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Computational prediction of transcription-factor binding site locations
Martha L Bulyk
Genome Biol. 2004; 5(1): 201. Published online 2003 December 23. doi: 10.1186/gb-2003-5-1-201
PMCID:
PMC395725
Abstract Full Text PDF–129K
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 Is Cited by the Following 62 Articles in this Archive:
Predicting Target DNA Sequences of DNA-Binding Proteins Based on Unbound Structures
Chien-Yu Chen, Ting-Ying Chien, Chih-Kang Lin, Chih-Wei Lin, Yi-Zhong Weng, Darby Tien-Hao Chang
PLoS One. 2012; 7(2): e30446. Published online 2012 February 1. doi: 10.1371/journal.pone.0030446
PMCID:
PMC3270014
Abstract Full Text PDF–710K
RegNetB: Predicting Relevant Regulator-Gene Relationships in Localized Prostate Tumor Samples
Angel Alvarez, Peter J Woolf
BMC Bioinformatics. 2011; 12: 243. Published online 2011 June 17. doi: 10.1186/1471-2105-12-243
PMCID:
PMC3128037
Abstract Full Text PDF–338K Supplementary Material
Quantitative Models of the Mechanisms That Control Genome-Wide Patterns of Transcription Factor Binding during Early Drosophila Development
Tommy Kaplan, Xiao-Yong Li, Peter J. Sabo, Sean Thomas, John A. Stamatoyannopoulos, Mark D. Biggin, Michael B. Eisen
PLoS Genet. 2011 February; 7(2): e1001290. Published online 2011 February 3. doi: 10.1371/journal.pgen.1001290
PMCID:
PMC3033374
Abstract Full Text PDF–2.2M Supplementary Material
UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein–DNA interactions
Kimberly Robasky, Martha L. Bulyk
Nucleic Acids Res. 2011 January; 39(Database issue): D124–D128. Published online 2010 October 30. doi: 10.1093/nar/gkq992
PMCID:
PMC3013812
Abstract Full Text PDF–6.7M
Using protein design algorithms to understand the molecular basis of disease caused by protein–DNA interactions: the Pax6 example
Andreu Alibés, Alejandro D. Nadra, Federico De Masi, Martha L. Bulyk, Luis Serrano, François Stricher
Nucleic Acids Res. 2010 November; 38(21): 7422–7431. Published online 2010 August 4. doi: 10.1093/nar/gkq683
PMCID:
PMC2995082
Abstract Full Text PDF–3.0M Supplementary Material
Conservation and Regulatory Associations of a Wide Affinity Range of Mouse Transcription Factor Binding Sites
Savina A. Jaeger, Esther T. Chan, Michael F. Berger, Rolf Stottmann, Timothy R. Hughes, Martha L. Bulyk
Genomics. Author manuscript; available in PMC 2011 April 1.
Published in final edited form as: Genomics. 2010 April; 95(4): 185–195. Published online 2010 January 15. doi: 10.1016/j.ygeno.2010.01.002
PMCID:
PMC2848887
Abstract Full Text PDF–2.1M Supplementary Material
Non-consensus GLI binding sites in Hedgehog target gene regulation
Martina Winklmayr, Carmen Schmid, Sandra Laner-Plamberger, Alexandra Kaser, Fritz Aberger, Thomas Eichberger, Anna-Maria Frischauf
BMC Mol Biol. 2010; 11: 2. Published online 2010 January 13. doi: 10.1186/1471-2199-11-2
PMCID:
PMC2830928
Abstract Full Text PDF–1.0M
DISPARE: DIScriminative PAttern REfinement for Position Weight Matrices
Isabelle da Piedade, Man-Hung Eric Tang, Olivier Elemento
BMC Bioinformatics. 2009; 10: 388. Published online 2009 November 26. doi: 10.1186/1471-2105-10-388
PMCID:
PMC2788558
Abstract Full Text PDF–1.7M Supplementary Material
Modeling the Quantitative Specificity of DNA-Binding Proteins from Example Binding Sites
Dana S. F. Homsi, Vineet Gupta, Gary D. Stormo
PLoS One. 2009; 4(8): e6736. Published online 2009 August 25. doi: 10.1371/journal.pone.0006736
PMCID:
PMC2726951
Abstract Full Text PDF–599K
An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia
Yair Benita, Hirotoshi Kikuchi, Andrew D. Smith, Michael Q. Zhang, Daniel C. Chung, Ramnik J. Xavier
Nucleic Acids Res. 2009 August; 37(14): 4587–4602. Published online 2009 August. doi: 10.1093/nar/gkp425
PMCID:
PMC2724271
Abstract Full Text PDF–2.3M Supplementary Material
Identifying regulatory elements in eukaryotic genomes
Leelavati Narlikar, Ivan Ovcharenko
Brief Funct Genomic Proteomic. 2009 July; 8(4): 215–230. Published online 2009 June 4. doi: 10.1093/bfgp/elp014
PMCID:
PMC2764519
Abstract Full Text PDF–177K
Prediction of mono- and di-nucleotide-specific DNA-binding sites in proteins using neural networks
Munazah Andrabi, Kenji Mizuguchi, Akinori Sarai, Shandar Ahmad
BMC Struct Biol. 2009; 9: 30. Published online 2009 May 13. doi: 10.1186/1472-6807-9-30
PMCID:
PMC2693520
Abstract Full Text PDF–1.9M Supplementary Material
An Integrated Approach to Identifying Cis-Regulatory Modules in the Human Genome
Kyoung-Jae Won, Saurabh Agarwal, Li Shen, Robert Shoemaker, Bing Ren, Wei Wang
PLoS ONE. 2009; 4(5): e5501. Published online 2009 May 12. doi: 10.1371/journal.pone.0005501
PMCID:
PMC2677454
Abstract Full Text PDF–675K
Evolutionary Conserved Motif Finder (ECMFinder) for genome-wide identification of clustered YY1- and CTCF-binding sites
Keunsoo Kang, Jae Hoon Chung, Joomyeong Kim
Nucleic Acids Res. 2009 April; 37(6): 2003–2013. Published online 2009 April. doi: 10.1093/nar/gkp077
PMCID:
PMC2665242
Abstract Full Text PDF–8.3M Supplementary Material
An Algorithm for Identifying Novel Targets of Transcription Factor Families: Application to Hypoxia-inducible Factor 1 Targets
Yue Jiang, Bojan Cukic, Donald A. Adjeroh, Heath D. Skinner, Jie Lin, Qingxi J. Shen, Bing-Hua Jiang
Cancer Inform. 2009; 7: 75–89. Published online 2009 March 4.
PMCID:
PMC2664698
Abstract Full Text PDF–355K
Caenorhabditis elegans cisRED: a catalogue of conserved genomic elements
Monica C. Sleumer, Mikhail Bilenky, An He, Gordon Robertson, Nina Thiessen, Steven J. M. Jones
Nucleic Acids Res. 2009 March; 37(4): 1323–1334. Published online 2009 March. doi: 10.1093/nar/gkn1041
PMCID:
PMC2651782
Abstract Full Text PDF–5.9M Supplementary Material
A SILAC-based DNA protein interaction screen that identifies candidate binding proteins to functional DNA elements
Gerhard Mittler, Falk Butter, Matthias Mann
Genome Res. 2009 February; 19(2): 284–293. doi: 10.1101/gr.081711.108
PMCID:
PMC2652210
Abstract Full Text PDF–988K
A Primer on Regression Methods for Decoding cis-Regulatory Logic
Debopriya Das, Matteo Pellegrini, Joe W. Gray
PLoS Comput Biol. 2009 January; 5(1): e1000269. Published online 2009 January 30. doi: 10.1371/journal.pcbi.1000269
PMCID:
PMC2607548
Full Text PDF–265K
Integrating sequence, evolution and functional genomics in regulatory genomics
Martin Vingron, Alvis Brazma, Richard Coulson, Jacques van Helden, Thomas Manke, Kimmo Palin, Olivier Sand, Esko Ukkonen
Genome Biol. 2009; 10(1): 202. Published online 2009 January 30. doi: 10.1186/gb-2009-10-1-202
PMCID:
PMC2687781
Abstract Full Text PDF–822K
CompMoby: Comparative MobyDick for detection of cis-regulatory motifs
Christina Chaivorapol, Collin Melton, Grace Wei, Ru-Fang Yeh, Miguel Ramalho-Santos, Robert Blelloch, Hao Li
BMC Bioinformatics. 2008; 9: 455. Published online 2008 October 27. doi: 10.1186/1471-2105-9-455
PMCID:
PMC2605473
Abstract Full Text PDF–1.6M Supplementary Material
A high-throughput percentage-of-binding strategy to measure binding energies in DNA–protein interactions: application to genome-scale site discovery
Xiaohu Wang, Haichun Gao, Yufeng Shen, George M. Weinstock, Jizhong Zhou, Timothy Palzkill
Nucleic Acids Res. 2008 September; 36(15): 4863–4871. Published online 2008 September. doi: 10.1093/nar/gkn477
PMCID:
PMC2528174
Abstract Full Text PDF–6.3M Supplementary Material
Design of Compact, Universal DNA Microarrays for Protein Binding Microarray Experiments
Anthony A. Philippakis, Aaron M. Qureshi, Michael F. Berger, Martha L. Bulyk
J Comput Biol. 2008 September; 15(7): 655–665. doi: 10.1089/cmb.2007.0114
PMCID:
PMC3203512
Abstract Full Text PDF–255K
STIF: Identification of stress-upregulated transcription factor binding sites in Arabidopsis thaliana
Ambika Shyam Sundar, Susan Mary Varghese, Khader Shameer, Nataraja Karaba, Makarla Udayakumar, Ramanathan Sowdhamini
Bioinformation. 2008; 2(10): 431–437. Published online 2008 July 30.
PMCID:
PMC2561162
Abstract Full Text PDF–299K Supplementary Material
Studies on DNA-binding selectivity of WRKY transcription factors lend structural clues into WRKY-domain function
Ingo Ciolkowski, Dierk Wanke, Rainer P. Birkenbihl, Imre E. Somssich
Plant Mol Biol. 2008 September; 68(1-2): 81–92. Published online 2008 June 4. doi: 10.1007/s11103-008-9353-1
PMCID:
PMC2493524
Abstract Full Text PDF–587K Supplementary Material
A generic approach to identify Transcription Factor-specific operator motifs; Inferences for LacI-family mediated regulation in Lactobacillus plantarum WCFS1
Christof Francke, Robert Kerkhoven, Michiel Wels, Roland J Siezen
BMC Genomics. 2008; 9: 145. Published online 2008 March 27. doi: 10.1186/1471-2164-9-145
PMCID:
PMC2329647
Abstract Full Text PDF–739K 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
DBD––taxonomically broad transcription factor predictions: new content and functionality
Derek Wilson, Varodom Charoensawan, Sarah K. Kummerfeld, Sarah A. Teichmann
Nucleic Acids Res. 2008 January; 36(Database issue): D88–D92. Published online 2008 January. doi: 10.1093/nar/gkm964
PMCID:
PMC2238844
Abstract Full Text PDF–4.6M
Architecture of the Sporulation-Specific Cdc14 Promoter from the Oomycete Phytophthora infestans
Audrey M. V. Ah-Fong, Qijun Xiang, Howard S. Judelson
Eukaryot Cell. 2007 December; 6(12): 2222–2230. Published online 2007 October 19. doi: 10.1128/EC.00328-07
PMCID:
PMC2168256
Abstract Full Text PDF–437K
Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses
Long Li, Qianqian Zhu, Xin He, Saurabh Sinha, Marc S Halfon
Genome Biol. 2007; 8(6): R101. Published online 2007 June 5. doi: 10.1186/gb-2007-8-6-r101
PMCID:
PMC2394749
Abstract Full Text PDF–1.1M Supplementary Material
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