Bibliography

Abul, Osman and Drabløs, Finn et al. (2006) "A Methodology for Motif Discovery Employing Iterated Cluster Re-Assignment" Comput . Syst. Bioinformatics Conf. 2006, August 14-18, 2006, Stanford University, California, USA : 257-268

Aerts, Stein and Thijs, Gert et al. (2004) "Comprehensive Analysis of the Base Composition Around the Transcription Start Site in Metazoa" BMC Genomics 5 : 34

Aerts, Stein and Van Loo, Peter et al. (2003) "Computational Detection of Cis-Regulatory Modules" Bioinformatics 19(Suppl. 2) : ii5-ii14

Aerts, Stein and Van Loo, Peter et al. (2004) "A Genetic Algorithm for the Detection of New Cis-Regulatory Modules in Sets of Coregulated Genes" Bioinformatics 20(12) : 1974-1976

Aerts, Stein and Van Loo, Peter et al. (2005) "TOUCAN 2: The All-Inclusive Open Source Workbench for Regulatory Sequence Analysis" Nucleic Acids Research 33 : W393-W396

Alkema, Wynand B and Johansson, Öjvind et al. (2004) "MSCAN: Identification of Functional Clusters of Transcription Factor Binding Sites" Nucleic Acids Research 32 : W195-W198

Allison, David B and Cui, Xiangqin et al. (2006) "Microarray Data Analysis: From Disarray to Consolidation and Consensus" Nature Reviews Genetics 7(1) : 55-65

Almeida, Jonas and Carriço, João A et al. (2001) "Analysis of Genomic Sequences by Chaos Game Representation" Bioinformatics 17(5) : 429-437

Altschul, Stephen F and Gish, Warren et al. (1990) "Basic Local Alignment Search Tool" Journal of Molecular Biology 215(3) : 403-410

Arnone, Maria I and Davidson, Eric H (1997) "The Hardwiring of Development: Organization and Function of Genomic Regulatory Systems" Development 124(10) : 1851-1864

Arthur, David and Vassilvitskii, Sergei (2007) "k-means++: The Advantages of Careful Seeding" Proc. SODA'07, January 7-9, 2007, New Orleans, Louisiana, USA : 1027-1035

Bailey, Timothy L and Bodén, Mikael et al. (2010) "The Value of Position-Specific Priors in Motif Discovery Using MEME" BMC Bioinformatics 11 : 179

Bailey, Timothy L and Elkan, Charles (1994) "Fitting a Mixture Model by Expectation Maximization to Discover Motifs in Biopolymers" Proc. 2nd Int. Conf. Intell. Syst. Mol. Biol., August 14-17, 1994, Stanford, California : 28-36

Bailey, Timothy L and Noble, William S (2003) "Searching for Statistically Significant Regulatory Modules" Bioinformatics 19(Suppl. 2) : ii16-ii25

Bajic, Vladimir B and Tan, Sin L et al. (2004) "Promoter Prediction Analysis on the Whole Human Genome" Nature Biotechnology 22(11) : 1467-1473

Barski, Artem and Cuddapah, Suresh et al. (2007) "High-Resolution Profiling of Histone Methylations in the Human Genome" Cell 129(4) : 823-827

Beiko, Robert G and Charlebois, Robert L (2005) "GANN: Genetic Algorithm Neural Networks for the Detection of Conserved Combinations of Features in DNA" BMC Bioinformatics 6 : 36

Beisvag, Vidar and Jünge, Frode K et al. (2006) "GeneTools - Application for Functional Annotation and Statistical Hypothesis Testing" BMC Bioinformatics 7 : 470

Bellora, Nicolás and Farré, Domènec et al. (2007) "PEAKS: Identification of Regulatory Motifs by their Position in DNA sequences" Bioinformatics 23(2) : 243-244

Bellora, Nicolás and Farré, Domènec et al. (2007) "Positional bias of general and tissue-specific regulatory motifs in mouse gene promoters" BMC Genomics 8 : 459

Berezikov, Eugene and Guryev, Victor et al. (2005) "CONREAL Web Server: Identification and Visualization of Conserved Transcription Factor Binding Sites" Nucleic Acids Research 33 : W447-W450

Bergman, Casey M and Carlson, Joseph W et al. (2005) "Drosophila DNase I Footprint Database: A Systematic Genome Annotation of Transcription Factor Binding Sites in the Fruitfly, Drosophila Melanogaster" Bioinformatics 21(8) : 1747-1749

Berman, Benjamin P and Nibu, Yutaka et al. (2002) "Exploiting Transcription Factor Binding Site Clustering to Identify Cis-Regulatory Modules Involved in Pattern Formation in the Drosophila Genome" Proc. Natl. Acad. Sci. USA 99(2) : 757-762

Bezdek, James C and Boggavarapu, Srinivas et al. (1994) "Genetic Algorithm Guided Clustering" Proc. 1st IEEE Conf. Evol. Comp., IEEE World Cong. Comp. Intel., June 27-29, 1994, Orlando, Florida, USA : 34-39

Bird, Adrian (1999) "DNA Methylation de Novo" Science 286(5448) : 2287-2288

Birney, Ewan and Andrews, T. Daniel et al. (2004) "An Overview of Ensembl" Genome Research 14(5) : 925-928

Blanchette, Mathieu and Sinha, Saurabh (2001) "Separating Real Motifs From Their Artifacts" Bioinformatics 17(Suppl) : S30-S38

Blanchette, Mathieu and Tompa, Martin (2003) "FootPrinter: A Program Designed for Phylogenetic Footprinting" Nucleic Acids Research 31(13) : 3840-3842

Blanco, Enrique and Farré, Domènec et al. (2006) "ABS: A Database of Annotated Regulatory Binding Sites from Orthologous Promoters" Nucleic Acids Research 34(Database issue) : D63-D67

Blanco, Enrique and Messeguer, Xavier et al. (2006) "Transcription Factor Map Alignment of Promoter Regions" PLoS Computational Biology 2(5) : 403-416

Boardman, Paul E and Oliver, Stephen G et al. (2003) "SiteSeer: Visualisation and Analysis of Transcription Factor Binding Sites in Nucleotide Sequences" Nucleic Acids Research 31(13) : 3572-3575

Bodén, Mikael and Bailey, Timothy L (2008) "Associating Transcription Factor-Binding Site Motifs With Target GO Terms and Target Genes" Nucleic Acids Research 36(12) : 4108-4117

Boehr, David D and Wright, Peter E (2008) "How Do Proteins Interact?" Science 320(5882) : 1429-1430

Boffelli, Dario and McAuliffe, Jon et al. (2003) "Phylogenetic shadowing of primate sequences to find functional regions of the human genome" Science 299(5611) : 1391-1394

Boutin, François and Hascoët, Mountaz (2004) "Cluster Validity Indices for Graph Partitioning" Proc. IV2004, July 14-16, 2004, London, UK : 376-381

Boyle, Alan P and Song, Lingyun et al. (2011) "High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells" Genome Research 21(3) : 456-464

Brazma, Alvis and Hingamp, Pascal et al. (2001) "Minimum Information about a Microarray Experiment (MIAME)-Toward Standards for Microarray Data" Nature Genetics 29(4) : 365-371

Brazma, Alvis and Parkinson, Helen et al. (2003) "ArrayExpress — A Public Repository for Microarray Gene Expression Data at the EBI" Nucleic Acids Research 31(1) : 68-71

Britten, Roy J (1996) "Cases of Ancient Mobile Element DNA Insertions That Now Affect Gene Regulation" Mol. Phylogenet. Evol. 5(1) : 13-17

Brown, Christopher D and Johnson, David S et al. (2007) "Functional Architecture and Evolution of Transcriptional Elements That Drive Gene Coexpression" Science 317(5844) : 1557-1560

Brun, Marcel and Sima, Chao et al. (2007) "Model-Based Evaluation of Clustering Validation Measures" Pattern Recognition 40(3) : 807-824

Buck, Michael J and Lieb, Jason D (2004) "ChIP-chip: Considerations for the Design, Analysis, and Application of Genome-Wide Chromatin Immunoprecipitation Experiments" Genomics 83(3) : 349-360

Bulyk, Martha L (2003) "Computational Prediction of Transcription-Factor binding Site Locations" Genome Biology 5 : 201

Burset, Moisès and Guigó, Roderic (1996) "Evaluation of Gene Structure Prediction Programs" Genomics 34(3) : 353-367

Bussemaker, Harmen J and Li, Hao et al. (2000) "Building a Dictionary for Genomes: Identification of Presumptive Regulatory Sites by Statistical Analysis" Prog. Nucleic Acid Res. Mol. Biol. 97(18) : 10096-10100

Bussemaker, Harmen J and Li, Hao et al. (2001) "Regulatory element detection using correlation with expression" Nature Genetics 27(2) : 167-171

Camon, Evelyn and Magrane, Michele et al. (2004) "The Gene Ontology Annotation (GOA) Database: Sharing Knowledge in Uniprot with Gene Ontology" Nucleic Acids Research 32 : D262-D266

Capelson, Maya and Corces, Victor G (2004) "Boundary elements and nuclear organization" Biology of the Cell 96(8) : 617-629

Carlson, Jonathan M and Chakravarty, Arijit et al. (2007) "SCOPE: A Web Server for Practical De Novo Motif Discovery" Nucleic Acids Research 35(Web Server issue) : W259-W264

Carninci, Piero and Sandelin, Albin et al. (2006) "Genome-Wide Analysis of Mammalian Promoter Architecture and Evolution" Nature Genetics 38(6) : 626-635

Carvalho, Alexandra M and Oliveira, Arlindo L (2011) "GRISOTTO: A greedy approach to improve combinatorial algorithms for motif discovery with prior knowledge" Algorithms for Molecular Biology 6 : 13

Casimiro, Ana C and Vinga, Susana et al. (2008) "An Analysis of the Positional Distribution of DNA Motifs in Promoter Regions and its Biological Relevance" BMC Bioinformatics 9 : 89

Chakravarty, Arijit and Carlson, Jonathan M et al. (2007) "A Novel Ensemble Learning Method for De Novo Computational Identification of DNA Binding Sites" BMC Bioinformatics 8 : 249

Chan, Bob Y and Kibler, Dennis (2005) "Using Hexamers to Predict Cis-Regulatory Motifs in Drosophila" BMC Bioinformatics 6 : 262

Che, Dongsheng and Jensen, Shane T et al. (2005) "BEST: Binding-site Estimation Suite of Tools" Bioinformatics 21(12) : 2909-2911

Che, Dongsheng and Song, Yinglei et al. (2005) "MDGA: Motif Discovery Using A Genetic Algorithm" Proc. GECCO'05, June 25-29, 2005, Washington D.C., USA : 447-452

Chen, Xin and Wu, Jian-min et al. (2006) "TiProD: The Tissue-Specific Promoter Database" Nucleic Acids Research 34 : D104-D107

Chenna, Ramu and Sugawara, Hideaki et al. (2003) "Multiple Sequence Alignment with the Clustal Series of Progams" Nucleic Acids Research 31(13) : 3497-3500

Choi, Jung K and Kim, Young-Joon (2008) "Epigenetic Regulation and the Variability of Gene Expression" Nature Genetics 40(2) : 141-147

Clarke, Neil D and Granek, Joshua A (2003) "Rank Order Metrics for Quantifying the Association of Sequence Features with Gene Regulation" Bioinformatics 19(2) : 212-218

Claverie, Jean-Michel and Audic, Stéphane (1996) "The Statistical Significance of Nucleotide Position-Weight Matrix Matches" Comput. Appl. Biosci. 12(5) : 431-439

Conlon, Erin M and Liu, Xiaole S et al. (2003) "Integrating Regulatory Motif Discovery and Genome-Wide Expression Analysis" Proc. Natl. Acad. Sci. USA 100(6) : 3339-3344

Corcoran, David L and Feingold, Eleanor et al. (2005) "FOOTER: A Web Tool for Finding Mammalian DNA Regulatory Regions Using Phylogenetic Footprinting" Nucleic Acids Research 33 : W442-W446

Cornish-Bowden, Athel (1985) "Nomenclature for Incompletely Specified bases in Nucleic Acid Sequences: Recommendations 1984" Nucleic Acids Research 13(9) : 3021-3030

Coward, Eivind (1999) "Shufflet: Shuffling Sequences While Conserving the k-let Counts" Bioinformatics 15(12) : 1058-1059

Crawford, Gregory E and Davis, Sean et al. (2006) "DNase-chip: A High-Resolution Method to Identify DNase I Hypersensitive Sites Using Tiled Microarrays." Nature Methods 3(7) : 503-509

Crawford, Gregory E and Holt, Ingeborg E et al. (2004) "Identifying Gene Regulatory Elements by Genome-Wide Recovery of DNase Hypersensitive Sites" Proc. Natl. Acad. Sci. USA 101(4) : 992-997

Crawford, Gregory E and Holt, Ingeborg E et al. (2006) "Genome-Wide Mapping of DNase Hypersensitive Sites Using Massively Parallel Signature Sequencing (MPSS)" Genome Research 16(1) : 123-131

Cucchiara, Rita (1998) "Genetic Algorithms for Clustering in Machine Vision" Machine Vision and Applications 11(1) : 1-6

D'haeseleer, Patrik (2005) "How Does Gene Expression Clustering Work?" Nature Biotechnology 23(12) : 1499-1501

D'haeseleer, Patrik (2006) "How Does DNA Sequence Motif Discovery Work?" Nature Biotechnology 24(8) : 959-961

D'haeseleer, Patrik (2006) "What Are DNA Sequence Motifs?" Nature Biotechnology 24(4) : 423-425

Daenen, Floris and van Roy, Frans et al. (2008) "Low nucleosome occupancy is encoded around functional human transcription factor binding sites" BMC Genomics 9 : 332

Dagan, Tal and Sorek, Rotem et al. (2004) "AluGene: A Database of Alu Elements Incorporated Within Protein-Coding Genes" Nucleic Acids Research 32 : D489-D492

Davidson, Eric H and Rast, Jonathan P et al. (2002) "A Genomic Regulatory Network for Development" Science 295(5560) : 1669-1678

de Lichtenberg, Ulrik and Jensen, Lars J et al. (2005) "Dynamic Complex Formation During the Yeast Cell Cycle" Science 307(5710) : 724-727

De Rasmo, Domenico and Signorile, Anna et al. (2010) "cAMP/Ca2+ response element-binding protein plays a central role in the biogenesis of respiratory chain proteins in mammalian cells" IUBMB Life 62(6) : 447-452

Di Cara, Alessandro and Schmidt, Karsten et al. (2005) "PromoterPlot: A Graphical Display of Promoter Similarities by Pattern Recognition" Nucleic Acids Research 33 : W423-W426

Doh, Sung T and Zhang, Yunyu et al. (2007) "Non-Coding Sequence Retrieval System for Comparative Genomic Analysis of Gene Regulatory Elements" BMC Bioinformatics 8 : 94

Donaldson, Ian J and Göttgens, Berthold (2006) "CoMoDis: Composite Motif Discovery in Mammalian Genomes" Nucleic Acids Research 35(1) : e1

Donaldson, Ian J and Göttgens, Berthold (2006) "TFBScluster Web Server for the Identification of Mammalian Composite Regulatory Elements" Nucleic Acids Research 34(Web Server issue) : W524-W528

Dowell, Robin D and Jokerst, Rodney M et al. (2001) "The Distributed Annotation System" BMC Bioinformatics 2 : 7

Down, Thomas and Leong, Bernard et al. (2006) "A Machine Learning Strategy to Identify Candidate Binding Sites in Human Protein-Coding Sequence" BMC Bioinformatics 7 : 419

Down, Thomas and Piipari, Matias et al. (2011) "Dalliance: interactive genome viewing on the web" Bioinformatics 27(6) : 889-890

Duret, Laurent and Bucher, Philipp (1997) "Searching for Regulatory Elements in Human Noncoding Sequences" Curr. Opin. Struct. Biol. 7(3) : 399-406

Eckhardt, Florian and Lewin, Joern et al. (2006) "DNA Methylation Profiling of Human Chromosomes 6, 20 and 22" Nature Genetics 38(12) : 1378-1384

Elnitski, Laura and Hardison, Ross C et al. (2003) "Distinguishing Regulatory DNA From Neutral Sites" Genome Research 13(1) : 64-72

Ercan, Sevinc and Lieb, Jason D (2006) "New Evidence That DNA Encodes Its Packaging" Nature Genetics 38(10) : 1104-1105

Ernst, Jason and Kellis, Manolis (2010) "Discovery and characterization of chromatin states for systematic annotation of the human genome" Nature Biotechnology 28(8) : 817-825

Ernst, Jason and Kheradpour, Pouya et al. (2011) "Mapping and analysis of chromatin state dynamics in nine human cell types" Nature 473(7345) : 43-49

Ernst, Jason and Plasterer, Heather L et al. (2010) "Integrating multiple evidence sources to predict transcription factor binding in the human genome" Genome Research 24(4) : 526-536

Errami, Mounir and Wren, Jonathan D et al. (2007) "eTBLAST: A Web Server to Identify Expert Reviewers, Appropriate Journals and Similar Publications" Nucleic Acids Research 35(Web Server issue) : W12-W15

Ettwiller, Laurence and Paten, Benedict et al. (2007) "Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation" Nature Methods 4(7) : 563-565

Eyre, Tina A and Ducluzeau, Fabrice et al. (2006) "The HUGO Gene Nomenclature Database, 2006 Updates" Nucleic Acids Research 34 : D319-D321

Farré, Domènec and Roset, Romà et al. (2003) "Identification of Patterns in Biological Sequences at the ALGGEN server: PROMO and MALGEN" Nucleic Acids Research 31(13) : 3651-3653

Fenstad, Mona H and Johnson, Matthew P et al. (2010) "Genetic and molecular functional characterization of variants within TNFSF13B, a positional candidate preeclampsia susceptibility gene on 13q" PLoS One 5(9) : e12993

Ferretti, Vincent and Poitras, Christian et al. (2007) "PReMod: A Database of Genome-Wide Mammalian Cis-Regulatory Module Predictions" Nucleic Acids Research 35(Database issue) : D122-D126

Feschotte, Cédric (2008) "Transposable Elements and the Evolution of Regulatory Networks" Nature Reviews Genetics 9(5) : 397-405

Finn, Robert D and Stalker, James et al. (2007) "ProServer: A Simple, Extensible Perl DAS Server" Bioinformatics 23(12) : 1568-1570

FitzGerald, Peter C and Shlyakhtenko, Andrey et al. (2004) "Clustering of DNA Sequences in Human Promotors" Genome Research 14(8) : 1562-1574

Floratos, Aris and Smith, Kenneth et al. (2010) "geWorkbench: an open source platform for integrative genomics" Bioinformatics 26(14) : 1779-1780

Florquin, Kobe and Saeys, Yvan et al. (2005) "Large-Scale Structural Analysis of the Core Promoter in Mammalian and Plant Genomes" Nucleic Acids Research 33(13) : 4255-4264

Fogel, Gary B and Weekes, Dana G et al. (2004) "Discovery of Sequence Motifs related to Coexpression of Genes Using Evolutionary Computation" Nucleic Acids Research 32(13) : 3826-3835

Fogel, Gary B and Weekes, Dana G et al. (2005) "A Statistical Analysis of the TRANSFAC Database" Biosystems 81(2) : 137-154

Fox, Joanne A and Butland, Stefanie L et al. (2005) "The Bioinformatics Links Directory: a Compilation of Molecular Biology Web Servers" Nucleic Acids Research 33(Web Server issue) : W3-W24

Frank, Eibe and Hall, Mark et al. (2004) "Data Mining in Bioinformatics Using Weka" Bioinformatics 20(15) : 2479-2481

Frech, Kornelie and Danescu-Mayer, Joana et al. (1997) "A Novel Method to Develop Highly Specific Models for Regulatory Units Detects a New LTR in GenBank which Contains a Functional Promoter" Journal of Molecular Biology 270(5) : 674-687

Frech, Kornelie and Quandt, Kerstin et al. (1997) "Finding Protein-Binding Sites in DNA Sequences: The Next Generation" Trends in Biochemical Sciences 22(3) : 103-104

Frith, Martin C and Fu, Yutao et al. (2004) "Detection of Functional DNA Motifs via Statistical Over-Representation" Nucleic Acids Research 32(4) : 1372-1381

Frith, Martin C and Hansen, Ulla et al. (2001) "Detection of Cis-Element Clusters in Higher Eukaryotic DNA" Bioinformatics 17(10) : 878-889

Frith, Martin C and Li, Michael C et al. (2003) "Cluster-Buster: Finding dense clusters of motifs in DNA sequences" Nucleic Acids Research 31(13) : 3666-3668

Frith, Martin C and Spouge, John L et al. (2002) "Statistical Significance of Clusters of Motifs Represented by Position Specific Scoring Matrices in Nucleotide Sequences" Nucleic Acids Research 30(14) : 3214-3224

Fu, Yutao and Frith, Martin C et al. (2004) "MotifViz: An Analysis and Visualization Tool for Motif Discovery" Nucleic Acids Research 32 : W420-W423

Fu, Yutao and Sinha, Manisha et al. (2008) "The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome" PLoS Genetics 4(7) : e1000138

Galas, David J and Schmitz, Albert (1978) "DNAse footprinting: a simple method for the detection of protein-DNA binding specificity" Nucleic Acids Research 5(9) : 3157-3170

Gallo, Steven M and Li, Long et al. (2006) "REDfly: a Regulatory Element Database for Drosophila" Bioinformatics 22(3) : 381-383

Gao, Feng and Foat, Barrett C et al. (2004) "Defining Transcriptional Networks Through Integrative Modeling of mRNA Expression and Transcription Factor Binding Data" BMC Bioinformatics 5 : 31

Gao, Ge and Zhong, Yingfu et al. (2006) "DRTF: A Database of Rice Transcription Factors" Bioinformatics 22(10) : 1286-1287

Ge, Hui and Walhout, Albertha J et al. (2003) "Integrating 'omic' Information: A Bridge Between Genomics and Systems Biology." Trends in Genetics 19(10) : 551-560

Gene Ontology Consortium (2004) "The Gene Ontology (GO) Database and Informatics Resource" Nucleic Acids Research 32 : D258-D261

Gentleman, Jane F and Mullin, Ronald C (1989) "The Distribution of the Frequency of Occurrence of Nucleotide Subsequences, Based on Their Overlap Capability" Biometrics 45 : 35-52

Gerstein, Mark and Bruce, Can et al. (2007) "What is a gene, post-ENCODE? History and updated definition" Genome Research 17(6) : 669-681

Gilbert, Walter (1978) "Why genes in pieces?" Nature 271(9) : 501

Ginalski, Krzysztof and Elofsson, Arne et al. (2003) "3D-Jury: A Simple Approach to Improce Protein Structure Predictions" Bioinformatics 19(8) : 1015-1018

Gordân, Raluca and Hartemink, Alexander (2008) "Using DNA duplex stability information for transcription factor binding site discovery" Proc. PSB, January 4-8, 2008, Kohala Coast, Hawaii, USA

Gordân, Raluca and Narlikar, Leelavati et al. (2008) "A Fast, Alignment-Free, Conservation-Based Method for Transcription Factor Binding Site Discovery" Proc. 12th Annual Int. Conf. on Computational Biology, March 30-April 2, 2008, Singapore : 98-111

Gordon, D. Benjamin and Nekludova, Lena et al. (2005) "TAMO: A Flexible, Object-Oriented Framework for Analyzing Transcriptional Regulation Using DNA-Sequence Motifs" Bioinformatics 21(14) : 3164-3165

Grant, Charles E and Bailey, Timothy L et al. (2011) "FIMO: scanning for occurrences of a given motif" Bioinformatics 27(7) : 1017-1018

Grover, Deepak and Mukerji, Mitali et al. (2004) "Alu Repeat Analysis in the Complete Human Genome: Trends and Variations with Respect to Genomic Composition" Bioinformatics 20(6) : 813-817

Guelen, Lars and Pagie, Ludo et al. (2008) "Domain Organization of Human Chromosomes Revealed by Mapping of Nuclear Lamina Interactions" Nature 453(7197) : 948-951

GuhaThakurta, Debraj and Stormo, Gary D (2001) "Identifying Target Sites for Cooperatively Binding Factors" Bioinformatics 17(7) : 608-621

Gupta, Mayetri and Liu, Jun S (2005) "De Novo Cis-Regulatory Module Elicitation for Eukaryotic Genomes" Proc. Natl. Acad. Sci. USA 102(20) : 7079-7084

Gupta, Shobhit and Stamatoyannopoulos, John A et al. (2007) "Quantifying similarity between motifs" Genome Biology 8(2) : R24

Halfon, Marc S (2006) "(Re)modeling the Transcriptional Enhancer" Nature Genetics 38(10) : 1102-1103

Halfon, Marc S and Gallo, Steven M et al. (2008) "REDfly 2.0: An Integrated Database of Cis-Regulatory Modules and Transcription Factor Binding Sites in Drosophila" Nucleic Acids Research 36 : D594-D598

Hannenhalli, Sridhar (2008) "Eukaryotic Transcription Factor Binding Sites - Modeling and Integrative Search Methods" Bioinformatics 24(11) : 1325-1331

Hannenhalli, Sridhar and Levy, Samuel (2001) "Promoter Prediction in the Human Genome" Bioinformatics 17(Suppl) : S90-S96

Harbison, Christopher T and Gordon, D. Benjamin et al. (2004) "Transcriptional Regulatory Code of a Eukaryotic Genome" Nature 431 : 99-104

Hardison, Ross C (2000) "Conserved Noncoding Sequences are Reliable Guides to Regulatory Elements" Trends in Genetics 16(9) : 369-372

Harris, Timothy D and Buzby, Phillip R et al. (2008) "Single-Molecule DNA Sequencing of a Viral Genome" Science 320(5872) : 106-109

Hartmann, Oliver (2005) "Quality Control for Microarray Experiments" Methods Inf. Med. 44(3) : 408-413

Haverty, Peter M and Weng, Zhiping (2004) "CisML: An XML-Based Format for Sequence Motif Detection Software" Bioinformatics 20(11) : 1815-1817

Heintzman, Nathaniel D and Hon, Gary et al. (2009) "Histone modifications at human enhancers reflect global cell-type-specific gene expression" Nature 459(7243) : 108-112

Heintzman, Nathaniel D and Stuart, Rhona K et al. (2007) "Distinct and Predictive Chromatin Signatures of Transcriptional Promoters and Enhancers in the Human Genome" Nature Genetics 39(3) : 311-318

Hermoso, Antoni and Aguilar, Daniel et al. (2004) "TrSDB: A Proteome Database of Transcription Factors" Nucleic Acids Research 32 : D171-D173

Hesselberth, Jay R and Chen, Xiaoyu et al. (2009) "Global mapping of protein-DNA interactions in vivo by digital genomic footprinting" Nature Methods 6(4) : 283-289

Hindemitt, Tobias and Mayer, Klaus F (2005) "CREDO: A Web-based Tool for Computational Detection of Conserved Sequence Motifs in Noncoding Sequences" Bioinformatics 21(23) : 4304-4306

Hinnebusch, Alan G and Lucchini, Giovanna et al. (1985) "A Synthetic HIS4 Regulatory Element Confers General Amino Acid Control on the Cytochrome c Gene (CYC1) of Yeast" Proc. Natl. Acad. Sci. USA 82(2) : 498-502

Holland, Richard C and Down, Thomas et al. (2008) "BioJava: An Open-Souce Framework for Bioinformatics" Bioinformatics 24(18) : 2096-2097

Homann, Oliver R and Johnson, Alexander D (2010) "MochiView: versatile software for genome browsing and DNA motif analysis" BMC Biology 8 : 49

Hon, Lawrence S and Jain, Ajay N (2003) "Compositional Structure of Repetitive Elements is Quantitatively Related to Co-expression of Gene Pairs" Journal of Molecular Biology 332(2) : 305-310

Ho Sui, Shannan J and Fulton, Debra L et al. (2007) "oPOSSUM: integrated tools for analysis of regulatory motif over-representation" Nucleic Acids Research 35(Web Server issue) : W245-W252

Howard, Daniel and Benson, Karl (2003) "Evolutionary Computation Method for Pattern Recognition of Cis-Acting Sites" Biosystems 72(1-2) : 19-27

Hsu, Chih-Wei and Chang, Chih-Chung et al. (2001) "A Practical Guide to Support Vector Classification" Department of Computer Science and Information Engineering, National University of Taiwan. Taipei, Taiwan.

Hu, Jianjun and Li, Bin et al. (2005) "Limitations and Potentials of Current Motif Discovery Algorithms" Nucleic Acids Research 33(15) : 4899-4913

Hu, Jianjun and Yang, Yifeng D et al. (2006) "EMD: An Ensemble Algorithm for Discovering Regulatory Motifs in DNA Sequences" BMC Bioinformatics 7 : 342

Hu, Yuh-Jyh and Sandmeyer, Suzanne et al. (2000) "Combinatorial Motif Analysis and Hypothesis Generation on Genomic Scale" Bioinformatics 16(3) : 222-232

Hu, Zhenjun and Frith, Martin C et al. (2003) "SeqVISTA: a graphical tool for sequence feature visualization and comparison" BMC Bioinformatics 4 : 1

Hu, Zhenjun and Fu, Yutao et al. (2004) "SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation" Nucleic Acids Research 32(Web Server Issue) : W235-W241

Huber, Bertrand R and Bulyk, Martha L (2006) "Meta-Analysis Discovery of Tissue-Specific DNA Sequence Motifs from Mammalian Gene Expression Data" BMC Bioinformatics 7 : 229

Hubert, Lawrence and Arabie, Phipps (1985) "Comparing Partitions" Journal of Classification 2 : 193-218

Hull, Duncan and Wolstencroft, Katy et al. (2006) "Taverna: A Tool for Building and Running Workflows of Services." Nucleic Acids Research 34(Web Server Issue) : W729-W732

Ideker, Trey and Thorsson, Vesteinn et al. (2001) "Integrated Genomic and Proteomic Analyses of A Systematically Perturbed Metabolic Network" Science 292(5518) : 929-934

Ioshikhes, Ilya P and Albert, Istvan et al. (2006) "Nucleosome Positions Predicted Through Comparative Genomics" Nature Genetics 38(10) : 1210-1215

Ioshikhes, Ilya P and Bolshoy, Alex et al. (1996) "Nucleosome DNA Sequence Pattern Revealed by Multiple Alignment of Experimentally Mapped Sequences" Journal of Molecular Biology 262(2) : 129-139

Ioshikhes, Ilya P and Trifonov, Edward N (1993) "Nucleosomal DNA Sequence Database" Nucleic Acids Research 21(21) : 4857-4859

Ioshikhes, Ilya P and Trifonov, Edward N et al. (1999) "Periodical Distribution of Transcription Factor Sites in Promoter Regions and Connection With Chromatin Structure" Proc. Natl. Acad. Sci. USA 96(6) : 2891-2895

Ioshikhes, Ilya P and Zhang, Michael Q (2000) "Large-Scale Human Promoter Mapping Using CpG Islands" Nature Genetics 26(1) : 61-63

Ivan, Andra and Halfon, Marc S et al. (2008) "Computational Discovery of Cis-Regulatory Modules in Drosophila Without Prior Knowledge of Motifs" Genome Biology 9 : R22

Jansen, Ritsert C (2003) "Studying Complex Biological Systems Using Multifactorial Perturbation." Nature Reviews Genetics 4(2) : 145-151

Janssens, Hilde and Hou, Shuling et al. (2006) "Quantitative and Predictive Model of Transcriptional Control of the Drosophila Melanogaster Even Skipped Gene" Nature Genetics 38(10) : 1159-1165

Jensen, Shane T and Liu, Jun S (2004) "BioOptimizer: a Bayesian Scoring Function Approach to Motif Discovery" Bioinformatics 20(10) : 1557-1564

Jensen, Shane T and Shen, Lei et al. (2005) "Combining Phylogenetic Motif Discovery and Motif Clustering to Predict Co-regulated Genes" Bioinformatics 21(20) : 3832-3839

Ji, Hongkai and Wong, Wing H (2006) "Computational Biology: Toward Deciphering Gene Regulatory Information in Mammalian Genomes" Biometrics 62(3) : 645-663

Johansson, Öjvind and Alkema, Wynand B et al. (2003) "Identification of Functional Clusters of Transcription Factor Binding Motifs in Genome Sequences: The MSCAN Algorithm" Bioinformatics 19(Suppl. 1) : i169-i176

Johnson, David S and Mortazavi, Ali et al. (2007) "Genome-Wide Mapping of in Vivo Protein-DNA Interactions" Science 316(5830) : 1497-1502

Jothi, Raja and Cuddapah, Suresh et al. (2008) "Genome-Wide Identification of In Vivo Protein-DNA Binding Sites from ChIP-Seq Data" Nucleic Acids Research

Junier, Thomas and Pagni, Marco (2000) "Dotlet: Diagonal Plots in a Web Browser" Bioinformatics 16(2) : 178-179

Jurka, Jerzy and Kapitonov, Vladimir V et al. (2005) "Repbase Update, A Database of Eukaryotic Repetitive Elements" Cytogenetic and Genome Research 110 : 462-467

Jurka, Jerzy and Smith, Temple F (1988) "A Fundamental Division in the Alu Family of Repeated Sequences" Proc. Natl. Acad. Sci. USA 85(13) : 4775-4778

Kadonaga, James T (1998) "Eukaryotic Transcription: An Interlaced Network of Transcription Factors and Chromatin-Modifying Machines" Cell 92(3) : 307-313

Kadonaga, James T (2004) "Regulation of RNA Polymerase II Transcription by Sequence-Specific DNA Binding Factors" Cell 116(2) : 247-257

Kagey, Michael H and Newman, Jamie J et al. (2010) "Mediator and cohesin connect gene expression and chromatin architecture" Nature 467(7314) : 430-435

Kanehisa, Minoru and Goto, Susumu et al. (2006) "From Genomics to Chemical Genomics: New Developments in KEGG" Nucleic Acids Research 34 : D354-D357

Kangaspeska, Sara and Stride, Brenda et al. (2008) "Transient Cyclical Methylation of Promoter DNA" Nature 452(7183) : 112-115

Kankainen, Matti and Holm, Liisa (2005) "POCO: Discovery of Regulatory Patterns from Promoters of Oppositely Expressed Gene Sets" Nucleic Acids Research 33 : W427-W431

Kankainen, Matti and Loytynoja, Ari (2007) "MATLIGN: A Motif Clustering, Comparison and Matching Tool" BMC Bioinformatics 8 : 189

Kantorovitz, Miriam R and Robinson, Gene E et al. (2007) "A Statistical Method for Alignment-Free Comparison of Regulatory Sequences" Bioinformatics 23 : i249-i255

Kanz, Carola and Aldebert, Philippe et al. (2005) "The EMBL Nucleotide Sequence Database" Nucleic Acids Research 33 : D29-D33

Karolchik, Donna and Hinrichs, Angela S et al. (2004) "The UCSC Table Browser Data Retrieval Tool" Nucleic Acids Research 32(Database issue) : D493-D496

Karpova, Tatiana S and Kim, Min J et al. (2008) "Concurrent Fast and Slow Cycling of a Transcriptional Activator at an Endogenous Promoter" Science 319(5862) : 466-469

Kasturi, Jyotsna and Acharya, Raj (2005) "Clustering of Diverse Genomic Data Using Information Fusion" Bioinformatics 21(4) : 423-429

Kato, Mamoru and Tsunoda, Tatsuhiko (2007) "MotifCombinator: A Web-Based Tool to Search for Combinations of Cis-Regulatory Motifs" BMC Bioinformatics 8 : 100

Kawas, Edward and Senger, Martin et al. (2006) "BioMoby extensions to the Taverna workflow management and enactment software" BMC Bioinformatics 7 : 523

Kel, Alexander E and Gößling, Ellen et al. (2003) "MATCH(TM): A Tool for Searching Transcription Factor Binding Sites in DNA Sequences" Nucleic Acids Research 31(13) : 3576-3579

Kel, Alexander E and Konovalova, Tatiana et al. (2006) "Composite Module Analyst: A Fitness-Based Tool for Identification of Transcription Factor Binding Site Combinations" Bioinformatics 22(10) : 1190-1197

Kel, Olga V and Romaschenko, Aida G et al. (1995) "A Compilation of Composite Regulatory Elements Affecting Gene Transcription in Vertebrates" Nucleic Acids Research 23(20) : 4097-4103

Kel, Olga V and Romaschenko, Aida G et al. (1995) "Data Representation in the TRRD - A Database of Transcription Regulatory Regions of the Eukaryotic Genome" Proc. HICSS'95, January 3-6, 1995, Kihei, Maui, Hawaii, USA : 42-51

Kel-Margoulis, Olga V and Kel, Alexander E et al. (2002) "TRANSCompel: A Database on Composite Regulatory Elements in Eukaryotic Genes" Nucleic Acids Research 30(1) : 332-334

Kel-Margoulis, Olga V and Romaschenko, Aida G et al. (2000) "COMPEL: A Database on Composite Regulatory Elements Providing Combinatorial Transcription Regulation" Nucleic Acids Research 28(1) : 311-315

Kerhornou, Arnaud and Guigó, Roderic (2007) "BioMoby Web Services to Support Clustering of Co-Regulated Genes Based on Similarity of Promoter Configurations" Bioinformatics 23(14) : 1831-1833

Kielbasa, Szymon M and Gonze, Didier et al. (2005) "Measuring similarities between transcription factor binding sites" BMC Bioinformatics 6 : 237

Kim, Ryung S and Ji, Hongkai et al. (2006) "An Improved Distance Measure Between the Expression Profiles Linking Co-Expression and Co-Regulation in Mouse" BMC Bioinformatics 7 : 44

Kim, Tae H and Abdullaev, Ziedulla K et al. (2007) "Analysis of the Vertebrate Insulator Protein CTCF-Binding Sites in the Human Genome" Cell 128(6) : 1231-1245

King, David C and Taylor, James et al. (2005) "Evaluation of Regulatory Potential and Conservation Scores for Detecting Cis-Regulatory Modules in Aligned Mammalian Genome Sequences" Genome Research 15(8) : 1051-1060

Klaerr-Blanchard, Maude and Chiapello, Hélène et al. (2000) "Detecting Localized Repeats in Genomic Sequences: A New Strategy and Its Application to Bacillus subtilis and Arabidopsis thaliana Sequences" Computers & Chemistry 24(1) : 57-70

Klepper, Kjetil and Sandve, Geir Kjetil et al. (2008) "Assessment of Composite Motif Discovery Methods" BMC Bioinformatics 9 : 123

Klingenhoff, Andreas and Frech, Kornelie et al. (1999) "Functional Promoter Modules can be detected by formal models independent of overall nucleotide sequence similarity" Bioinformatics 15(3) : 180-186

Kolbe, Diana and Taylor, James et al. (2004) "Regulatory Potential Scores From Genome-Wide Three-Way Alignments of Human, Mouse, and Rat" Genome Research 14(4) : 700-707

Korhonen, Janne and Martinmäki, Petri et al. (2009) "MOODS: fast search for position weight matrix matches in DNA sequences" Bioinformatics 25(23) : 3181-3182

Kornberg, Roger D (2007) "The Molecular Basis of Eukaryotic Transcription" Proc. Natl. Acad. Sci. USA 104(32) : 12955-12961

Krasnogor, Natalio and Pelta, David A (2004) "Measuring the Similarity of Protein Structures by Means of the Universal Similarity Metric" Bioinformatics 20(7) : 1015-1021

Krivan, William and Wasserman, Wyeth W (2001) "A Predictive Model for Regulatory Sequences Directing Liver-Specific Transcription" Genome Research 11(9) : 1159-1566

Krovi, Ravindra (1992) "Genetic Algorithms for Clustering: A Preliminary Investigation" Proc. HICSS'92, January 7-10, 1992, Kihei, Maui, Hawaii, USA : 540-544

Kuttippurathu, Lakshmi and Hsing, Michael et al. (2011) "CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments" Bioinformatics 27(5) : 715-717

Lähdesmäki, Harri and Rust, Alistair G et al. (2008) "Probabilistic Inference of Transcription Factor Binding from Multiple Data Sources" PLoS One 3(3) : e1820

La, David and Livesay, Dennis R (2005) "MINER: Software for Phylogenetic Motif Identification" Nucleic Acids Research 33 : W267-W270

Lajugie, Julien and Bouhassira, Eric E (2011) "GenPlay, a multipurpose genome analyzer and browser" Bioinformatics 27(14) : 1889-1893

Lawrence, Charles E and Altschul, Stephen F et al. (1993) "Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy for Multiple Alignment" Science 262(5131) : 208-214

Lee, Jung-Shin and Smith, Edwin et al. (2010) "The language of histone crosstalk" Cell 142(5) : 682-685

Lee, Tong I and Rinaldi, Nicola J et al. (2002) "Transcriptional Regulatory Networks in Saccharomyces cerevisiae" Science 298(5594) : 799-804

Leek, Jeffrey T and Monsen, Eva et al. (2006) "EDGE: Extraction and Analysis of Differential Gene Expression" Bioinformatics 22(4) : 507-508

Lenhard, Boris and Wasserman, Wyeth W (2002) "TFBS: Computational Framework for Transcription Factor Binding Site Analysis" Bioinformatics 18(8) : 1135-1136

Levine, Michael and Tijan, Robert (2003) "Transcription Regulation and Animal Diversity" Nature 424(6945) : 147-151

Levitsky, Viktor G and Ponomarenko, Mikhail P et al. (1999) "Nucleosomal DNA property database" Bioinformatics 15(7-8) : 582-592

Li, Leping and Liang, Yu et al. (2007) "GAPWM: A Genetic Algorithm Method for Optimizing a Position Weight Matrix" Bioinformatics 23(10) : 1188-1194

Li, Meng and Paik, Hyun-il H et al. (2008) "Enriched Transcription Factor Binding Sites in Hypermethylated Gene Promoters in Drug Resistant Cancer Cells" Bioinformatics 24(16) : 1745-1748

Li, Ruiqiang and Li, Yingrui et al. (2008) "SOAP: short oligonucleotide alignment program" Bioinformatics 24(5) : 713-714

Li, Ruiqiang and Yu, Chang et al. (2009) "SOAP2: an improved ultrafast tool for short read alignment" Bioinformatics 25(15) : 1966-1967

Liang, Faming and Wong, Wing H (2000) "Evolutionary Monte Carlo: Applications to Cp Model Sampling and Change Point Problem" Statistica Sinica 10 : 317-342

Liao, Guo-chun and Rehm, E. Jay et al. (2000) "Insertion Site Preferences of the P Transposable Element in Drosophila Melanogaster" Proc. Natl. Acad. Sci. USA 97(7) : 3347-3351

Lichtarge, Olivier and Sowa, Mathew E (2002) "Evolutionary Predictions of Binding Surfaces and Interactions" Curr. Opin. Struct. Biol. 12(1) : 21-27

Lin, Hwei-Jen and Yang, Fu-Wen et al. (2005) "An Efficient GA-based Clustering Technique" Tamkang J. Sci. Eng. 8(2) : 113-122

Lipman, David J and Pearson, William R (1985) "Rapid and Sensitive Protein Similarity Searches" Science 227(4693) : 1435-1441

Liu, Falcon F and Tsai, Jeffrey J et al. (2005) "FMGA: Finding Motifs by Genetic Algorithm" Proc. BIBE'04, May 19-21, 2004, Taichung, Taiwan : 459-466

Liu, Fang and Tøstesen, Eivind et al. (2007) "The Human Genomic Melting Map" PLoS Computational Biology 3(5) : e93

Liu, Xiaole S and Brutlag, Douglas L et al. (2001) "BioProspector: Discovering Conserved DNA Motifs in Upstream Regulatory Regions of Co-Expressed Genes" Proc. PSB'01, January 3-7, 2001, Hawaii : 127-138

Liu, Xiaole S and Brutlag, Douglas L et al. (2002) "An Algorithm for Finding Protein−DNA Binding Sites With Applications to Chromatin-Immunoprecipitation Microarray Experiments" Nature Biotechnology 20(8) : 835-839

Liu, Xiong and Yu, Xueping et al. (2008) "TiGER: a database for tissue-specific gene expression and regulation" BMC Bioinformatics 9 : 271

Lones, Michael A and Tyrrell, Andy M (2007) "Regulatory Motif Discovery Using a Population Clustering Evolutionary Algorithm" IEEE/ACM Trans. Comput. Biol. Bioinform. 4(3) : 403-414

Loots, Gabriela G and Ovcharenko, Ivan (2004) "rVISTA 2.0: Evolutionary Analysis of Transcription Factor Binding Sites" Nucleic Acids Research 32 : W217-W221

Loots, Gabriela G and Ovcharenko, Ivan (2007) "ECRbase: Database of Evolutionary Conserved Regions, Promoters, and Transcription Factor Binding Sites in Vertebrate Genomes" Bioinformatics 23(1) : 122-124

Lu, Yi and Lu, Shiyong et al. (2004) "FGKA: A Fast Genetic K-means Clustering Algorithm" Proc. SAC'04, March 14-17, 2004, Nicosia, Cyprus : 622-623

Ludlow, Laural B and Schick, Barbara P et al. (1996) "Identification of a mutation in a GATA binding site of the platelet glycoprotein Ibbeta promoter resulting in the Bernard-Soulier syndrome" Journal of Biological Chemistry 271(36) : 22076-22080

Métivier, Raphaël and Gallais, Rozenn et al. (2008) "Cyclical DNA Methylation of a Transcriptionally Active Promoter" Nature 452(7183) : 45-50

MacCarthy, Thomas and Pomiankowski, Andrew et al. (2005) "Using Large-Scale Perturbations in Gene Network Reconstruction." BMC Bioinformatics 6(11)

Macisaac, Kenzie D and Gordon, D. Benjamin et al. (2006) "A Hypothesis-Based Approach for Identifying the Binding Specificity of Regulatory Proteins from Chromatin Immunoprecipitation Data" Bioinformatics 22(4) : 423-429

Maerkl, Sebastian J and Quake, Stephen R (2007) "A Systems Approach to Measuring the Binding Energy Landscapes of Transcription Factors" Science 315(5809) : 233-237

Mahony, Shaun and Benos, Panayiotis V (2007) "STAMP: A Web Tool for Exploring DNA-Binding Motif Similarities" Nucleic Acids Research 35(Web Server issue) : W253-W258

Makalowski, Wojciech (2003) "Not Junk After All" Science 300(5623) : 1246-1247

Marinescu, Voichita D and Kohane, Isaac S et al. (2005) "The MAPPER Database: A Multi-Genome Catalog of Putative Transcription Factor Binding Sites" Nucleic Acids Research 33 : D91-D97

Marstrand, Troels T and Frellsen, Jes et al. (2008) "Asap: A Framework for Over-Representation Statistics for Transcription Factor Binding Sites" PLoS One 3(2) : e1623

Maston, Glenn A and Evans, Sara K et al. (2006) "Transcriptional Regulatory Elements in the Human Genome" Annu. Rev. Genomics Hum. Genet. 7 : 29-59

Matys, Volker and Fricke, Ellen et al. (2003) "TRANSFAC: Transcriptional Regulation, From Patterns to Profiles" Nucleic Acids Research 31(1) : 374-378

Matys, Volker and Kel-Margoulis, Olga V et al. (2006) "TRANSFAC® and its module TRANSCompel®: Transcriptional Gene Regulation in Eukaryotes" Nucleic Acids Research 34 : D108-D110

Maxam, Allan M and Gilbert, Walter (1977) "A New Method for Sequencing DNA" Proc. Natl. Acad. Sci. USA 74(2) : 560-564

McGall, Glenn H and Christians, Fred C (2002) "High-Density Genechip Oligonucleotide Probe Arrays" Advances in Biochemical Engineering / Biotechnology 77 : 21-42

Meng, Guofeng and Mosig, Axel et al. (2010) "A computational evaluation of over-representation of regulatory motifs in the promoter regions of differentially expressed genes" BMC Bioinformatics 11 : 267

Miller, Webb (2001) "Comparison of Genomic DNA Sequences: Solved and Unsolved Problems" Bioinformatics 17(5) : 391-397

Mito, Yoshiko and Henikoff, Jorja G et al. (2007) "Histone Replacement Marks the Boundaries of cis-Regulatory Domains" Science 315(5817) : 1408-1411

Montgomery, Stephen B and Griffith, Obi L et al. (2006) "ORegAnno: An Open Access Database and Curation System for Literature-Derived Promoters, Transcription Factor Binding Sites and Regulatory Variation" Bioinformatics 22(5) : 637-640

Moorman, Celine and Sun, Ling V et al. (2006) "Hotspots of Transcription Factor Colocalization in the Genome of Drosophila Melanogaster" Proc. Natl. Acad. Sci. USA 103(32) : 12027-12032

Narlikar, Leelavati and Gordân, Raluca et al. (2006) "Informative Priors Based on Transcription Factor Structural Class Improve De Novo Motif Discovery" Bioinformatics 22(14) : e384-e392

Narlikar, Leelavati and Gordân, Raluca et al. (2007) "A Nucleosome-Guided Map of Transcription Factor Binding Sites in Yeast" PLoS Computational Biology 3(11) : e215

Narlikar, Leelavati and Hartemink, Alexander (2005) "Sequence Features of DNA Binding Sites Reveal Structural Class of Associated Transcription Factor" Bioinformatics 22(2) : 157-163

Nobrega, Marcelo A and Ovcharenko, Ivan et al. (2003) "Scanning Human Gene Deserts for Long-Range Enhancers" Science 302(5644) : 413

Norambuena, Tomás and Melo, Francisco (2010) "The Protein-DNA Interface database" BMC Bioinformatics 11 : 262

Obayashi, Takeshi and Hayashi, Shinpei et al. (2008) "COXPRESdb: a database of coexpressed gene networks in mammals" Nucleic Acids Research 36(Database issue) : D77-D82

Obayashi, Takeshi and Kinoshita, Kengo (2011) "COXPRESdb: a database to compare gene coexpression in seven model animals" Nucleic Acids Research 39(Suppl. 1) : D1016–D1

Ohler, Uwe and Niemann, Heinrich (2001) "Identification and Analysis of Eukaryotic Promoters: Recent Computational Approaches" Trends in Genetics 17(2) : 56-60

Oinn, Tom (2003) "Talisman - Rapid Application Development for the Grid" Bioinformatics 19(Suppl. 1) : i212-i214

Oinn, Tom and Addis, Matthew et al. (2004) "Taverna: A Tool for the Composition and Enactment of Bioinformatics Workflows" Bioinformatics 20(17) : 3045-3054

Okumura, Toshiyuki and Makiguchi, Hiroki et al. (2007) "Melina II: A Web Tool for Comparisons Among Several Predictive Algorithms to Find Potential Motifs from Promoter Regions" Nucleic Acids Research 35(Web Server issue) : W227-W231

Orgel, Leslie E and Crick, Francis H (1980) "Selfish DNA: The Ultimate Parasite" Nature 284(5757) : 604-607

Orlando, Valerio (2000) "Mapping Chromosomal Proteins In Vivo by Formaldehyde-Crosslinked-Chromatin Immunoprecipitation" Trends in Biochemical Sciences 25(3) : 99-104

Osborne, Cameron S and Chakalova, Lyubomira et al. (2004) "Active Genes Dynamically Colocalize to Shared Sites of Ongoing Transcription" Nature Genetics 36(10) : 1065-1071

Ozsolak, Fatih and Song, Jun S et al. (2007) "High-Throughput Mapping of the Chromatin Structure of Human Promoters" Nature Biotechnology 25(2) : 244-248

Périer, Rouaïda C and Junier, Thomas et al. (1998) "The Eukaryotic Promoter Database EPD" Nucleic Acids Research 26(1) : 353-357

Papatsenko, Dmitri (2007) "ClusterDraw Web Server: A Tool to Identify and Visualize Clusters of Binding Motifs for Transcription Factors" Bioinformatics 23(8) : 1032-1034

Papavassiliou, Athanasios G (1995) "Molecular Medicine. Transcription Factors" New England Journal of Medicine 332(1) : 45-47

Papin, Jason A and Reed, Jennifer L et al. (2004) "Hierarchical Thinking in Network Biology: The Unbiased Modularization of Biochemical Networks" Trends in Biochemical Sciences 29(12) : 641-647

Park, Nam H and Ahn, Chang W et al. (2005) "Adaptive Clustering Technique Using Genetic Algorithms" IEICE Trans. Inf. Syst. 88(12) : 2880-2882

Park, Peter J and Butte, Atul J et al. (2002) "Comparing Expression Profiles of Genes with Similar Promoter Regions" Bioinformatics 18(12) : 1576-1584

Parkinson, Helen and Kapushesky, Misha et al. (2006) "ArrayExpress-A Public Database of Microarray Experiments and Gene Expression Profiles" Nucleic Acids Research 35 : D747-D750

Parsons, Lance and Haque, Ehtesham et al. (2004) "Evaluating Subspace Clustering Algorithms" Workshop on Clustering High Dimensional Data and its Applications. SIAM International Conference on Data Mining, Lake Buena Vista, Florida : 48-56

Partida, Gabriel C and Buske, Fabian A et al. (2012) "Epigenetic priors for identifying active transcription factor binding sites" Bioinformatics 28(1) : 56-62

Patil, Kiran R and Nielsen, Jens (2005) "Uncovering Transcriptional Regulation of Metabolism by Using Metabolic Network Topology" Proc. Natl. Acad. Sci. USA 102(8) : 2685-2689

Pavesi, Giulio and Mauri, Giancarlo et al. (2001) "An Algorithm for Finding Signals of Unknown Length in DNA Sequences" Bioinformatics 17(Suppl) : S207-S214

Pavesi, Giulio and Mereghetti, Paolo et al. (2004) "Weeder Web: Discovery of Transcription Factor Binding Sites in A Set of Sequences From Co-Regulated Genes" Nucleic Acids Research 32 : W199-W203

Pavlidis, Paul and Furey, Terrence S et al. (2001) "Promoter Region-Based Classification of Genes" Proc. PSB'01, January 3-7, 2001, Hawaii : 151-164

Pedersen, Anders G and Baldi, Pierre et al. (1999) "The Biology of Eukaryotic Promoter Prediction - A Review" Computers & Chemistry 23(3-4) : 191-207

Pennacchio, Len A and Ahituv, Nadav et al. (2006) "In Vivo Enhancer Analysis of Human Conserved Non-Coding Sequences." Nature 444(7118) : 499-502

Perco, Paul and Kainz, Alexander et al. (2005) "Detection of Coregulation in Differential Gene Expression Profiles" Biosystems 82(3) : 235-247

Perez, Olga M and Marin, Francisco J et al. (2001) "Improving Biological Sequence Property Distances by Using a Genetic Algorithm" Proc. IWANN'2001, June 13-15, 2001, Granada, Spain : 539-546

Pham, Tuan D and Zuegg, Johannes (2004) "A Probabilistic Measure for Alignment-Free Sequence Comparison" Bioinformatics 20(18) : 3455-3461

Phan, Vinhthuy and Furlotte, Nicholas A (2008) "Motif Tool Manager: a web-based framework for motif discovery" Bioinformatics 24(24) : 2930-2931

Philippakis, Anthony A and He, Fangxue S et al. (2005) "ModuleFinder: A Tool for Computational Discovery of Cis Regulatory Modules" Proc. PSB'01, January 4-8, 2005, Hawaii : 519-530

Pierstorff, Nora and Bergman, Casey M et al. (2006) "Identifying Cis-Regulatory Modules by Combining Comparative and Compositional Analysis of DNA" Bioinformatics 22(23) : 2858-2864

Pique-Regi, Roger and Degner, Jacob F et al. (2010) "Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data" Genome Research

Polouliakh, Natalia and Konno, Michiko et al. (2005) "Parameter Landscape Analysis of Common Motif Discovery Programs" RECOMB 2004 Ws on Regulatory Genomics, March 26-27, 2004, San Diego, CA, USA : 79-87

Poluliakh, Natalia and Takagi, Toshihisa et al. (2003) "MELINA: Motif Extraction From Promoter Regions of Potentially Co-Regulated Genes" Bioinformatics 19(3) : 423-424

Ponger, Loïc and Mouchiroud, Dominique (2002) "CpGProD: Identifying CpG Islands Associated with Transcription Start Sites in Large Genomic Mammalian Sequences" Bioinformatics 18(4) : 631-633

Ponomarenko, Julia V and Merkulova, Tatyana I et al. (2001) "rSNP_Guide, a database system for analysis of transcription factor binding to target sequences: application to SNPs and site-directed mutations" Nucleic Acids Research 29(1) : 312-316

Ponty, Yann and Termier, Michel et al. (2006) "GenRGenS: Software for Generating Random Genomic Sequences and Structures" Bioinformatics 22(12) : 1534-1535

Portales-Casamar, Elodie and Thongjuea, Supat et al. (2010) "JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles" Nucleic Acids Research

Prakash, Amol and Tompa, Martin (2005) "Discovery of Regulatory Elements in Vertebrates Through Comparative Genomics" Nature Biotechnology 23(10) : 1249-1256

Pribnow, David (1975) "Nucleotide Sequence of an RNA Polymerase Binding Site at an Early T7 Promoter" Proc. Natl. Acad. Sci. USA 72(3) : 784-788

Pruitt, Kim D and Katz, Kenneth S et al. (2000) "Introducing RefSeq and LocusLink: Curated Human Genome Resources at the NCBI" Trends in Genetics 16(1) : 44-47

Pruitt, Kim D and Tatusova, Tatiana et al. (2005) "NCBI Reference Sequence (RefSeq): A Curated Non-Redundant Sequence Database of Genomes, Transcripts and Proteins" Nucleic Acids Research 33 : D501-D504

Pudimat, Rainer and Schukat-Talamazzini, Ernst-Günter et al. (2005) "A multiple-feature framework for modelling and predicting transcription factor binding sites" Bioinformatics 21(14) : 3082-3088

Purmann, Antje and Toedling, Joern et al. (2007) "Genomic Organization of Transcriptomes in Mammals: Coregulation and Cofunctionality" Genomics 89(5) : 580-587

Qian, Ziliang and Cai, Yu-Dong et al. (2006) "A Novel Computational Method to Predict Transcription Factor DNA Binding Preference" Biochem. Biophys. Res. Commun. 348(3) : 1034-1037

Qian, Ziliang and Cai, Yu-Dong et al. (2006) "Automatic Transcription Factor Classifier Based on Functional Domain Composition" Biochem. Biophys. Res. Commun. 347(1) : 141-144

Qian, Ziliang and Lu, Lingyi et al. (2007) "An Approach to Predict Transcription Factor DNA Binding Site Specificity Based Upon Gene and Transcription Factor Functional Categorization" Bioinformatics 23(18) : 2449-2454

Qiu, Ping (2003) "Recent Advances in Computational Promoter Analysis in Understanding the Transcriptional Regulatory Network" Biochem. Biophys. Res. Commun. 309(3) : 495-501

Quackenbush, John (2006) "Microarray Analysis and Tumor Classification" New England Journal of Medicine 354(23) : 2463-2472

Quandt, Kerstin and Frech, Kornelie et al. (1995) "MatInd and MatInspector: New Fast And Versatile Tools for Detection of Consensus Matches in Nucleotide Sequence Data" Nucleic Acids Research 23(23) : 4878-4884

Quandt, Kerstin and Grote, Korbinian et al. (1996) "GenomeInspector: Basic Software Tools for Analysis of Spatial Correlations between Genomic Structures within Megabase Sequences" Genomics 33(2) : 301-304

Quest, Daniel and Dempsey, Kathryn et al. (2008) "MTAP: The Motif Tool Assessment Platform" BMC Bioinformatics 9(Suppl 9) : S6

Quinlan, Aaron R and Hall, Ira M (2010) "BEDTools: a flexible suite of utilities for comparing genomic features" Bioinformatics 26(6) : 841-842

Régnier, Mireille (2000) "A Unified Approach to Word Occurrence Probabilities" Discrete Applied Mathematics 104 : 259-280

Régnier, Mireille and Denise, Alain (2004) "Rare Events and Conditional Events on Random Strings" Discrete Math. Theor. Comput. Sci. 6 : 191-214

Régnier, Mireille and Szpankowski, Wojciech (1998) "On Pattern Frequency Occurrences in a Markovian Sequence" Algorithmica 22(4) : 631-649

Ramsey, Stephen A and Knijnenburg, Theo A et al. (2010) "Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites" Bioinformatics 26(17) : 2071-2075

Reinert, Gesine and Schbath, Sophie et al. (2000) "Probabilistic and Statistical Properties of Words: An Overview" Algorithmica 7(1-2) : 1-46

Ren, Bing and Robert, François et al. (2000) "Genome-Wide Location and Function of DNA Binding Proteins" Science 290(5500) : 2306-2309

Rice, Peter and Longden, Ian et al. (2000) "EMBOSS: the European Molecular Biology Open Software Suite" Trends in Genetics 16(6) : 276-277

Ringe, Dagmar and Petsko, Gregory A (2008) "How Enzymes Work" Science 320(5882) : 1428-1429

Riva, Alberto (2012) "The MAPPER2 Database: a multi-genome catalog of putative transcription factor binding sites" Nucleic Acids Research 40(Database issue) : D155-D161

Robertson, Gordon and Bilenky, Misha et al. (2006) "cisRED: A Database System for Genome-Scale Computational Discovery of Regulatory Elements" Nucleic Acids Research 34 : D68-D73

Robinson, James T and Thorvaldsdóttir, Helga et al. (2011) "Integrative genomics viewer" Nature Biotechnology 29(1) : 24-26

Robinson, Mark D and Grigull, Jörg et al. (2002) "FunSpec: A Web-Based Cluster Interpreter for Yeast" BMC Bioinformatics 3 : 35

Robinson-Rechavi, Marc and Garcia, Hector E et al. (2003) "The Nuclear Receptor Superfamily" Journal of Cell Science 116 : 585-586

Roepcke, Stefan and Grossmann, Steffen et al. (2005) "T-Reg Comparator: An Analysis Tool for the Comparison of Position Weight Matrices" Nucleic Acids Research 33 : W438-W441

Rohs, Remo and West, Sean M et al. (2009) "The role of DNA shape in protein-DNA recognition" Nature 461(7268) : 1225-1226

Rokas, Antonis and Hittinger, Chris T (2007) "Transcriptional rewiring: the proof is in the eating" Current Biology 17(16) : R626-R628

Romer, Katherine A and Kayombya, Guy-Richard et al. (2007) "WebMOTIFS: automated discovery, filtering and scoring of DNA sequence motifs using multiple programs and Bayesian approaches" Nucleic Acids Research 35(Web Server issue) : W217-W220

Rubio, Eric D and Reiss, David J et al. (2008) "CTCF Physically Links Cohesin to Chromatin" Proc. Natl. Acad. Sci. USA 105(24) : 8309-8314

Rutherford, Kim and Parkhill, Julian et al. (2000) "Artemis: sequence visualization and annotation" Bioinformatics 16(10) : 944-945

Sabatti, Chiara and Rohlin, Lars et al. (2005) "Vocabulon: A Dictionary Model Approach for Reconstruction and Localization of Transcription Factor Binding Sites" Bioinformatics 21(7) : 922-931

Saha, Saurabh and Sparks, Andrew B et al. (2002) "Using the Transcriptome to Annotate the Genome" Nature Biotechnology 20(5) : 508-512

Sammeth, Michael and Griebel, Thasso et al. (2006) "Panta Rhei (QAlign2): An Open Graphical Environment for Sequence Analysis" Bioinformatics 22(7) : 889-890

Sandelin, Albin and Alkema, Wynand B et al. (2004) "JASPAR: An Open-Access Database for Eukaryotic Transcription Factor Binding Profiles" Nucleic Acids Research 32 : D91-D94

Sandelin, Albin and Wasserman, Wyeth W (2004) "Constrained Binding Site Diversity within Families of Transcription Factors Enhances Pattern Discovery Bioinformatics" Journal of Molecular Biology 338(2) : 207-215

Sandelin, Albin and Wasserman, Wyeth W et al. (2004) "ConSite: Web-Based Prediction of Regulatory Elements Using Cross-Species Comparison" Nucleic Acids Research 32 : W249-W252

Sandve, Geir Kjetil and Abul, Osman et al. (2007) "Improved benchmarks for computational motif discovery" Bioinformatics 8 : 193

Sandve, Geir Kjetil and Drabløs, Finn (2005) "Generalized Composite Motif Discovery" Proc. KES'05, September 14-16, 2005, Melbourne, Australia : 763-769

Sandve, Geir Kjetil and Drabløs, Finn (2006) "A Survey of Motif Discovery Methods in an Integrated Framework" Biology Direct 1 : 11

Sandvik, Arne K and Alsberg, Bjørn K et al. (2006) "Gene Expression Analysis and Clinical Diagnosis" Clinica Chimica Acta 363(1-2) : 157-164

Sanger, Frederick and Nicklen, Steve et al. (1977) "DNA Sequencing With Chain-Terminating Inhibitors" Proc. Natl. Acad. Sci. USA 74(12) : 5463-5467

Schmid, Carl W (1996) "Alu: Structure, Origin, Evolution, Significance, and Function of One-Tenth of Human DNA" Prog. Nucleic Acid Res. Mol. Biol. 53 : 283-319

Schmid, Christoph D and Périer, Rouaïda C et al. (2006) "EPD in its Twentieth Year: Towards Complete Promoter Coverage of Selected Model Organisms" Nucleic Acids Research 34 : D82-D85

Schneider, Thomas D and Stephens, R. Michael (1990) "Sequence Logos: A New Way to Display Consensus Sequences" Nucleic Acids Research 18(20) : 6097-6100

Schneider, Thomas D and Stormo, Gary D et al. (1986) "Information Content of Binding Sites on Nucleotide Sequences" Journal of Molecular Biology 188(3) : 415-431

Schones, Dustin E and Cui, Kairong et al. (2008) "Dynamic Regulation of Nucleosome Positioning in the Human Genome" Cell 132(5) : 887-898

Schones, Dustin E and Sumazin, Pavel et al. (2005) "Similarity of Position Frequency Matrices for Transcription Factor Binding Sites" Bioinformatics 21(3) : 307-313

Seehuus, Rolv and Tveit, Amund et al. (2005) "Discovering Biological Motifs With Genetic Programming" Proc. GECCO'05, June 25-29, 2005, Washington D.C., USA : 401-408

Segal, Eran and Fondufe-Mittendorf, Yvonne et al. (2006) "A Genomic Code for Nucleosome Positioning" Nature 442 : 772-778

Segal, Eran and Raveh-Sadka, Tali et al. (2008) "Predicting Expression Patterns from Regulatory Sequence in Drosophila Segmentation" Nature 451(7178) : 535-540

Segal, Eran and Sharan, Roded (2004) "A Discriminative Model for Identifying Spatial cis-Regulatory Modules" Proceedings of RECOMB'04, March 27-31, 2004, San Diego, CA, USA : 141-149

Semeiks, Jeremy R and Rizki, Aylin et al. (2006) "Ensemble Attribute Profile Clustering: Discovering and Characterizing Groups of Genes with Similar Patterns of Biological Features" BMC Bioinformatics 7 : 147

Senger, Martin and Rice, Peter et al. (2003) "Soaplab - A Unified Sesame Door To Analysis Tools" Proc. UK e-Science All Hands Meeting 2003, September 2-4, 2003, Nottingham, UK : 509-513

Shankar, Ravi and Grover, Deepak et al. (2004) "Evolution and Distribution of RNA Polymerase II Regulatory Sites from RNA Polymerase III Dependant Mobile Alu Elements" BMC Evolutionary Biology 4 : 37

Sharan, Roded and Ben-Hur, Asa et al. (2004) "CREME: Cis-Regulatory Module Explorer for the Human Genome" Nucleic Acids Research 32 : W253-W256

Shelest, Vladimir and Albrecht, Daniela et al. (2010) "DistanceScan: a tool for promoter modeling" Bioinformatics 26(11) : 1460-1462

Shen-Orr, Shai S and Milo, Ron et al. (2002) "Network Motifs in the Transcriptional Regulation Network of Escherichia Coli" Nature Genetics 31(1) : 64-68

Shiraki, Toshiyuki and Kondo, Shinji et al. (2004) "Cap Analysis Gene Expression for High-Throughput Analysis of Transcriptional Starting Point and Identification of Promoter Usage." Proc. Natl. Acad. Sci. USA 100(26) : 15776-15781

Simonis, Nicolas and Wodak, Shoshana J et al. (2004) "Combining Pattern Discovery and Discriminant Analysis to Predict Gene Co-Regulation" Bioinformatics 20(15) : 2370-2379

Sinha, Saurabh (2002) "Discriminative Motifs" Proc. 6th Annual Int. Conf. on Computational Biology, April 18-21, 2002, Washington, USA : 291-298

Sinha, Saurabh and Liang, Yupu et al. (2006) "Stubb: A Program for Discovery and Analysis of Cis-Regulatory Modules" Nucleic Acids Research 34 : W555-559

Sinha, Saurabh and Tompa, Martin (2003) "YMF: A Program for Discovery of Novel Transcription Factor Binding Sites by Statistical Overrepresentation" Nucleic Acids Research 31(13) : 3586-3588

Sinha, Saurabh and van Nimwegen, Erik et al. (2003) "A Probabilistic Method to Detect Regulatory Modules" Bioinformatics 19(Suppl.1) : i292-i301

Smedley, Damian and Haider, Syed et al. (2009) "BioMart - biological queries made easy" BMC Genomics 10 : 22

Smith, Temple F and Waterman, Michael S (1981) "Identification of Common Molecular Subsequences" Journal of Molecular Biology 147(1) : 195-197

Spivak, Aaron T and Stormo, Gary D (2012) "ScerTF: a comprehensive database of benchmarked position weight matrices for Saccharomyces species" Nucleic Acids Research 40(Database issue) : D162-D168

Staden, Rodger (1984) "Computer Methods to Locate Signals in Nucleic Acid Sequences" Nucleic Acids Research 12(1) : 505-519

Stegmaier, Philip and Kel, Alexander E et al. (2004) "Systematic DNA-Binding Domain Classification of Transcription Factors" Genome Informatics 15(2) : 276-286

Stein, Lincoln (2002) "Creating a Bioinformatics Nation" Nature 417(6885) : 119-120

Stephanopoulos, Gregory and Alper, Hal et al. (2004) "Exploiting Biological Complexity for Strain Improvement Through Systems Biology" Nature Biotechnology 22(10) : 1261-1267

Stevens, Robert D and Robinson, Alan J et al. (2003) "myGrid: Personalised Bioinformatics on the Information Grid" Bioinformatics 19(Suppl. 1) : i302-304

Stormo, Gary D (2000) "DNA Binding Sites: Representation and Discovery" Bioinformatics 16(1) : 16-23

Stormo, Gary D and Hartzell, George W (1989) "Identifying Protein-Binding Sites from Unaligned DNA Fragments" Proc. Natl. Acad. Sci. USA 86(4) : 1183-1187

Strahl, Brian D and Allis, C. David (2000) "The Language of Covalent Histone Modifications" Nature 403(6765) : 41-45

Sumazin, Pavel and Chen, Gengxin et al. (2005) "DWE: Discriminating Word Enumerator" Bioinformatics 21(1) : 31-38

Sun, Hanchang and Yuan, Yuan et al. (2010) "Tmod: toolbox of motif discovery" Bioinformatics 26(3) : 405-407

Sze, Sing-Hoi and Gelfand, Mikhail S et al. (2002) "Finding Weak Motifs in DNA Sequences" Proc. PSB'02, January 3-7, 2002, Lihue, Hawaii : 235-246

Taatjes, Dylan J (2010) "The human Mediator complex: a versatile, genome-wide regulator of transcription" Trends in Biochemical Sciences 35(6) : 315-322

Takai, Daiya and Jones, Peter A (2002) "Comprehensive Analysis of CpG Islands in Human Chromosomes 21 and 22" Proc. Natl. Acad. Sci. USA 99(6) : 3740-3745

Tatarinova, Tatiana and Brover, Vyacheslav et al. (2003) "Skew in CG content near the transcription start site in Arabidopsis thaliana" Bioinformatics 19(Suppl. 1) : i313-i314

Teixeira, Miguel C and Monteiro, Pedro et al. (2006) "The YEASTRACT Database: A Tool for the Analysis of Transcription Regulatory Associations in Saccharomyces Cerevisiae" Nucleic Acids Research 34 : D446-D451

The ENCODE Project Consortium (2004) "The ENCODE (ENCyclopedia Of DNA Elements) Project" Science 306(5696) : 636-640

Thomas-Chollier, Morgane and Sand, Olivier et al. (2008) "RSAT: regulatory sequence analysis tools" Nucleic Acids Research 36(Web Server Issue) : W119-W127

Thompson, Catherine C and McKnight, Steven L (1992) "Anatomy of an Enhancer" Trends in Genetics 8(7) : 232-236

Thompson, William and Palumbo, Michael J et al. (2004) "Decoding Human Regulatory Circuits" Genome Research 14(10a) : 1967-1974

Thornburg, Bartley G and Gotea, Valer et al. (2006) "Transposable Elements as a Significant Source of Transcription Regulating Signals" Gene 365 : 104-110

Tolstorukov, Michael Y and Choudhary, Vidhu et al. (2008) "nuScore: A Web-Interface for Nucleosome Positioning Predictions" Bioinformatics 24(12) : 1456-1458

Tompa, Martin and Li, Nan (2006) "Analysis of Computational Approaches for Motif Discovery" Algorithms for Molecular Biology 1 : 8

Tompa, Martin and Li, Nan et al. (2005) "Assessing Computational Tools for the Discovery of Transcription Factor Binding Sites" Nature Biotechnology 23(1) : 137-144

Travers, Andrew A (2004) "The Structural Basis of DNA Flexibility" Phil. Trans. R. Soc. A 362(1820) : 1423-1438

Tuteja, Geetu and White, Peter et al. (2009) "Extracting transcription factor targets from ChIP-Seq data" Nucleic Acids Research 37(17) : e113

Ucar, Duygu and Beyer, Andreas et al. (2009) "Predicting functionality of protein-DNA interactions by integrating diverse evidence" Bioinformatics 25(12) : i137-i144

Ucar, Duygu and Hu, Qingyang et al. (2011) "Combinatorial chromatin modification patterns in the human genome revealed by subspace clustering" Nucleic Acids Research 39(10) : 4063-4075

van Dijk, Marc and Bonvin, Alexandre M (2008) "A Protein-DNA Docking Benchmark" Nucleic Acids Research 36(14) : e88

van Heeringen, Simon J and Veenstra, Gert J (2011) "GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments" Bioinformatics 27(2) : 270-271

van Helden, Jacques (2003) "Regulatory Sequence Analysis Tools" Nucleic Acids Research 31(13) : 3593-3596

van Helden, Jacques (2004) "Metrics for Comparing Regulatory Sequences on the Basis of Pattern Counts" Bioinformatics 20(3) : 399-406

van Helden, Jacques and André, Bruno et al. (1998) "Extracting Regulatory Sites from the Upstream Region of Yeast Genes by Computational Analysis of Oligonucleotide Frequencies" Journal of Molecular Biology 281(5) : 827-842

van Helden, Jacques and Rios, Alma F et al. (2000) "Discovering Regulatory Elements in Non-Coding Sequences by Analysis of Spaced Dyads" Nucleic Acids Research 28(8) : 1808-1818

Vaquerizas, Juan M and Kummerfeld, Sarah K et al. (2009) "A census of human transcription factors: function, expression and evolution" Nature Reviews Genetics 10(4) : 252-263

Velculescu, Victor E and Zhang, Lin et al. (1995) "Serial Analysis of Gene Expression" Science 270(5235) : 484-487

Venkatasubbarao, Srivatsa (2004) "Microarrays - status and prospects" Trends in Biotechnology 22(12) : 630-637

Venter, J. Craig and Smith, Hamilton O et al. (1996) "A New Strategy for Genome Sequencing" Nature 381(6581) : 364-366

Vinga, Susana and Almeida, Jonas (2003) "Alignment-free Sequence Comparison - A Review" Bioinformatics 19(4) : 513-523

Visel, Axel and Minovitsky, Simon et al. (2006) "VISTA Enhancer Browser - A Database of Tissue-Specific Human Enhancers" Nucleic Acids Research 35(Database Issue) : D88-D92

Vishnevsky, Oleg V and Kolchanov, Nikolay A (2005) "ARGO: A Web System for the Detection of Degenerate Motifs and Large-Scale Recognition of Eukaryotic Promoters" Nucleic Acids Research 33 : W417-W422

Vlieghe, Dominique and Sandelin, Albin et al. (2006) "A new generation of JASPAR, the open-access repository for transcription factor binding site profiles" Nucleic Acids Research 34 : D95-D97

Wakaguri, Hiroyuki and Yamashita, Riu et al. (2008) "DBTSS: database of transcription start sites, progress report 2008" Nucleic Acids Research 36(Database issue) : D97-D101

Waleev, Tagir and Shtokalo, Dmitry et al. (2006) "Composite Module Analyst: Identification of Transcription Factor Binding Site Combinations Using Genetic Algorithm" Nucleic Acids Research 34(Web Server issue) : W541-W545

Wang, Guandong and Yu, Taotao et al. (2005) "WordSpy: Identifying Transcription Factor Binding Motifs by Building a Dictionary and Learning a Grammar" Nucleic Acids Research 33 : W412-W416

Wang, Guandong and Zhang, Weixiong (2005) "An Iterative Learning Algorithm for Deciphering Stegoscripts: A Grammatical Approach for Motif Discovery" Washington University, Department of Computer Science and Engineering. Technical Report No. 12, 2005. St. Louis, MO, USA.

Wang, Ting and Stormo, Gary D (2003) "Combining Phylogenetic Data with Co-Regulated Genes to Identify Regulatory Motifs" Bioinformatics 19(18) : 2369-2380

Wang, Zhibin and Zang, Chongzhi et al. (2008) "Combinatorial Patterns of Histone Acetylations and Methylations in the Human Genome" Nature Genetics 40(7) : 897-903

Wasserman, Wyeth W and Fickett, James W (1998) "Identification of Regulatory Regions Which Confer Muscle-Specific Gene Expression" Journal of Molecular Biology 278(1) : 167-181

Wasserman, Wyeth W and Palumbo, Michael J et al. (2000) "Human-Mouse Genome Comparison to Locate Regulatory Sites" Nature Genetics 26(2) : 225-228

Wasserman, Wyeth W and Sandelin, Albin (2004) "Applied Bioinformatics for the Identification of Regulatory Elements" Nature Reviews Genetics 5(4) : 276-287

Wasserman, Wyeth W and Sandelin, Albin (2004) "Applied Bioinformatics for the Identification of Regulatory Elements" Nature Reviews Genetics 5(4) : 276-287

Watson, James D and Crick, Francis H (1953) "Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid" Nature 171(4356) : 737-738

Weber, Michael and Hellmann, Ines et al. (2007) "Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome" Nature Genetics 39(4) : 457-466

Wei, Wei and Yu, Xiao-Dan (2007) "In the post-genomic era, identification of specific regulatory motifs or transcription factor binding sites (TFBSs) in non-coding DNA sequences, which is essential to elucidate transcriptional regulatory networks, has emerged as an obstacle that frustrate" Genomics, Proteomics & Bioinformatics 5(2) : 131-142

Werner, Thomas (1999) "Models for Prediction and Recognition of Eukaryotic Promoters" Mammalian Genome 10(2) : 168-175

Werner, Thomas (2001) "Target Gene Identification from Expression Array Data by Promoter Analysis" Biomolecular Engineering 17(3) : 87-94

Werner, Thomas and Fessele, Sabine et al. (2003) "Computer Modeling of Promoter Organization as a Tool to Study Transcriptional Coregulation" The FASEB Journal 17(10) : 1228-1237

Wijaya, Edward and Yiu, Siu-Ming et al. (2008) "MotifVoter: a novel ensemble method for fine-grained integration of generic motif finders" Bioinformatics 24(20) : 2288-2295

Wilkinson, Mark D and Links, Matthew (2002) "BioMOBY: An Open Source Biological Web Services Proposal" Briefings in Bioinformatics 3(4) : 331-341

Wingender, Edgar (1988) "Compilation of Transcription Regulating Proteins" Nucleic Acids Research 16(5) : 1879-1902

Wingender, Edgar and Dietze, Peter et al. (1996) "TRANSFAC: A Database on Transcription Factors and their DNA Binding Sites" Nucleic Acids Research 24(1) : 238-241

Won, Kyoung-Jae and Agarwal, Saurabh et al. (2008) "An integrated approach to identifying cis-regulatory modules in the human genome" PLoS One 4(5) : e5501

Won, Kyoung-Jae and Ren, Bing et al. (2010) "Genome-wide prediction of transcription factor binding sites using an integrated model" Genome Biology 11 : R7

Won, Kyoung-Jae and Sandelin, Albin et al. (2008) "Modeling Promoter Grammars with Evolving Hidden Markov Models" Bioinformatics 24(15) : 1669-1675

Wrzodek, Clemens and Schröder, Adrian et al. (2010) "ModuleMaster: a new tool to decipher transcriptional regulatory networks" Biosystems 99(1) : 79-81

Wu, Tiee-Jian and Burke, John P et al. (1997) "A Measure of DNA Sequence Dissimilarity Based on Mahalanobis Distance Between Frequencies of Words" Biometrics 53(4) : 1431-1439

Wu, Tiee-Jian and Huang, Ying-Hsueh et al. (2005) "Optimal Word Sizes for Dissimilarity Measures and Estimation of the Degree of Dissimilarity Between DNA Sequences" Bioinformatics 21(22) : 4125-4132

Xing, Eric P and Wu, Wei et al. (2004) "LOGOS: A Modular Bayesian Model For De Novo Motif Detection" J. Bioinf. Comput. Biol. 2(1) : 127-154

Yamashita, Riu and Suzuki, Yutaka et al. (2006) "DBTSS: DataBase of Human Transcription Start Sites, progress report 2006" Nucleic Acids Research 34(Database issue) : D86-D89

Yang, Yee H and Speed, Terry (2007) "Design Issues for cDNA Microarray Experiments" Nature Reviews Genetics 3(8) : 579-588

Yuan, Guo-Cheng and Liu, Yuen-Jong et al. (2005) "Genome-Scale Identification of Nucleosome Positions in S. cerevisiae" Science 309(5734) : 626-630

Zdobnov, Evgeny M and Lopez, Rodrigo et al. (2002) "The EBI SRS Server - New Features" Bioinformatics 18(8) : 1149-1150

Zeng, Jue and Yan, Jizhou et al. (2008) "Genome Wide Screens in Yeast to Identify Potential Binding Sites and Target Genes of DNA-Binding Proteins" Nucleic Acids Research 36(1) : e8

Zhang, Ching (1994) "A Genetic Algorithm for Molecular Sequence Comparison" Proc. ICSMC'94, October 2-5, 1994, San Antonio, Texas, USA : 1926-1931

Zhang, Yan and Lv, Jie et al. (2010) "HHMD: the human histone modification database" Nucleic Acids Research 38(Database issue) : D149-D154

Zhang, Zhaolei and Gerstein, Mark (2003) "Of Mice and Men: Phylogenetic Footprinting Aids the Discovery of Regulatory Elements" Journal of Biology 2(2) : 11

Zhang, Zhengdong D and Paccanaro, Alberto et al. (2007) "Statistical Analysis of the Genomic Distribution and Correlation of Regulatory Elements in the ENCODE Regions" Genome Research 17(6) : 787-797

Zheng, Ming and Barrera, Leah O et al. (2005) "ChIP-chip: Data, Model, and Analysis" Department of Statistics. Technical Report No. 2005102801, 2005. UCLA.

Zhou, Qing and Wong, Wing H (2004) "CisModule: De Novo Discovery of Cis-Regulatory Modules by Hierarchical Mixture Modeling" Proc. Natl. Acad. Sci. USA 101(33) : 12114-12119

Zhu, Jian and Zhang, Michael Q (1999) "SCPD: A Promoter Database of the Yeast Saccharomyces Cerevisiae" Bioinformatics 15(7-8) : 607-611

Zhu, Jiang and He, Fuhong et al. (2008) "How many human genes can be defined as housekeeping with current expression data?" BMC Genomics 9 : 172

Ziegler, Slava and Röhrs, Sonja et al. (2005) "Novel Target Genes of the Wnt Pathway and Statistical Insights into Wnt Target Promoter Regulation" FEBS Journal 272(7) : 1600-1615



457 entries, 3910 pages (approximately), 8.555 pages on average per article