My NCBISign In
Quantifying similarity between motifs
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 61 Articles in this Archive:

Deep RNA Sequencing Reveals Novel Cardiac Transcriptomic Signatures for Physiological and Pathological Hypertrophy
Hong Ki Song, Seong-Eui Hong, Taeyong Kim, Do Han Kim
PLoS One. 2012; 7(4): e35552. Published online 2012 April 16. doi: 10.1371/journal.pone.0035552
PMCID:
PMC3327670
Abstract Full Text PDF–1.6M Supplementary Material
Mutant p53 cooperates with ETS2 to promote etoposide resistance
Phi M. Do, Lakshman Varanasi, Songqing Fan, Chunyang Li, Iwona Kubacka, Virginia Newman, Krishna Chauhan, Silvano Rakeem Daniels, Maurizio Boccetta, Michael R. Garrett, Runzhao Li, Luis A. Martinez
Genes Dev. 2012 April 15; 26(8): 830–845. doi: 10.1101/gad.181685.111
PMCID:
PMC3337457
Free in PMC on 2012/10/15
Computational Characterization of 3′ Splice Variants in the GFAP Isoform Family
Sarah E. Boyd, Betina Nair, Sze Woei Ng, Jonathan M. Keith, Jacqueline M. Orian
PLoS One. 2012; 7(3): e33565. Published online 2012 March 30. doi: 10.1371/journal.pone.0033565
PMCID:
PMC3316583
Abstract Full Text PDF–1012K Supplementary Material
Intronic Cis-Regulatory Modules Mediate Tissue-Specific and Microbial Control of angptl4/fiaf Transcription
J. Gray Camp, Amelia L. Jazwa, Chad M. Trent, John F. Rawls
PLoS Genet. 2012 March; 8(3): e1002585. Published online 2012 March 29. doi: 10.1371/journal.pgen.1002585
PMCID:
PMC3315460
Abstract Full Text PDF–3.3M Supplementary Material
Sequence signatures involved in targeting the male-specific lethal complex to X-chromosomal genes in Drosophila melanogaster
Philge Philip, Fredrik Pettersson, Per Stenberg
BMC Genomics. 2012; 13: 97. Published online 2012 March 19. doi: 10.1186/1471-2164-13-97
PMCID:
PMC3355045
Abstract Full Text PDF–1.7M Supplementary Material
A Conserved Transcriptional Regulator Governs Fungal Morphology in Widely Diverged Species
Christopher W. Cain, Matthew B. Lohse, Oliver R. Homann, Anita Sil, Alexander D. Johnson
Genetics. 2012 February; 190(2): 511–521. doi: 10.1534/genetics.111.134080
PMCID:
PMC3276625
Free in PMC on 2013/02/01
A Whole-Chromosome Analysis of Meiotic Recombination in Drosophila melanogaster
Danny E. Miller, Satomi Takeo, Kavyasree Nandanan, Ariel Paulson, Madelaine M. Gogol, Aaron C. Noll, Anoja G. Perera, Kendra N. Walton, William D. Gilliland, Hua Li, Karen K. Staehling, Justin P. Blumenstiel, R. Scott Hawley
G3 (Bethesda) 2012 February; 2(2): 249–260. Published online 2012 February 1. doi: 10.1534/g3.111.001396
PMCID:
PMC3284332
Abstract Full Text PDF–1.7M
Genome-wide landscape of liver X receptor chromatin binding and gene regulation in human macrophages
Petri Pehkonen, Lynn Welter-Stahl, Janine Diwo, Jussi Ryynänen, Anke Wienecke-Baldacchino, Sami Heikkinen, Eckardt Treuter, Knut R Steffensen, Carsten Carlberg
BMC Genomics. 2012; 13: 50. Published online 2012 January 31. doi: 10.1186/1471-2164-13-50
PMCID:
PMC3295715
Abstract Full Text PDF–2.1M Supplementary Material
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
Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights
Raluca Gordân, Kevin F Murphy, Rachel P McCord, Cong Zhu, Anastasia Vedenko, Martha L Bulyk
Genome Biol. 2011; 12(12): R125. Published online 2011 December 21. doi: 10.1186/gb-2011-12-12-r125
PMCID:
PMC3334620
Abstract Full Text PDF–3.3M Supplementary Material
Identification of tumor-specific Salmonella Typhimurium promoters and their regulatory logic
Sara Leschner, Igor V. Deyneko, Stefan Lienenklaus, Kathrin Wolf, Helmut Bloecker, Dirk Bumann, Holger Loessner, Siegfried Weiss
Nucleic Acids Res. 2012 April; 40(7): 2984–2994. Published online 2011 December 2. doi: 10.1093/nar/gkr1041
PMCID:
PMC3326293
Abstract Full Text PDF–5.7M Supplementary Material
Discriminative prediction of mammalian enhancers from DNA sequence
Dongwon Lee, Rachel Karchin, Michael A. Beer
Genome Res. 2011 December; 21(12): 2167–2180. doi: 10.1101/gr.121905.111
PMCID:
PMC3227105
Free in PMC on 2012/06/01
The Transcriptional Coactivator Cbp Regulates Self-Renewal and Differentiation in Adult Hematopoietic Stem Cells
Wai-In Chan, Rebecca L. Hannah, Mark A. Dawson, Clare Pridans, Donna Foster, Anagha Joshi, Berthold Göttgens, Jan M. Van Deursen, Brian J. P. Huntly
Mol Cell Biol. 2011 December; 31(24): 5046–5060. doi: 10.1128/MCB.05830-11
PMCID:
PMC3233028
Free in PMC on 2012/06/01
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
Ehrlichia chaffeensis TRP120 Binds a G+C-Rich Motif in Host Cell DNA and Exhibits Eukaryotic Transcriptional Activator Function
Bing Zhu, Jeeba A. Kuriakose, Tian Luo, Efren Ballesteros, Sharu Gupta, Yuriy Fofanov, Jere W. McBride
Infect Immun. 2011 November; 79(11): 4370–4381. doi: 10.1128/IAI.05422-11
PMCID:
PMC3257946
Abstract Full Text PDF–1.2M Supplementary Material
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
Intersection of FOXO- and RUNX1-mediated gene expression programs in single breast epithelial cells during morphogenesis and tumor progression
Lixin Wang, Joan S. Brugge, Kevin A. Janes
Proc Natl Acad Sci U S A. 2011 October 4; 108(40): E803–E812. Published online 2011 August 22. doi: 10.1073/pnas.1103423108
Includes additional comments & authors
PMCID:
PMC3189061
Abstract Full Text PDF–1.5M 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
Androgen receptor driven transcription in molecular apocrine breast cancer is mediated by FoxA1
Jessica L L Robinson, Stewart MacArthur, Caryn S Ross-Innes, Wayne D Tilley, David E Neal, Ian G Mills, Jason S Carroll
EMBO J. 2011 August 3; 30(15): 3019–3027. Published online 2011 June 24. doi: 10.1038/emboj.2011.216
Correction in:
EMBO J. 2012 March 21; 31(6): 1617.
PMCID:
PMC3160190
Free in PMC on 2012/08/03
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
The BTB and CNC Homology 1 (BACH1) Target Genes Are Involved in the Oxidative Stress Response and in Control of the Cell Cycle
Hans-Jörg Warnatz, Dominic Schmidt, Thomas Manke, Ilaria Piccini, Marc Sultan, Tatiana Borodina, Daniela Balzereit, Wasco Wruck, Alexey Soldatov, Martin Vingron, Hans Lehrach, Marie-Laure Yaspo
J Biol Chem. 2011 July 1; 286(26): 23521–23532. Published online 2011 May 9. doi: 10.1074/jbc.M111.220178
PMCID:
PMC3123115
Free in PMC on 2012/07/01
Improved similarity scores for comparing motifs
Emi Tanaka, Timothy Bailey, Charles E. Grant, William Stafford Noble, Uri Keich
Bioinformatics. 2011 June 15; 27(12): 1603–1609. Published online 2011 May 4. doi: 10.1093/bioinformatics/btr257
PMCID:
PMC3106196
Free in PMC on 2012/06/15
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
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