Bioinformatics, 7:114 (7 March 2006)
    [abstract]

  46. alternative-splicing
    Jennifer L Kabat, Sergio Barberan-Soler, Paul McKenna, Hiram Clawson, Tracy Farrer, Alan M Zahler (2006), "Intronic alternative splicing regulators identified by comparative genomics in Nematodes", PLoS Computational Biology, 2(7):e86.
    [abstract ]

  47. Luv Kashyap and Mohammad Tabish (2006), "Comparative analysis of various gene finders specific to Caenorhabditis elegans genome", Bioinformation, 1(6):203-207.
    [abstract]

  48. James P. Kastenmayer, Li Ni, Angela Chu, Lauren E. Kitchen, Wei-Chun Au, Hui Yang, Carole D. Carter, David Wheeler, Ronald W. Davis, Jef D. Boeke, Michael A. Snyder, and Munira A. Basrai (2006), "Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae", Genome Research, 16(3):365-373.
    [abstract]

  49. promoter/TF
    Nak-Kyeong Kim, Kannan Tharakaraman, and John L Spouge (2006), "Adding sequence context to a Markov background model improves the identification of regulatory elements", Bioinformatics, 22(23):2870-2875.
    [abstract]

  50. promoter/TF
    Kouichi Kimura, Ai Wakamatsu, Yutaka Suzuki, Toshio Ota, Tetsuo Nishikawa, Riu Yamashita, Jun-ichi Yamamoto, Mitsuo Sekine, Katsuki Tsuritani, Hiroyuki Wakaguri, Shizuko Ishii, Tomoyasu Sugiyama, Kaoru Saito, Yuko Isono, Ryotaro Irie, Norihiro Kushida, Takahiro Yoneyama, Rie Otsuka, Katsuhiro Kanda, Takahide Yokoi, Hiroshi Kondo, Masako Wagatsuma, Katsuji Murakawa, Shinichi Ishida, Tadashi Ishibashi, Asako Takahashi-Fujii, Tomoo Tanase, Keiichi Nagai, Hisashi Kikuchi, Kenta Nakai, Takao Isogai, and Sumio Sugano (2006), "Diversification of transcriptional modulation: Large-scale identification and characterization of putative alternative promoters of human genes", Genome Research, 16(1):55-65.
    [abstract]

  51. expression
    A. Kel, T. Konovalova, T. Waleev, E. Cheremushkin, O. Kel-Margoulis, and E. Wingender "Composite Module Analyst: a fitness-based tool for identification of transcription factor binding site combinations", Bioinformatics, 22(10):1190-1197.
    [abstract]

  52. promoter/TF
    Imtiaz A. Khan, Matthew Mort, Paul R. Buckland, Michael C. O'Donovan, David N. Cooper and Nadia A. Chuzhanova (2006), "In silico discrimination of single nucleotide polymorphisms and pathological mutations in human gene promoter regions by means of local DNA sequence context and regularity", In Silico Biology, 6:0003.

  53. Lutz Krause, Naryttza N. Diaz, Daniela Bartels, Robert A. Edwards, Alfred Pühler, Forest Rohwer, Folker Meyer, and Jens Stoye (2006), "Finding novel genes in bacterial communities isolated from the environment", Bioinformatics, 22:e281-e289.
    [abstract]

  54. Ngai-Fong Law, Kin-On Cheng, Wan-Chi Siu (2006), "On relationship of Z-curve and Fourier approaches for DNA coding sequence classification", Bioinformation, 1(7): 242-246.
    [abstract]

  55. annotation
    Luca Lenzi, Flavia Frabetti, Federica Facchin, Raffaella Casadei, Lorenza Vitale, Silvia Canaider, Paolo Carinci, Maria Zannotti, and Pierluigi Strippoli (2006), "UniGene Tabulator: a full parser for the UniGene format", Bioinformatics, 22(20):2570-2571.
    [abstract]

  56. promoter/TF
    Henry C.M. Leung, Francis Y.L. Chin (2006), "An efficient motif discovery algorithm with unknown motif length and number of binding sites", International Journal of Data Mining and Bioinformatics, 1(2):201-215.
    [abstract]

  57. promoter/TF
    Henry C. M. Leung and Francis Y. L. Chin (2006), "Finding motifs from all sequences with and without binding sites", Bioinformatics, 22(18):2217-2223.
    [abstract]

  58. promoter/TF
    Lang Li, Alfred S. L. Cheng, Victor X. Jin, Henry H. Paik, Meiyun Fan, Xiaoman Li, Wei Zhang, Jason Robarge, Curtis Balch, Ramana V. Davuluri, Sun Kim, Tim H.-M. Huang, and Kenneth P. Nephew (2006), "A mixture model-based discriminate analysis for identifying ordered transcription factor binding site pairs in gene promoters directly regulated by estrogen receptor-alpha", Bioinformatics, 22(18):2210-2216.
    [abstract]

  59. promoter/TF
    Nan Li, Martin Tompa (2006), "Analysis of computational approaches for motif discovery", Algorithms for Molecular Biology, 1:8.
    [abstract]

  60. promoter/TF
    Qian-Zhong Li, Hao Lin (2006), "The recognition and prediction of sigma70 promoters in Escherichia coli K-12", Journal of Theoretical Biology, 242:135-141.
    [abstract ]

  61. alternative-splicing
    Han Liang and Laura F. Landweber (2006), "A genome-wide study of dual coding regions in human alternatively spliced genes", Genome Research, 16(2):190-196.
    [abstract]

  62. Burkhard Linke, Alice C McHardy, Heiko Neuweger, Lutz Krause, Folker Meyer (2006), "REGANOR: a gene prediction server for prokaryotic genomes and a database of high quality gene predictions for prokaryotes", Applied Bioinformatics, 5(3):193-198.

  63. Leonard Lipovich and Mary-Claire King (2006), "Abundant novel transcriptional units and unconventional gene pairs on human chromosome 22", Genome Research, 16(1):45-54.
    [abstract]

  64. J Liu, J Gough, B Rost (2006), "Distinguishing protein-coding from non-coding RNAs through support vector machines", PLoS Genetics, 2(4):e29

  65. splicing
    Sayed-Amir Marashi, Changiz Eslahchi, Hamid Pezeshk and Mehdi Sadeghi (2006), "Impact of RNA structure on the prediction of donor and acceptor splice sites", BMC Bioinformatics, 7:297.
    [abstract]

  66. splicing
    Sayed-Amir Marashi, Hani Goodarzi, Mehdi Sadeghi, Changiz Eslahchi, Hamid Pezeshk (2006), "Importance of RNA secondary structure information for yeast donor and acceptor splice site predictions by neural networks", Computational Biology and Chemistry, 30(1):50-57.
    [abstract ]

  67. promoter/TF
    Kenzie D MacIsaac, Ting Wang, Benjamin D. Gordon, David K Gifford, Gary D Stormo, Ernest Fraenkel (2006), "An improved map of conserved regulatory sites for Saccharomyces cerevisiae", BMC Bioinformatics, 7:113.
    [abstract]

  68. alternative-splicing
    Dmitry B. Malko, Vsevolod J. Makeev, Andrey A. Mironov, and Mikhail S. Gelfand (2006), "Evolution of exon-intron structure and alternative splicing in fruit flies and malarial mosquito genomes", Genome Research, 16(4):505-509.
    [abstract]

  69. promoter/TF
    L Mao, WJ Zheng (2006), "Combining comparative genomics with de novo motif discovery to identify human transcription factor DNA-binding motifs", BMC Bioinformatics, 7(Suppl 4):S21.

  70. expression
    Joe Mellor and Charles DeLisi (2006), "An equilibrium partitioning model connecting gene expression and cis-motif content", Bioinformatics, 22:e368-e374.
    [abstract]

  71. promoter/TF
    Sauro Menchetti, Andrea Passerini, Paolo Frasconi, Claudia Andreini, Antonio Rosato (2006), "Improving prediction of Zinc binding sites by modeling the linkage between redidues close in sequence", Proceedings of the Tenth International Conference on Research in Computational Molecular Biology , pp.?-?

  72. promoter/TF
    Nuno D. Mendes, Ana C. Casimiro, Pedro M. Santos, Isabel Sá-Correia, Arlindo L. Oliveira, and Ana T. Freitas (2006), "MUSA: a parameter free algorithm for the identification of biologically significant motifs", Bioinformatics, 22(24):2996-3002.
    [abstract]

  73. Giulia Menconi, Roberto Marangoni (2006), "A compression-based approach for coding sequences identification. I. application to prokaryotic genomes", Journal of Computational Biology, 13(8):1477-1488.
    [abstract]

  74. K Munch, A Krogh (2006), "Automatic generation of gene finders for eukaryotic species", BMC Bioinformatics, 7:263.
    [abstract]

  75. alternative-splicing
    Hideki Nagasaki, Masanori Arita, Tatsuya Nishizawa, Makiko Suwa, and Osamu Gotoh (2006), "Automated classification of alternative splicing and transcriptional initiation and construction of visual database of classified patterns", Bioinformatics, 22(10):1211-1216.
    [abstract]

  76. Achuthsankar S. Nair, Sivarama Pillai Sreenadhan (2006), "A coding measure scheme employing electron-ion interaction pseudopotential (EIIP)", Bioinformation, 1(6): 197-202.
    [abstract]

  77. promoter/TF
    Leelavati Narlikar, Raluca Gordân, Uwe Ohler, and Alexander J. Hartemink (2006), "Informative priors based on transcription factor structural class improve de novo motif discovery", Bioinformatics, 22:e384-e392.
    [abstract]

  78. Patrick Ng, Niranjan Nagarajan, Neil Jones, and Uri Keich (2006), "Apples to apples: improving the performance of motif finders and their significance analysis in the Twilight Zone", Bioinformatics, 22:e393-e401.
    [abstract]

  79. alternative-splicing
    Seung-Jae Noh, Kyooyeol Lee, Hyojung Paik, and Cheol-Goo Hur (2006), "TISA: tissue-specific alternative splicing in human and mouse genes", DNA Research, 13:229-243.
    [abstract]

  80. Brian Oliver (2006), "Tiling DNA microarrays for fly genome cartography" (news and views), Nature Genetics, 38:1101-1102.
    [PDF]

  81. annotation
    Debnath Pal (2006), "On gene ontology and function annotation" Bioinformation, 1(3): 97-98.
    [abstract]

  82. expression
    Q Pan, AL Saltzman, YK Kim, C Misquitta, O Shai, LE Maquat, BJ Frey, BJ Blencowe (2006), "Quantitative microarray profiling provides evidence against widespread coupling of alternative splicing with nonsense-mediated mRNA decay to control gene expression", Genes and Development, 20(2):153-158.

  83. similarity
    Bradford C Powell, Clyde A Hutchison III (2006), "Similarity-based gene detection: using COGs to find evolutionarily-conserved ORFs", BMC Bioinformatics, 7:31.
    [abstract]

  84. promoter/TF
    Shyam Prabhakar, Francis Poulin, Malak Shoukry, Veena Afzal, Edward M. Rubin, Olivier Couronne, and Len A. Pennacchio (2006), "Close sequence comparisons are sufficient to identify human cis-regulatory elements", Genome Research, 16(7):855-863.
    [abstract]

  85. promoter/TF
    Jiang Qian, Jimmy Lin and Donald J. Zack (2006), "Characterization of binding sites of eukaryotic transcription factors", Genomics, Proteomics & Bioinformatics, 4(3):67-79.
    [abstract ]

  86. D. Ashok Reddy and Chanchal K. Mitra (2006), "Comparative analysis of transcription start sites using mutual information", Genomics, Proteomics & Bioinformatics, 4(3):189-195.
    [abstract ]

  87. promoter/TF
    DA Reddya, BVL Prasadb, Chanchal K Mitra (2006), "Comparative analysis of core promoter region: Information content from mono and dinucleotide substitution matrices", Computational Biology and Chemistry, 30(1):58-62.

  88. annotation
    Jennifer L. Reed, Iman Famili, Ines Thiele and Bernhard O. Palsson (2006) "Towards multidimensional genome annotation", Nature Reviews Genetics, 7(2):130-141.
    [abstract]

  89. annotation
    Jennifer L. Reed, Trina R. Patel, Keri H. Chen, Andrew R. Joyce, Margaret K. Applebee, Christopher D. Herring, Olivia T. Bui, Eric M. Knight, Stephen S. Fong, and Bernhard O. Palsson (2006), "Systems approach to refining genome annotation", Proceedings of National Academy of Sciences, 103:17480-17484.

  90. splicing
    Scott William Roy and Walter Gilbert (2006), "The evolution of spliceosomal introns: patterns, puzzles and progress", Nature Reviews Genetics, 7(3):211-221.
    [abstract]

  91. Chiara Sabatti and Gareth M. James (2006), "Bayesian sparse hidden components analysis for transcription regulation networks", Bioinformatics, 22(6):739-746.
    [abstract]

  92. Manoj P. Samanta, Waraporn Tongprasit, Sorin Istrail, R. Andrew Cameron, Qiang Tu, Eric H. Davidson, and Viktor Stolc (2006), "The transcriptome of the sea urchin embryo", Science, 314:960-962.

  93. expression
    Guido Sanguinetti, Neil D. Lawrence, and Magnus Rattray (2006), "Probabilistic inference of transcription factor concentrations and gene-specific regulatory activities", Bioinformatics, 22(22):2775-2781.
    [abstract]

  94. expression
    Guido Sanguinetti, Magnus Rattray, and Neil D. Lawrence (2006), "A probabilistic dynamical model for quantitative inference of the regulatory mechanism of transcription", Bioinformatics, 22(14):1753-1759.
    [abstract]

  95. Michael Seringhaus, Alberto Paccanaro, Anthony Borneman, Michael Snyder, and Mark Gerstein (2006), "Predicting essential genes in fungal genomes", Genome Research, 16(9):1126-1135.
    [abstract]

  96. alternative-splicing
    Parantu K. Shah and Peer Bork (2006), "LSAT: learning about alternative transcripts in MEDLINE", Bioinformatics, 22:857-865.
    [abstract]

  97. expression
    alternative-splicing
    O Shai, QD Morris, BJ Blencowe, BJ Frey (2006), "Inferring global levels of alternative splicing isoforms using a generative model of microarray data", Bioinformatics, 22(5):606-613.
    [abstract]

  98. Xiang Shao, Valery Shepelev, and Alexei Fedorov (2006), "Bioinformatic analysis of exon repetition, exon scrambling and trans-splicing in humans", Bioinformatics, 22(6): 692-698.
    [abstract]

  99. promoter/TF
    Alexei A. Sharov, Dawood B. Dudekula, and Minoru S. H. Ko (2006) "CisView: a browser and database of cis-regulatory modules predicted in the mouse genome", DNA Research, 13:123-134.
    [abstract]

  100. Valery Shepelev and Alexei Fedorov (2006), "Advances in the Exon?Intron Database (EID)", Briefings in Bioinformatics, 7:178-185.
    [abstract]

  101. Sören Sonnenburg, Alexander Zien, and Gunnar Rätsch (2006), "ARTS: accurate recognition of transcription starts in human", Bioinformatics, 22:e472-e480.
    [abstract]

  102. Richelle Sopko and Brenda Andrews (2006), "Small open reading frames: Not so small anymore", Genome Research, 16(3):314-315.
    [abstract]

  103. Mario Stanke, Oliver Schöffmann, Burkhard Morgenstern, Stephan Waack (2006), "Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources", BMC Bioinformatics, 7:62.
    [abstract]

  104. promoter/TF
    Gang Su, Binchen Mao, Jin Wang (2006), "A web server for transcription factor binding site prediction", Bioinformation, 1(5): 156-157.
    [abstract]

  105. alternative-splicing
    Zhixi Su, Jianmin Wang, Jun Yu, Xiaoqiu Huang, and Xun Gu (2006), "Evolution of alternative splicing after gene duplication", Genome Research, 16(2):182-189.
    [abstract]

  106. Amos Tanay (2006), "Extensive low-affinity transcriptional interactions in the yeast genome", Genome Research, 16(8):962-972.
    [abstract]

  107. translation
    Maike Tech, Peter Meinicke (2006), "An unsupervised classification scheme for improving predictions of prokaryotic TIS", BMC Bioinformatics, 7:121.
    [abstract]

  108. alternative-splicing
    Gilbert Thill, Vanina Castelli, Sophie Pallud, Marcel Salanoubat, Patrick Wincker, Pierre de la Grange, Didier Auboeuf, Vincent Schächter, and Jean Weissenbach (2006), "ASEtrap: A biological method for speeding up the exploration of spliceomes", Genome Research, 16(6):776-786.
    [abstract]

  109. Suhas Tikole, Ramasubbu Sankararamakrishnan (2006), "A survey of mRNA sequences with a Non-AUG start codon in RefSeq database", Journal of Biomolecular Structure and Dynamics 24(1):33-42.
    [abstract]

  110. promoter/TF
    Huai-Kuang Tsai, Grace Tzu-Wei Huang, Meng-Yuan Chou, Henry Horng-Shing Lu, and Wen-Hsiung Li (2006), "Method for identifying transcription factor binding sites in yeast", Bioinformatics, 22(14):1675-1681.
    [abstract]

  111. Marijke J van Baren, Michael R Brent (2006), "Iterative gene prediction and pseudogene removal improves genome annotation", Genome Research, 16(5):678-685.
    [abstract]

  112. Mireia Vilardell and Alex Sánchez-Pla (2006), "Hypothesis testing approaches to the exon prediction problem", Bioinformatics, 22(24):3003-3008.
    [abstract]

  113. Chunlin Wang, Chris Ding, Richard F. Meraz, and Stephen R. Holbrook (2006), "PSoL: a positive sample only learning algorithm for finding non-coding RNA genes", Bioinformatics, 22(21):2590-2596.
    [abstract]

  114. promoter/TF
    Yu Wang, Tobias Hindemitt, and Klaus F. X. Mayer (2006), "Significant sequence similarities in promoters and precursors of Arabidopsis thaliana non-conserved microRNAs", Bioinformatics, 22(21):2585-2589.
    [abstract]

  115. promoter/TF
    Zhi Wei and Shane T. Jensen (2006), "GAME: detecting cis-regulatory elements using a genetic algorithm", Bioinformatics, 22(13):1577-1584.
    [abstract]

  116. expression
    Adriano V. Werhli, Marco Grzegorczyk, and Dirk Husmeier (2006), "Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks", Bioinformatics, 22(20):2523-2531.
    [abstract]

  117. similarity
    Jing Wu, David Haussler (2006), "Coding exon detection using comparative sequences", Journal of Computational Biology, 13(6):1148-1164.
    [abstract]

  118. promoter/TF
    Xudong Xie, Shuanhu Wu, Kin-Man Lam, and Hong Yan (2006), "PromoterExplorer: an effective promoter identification method based on the AdaBoost algorithm", Bioinformatics, 22(22):2722-2728.
    [abstract]

  119. alternative-splicing
    Yi Xing and Christopher Lee (2006), "Alternative splicing and RNA selection pressure ? evolutionary consequences for eukaryotic genomes", Nature Reviews Genetics, 7(7):499-509.
    [abstract]

  120. Malik Yousef, Michael Nebozhyn, Hagit Shatkay, Stathis Kanterakis, Louise C. Showe, and Michael K. Showe (2006), "Combining multi-species genomic data for microRNA identification using a Naïve Bayes classifier", Bioinformatics, 22(11):1325-1334.
    [abstract]

  121. promoter/TF
    Guo-qing Zhang, Zhi-wei Cao, Qing-ming Luo, Yu-dong Cai (2006), "Operon prediction based on SVM", Computational Biology and Chemistry, 30(3):233-240.
    [abstract ]

  122. Jiexin Zhang, Li Zhang, and Kevin R. Coombes (2006), "Gene sequence signatures revealed by mining the UniGene affiliation network", Bioinformatics, 22(4):385-391.
    [abstract]

  123. similarity
    splicing
    Miao Zhang, and Warren Gish (2006), "Improved spliced alignment from an information theoretic approach", Bioinformatics, 22(1):13-20.
    [abstract]