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Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach
Olivier Elemento, Saeed Tavazoie
Genome Biol. 2005; 6(2): R18. Published online 2005 January 26. doi: 10.1186/gb-2005-6-2-r18
PMCID:
PMC551538
Abstract Full Text PDF–1.0M

Is Cited by the Following 48 Articles in this Archive:

MotifMap: integrative genome-wide maps of regulatory motif sites for model species
Kenneth Daily, Vishal R Patel, Paul Rigor, Xiaohui Xie, Pierre Baldi
BMC Bioinformatics. 2011; 12: 495. Published online 2011 December 30. doi: 10.1186/1471-2105-12-495
PMCID:
PMC3293935
Abstract Full Text PDF–2.3M Supplementary Material
Chromatin-driven de novo discovery of DNA binding motifs in the human malaria parasite
Elena Y Harris, Nadia Ponts, Karine G Le Roch, Stefano Lonardi
BMC Genomics. 2011; 12: 601. Published online 2011 December 13. doi: 10.1186/1471-2164-12-601
PMCID:
PMC3282892
Abstract Full Text PDF–951K Supplementary Material
Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data
Roger Pique-Regi, Jacob F. Degner, Athma A. Pai, Daniel J. Gaffney, Yoav Gilad, Jonathan K. Pritchard
Genome Res. 2011 March; 21(3): 447–455. doi: 10.1101/gr.112623.110
PMCID:
PMC3044858
Abstract Full Text PDF–1.4M
Identification and Genome-Wide Prediction of DNA Binding Specificities for the ApiAP2 Family of Regulators from the Malaria Parasite
Tracey L. Campbell, Erandi K. De Silva, Kellen L. Olszewski, Olivier Elemento, Manuel Llinás
PLoS Pathog. 2010 October; 6(10): e1001165. Published online 2010 October 28. doi: 10.1371/journal.ppat.1001165
PMCID:
PMC2965767
Abstract Full Text PDF–2.9M Supplementary Material
Multi-species integrative biclustering
Peter Waltman, Thadeous Kacmarczyk, Ashley R Bate, Daniel B Kearns, David J Reiss, Patrick Eichenberger, Richard Bonneau
Genome Biol. 2010; 11(9): R96. Published online 2010 September 29. doi: 10.1186/gb-2010-11-9-r96
PMCID:
PMC2965388
Abstract Full Text PDF–2.6M Supplementary Material
Finding regulatory DNA motifs using alignment-free evolutionary conservation information
Raluca Gordân, Leelavati Narlikar, Alexander J. Hartemink
Nucleic Acids Res. 2010 April; 38(6): e90. Published online 2010 April. doi: 10.1093/nar/gkp1166
PMCID:
PMC2847231
Abstract Full Text PDF–2.2M Supplementary Material
Systematic discovery of regulatory motifs in Fusarium graminearum by comparing four Fusarium genomes
Lokesh Kumar, Andrew Breakspear, Corby Kistler, Li-Jun Ma, Xiaohui Xie
BMC Genomics. 2010; 11: 208. Published online 2010 March 26. doi: 10.1186/1471-2164-11-208
PMCID:
PMC2853525
Abstract Full Text PDF–2.0M Supplementary Material
Evidence-ranked motif identification
Stoyan Georgiev, Alan P Boyle, Karthik Jayasurya, Xuan Ding, Sayan Mukherjee, Uwe Ohler
Genome Biol. 2010; 11(2): R19. Published online 2010 February 15. doi: 10.1186/gb-2010-11-2-r19
PMCID:
PMC2872879
Abstract Full Text PDF–2.3M Supplementary Material
Revealing global regulatory perturbations across human cancers
Hani Goodarzi, Olivier Elemento, Saeed Tavazoie
Mol Cell. Author manuscript; available in PMC 2010 December 11.
Published in final edited form as: Mol Cell. 2009 December 11; 36(5): 900–911. doi: 10.1016/j.molcel.2009.11.016
PMCID:
PMC2900319
Abstract Full Text PDF–3.3M Supplementary Material
Profiling the Human Protein-DNA Interactome Reveals MAPK1 as a Transcriptional Repressor of Interferon Signalling
Shaohui Hu, Zhi Xie, Akishi Onishi, Xueping Yu, Lizhi Jiang, Jimmy Lin, Hee-sool Rho, Crystal Woodard, Hong Wang, Jun-Seop Jeong, Shunyou Long, Xiaofei He, Herschel Wade, Seth Blackshaw, Jiang Qian, Heng Zhu
Cell. Author manuscript; available in PMC 2010 October 30.
Published in final edited form as: Cell. 2009 October 30; 139(3): 610–622. doi: 10.1016/j.cell.2009.08.037
PMCID:
PMC2774939
Abstract Full Text PDF–4.1M Supplementary Material
Mechanisms and Evolution of Control Logic in Prokaryotic Transcriptional Regulation
Sacha A. F. T. van Hijum, Marnix H. Medema, Oscar P. Kuipers
Microbiol Mol Biol Rev. 2009 September; 73(3): 481–509. doi: 10.1128/MMBR.00037-08
PMCID:
PMC2738135
Abstract Full Text PDF–4.4M
Discovery of cis-elements between sorghum and rice using co-expression and evolutionary conservation
Xi Wang, Georg Haberer, Klaus FX Mayer
BMC Genomics. 2009; 10: 284. Published online 2009 June 26. doi: 10.1186/1471-2164-10-284
PMCID:
PMC2714861
Abstract Full Text PDF–1.9M Supplementary Material
Unraveling Transcriptional Control in Arabidopsis Using cis-Regulatory Elements and Coexpression Networks
Klaas Vandepoele, Mauricio Quimbaya, Tine Casneuf, Lieven De Veylder, Yves Van de Peer
Plant Physiol. 2009 June; 150(2): 535–546. doi: 10.1104/pp.109.136028
PMCID:
PMC2689962
Abstract Full Text PDF–674K Supplementary Material
A combinatorial approach to determine the context-dependent role in transcriptional and posttranscriptional regulation in Arabidopsis thaliana
Le Lu, Jinming Li
BMC Syst Biol. 2009; 3: 43. Published online 2009 April 28. doi: 10.1186/1752-0509-3-43
PMCID:
PMC2694151
Abstract Full Text PDF–814K
Microarray Profiling of Phage-Display Selections for Rapid Mapping of Transcription Factor–DNA Interactions
Gordon Freckleton, Soyeon I. Lippman, James R. Broach, Saeed Tavazoie
PLoS Genet. 2009 April; 5(4): e1000449. Published online 2009 April 10. doi: 10.1371/journal.pgen.1000449
PMCID:
PMC2659770
Abstract Full Text PDF–614K
Genome-wide discovery of functional transcription factor binding sites by comparative genomics: The case of Stat3
Francesco Vallania, Davide Schiavone, Sarah Dewilde, Emanuela Pupo, Serge Garbay, Raffaele Calogero, Marco Pontoglio, Paolo Provero, Valeria Poli
Proc Natl Acad Sci U S A. 2009 March 31; 106(13): 5117–5122. Published online 2009 March 12. doi: 10.1073/pnas.0900473106
PMCID:
PMC2664024
Abstract Full Text PDF–750K Supplementary Material
Comparative genomics allows the discovery of cis-regulatory elements in mosquitoes
Douglas H. Sieglaff, W. Augustine Dunn, Xiaohui S. Xie, Karyn Megy, Osvaldo Marinotti, Anthony A. James
Proc Natl Acad Sci U S A. 2009 March 3; 106(9): 3053–3058. Published online 2009 February 11. doi: 10.1073/pnas.0813264106
PMCID:
PMC2640218
Abstract Full Text PDF–845K Supplementary Material
A new library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters
Gwenael Badis, Esther T. Chan, Harm van Bakel, Lourdes Pena-Castillo, Desiree Tillo, Kyle Tsui, Clayton D. Carlson, Andrea J. Gossett, Michael J. Hasinoff, Christopher L. Warren, Marinella Gebbia, Shaheynoor Talukder, Ally Yang, Sanie Mnaimneh, Dimitri Terterov, David Coburn, Ai Li Yeo, Zhen Xuan Yeo, Neil D. Clarke, Jason D. Lieb, Aseem Z. Ansari, Corey Nislow, Timothy R. Hughes
Mol Cell. Author manuscript; available in PMC 2009 December 26.
Published in final edited form as: Mol Cell. 2008 December 26; 32(6): 878–887. doi: 10.1016/j.molcel.2008.11.020
PMCID:
PMC2743730
Abstract Full Text PDF–4.9M Supplementary Material
c-REDUCE: Incorporating sequence conservation to detect motifs that correlate with expression
Katerina Kechris, Hao Li
BMC Bioinformatics. 2008; 9: 506. Published online 2008 November 28. doi: 10.1186/1471-2105-9-506
PMCID:
PMC2626603
Abstract Full Text PDF–288K Supplementary Material
MotifMap: a human genome-wide map of candidate regulatory motif sites
Xiaohui Xie, Paul Rigor, Pierre Baldi
Bioinformatics. 2009 January 15; 25(2): 167–174. Published online 2008 November 18. doi: 10.1093/bioinformatics/btn605
PMCID:
PMC2732295
Abstract Full Text PDF–255K Supplementary Material
Classifying transcription factor targets and discovering relevant biological features
Dustin T Holloway, Mark Kon, Charles DeLisi
Biol Direct. 2008; 3: 22. Published online 2008 May 30. doi: 10.1186/1745-6150-3-22
PMCID:
PMC2441612
Abstract Full Text PDF–836K Supplementary Material
Systematic identification of mammalian regulatory motifs' target genes and functions
Jason B. Warner, Anthony A. Philippakis, Savina A. Jaeger, Fangxue Sherry He, Jolinta Lin, Martha L. Bulyk
Nat Methods. Author manuscript; available in PMC 2009 July 10.
Published in final edited form as: Nat Methods. 2008 April; 5(4): 347–353. Published online 2008 March 2. doi: 10.1038/nmeth.1188
PMCID:
PMC2708972
Abstract Full Text PDF–1.6M Supplementary Material
Discovering gapped binding sites of yeast transcription factors
Chien-Yu Chen, Huai-Kuang Tsai, Chen-Ming Hsu, Mei-Ju May Chen, Hao-Geng Hung, Grace Tzu-Wei Huang, Wen-Hsiung Li
Proc Natl Acad Sci U S A. 2008 February 19; 105(7): 2527–2532. Published online 2008 February 13. doi: 10.1073/pnas.0712188105
PMCID:
PMC2268170
Abstract Full Text PDF–955K Supplementary Material
Transcriptional profiling of MnSOD-mediated lifespan extension in Drosophila reveals a species-general network of aging and metabolic genes
Christina Curtis, Gary N Landis, Donna Folk, Nancy B Wehr, Nicholas Hoe, Morris Waskar, Diana Abdueva, Dmitriy Skvortsov, Daniel Ford, Allan Luu, Ananth Badrinath, Rodney L Levine, Timothy J Bradley, Simon Tavaré, John Tower
Genome Biol. 2007; 8(12): R262. Published online 2007 December 9. doi: 10.1186/gb-2007-8-12-r262
PMCID:
PMC2246264
Abstract Full Text PDF–1.7M Supplementary Material
Predicting combinatorial binding of transcription factors to regulatory elements in the human genome by association rule mining
Xochitl C Morgan, Shulin Ni, Daniel P Miranker, Vishwanath R Iyer
BMC Bioinformatics. 2007; 8: 445. Published online 2007 November 15. doi: 10.1186/1471-2105-8-445
PMCID:
PMC2211755
Abstract Full Text PDF–1.1M Supplementary Material
Identifications of conserved 7-mers in 3'-UTRs and microRNAs in Drosophila
Jin Gu, Hu Fu, Xuegong Zhang, Yanda Li
BMC Bioinformatics. 2007; 8: 432. Published online 2007 November 8. doi: 10.1186/1471-2105-8-432
PMCID:
PMC2241842
Abstract Full Text PDF–405K Supplementary Material
A universal framework for regulatory element discovery across all genomes and data-types
Olivier Elemento, Noam Slonim, Saeed Tavazoie
Mol Cell. Author manuscript; available in PMC 2010 July 8.
Published in final edited form as: Mol Cell. 2007 October 26; 28(2): 337–350. doi: 10.1016/j.molcel.2007.09.027
PMCID:
PMC2900317
Abstract Full Text PDF–2.0M Supplementary Material
Sequences conserved by selection across mouse and human malaria species
Hideo Imamura, Jason H Persampieri, Jeffrey H Chuang
BMC Genomics. 2007; 8: 372. Published online 2007 October 15. doi: 10.1186/1471-2164-8-372
PMCID:
PMC2174483
Abstract Full Text PDF–467K Supplementary Material
Genome Dynamics of Short Oligonucleotides: The Example of Bacterial DNA Uptake Enhancing Sequences
Mohammed Bakkali
PLoS ONE. 2007; 2(8): e741. Published online 2007 August 15. doi: 10.1371/journal.pone.0000741
PMCID:
PMC1939737
Abstract Full Text PDF–536K Supplementary Material
Identification of candidate regulatory sequences in mammalian 3' UTRs by statistical analysis of oligonucleotide distributions
Davide Corà, Ferdinando Di Cunto, Michele Caselle, Paolo Provero
BMC Bioinformatics. 2007; 8: 174. Published online 2007 May 24. doi: 10.1186/1471-2105-8-174
PMCID:
PMC1904458
Abstract Full Text PDF–381K Supplementary Material
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