gene recognition papers (2007)

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2007

splicing

Tyler S. Alioto (2007), "U12DB: a database of orthologous U12-type spliceosomal introns", Nucleic Acids Research, 35(Database issue):D110-D115.
annotation

Irena I Artamonova, Goar Frishman, Dmitrij Frishman (2007), "Applying negative rule mining to improve genome annotation", BMC Bioinformatics, 8:261.
[abstract]
Abha Singh Bais, Steffen Grossmann, and Martin Vingron (2007), "Simultaneous alignment and annotation of cis-regulatory regions", Bioinformatics, 23:e44-e49.
[abstract]
Benjamin B Andken, In Lim, Gary Benson, John J Vincent, Matthew T Ferenc, Bianca Heinrich, Larissa A Jarzylo, Heng-Ye Man, James O Deshler (2007), "3'-UTR SIRF: A database for identifying clusters of short interspersed repeats in 3' untranslated regions", BMC Bioinformatics, 8:274.
[abstract]
Evert-Jan Blom, Dinne W. J. Bosman, Sacha A. F. T. van Hijum, Rainer Breitling, Lars Tijsma, Remko Silvis, Jos B. T. M. Roerdink, and Oscar P. Kuipers (2007), "FIVA: Functional Information Viewer and Analyzer extracting biological knowledge from transcriptome data of prokaryotes", Bioinformatics, 23:1161-1163.
[abstract]
expression

Matteo Brilli, Renato Fani, and Pietro Lió (2007), "MotifScorer: using a compendium of microarrays to identify regulatory motifs", Bioinformatics, 23:493-495.
[abstract]
Arijit Chakravarty, Jonathan M. Carlson, Radhika S. Khetani, Charles E. DeZiel, and Robert H. Gross (2007), "SPACER: identification of cis-regulatory elements with non-contiguous critical residues", Bioinformatics, 23:1029-1031.
[abstract]
promoter/TF

Arijit Chakravarty, Jonathan M Carlson, Radhika S Khetani, Robert H Gross (2007), "A novel ensemble learning method for de novo computational identification of DNA binding sites", BMC Bioinformatics, 8:249.
[abstract]
expression

Chao Cheng, Xiting Yan, Fengzhu Sun, Lei M Li (2007), "Inferring activity changes of transcription factors by binding association with sorted expression profiles", BMC Bioinformatics, 8:452.
[abstract]
promoter/TF

M Comin, L Parida (2007), "Subtle motif discovery for detection of DNA regulatory sites", Proceedings of the 5th Asia-Pacific Bioinformatics Conference eds. D Sankoff, L Wang, F Chin, pp. 27-36 (Imperial College Press, London).
S Cruveiller, O Clay, K Jabbari, G Bernardi (2007), "Simple proteomic checks for detecting noncoding RNA", Proteomics, 7(3):361-363.
promoter/TF

Marija Cvijovic, Daniel Dalevi, Elizabeth Bilsland, Graham JL Kemp, Per Sunnerhagen (2007), "Identification of putative regulatory upstream ORFs in the yeast genome using heuristics and evolutionary conservation", BMC Bioinformatics, 8:295.
[abstract]
Arthur L Delcher, Kirsten A Bratke, Edwin C Powers, and Steven L Salzberg (2007), "Identifying bacterial genes and endosymbiont DNA with Glimmer", Bioinformatics, 23:673-679.
[abstract]
Richard J. Dixon, Ian C. Eperon, and Nilesh J. Samani (2007), "Complementary intron sequence motifs associated with human exon repetition: a role for intragenic, inter-transcript interactions in gene expression", Bioinformatics, 23:150-155.
[abstract]
splicing

Rezarta Islamaj Dogan, Lise Getoor, W John Wilbur, Stephen M Mount (2007), "Features generated for computational splice-site prediction correspond to functional elements", BMC Bioinformatics, 8:410.
[abstract]
promoter/TF

Ian J. Donaldson, Berthold Göttgens (2007), "CoMoDis: composite motif discovery in mammalian genomes", a href="/j/nar.html" target=_> Nucleic Acids Research, 35(1):e1.
promoter/TF

Fathi Elloumi, Martha Nason (2007), "SEARCHPATTOOL: a new method for mining the most specific frequent patterns for binding sites with application to prokaryotic DNA sequences", BMC Bioinformatics, 8:354.
[abstract]
Christine G Elsik, Aaron J Mackey, Justin T Reese, Natalia V Milshina, David S Roos, George M Weinstock (2007), "Creating a honey bee consensus gene set", Genome Biology, 8:R13
O Emanuelsson, U Nagalakshmi, D Zheng, J S Rozowsky, A E Urban, J Du, Z Lian, V Stolc, S Weissman, M Snyder, Mark B Gerstein (2007), "Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome", Genome Research, 17(6):886-897.
[abstract]
similarity

Xiaodan Fan, Jun Zhu, Eric E Schadt, Jun S Liu (2007) "Statistical power of phylo-HMM for evolutionarily conserved element detection", BMC Bioinformatics, 8:374.
[abstract]
promoter/TF

Vincent Ferretti, Christian Poitras, Dominique Bergeron, Benoit Coulombe, François Robert, and Mathieu Blanchette (2007), "PReMod: a database of genome-wide mammalian cis-regulatory module predictions", Nucleic Acids Research, 35(Database issue): D122-D126.
annotation

Robert D Finn, James W Stalker, David K Jackson, Eugene Kulesha, Jody Clements, Roger Pettett (2007), "ProServer: A simple, extensible Perl DAS server", Bioinformatics, 23(12):1568-1570.
[abstract]
promoter/TF

Tancred Frickey and Georg Weiller (2007), "Mclip: motif detection based on cliques of gapped local profile-to-profile alignments", Bioinformatics, 23(4):502-503.
[abstract]
Wataru Fujibuchi, Tsuyoshi Kato (2007), "Classification of heterogeneous microarray data by maximum entropy kernel", BMC Bioinformatics, 8:267.
[abstract]
Masashi Fujita, Hisaaki Mihara, Susumu Goto, Nobuyoshi Esaki, Minoru Kanehisa (2007), "Mining prokaryotic genomes for unknown amino acids: a stop-codon-based approach", BMC Bioinformatics, 8:225.
[abstract]
F Gao, CT Zhang (2007), "DoriC: a database of oriC regions in bacterial genomes", Bioformatics, 23(14):1866-1867.
[abstract]
Matan Gavish, Amnon Peled, and Benny Chor (2007), "Genetic code symmetry and efficient design of GC-constrained coding sequences", Bioinformatics, 23: e57-e63.
[abstract]
Mark B. Gerstein, Can Bruce, Joel S. Rozowsky, Deyou Zheng, Jiang Du, Jan O. Korbel, Olof Emanuelsson, Zhengdong D. Zhang, Sherman Weissman, and Michael Snyder (2007) "What is a gene, post-ENCODE? History and updated definition", Genome Research, 17:669-681.
[abstract]
Thomas R. Gingeras (2007), "Origin of phenotypes: Genes and transcripts", Genome Research, 17:682-690.
[abstract]
Charles Girardot, Oleg Sklyar, Sophie Grosz, Wolfgang Huber, and Eileen E. M. Furlong (2007), "CoCo: a web application to display, store and curate ChIP-on-chip data integrated with diverse types of gene expression data", Bioinformatics, 23:771-773.
[abstract]
Srinka Ghosh, Heather A Hirsch, Edward A Sekinger, Philipp Kapranov, Kevin Struhl (2007) "Differential analysis for high density tiling microarray data", BMC Bioinformatics, 8:359.
[abstract]
annotation

Sam Griffiths-Jones (2007), "Annotating noncoding RNA genes", Annual Review of Genomics and Human Genetics, 8:279-298.
[abstract]
Snorre A. Helvik, Ola Snøve, Jr, and Pål Sætrom (2007), "Reliable prediction of Drosha processing sites improves microRNA gene prediction", Bioinformatics, 23:142-149
[abstract]
alternative-splicing

Michael Hiller, Swetlana Nikolajewa, Klaus Huse, Karol Szafranski, Philip Rosenstiel, Stefan Schuster, Rolf Backofen, and Matthias Platzer (2007), "TassDB: a database of alternative tandem splice sites", Nucleic Acids Research, 35(Database issue):D188-D192.
Ian B. Jeffery, Stephen F. Madden, Paul A. McGettigan, Guy Perrière, Aedín C. Culhane, and Desmond G. Higgins (2007), "Integrating transcription factor binding site information with gene expression datasets", Bioinformatics, 23:298-305.
[abstract]
Anil G. Jegga, Jing Chen, Sivakumar Gowrisankar, Mrunal A. Deshmukh, RangaChandra Gudivada, Sue Kong, Vivek Kaimal, and Bruce J. Aronow (2007), "GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs", Nucleic Acids Research, 35(Database issue):D116-D121.
promoter/TF

C. Jiang, Z. Xuan, F. Zhao, and M. Q. Zhang (2007), "TRED: a transcriptional regulatory element database, new entries and other development", Nucleic Acids Reseach, 35(Database issue):D137-D140.
alternative-splicing

L Kashyap, RK Sharma (2007), "Alternative splicing: a paradoxical qudo in eukaryotic genomes", Bioinformation, 2(4):155-156.
[PDF]
Jun Kawai, Piero Carninci, Yoshihide Hayashizaki (2007), "Transcriptomics resources for functional genomics", Briefings in Functional Genomics and Proteomics, 6(3):171-179.
[abstract]
alternative-splicing

Namshin Kim, Alexander V. Alekseyenko, Meenakshi Roy, and Christopher Lee (2007), "The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species", Nucleic Acids Research, 35(Database issue):D93-D98.
expression

Tae-Min Kim, Yeun-Jun Chung, Mun-Gan Rhyu, Myeong Ho Jung (2007), "Inferring biological functions and associated transcriptional regulators using gene set expression coherence analysis", BMC Bioinformatics, 8:453.
[abstract]
Keith Knapp and Yi-Ping Phoebe Chen (2007), "An evaluation of contemporary hidden Markov model genefinders with a predicted exon taxonomy", Nucleic Acids Research, 35:317-324.
promoter/TF

Nikolay A. Kolchanov, Tatyana I. Merkulova, Elena V. Ignatieva, Elena A. Ananko, Dmitry Yu. Oshchepkov, Viktor G. Levitsky, Gennady V. Vasiliev, Nataly V. Klimova, Vasily M. Merkulov, and T. Charles Hodgman (2007), "Combined experimental and computational approaches to study the regulatory elements in eukaryotic genes", Briefings in Bioinformatics, 8:266-274.
[abstract]
Lutz Krause, Alice C. McHardy, Tim W. Nattkemper, Alfred Pühler, Jens Stoye Folker Meyer (2007), "GISMO -- gene identification using a support vector machine for ORF classification", Nucleic Acids Research, 35(2):540-549.
expression

Peter Larsen, Eyad Almasri, Guanrao Chen, Yang Dai (2007), "A statistical method to incorporate biological knowledge for generating testable novel gene regulatory interactions from microarray experiments", BMC Bioinformatics, 8:317.
[abstract]
alternative-splicing

Yeunsook Lee, Younghee Lee, Bumjin Kim, Youngah Shin, Seungyoon Nam, Pora Kim, Namshin Kim, Won-Hyong Chung, Jaesang Kim, and Sanghyuk Lee (2007), "ECgene: an alternative splicing database update", Nucleic Acids Research, 35(Database issue):D99-D103.
expression

Huai Li, Yu Sun, and Ming Zhan (2007), "The discovery of transcriptional modules by a two-stage matrix decomposition approach", Bioinformatics, 23:473-479.
[abstract]
Li-Hsieh Lin, Hsiao-Ching Lee, Wen-Hsiung Li, Bor-Sen Chen (2007), "A systematic approach to detecting transcription factors in response to environmental stresses", BMC Bioinformatics, 8:473.
[abstract]
promoter/TF

Xiangdong Liu, Walter J Jessen, Siva Sivaganesan, Bruce J Aronow, Mario Medvedovic (2007), "Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP-chip data", BMC Bioinformatics, 8:283.
[abstract]
WH Majoros (2007), Methods for Computational Gene Prediction (Cambridge University Press).
http://geneprediction.org/book/
http://www.cambridge.org/catalogue/catalogue.asp?isbn=9780521706940
W Majoros, U Ohler (2007), "Spatial preferences of microRNA targets in 3' untranslated regions", BMC Genomics, 8:152.
Scott Mann, Jinyan Li, Yi-Ping Phoebe Chen (2007), "A pHMM-ANN based discriminative approach to promoter identification in prokaryote genomic contexts", Nucleic Acids Research, 35(2):e12.
Irmtraud M. Meyer (2007), "A practical guide to the art of RNA gene predictio", Briefings in Bioinformatics, 8:396-414.
[abstract]
promoter/TF

Xochitl C Morgan, Shulin Ni, Daniel P Miranker, Vishwanath R Iyer (2007), "Predicting combinatorial binding of transcription factors to regulatory elements in the human genome by association rule mining", BMC Bioinformatics, 8:445.
[abstract]
promoter/TF

Leelavati Narlikar, Raluca Gordân, Alexander J. Hartemink (2007) "A nucleosome-guided map of transcription factor binding sites in yeast", PLoS Computational Biology, 3(11):e215.
[abstract]
promoter/TF

Keith Noto and Mark Craven (2007), "Learning probabilistic models of cis-regulatory modules that represent logical and spatial aspects", Bioinformatics, 23:e156-e162.
[abstract]
promoter/TF

Mikhail Pachkov, Ionas Erb, Nacho Molina, and Erik van Nimwegen (2007), "SwissRegulon: a database of genome-wide annotations of regulatory sites", Nucleic Acids Research, 35(Database issue): D127-D131.
Dmitri Papatsenko (2007), "ClusterDraw web server: a tool to identify and visualize clusters of binding motifs for transcription factors", Bioinformatics, 23:1032-1034.
[abstract]
Laxmi Parida (2007), "Statistical significance of large gene clusters", Journal of Computational Biology, 14(9):1145-1159.
[abstract]
Shouyong Peng, Artyom A Alekseyenko, Erica Larschan, Mitzi I Kuroda, Peter J Park (2007), "Normalization and experimental design for ChIP-chip data", BMC Bioinformatics, 8:219.
[abstract]
promoter/TF

LA Pennacchio, GG Loots, MA Nobrega, I Ovcharenko (2007), "Predicting tissue-specific enhancers in the human genome", Genome Research, 17:201-211.
[abstract]
Michael Pheasant and John S. Mattick (2007), "Raising the estimate of functional human sequences", Genome Research, 17:1245-1253.
[abstract]
expression

Carmen Pin, Mark Reuter (2007), "Use of genomic DNA control features and predicted operon structure in microarray data analysis: ArrayLeaRNA - a Bayesian approach", BMC Bioinformatics, 8:455.
[abstract]
promoter/TF

Ziliang Qian, Lingyi Lu, Liu Qi, Yixue Li (2007), "An Efficient method for statistical significance calculation of transcription factor binding sites", Bioinformation, 2(5):169-174.
[PDF]
expression

Henning Redestig, Daniel Weicht, Joachim Selbig, Matthew A Hannah (2007), "Transcription factor target prediction using multiple short expression time series from Arabidopsis thaliana", BMC Bioinformatics, 8:454.
[abstract]
promoter/TF

Emma Redhead, Timothy L Bailey (2007), "Discriminative motif discovery in DNA and protein sequences using the DEME Algorithm", BMC Bioinformatics, 8:385.
[abstract]
translation

Y Saeys, T Abeel, S Degroeve, Y Van de Peer (2007), "Translation initiation site prediction on a genomic scale: beauty in simplicity", Bioinformatics, 23:418-23.
Y Saeys, Y Van de Peer (2007), "Enhancing coding potential prediction for short sequences using complementary sequence features and feature selection", Lecture Notes in Bioinformatics, 4366:107-118.
Yvan Saeys, Pierre Rouzé, and Yves Van de Peer (2007), "In search of the small ones: improved prediction of short exons in vertebrates, plants, fungi and protists", Bioinformatics, 23:414-420.
[abstract]
promoter/TF

Yuta Sakakibara, Takuma Irie, Yutaka Suzuki, Riu Yamashita, Hiroyuki Wakaguri, Akinori Kanai, Joe Chiba, Toshihisa Takagi, Junko Mizushima-Sugano, Shin-ichi Hashimoto, Kenta Nakai, and Sumio Sugano (2007), "Intrinsic promoter activities of primary DNA sequences in the human genome", DNA Research, 14:71-77.
[abstract]
annotation

Steven Salzberg (2007), "Genome re-annotation: a wiki solution?", Genome Biology, 8(1):102.
[abstract]
Giulietta Spudich, Xosé M Fernández-Suárez, Ewan Birney (2007), "Genome browsing with Ensembl: a practical overview", Briefings in Functional Genomics and Proteomics, 6(3):202-219.
[abstract]
L Sterck, S Rombauts, K Vandepoele, P Rouzé, Y Van de Peer (2007), "How many genes are there in plants (... and why are they there)?", Current Opinions on Plant Biology, 10:199-203.
alternative-splicing

Jun-ichi Takeda, Yutaka Suzuki, Mitsuteru Nakao, Tsuyoshi Kuroda, Sumio Sugano, Takashi Gojobori, and Tadashi Imanishi (2007), "H-DBAS: Alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-Invitational", Nucleic Acids Research, 35(Database issue):D104-D109.
alternative-splicing

David Talavera, Adam Hospital, Modesto Orozco, Xavier de la Cruz (2007), "A procedure for identifying homologous alternative splicing events", BMC Bioinformatics, 8:260.
[abstract]
expression

Reuben Thomas, Carlos J Paredes, Sanjay Mehrotra, Vassily Hatzimanikatis, Eleftherios T Papoutsakis (2007), "A model-based optimization framework for the inference of regulatory interactions using time-course DNA microarray expression data", BMC Bioinformatics, 8:228.
[abstract]
Joern Toedling, Oleg Sklyar, Wolfgang Huber (2007), "Ringo - an R/Bioconductor package for analyzing ChIP-chip readouts", BMC Bioinformatics, 8:221.
[abstract]
Andrija Tomovic and Edward J. Oakeley (2007), "Position dependencies in transcription factor binding sites", Bioinformatics, 23:933-941.
[abstract]
annotation

L Tripathi (2007), "Integrating information from existing databases for enhanced function annotation of genes, genomes and networks", Bioinformation, 2(4):132-134.
[PDF]
Angelica Tulipano, Giacinto Donvito, Flavio Licciulli, Giorgio Maggi, Andreas Gisel (2007), "Gene analogue finder: a GRID solution for finding functionally analogous gene products", BMC Bioinformatics, 8:329.
[abstract]
Axel Visel, Simon Minovitsky, Inna Dubchak, and Len A. Pennacchio (2007), "VISTA Enhancer Browser?a database of tissue-specific human enhancers", Nucleic Acids Research, 35 (Database issue):D88-D92.
Michael Weber, Dirk Schübeler (2007), "Genomic patterns of DNA methylation: targets and function of an epigenetic mark", Currnet Opinion in Cell Biology, 19(3):273-280.
[abstract]
expression

Randy Z Wu, Christina Chaivorapol, Jiashun Zheng, Hao Li, Shoudan Liang (2007), "fREDUCE: Detection of degenerate regulatory elements using correlation with expression", BMC Bioinformatics, 8:399.
[abstract]
promoter/TF

X Xie, S Wu, KM Lam, H Yan (2007), "An effective promoter detection method using the adaboost algorithm", Proceedings of the 5th Asia-Pacific Bioinformatics Conference eds. D Sankoff, L Wang, F Chin, pp. 37-46 (Imperial College Press, London).
Gangman Yi, Sing-Hoi Sze, and Michael R. Thon (2007) "Identifying clusters of functionally related genes in genomes", Bioinformatics, 23:1053-1060.
[abstract]
Changchuan Yin, Stephen ST Yau (2007), "Prediction of protein coding regions by the 3-base periodicity analysis of a DNA sequence", Journal of Theoretical Biology, 247:687-694.
[PDF]
promoter/TF

Xueping Yu, Jimmy Lin, Donald J Zack, Jiang Qian (2007), "Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors", BMC Bioinformatics, 8:437.
[abstract]
promoter/TF

Michael Q Zhang (2007), "Computational analyses of eukaryotic promoters", BMC Bioinformatics, 8(suppl 6):S3.
[html]
Fangcui Zhao, Huijie Yang, Binghong Wang (2007), "Complexity of human promoter sequences", Journal of Theoretical Biology, 247:645-649.
Leming Zhou, Liliana Florea (2007), "Designing sensitive and specific spaced seeds for cross-species mRNA-to-genome alignment", Journal of Computational Biology, 14(2):113-130.
[abstract]
Qi-Hui Zhu, An-Yuan Guo, Ge Gao, Ying-Fu Zhong, Meng Xu, Minren Huang, and Jinchu Luo (2007), "DPTF: a database of poplar transcription factors", Bioinformatics, 23:1307-1308.
[abstract]