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PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation
Elodie Portales-Casamar, Stefan Kirov, Jonathan Lim, Stuart Lithwick, Magdalena I Swanson, Amy Ticoll, Jay Snoddy, Wyeth W Wasserman
Genome Biol. 2007; 8(10): R207. Published online 2007 September 28. doi: 10.1186/gb-2007-8-10-r207
PMCID:
PMC2246282
Abstract Full Text PDF–1.6M

Is Cited by the Following 18 Articles in this Archive:

Validation of Skeletal Muscle cis-Regulatory Module Predictions Reveals Nucleotide Composition Bias in Functional Enhancers
Andrew T. Kwon, Alice Yi Chou, David J. Arenillas, Wyeth W. Wasserman
PLoS Comput Biol. 2011 December; 7(12): e1002256. Published online 2011 December 1. doi: 10.1371/journal.pcbi.1002256
PMCID:
PMC3228787
Abstract Full Text PDF–788K Supplementary Material
Identification of cis-regulatory sequence variations in individual genome sequences
Rebecca Worsley-Hunt, Virginie Bernard, Wyeth W Wasserman
Genome Med. 2011; 3(10): 65. Published online 2011 October 10. doi: 10.1186/gm281
PMCID:
PMC3239227
Abstract Full Text PDF–1.0M
Towards resolving the transcription factor network controlling myelin gene expression
Debra L. Fulton, Eric Denarier, Hana C. Friedman, Wyeth W. Wasserman, Alan C. Peterson
Nucleic Acids Res. 2011 October; 39(18): 7974–7991. Published online 2011 July 5. doi: 10.1093/nar/gkr326
PMCID:
PMC3185407
Abstract Full Text PDF–6.0M Supplementary Material
Evolution of gene regulation of pluripotency - the case for wiki tracks at genome browsers
Georg Fuellen, Stephan Struckmann
Biol Direct. 2010; 5: 67. Published online 2010 December 29. doi: 10.1186/1745-6150-5-67
PMCID:
PMC3024949
Abstract Full Text PDF–819K Supplementary Material
The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources
Marion Gremse, Antje Chang, Ida Schomburg, Andreas Grote, Maurice Scheer, Christian Ebeling, Dietmar Schomburg
Nucleic Acids Res. 2011 January; 39(Database issue): D507–D513. Published online 2010 October 28. doi: 10.1093/nar/gkq968
PMCID:
PMC3013802
Abstract Full Text PDF–12M
A regulatory toolbox of MiniPromoters to drive selective expression in the brain
Elodie Portales-Casamar, Douglas J. Swanson, Li Liu, Charles N. de Leeuw, Kathleen G. Banks, Shannan J. Ho Sui, Debra L. Fulton, Johar Ali, Mahsa Amirabbasi, David J. Arenillas, Nazar Babyak, Sonia F. Black, Russell J. Bonaguro, Erich Brauer, Tara R. Candido, Mauro Castellarin, Jing Chen, Ying Chen, Jason C. Y. Cheng, Vik Chopra, T. Roderick Docking, Lisa Dreolini, Cletus A. D'Souza, Erin K. Flynn, Randy Glenn, Kristi Hatakka, Taryn G. Hearty, Behzad Imanian, Steven Jiang, Shadi Khorasan-zadeh, Ivana Komljenovic, Stéphanie Laprise, Nancy Y. Liao, Jonathan S. Lim, Stuart Lithwick, Flora Liu, Jun Liu, Meifen Lu, Melissa McConechy, Andrea J. McLeod, Marko Milisavljevic, Jacek Mis, Katie O'Connor, Betty Palma, Diana L. Palmquist, Jean-François Schmouth, Magdalena I. Swanson, Bonny Tam, Amy Ticoll, Jenna L. Turner, Richard Varhol, Jenny Vermeulen, Russell F. Watkins, Gary Wilson, Bibiana K. Y. Wong, Siaw H. Wong, Tony Y. T. Wong, George S. Yang, Athena R. Ypsilanti, Steven J. M. Jones, Robert A. Holt, Daniel Goldowitz, Wyeth W. Wasserman, Elizabeth M. Simpson
Proc Natl Acad Sci U S A. 2010 September 21; 107(38): 16589–16594. Published online 2010 August 31. doi: 10.1073/pnas.1009158107
PMCID:
PMC2944712
Abstract Full Text PDF–1.4M Supplementary Material
Global mapping of binding sites for Nrf2 identifies novel targets in cell survival response through ChIP-Seq profiling and network analysis
Deepti Malhotra, Elodie Portales-Casamar, Anju Singh, Siddhartha Srivastava, David Arenillas, Christine Happel, Casper Shyr, Nobunao Wakabayashi, Thomas W. Kensler, Wyeth W. Wasserman, Shyam Biswal
Nucleic Acids Res. 2010 September; 38(17): 5718–5734. Published online 2010 May 11. doi: 10.1093/nar/gkq212
PMCID:
PMC2943601
Abstract Full Text PDF–4.6M Supplementary Material
Five vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding
Dominic Schmidt, Michael D. Wilson, Benoit Ballester, Petra C. Schwalie, Gordon D. Brown, Aileen Marshall, Claudia Kutter, Stephen Watt, Celia P. Martinez-Jimenez, Sarah Mackay, Iannis Talianidis, Paul Flicek, Duncan T. Odom
Science. Author manuscript; available in PMC 2010 December 23.
Published in final edited form as: Science. 2010 May 21; 328(5981): 1036–1040. Published online 2010 April 8. doi: 10.1126/science.1186176
PMCID:
PMC3008766
Abstract Full Text PDF–1.0M Supplementary Material
Transcription factor regulation can be accurately predicted from the presence of target gene signatures in microarray gene expression data
Ahmed Essaghir, Federica Toffalini, Laurent Knoops, Anders Kallin, Jacques van Helden, Jean-Baptiste Demoulin
Nucleic Acids Res. 2010 June; 38(11): e120. Published online 2010 March 9. doi: 10.1093/nar/gkq149
PMCID:
PMC2887972
Abstract Full Text PDF–3.3M Supplementary Material
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles
Elodie Portales-Casamar, Supat Thongjuea, Andrew T. Kwon, David Arenillas, Xiaobei Zhao, Eivind Valen, Dimas Yusuf, Boris Lenhard, Wyeth W. Wasserman, Albin Sandelin
Nucleic Acids Res. 2010 January; 38(Database issue): D105–D110. Published online 2010 January. doi: 10.1093/nar/gkp950
PMCID:
PMC2808906
Abstract Full Text PDF–1.1M
Discovery of Regulatory Elements is Improved by a Discriminatory Approach
Eivind Valen, Albin Sandelin, Ole Winther, Anders Krogh
PLoS Comput Biol. 2009 November; 5(11): e1000562. Published online 2009 November 13. doi: 10.1371/journal.pcbi.1000562
PMCID:
PMC2770120
Abstract Full Text PDF–290K Supplementary Material
The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences
Elodie Portales-Casamar, David Arenillas, Jonathan Lim, Magdalena I. Swanson, Steven Jiang, Anthony McCallum, Stefan Kirov, Wyeth W. Wasserman
Nucleic Acids Res. 2009 January; 37(Database issue): D54–D60. Published online 2009 January. doi: 10.1093/nar/gkn783
PMCID:
PMC2686574
Abstract Full Text PDF–3.8M
UniPROBE: an online database of protein binding microarray data on protein–DNA interactions
Daniel E. Newburger, Martha L. Bulyk
Nucleic Acids Res. 2009 January; 37(Database issue): D77–D82. Published online 2009 January. doi: 10.1093/nar/gkn660
PMCID:
PMC2686578
Abstract Full Text PDF–4.0M
Identification of a set of genes showing regionally enriched expression in the mouse brain
Cletus A D'Souza, Vikramjit Chopra, Richard Varhol, Yuan-Yun Xie, Slavita Bohacec, Yongjun Zhao, Lisa LC Lee, Mikhail Bilenky, Elodie Portales-Casamar, An He, Wyeth W Wasserman, Daniel Goldowitz, Marco A Marra, Robert A Holt, Elizabeth M Simpson, Steven JM Jones
BMC Neurosci. 2008; 9: 66. Published online 2008 July 14. doi: 10.1186/1471-2202-9-66
PMCID:
PMC2483290
Abstract Full Text PDF–364K Supplementary Material
ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species
Bart Hooghe, Paco Hulpiau, Frans van Roy, Pieter De Bleser
Nucleic Acids Res. 2008 July 1; 36(Web Server issue): W128–W132. Published online 2008 July 1. doi: 10.1093/nar/gkn195
PMCID:
PMC2447729
Abstract Full Text PDF–4.3M Supplementary Material
ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues?
Peter Van Loo, Stein Aerts, Bernard Thienpont, Bart De Moor, Yves Moreau, Peter Marynen
Genome Biol. 2008; 9(4): R66. Published online 2008 April 7. doi: 10.1186/gb-2008-9-4-r66
PMCID:
PMC2643937
Abstract Full Text PDF–817K
Text-mining assisted regulatory annotation
Stein Aerts, Maximilian Haeussler, Steven van Vooren, Obi L Griffith, Paco Hulpiau, Steven JM Jones, Stephen B Montgomery, Casey M Bergman, The Open Regulatory Annotation Consortium
Genome Biol. 2008; 9(2): R31. Published online 2008 February 13. doi: 10.1186/gb-2008-9-2-r31
PMCID:
PMC2374703
Abstract Full Text PDF–538K Supplementary Material
ORegAnno: an open-access community-driven resource for regulatory annotation
Obi L. Griffith, Stephen B. Montgomery, Bridget Bernier, Bryan Chu, Katayoon Kasaian, Stein Aerts, Shaun Mahony, Monica C. Sleumer, Mikhail Bilenky, Maximilian Haeussler, Malachi Griffith, Steven M. Gallo, Belinda Giardine, Bart Hooghe, Peter Van Loo, Enrique Blanco, Amy Ticoll, Stuart Lithwick, Elodie Portales-Casamar, Ian J. Donaldson, Gordon Robertson, Claes Wadelius, Pieter De Bleser, Dominique Vlieghe, Marc S. Halfon, Wyeth Wasserman, Ross Hardison, Casey M. Bergman, Steven J.M. Jones, The Open Regulatory Annotation Consortium
Nucleic Acids Res. 2008 January; 36(Database issue): D107–D113. Published online 2008 January. doi: 10.1093/nar/gkm967
PMCID:
PMC2239002
Abstract Full Text PDF–360K
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