Cited by ..

Shobhit Gupta, John A Stamatoyannopoulos, Timothy L Bailey, William Stafford Noble

Genome Biol. 2007; 8(2): R24. Published online 2007 February 26. doi: 10.1186/gb-2007-8-2-r24

PMCID:: PMC1852410

Abstract Full Text PDF–403K Supplementary Material

Is Cited by the Following 44 Articles in this Archive:

Genome-Wide Progesterone Receptor Binding: Cell Type-Specific and Shared Mechanisms in T47D Breast Cancer Cells and Primary Leiomyoma Cells

Ping Yin, Damian Roqueiro, Lei Huang, Jonas K. Owen, Anna Xie, Antonia Navarro, Diana Monsivais, John S. Coon V, J. Julie Kim, Yang Dai, Serdar E. Bulun

PLoS One. 2012; 7(1): e29021. Published online 2012 January 17. doi: 10.1371/journal.pone.0029021

PMCID:: PMC3260146

Abstract Full Text PDF–579K Supplementary Material

YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities

Carl G. de Boer, Timothy R. Hughes

Nucleic Acids Res. 2012 January; 40(D1): D169–D179. Published online 2011 November 17. doi: 10.1093/nar/gkr993

PMCID:: PMC3245003

Abstract Full Text PDF–7.4M

Genome-wide mapping of Sox6 binding sites in skeletal muscle reveals both direct and indirect regulation of muscle terminal differentiation by Sox6

Chung-Il An, Yao Dong, Nobuko Hagiwara

BMC Dev Biol. 2011; 11: 59. Published online 2011 October 10. doi: 10.1186/1471-213X-11-59

PMCID:: PMC3239296

Abstract Full Text PDF–5.4M Supplementary Material

The Evolutionarily Conserved Longevity Determinants HCF-1 and SIR-2.1/SIRT1 Collaborate to Regulate DAF-16/FOXO

Gizem Rizki, Terri Naoko Iwata, Ji Li, Christian G. Riedel, Colette Lafontaine Picard, Max Jan, Coleen T. Murphy, Siu Sylvia Lee

PLoS Genet. 2011 September; 7(9): e1002235. Published online 2011 September 1. doi: 10.1371/journal.pgen.1002235

PMCID:: PMC3164695

Abstract Full Text PDF–1.9M Supplementary Material

ChIP-seq reveals cell type-specific binding patterns of BMP-specific Smads and a novel binding motif

Masato Morikawa, Daizo Koinuma, Shuichi Tsutsumi, Eleftheria Vasilaki, Yasuharu Kanki, Carl-Henrik Heldin, Hiroyuki Aburatani, Kohei Miyazono

Nucleic Acids Res. 2011 November; 39(20): 8712–8727. Published online 2011 July 15. doi: 10.1093/nar/gkr572

PMCID:: PMC3203580

Abstract Full Text PDF–1.9M Supplementary Material

Identification of Mycoparasitism-Related Genes in Trichoderma atroviride

Barbara Reithner, Enrique Ibarra-Laclette, Robert L. Mach, Alfredo Herrera-Estrella

Appl Environ Microbiol. 2011 July; 77(13): 4361–4370. doi: 10.1128/AEM.00129-11

PMCID:: PMC3127718

Abstract Full Text PDF–905K Supplementary Material

RSAT 2011: regulatory sequence analysis tools

Morgane Thomas-Chollier, Matthieu Defrance, Alejandra Medina-Rivera, Olivier Sand, Carl Herrmann, Denis Thieffry, Jacques van Helden

Nucleic Acids Res. 2011 July 1; 39(Web Server issue): W86–W91. Published online 2011 June 27. doi: 10.1093/nar/gkr377

PMCID:: PMC3125777

Abstract Full Text PDF–4.4M

A Linear Model for Transcription Factor Binding Affinity Prediction in Protein Binding Microarrays

Matti Annala, Kirsti Laurila, Harri Lähdesmäki, Matti Nykter

PLoS One. 2011; 6(5): e20059. Published online 2011 May 26. doi: 10.1371/journal.pone.0020059

PMCID:: PMC3102690

Abstract Full Text PDF–933K Supplementary Material

DREME: motif discovery in transcription factor ChIP-seq data

Timothy L. Bailey

Bioinformatics. 2011 June 15; 27(12): 1653–1659. Published online 2011 May 4. doi: 10.1093/bioinformatics/btr261

PMCID:: PMC3106199

Abstract Full Text PDF–434K

The CRISPR/Cas Immune System Is an Operon Regulated by LeuO, H-NS, and Leucine-Responsive Regulatory Protein in Salmonella enterica Serovar Typhi

L. Medina-Aparicio, J. E. Rebollar-Flores, A. L. Gallego-Hernández, A. Vázquez, L. Olvera, R. M. Gutiérrez-Ríos, E. Calva, I. Hernández-Lucas

J Bacteriol. 2011 May; 193(10): 2396–2407. doi: 10.1128/JB.01480-10

PMCID:: PMC3133143

Abstract Full Text PDF–1.5M Supplementary Material

Extensive DNA-binding specificity divergence of a conserved transcription regulator

Christopher R. Baker, Brian B. Tuch, Alexander D. Johnson

Proc Natl Acad Sci U S A. 2011 May 3; 108(18): 7493–7498. Published online 2011 April 15. doi: 10.1073/pnas.1019177108

PMCID:: PMC3088634

Abstract Full Text PDF–767K Supplementary Material

MEME-ChIP: motif analysis of large DNA datasets

Philip Machanick, Timothy L. Bailey

Bioinformatics. 2011 June 15; 27(12): 1696–1697. Published online 2011 April 12. doi: 10.1093/bioinformatics/btr189

PMCID:: PMC3106185

Abstract Full Text PDF–215K Supplementary Material

The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding

Xiao-Yong Li, Sean Thomas, Peter J Sabo, Michael B Eisen, John A Stamatoyannopoulos, Mark D Biggin

Genome Biol. 2011; 12(4): R34. Published online 2011 April 7. doi: 10.1186/gb-2011-12-4-r34

PMCID:: PMC3218860

Abstract Full Text PDF–787K Supplementary Material

FLOWERING LOCUS C (FLC) regulates development pathways throughout the life cycle of Arabidopsis

Weiwei Deng, Hua Ying, Chris A. Helliwell, Jennifer M. Taylor, W. James Peacock, Elizabeth S. Dennis

Proc Natl Acad Sci U S A. 2011 April 19; 108(16): 6680–6685. Published online 2011 April 4. doi: 10.1073/pnas.1103175108

PMCID:: PMC3081018

Abstract Full Text PDF–594K Supplementary Material

Modulation of chromatin position and gene expression by HDAC4 interaction with nucleoporins

Izhak Kehat, Federica Accornero, Bruce J. Aronow, Jeffery D. Molkentin

J Cell Biol. 2011 April 4; 193(1): 21–29. doi: 10.1083/jcb.201101046

PMCID:: PMC3082185

Abstract Full Text PDF–2.2M

An Integrated Pipeline for the Genome-Wide Analysis of Transcription Factor Binding Sites from ChIP-Seq

Eloi Mercier, Arnaud Droit, Leping Li, Gordon Robertson, Xuekui Zhang, Raphael Gottardo

PLoS One. 2011; 6(2): e16432. Published online 2011 February 16. doi: 10.1371/journal.pone.0016432

PMCID:: PMC3040171

Abstract Full Text PDF–689K Supplementary Material

Genome-wide chromatin occupancy analysis reveals a role for ASH2 in transcriptional pausing

Sílvia Pérez-Lluch, Enrique Blanco, Albert Carbonell, Debasish Raha, Michael Snyder, Florenci Serras, Montserrat Corominas

Nucleic Acids Res. 2011 June; 39(11): 4628–4639. Published online 2011 February 9. doi: 10.1093/nar/gkq1322

PMCID:: PMC3113561

Abstract Full Text PDF–8.8M Supplementary Material

Scaffolding a Caenorhabditis nematode genome with RNA-seq

Ali Mortazavi, Erich M. Schwarz, Brian Williams, Lorian Schaeffer, Igor Antoshechkin, Barbara J. Wold, Paul W. Sternberg

Genome Res. 2010 December; 20(12): 1740–1747. doi: 10.1101/gr.111021.110

PMCID:: PMC2990000

Abstract Full Text PDF–525K

FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system

Lihua Julie Zhu, Ryan G. Christensen, Majid Kazemian, Christopher J. Hull, Metewo Selase Enuameh, Matthew D. Basciotta, Jessie A. Brasefield, Cong Zhu, Yuna Asriyan, David S. Lapointe, Saurabh Sinha, Scot A. Wolfe, Michael H. Brodsky

Nucleic Acids Res. 2011 January; 39(Database issue): D111–D117. Published online 2010 November 19. doi: 10.1093/nar/gkq858

PMCID:: PMC3013762

Abstract Full Text PDF–5.1M

Activation of a Silent Fungal Polyketide Biosynthesis Pathway through Regulatory Cross Talk with a Cryptic Nonribosomal Peptide Synthetase Gene Cluster

Sebastian Bergmann, Alexander N. Funk, Kirstin Scherlach, Volker Schroeckh, Ekaterina Shelest, Uwe Horn, Christian Hertweck, Axel A. Brakhage

Appl Environ Microbiol. 2010 December; 76(24): 8143–8149. Published online 2010 October 15. doi: 10.1128/AEM.00683-10

PMCID:: PMC3008269

Abstract Full Text PDF–758K Supplementary Material

A ChIP-seq defined genome-wide map of vitamin D receptor binding: Associations with disease and evolution

Sreeram V. Ramagopalan, Andreas Heger, Antonio J. Berlanga, Narelle J. Maugeri, Matthew R. Lincoln, Amy Burrell, Lahiru Handunnetthi, Adam E. Handel, Giulio Disanto, Sarah-Michelle Orton, Corey T. Watson, Julia M. Morahan, Gavin Giovannoni, Chris P. Ponting, George C. Ebers, Julian C. Knight

Genome Res. 2010 October; 20(10): 1352–1360. doi: 10.1101/gr.107920.110

PMCID:: PMC2945184

Abstract Full Text PDF–1.1M

Motif prediction to distinguish LPS-stimulated pro-inflammatory vs. antibacterial macrophage genes

Rahul K Kollipara, Narayanan B Perumal

Immunome Res. 2010; 6: 5. Published online 2010 September 21. doi: 10.1186/1745-7580-6-5

PMCID:: PMC2949756

Abstract Full Text PDF–1.1M Supplementary Material

Dual-functioning transcription factors in the developmental gene network of Drosophila melanogaster

Denis C Bauer, Fabian A Buske, Timothy L Bailey

BMC Bioinformatics. 2010; 11: 366. Published online 2010 July 2. doi: 10.1186/1471-2105-11-366

PMCID:: PMC2912886

Abstract Full Text PDF–790K Supplementary Material

Identification of novel non-coding small RNAs from Streptococcus pneumoniae TIGR4 using high-resolution genome tiling arrays

Ranjit Kumar, Pratik Shah, Edwin Swiatlo, Shane C Burgess, Mark L Lawrence, Bindu Nanduri

BMC Genomics. 2010; 11: 350. Published online 2010 June 3. doi: 10.1186/1471-2164-11-350

PMCID:: PMC2887815

Abstract Full Text PDF–1.3M Supplementary Material

Combining ChIP-chip and Expression Profiling to Model the MoCRZ1 Mediated Circuit for Ca²⁺/Calcineurin Signaling in the Rice Blast Fungus

Soonok Kim, Jinnan Hu, Yeonyee Oh, Jongsun Park, Jinhee Choi, Yong-Hwan Lee, Ralph A. Dean, Thomas K. Mitchell

PLoS Pathog. 2010 May; 6(5): e1000909. Published online 2010 May 20. doi: 10.1371/journal.ppat.1000909

PMCID:: PMC2873923

Abstract Full Text PDF–1.5M Supplementary Material

Human RNA Polymerase III transcriptomes and relationships to Pol II promoters, enhancer-binding factors and chromatin domains

Andrew J. Oler, Ravi K. Alla, Douglas N. Roberts, Alexander Wong, Peter C. Hollenhorst, Katherine J. Chandler, Patrick A. Cassiday, Cassie A. Nelson, Curt H. Hagedorn, Barbara J. Graves, Bradley R. Cairns

Nat Struct Mol Biol. Author manuscript; available in PMC 2010 November 1.

Published in final edited form as: Nat Struct Mol Biol. 2010 May; 17(5): 620–628. Published online 2010 April 25. doi: 10.1038/nsmb.1801