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	Diversity and complexity in DNA recognition by transcription factors. [My Copy] Science (New York, N.Y.), Vol. 324, No. 5935. (26 June 2009), pp. 1720-1723. by Gwenael Badis, Michael F. Berger, Anthony A. Philippakis, et al.Shaheynoor Talukder, Andrew R. Gehrke, Savina A. Jaeger, Esther T. Chan, Genita Metzler, Anastasia Vedenko, Xiaoyu Chen, Hanna Kuznetsov, Chi-Fong F. Wang, David Coburn, Daniel E. Newburger, Quaid Morris, Timothy R. Hughes, Martha L. Bulyk posted to no-tag by nklee on 2009-11-18 04:56:23 as along with 25 people and 1 group vingron bsamal sebastien_vigneau sconlan isimpson jbhiatt daforerog absterga mingzhi galka8_diploma fenghezi TRHvidsten ilyashl cambray rpatward tibbitts dpollard siebert JustinCrocker burak aalibes dipenps roys emptyhb tmmurali RockmanLab
	Distinguishing direct versus indirect transcription factor-DNA interactions. [My Copy] Genome research, Vol. 19, No. 11. (3 November 2009), pp. 2090-2100. by Raluca Gordân, Alexander J. Hartemink, Martha L. Bulyk posted to no-tag by nklee on 2009-11-18 04:54:37 as along with 13 people roys sebastien_vigneau oannes djkt vingron venancio owhitney tmmurali emptyhb idonaldson maximilianh jbhiatt frohike
	Exhaustive Search for Over-represented DNA Sequence Motifs with CisFinder [My Copy] DNA Res In DNA Res, Vol. 16, No. 5. (1 October 2009), pp. 261-273. by Alexei A. Sharov, Minoru S. H. Ko posted to no-tag by nklee on 2009-11-18 04:54:01 as along with 4 people and 2 groups bsamal sebastien_vigneau operon polivares CTCF BergmanLab
	Quantitative evaluation of protein-DNA interactions using an optimized knowledge-based potential [My Copy] Nucl. Acids Res., Vol. 33, No. 2. (26 January 2005), pp. 546-558. by Zhijie Liu, Fenglou Mao, Jun-tao Guo, et al.Bo Yan, Peng Wang, Youxing Qu, Ying Xu posted to no-tag by nklee on 2009-11-13 05:20:09 as along with 2 people and 1 group kaarsinogen oannes Regulomics_UCHSC
	Chipper: discovering transcription-factor targets from chromatin immunoprecipitation microarrays using variance stabilization [My Copy] Genome Biology, Vol. 6, No. 11. (2005), R96. by Francis Gibbons, Markus Proft, Kevin Struhl, Frederick Roth posted to no-tag by nklee on 2009-10-03 03:54:58 as along with 3 people and 1 group humburg oelemento blobbybirdman Myxo group
	A Semi-Supervised Method for Predicting Transcription Factor–Gene Interactions in Escherichia coli [My Copy] PLoS Comput Biol, Vol. 4, No. 3. (28 March 2008), e1000044. by Jason Ernst, Qasim K. Beg, Krin A. Kay, Gábor Balázsi, Zoltán N. Oltvai, Ziv Bar-Joseph posted to no-tag by nklee on 2009-08-05 08:21:56 as along with 4 people tienholin roys xili03 eskay
	A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes [My Copy] BMC Genomics, Vol. 9, No. 1. (31 October 2008), 517. by Stefan Kurtz, Apurva Narechania, Joshua Stein, Doreen Ware posted to no-tag by nklee on 2009-07-06 08:29:51 as along with 5 people skembel timflutre malcook operon treangen
	Estimating the posterior probability that genome-wide association findings are true or false [My Copy] Bioinformatics, Vol. 25, No. 14. (15 July 2009), pp. 1807-1813. by Jozsef Bukszar, Joseph L. McClay, Edwin J. C. G. van den Oord posted to no-tag by nklee on 2009-07-03 02:50:01 as along with 3 people zufar djkt guhjy
	SPACER: identification of cis-regulatory elements with non-contiguous critical residues [My Copy] Bioinformatics In Bioinformatics, Vol. 23, No. 8. (15 April 2007), pp. 1029-1031. by Arijit Chakravarty, Jonathan M. Carlson, Radhika S. Khetani, Charles E. DeZiel, Robert H. Gross posted to no-tag by nklee on 2009-07-02 02:46:43 as along with 4 people bsamal maximilianh wenhan csdhwang
	Binding Site Graphs: A New Graph Theoretical Framework for Prediction of Transcription Factor Binding Sites [My Copy] PLoS Comput Biol, Vol. 3, No. 5. (11 May 2007), e90. by Timothy E. Reddy, Charles DeLisi, Boris E. Shakhnovich posted to no-tag by nklee on 2009-07-02 02:25:14 as along with 7 people and 1 group pradiptaray aalibes dpollard medic0747 GustavoLacerda mircea marti EisenLab
	Affinity Density: a novel genomic approach to the identification of transcription factor regulatory targets. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 13. (1 July 2009), pp. 1617-1624. by Dennis J. Hazelett, Daniel L. Lakeland, Joseph B. Weiss posted to no-tag by nklee on 2009-06-26 02:28:08 as along with 5 people and 2 groups maximilianh guhjy TRHvidsten nuin cisevol cis-regulatory-evolution BergmanLab
	Compound poisson approximation of the number of occurrences of a position frequency matrix (PFM) on both strands. [My Copy] Journal of computational biology : a journal of computational molecular cell biology, Vol. 15, No. 6. (g 2008), pp. 547-564. by U. J. Pape, S. Rahmann, F. Sun, M. Vingron posted to no-tag by nklee on 2009-01-21 08:11:18 as along with 1 person wowalz
	Motif Tool Manager: a web-based framework for motif discovery [My Copy] Bioinformatics (Oxford, England) In Bioinformatics, Vol. 24, No. 24. (15 December 2008), pp. 2930-2931. by Vinhthuy Phan, Nicholas A. Furlotte posted to no-tag by nklee on 2008-11-24 06:11:12 as along with 6 people bsamal wowalz maximilianh nuin natstreet druvus
	Factors affecting the concordance between orthologous gene trees and species tree in bacteria [My Copy] BMC Evolutionary Biology, Vol. 8 (30 October 2008), 300. by Santiago Castillo-Ramirez, Victor Gonzalez posted to no-tag by nklee on 2008-11-01 23:29:04 as along with 1 person and 1 group djkt iSEEM
	Distance conservation of transcription regulatory motifs in human promoters [My Copy] Computational Biology and Chemistry (10 July 2008) by J. Lu, L. Luo, Y. Zhang posted to no-tag by nklee on 2008-10-24 05:17:25 as
	Automated Hierarchical Density Shaving: A robust, automated clustering and visualization framework for large biological datasets [My Copy] Computational Biology and Bioinformatics, IEEE/ACM Transactions on, Vol. 11, No. 1. (2009), pp. 1-1. by G. Gupta, A. Liu, Ghosh posted to no-tag by nklee on 2008-09-25 05:32:25 as
	Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology [My Copy] Systematic Zoology, Vol. 20, No. 4. (1971), pp. 406-416. by Walter M. Fitch posted to no-tag by nklee on 2008-08-27 01:44:34 as along with 1 person BioNica
	Deterministic annealing EM algorithm [My Copy] Neural Networks, Vol. 11, No. 2. (31 March 1998), pp. 271-282. by N. Ueda posted to no-tag by nklee on 2008-07-16 07:07:00 as along with 1 person zhengyun
	A profile-based deterministic sequential Monte Carlo algorithm for motif discovery. [My Copy] Bioinformatics (Oxford, England), Vol. 24, No. 1. (1 January 2008), pp. 46-55. by K. C. Liang, X. Wang, D. Anastassiou posted to no-tag by nklee on 2008-04-01 08:23:43 as along with 7 people and 1 group bsamal wowalz grahamc cjeans maximilianh idonaldson isimpson Motif Discovery
	SCPD: a promoter database of the yeast Saccharomyces cerevisiae. [My Copy] Bioinformatics, Vol. 15, No. 7-8. (g 1999), pp. 607-611. by J. Zhu, M. Q. Zhang posted to no-tag by nklee on 2008-04-01 02:00:27 as along with 4 people chad_davis xiaobeizhao lusk njcitulike
	An Efficient Cis-Element Discovery Method Using Multiple Sequence Comparisons Based on Evolutionary Relationships [My Copy] Genomics, Vol. 71, No. 2. (15 January 2001), pp. 260-262. by Kenta Sumiyama, Chang-Bae Kim, Frank H. Ruddle posted to no-tag by nklee on 2008-03-25 21:28:19 as
	Motif discovery by monotone scores [My Copy] Discrete Applied Mathematics In Computational Molecular Biology Series, Issue V, Vol. 155, No. 6-7. (1 April 2007), pp. 695-706. by Alberto Apostolico, Cinzia Pizzi posted to no-tag by nklee on 2008-03-25 21:22:39 as along with 1 person wowalz
	SeqAn an efficient, generic C++ library for sequence analysis. [My Copy] BMC bioinformatics, Vol. 9, No. 1. (2008) by Andreas Döring, David Weese, Tobias Rausch, Knut Reinert posted to no-tag by nklee on 2008-01-10 05:18:25 as along with 16 people aheilbut MarcelSchulz n00c druvus mmartin dquest daforerog groepl guhjy chad_davis laughcry ryanraaum barriot mailund magusina reyez
	Informative priors based on transcription factor structural class improve de novo motif discovery [My Copy] Bioinformatics, Vol. 22, No. 14. (15 July 2006), pp. e384-392. by Leelavati Narlikar, Raluca Gordan, Uwe Ohler, Alexander J. Hartemink posted to no-tag by nklee on 2008-01-01 04:36:14 as along with 6 people frohike megraw maximilianh dquest idonaldson yevishere
	A Universal Framework for Regulatory Element Discovery across All Genomes and Data Types [My Copy] Molecular Cell, Vol. 28, No. 2. (26 October 2007), pp. 337-350. by Olivier Elemento, Noam Slonim, Saeed Tavazoie posted to no-tag by nklee on 2008-01-01 04:35:44 as along with 17 people and 2 groups cerca ilyashl TRHvidsten leelarcombe kieran101 ana brant cwbrown aswin cjeans zwang cabbagezs maximilianh idonaldson sb_journal_club kristen barwil EisenLab Motif Discovery
	Data Augmentation Algorithms for Detecting Conserved Domains in Protein Sequences: A Comparative Study [My Copy] J. Proteome Res. (15 December 2007) by Chengpeng Bi posted to no-tag by nklee on 2008-01-01 01:08:03 as
	Getting Started in Probabilistic Graphical Models [My Copy] PLoS Computational Biology, Vol. 3, No. 12. (1 December 2007), e252. by Edoardo M. Airoldi posted to no-tag by nklee on 2008-01-01 01:07:27 as along with 14 people and 1 group buyske mhamada guhjy balicea AbnerCYH stajich cjeans GustavoLacerda GeeSharpMinor sobolevnrm cabbagezs biehl softsimu jfr baker-group
	Exploring Conservation of Transcription Factor Binding Sites with CONREAL. [My Copy] Methods Mol Biol, Vol. 395 (2007), pp. 437-448. by E. Berezikov, V. Guryev, E. Cuppen posted to no-tag by nklee on 2007-12-19 21:20:26 as along with 1 person maximilianh
	TFCONES: A database of vertebrate transcription factor-encoding genes and their associated conserved noncoding elements [My Copy] BMC Genomics, Vol. 8 (29 November 2007), 441. by Alison P. Lee, Yuchen Yang, Sydney Brenner, Byrappa Venkatesh posted to no-tag by nklee on 2007-12-19 21:20:18 as along with 3 people maximilianh yevishere guhjy
	Transcriptional similarities, dissimilarities, and conservation of cis-elements in duplicated genes of Arabidopsis. [My Copy] Plant Physiol, Vol. 136, No. 2. (October 2004), pp. 3009-3022. by G. Haberer, T. Hindemitt, B. C. Meyers, K. F. Mayer posted to no-tag by nklee on 2007-12-19 03:21:13 as along with 2 people and 1 group ushishir cisevol cis-regulatory-evolution
	Efficient and accurate P-value computation for Position Weight Matrices [My Copy] Algorithms for Molecular Biology, Vol. 2, No. 1. (2007) by Helene Touzet, Jean S. Varre posted to no-tag by nklee on 2007-12-12 05:56:53 as along with 2 people barriot xili03
	Determining promoter location based on DNA structure first-principles calculations. [My Copy] Genome Biology, Vol. 8, No. 12. (2007) by Ramon J. Goni, Alberto Perez, David Torrents, Modesto Orozco posted to no-tag by nklee on 2007-12-12 04:40:44 as along with 4 people orzenil megraw cjeans maximilianh
	Penalized likelihood for sparse contingency tables with an application to full-length cDNA libraries [My Copy] BMC Bioinformatics, Vol. 8 (11 December 2007), 476. by Corinne Dahinden, Giovanni Parmigiani, Mark C. Emerick, Peter Buhlmann posted to no-tag by nklee on 2007-12-12 03:32:45 as along with 1 person ryanraaum
	Integrating genomic data to predict transcription factor binding. [My Copy] Genome Inform Ser Workshop Genome Inform, Vol. 16, No. 1. (2005), pp. 83-94. by D. T. Holloway, M. Kon, C. DeLisi posted to no-tag by nklee on 2007-11-29 21:55:02 as along with 3 people and 2 groups dpollard malcook adsmitty SIMR bioinformatics EisenLab
	Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors [My Copy] BMC Bioinformatics, Vol. 8, No. 1. (09 November 2007), 437. by Xueping Yu, Jimmy Lin, Donald Zack, Jiang Qian posted to no-tag by nklee on 2007-11-12 00:59:03 as along with 10 people roys isimpson guhjy chad_davis mikaelhuss maximilianh idonaldson njcitulike bootsy snow_dragon
	Reliable prediction of transcription factor binding sites by phylogenetic verification. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 47. (22 November 2005), pp. 16945-16950. by X. Li, S. Zhong, W. H. Wong posted to no-tag by nklee on 2007-10-23 06:21:49 as along with 2 people xwbcn postrational
	fREDUCE: Detection of degenerate regulatory elements using correlation with expression [My Copy] BMC Bioinformatics, Vol. 8, No. 1. (2007) by Randy Wu, Christina Chaivorapol, Jiashun Zheng, Hao Li, Shoudan Liang posted to no-tag by nklee on 2007-10-18 05:55:58 as along with 1 person maximilianh
	Computational identification of transcription factor binding sites by functional analysis of sets of genes sharing overrep-resented upstream motifs [My Copy] BMC Bioinformatics, Vol. 5, No. 1. (2004) by Davide Cora, Ferdinando Di Cunto, Paolo Provero, Lorenzo Silengo, Michele Caselle posted to no-tag by nklee on 2007-10-17 04:05:19 as along with 1 person nuin
	A bottom-up approach to gene regulation. [My Copy] Nature, Vol. 439, No. 7078. (16 February 2006), pp. 856-860. by Nicholas J. Guido, Xiao Wang, David Adalsteinsson, et al.David McMillen, Jeff Hasty, Charles R. Cantor, Timothy C. Elston, J. J. Collins posted to no-tag by nklee on 2007-10-10 23:26:06 as along with 18 people and 2 groups genocad bertelsen Scis0000002 raik rklancer snuppepuppan guhjy okarsligil bayesian balicea samal madhadron balabu johncumbers mmt proulx dbikard tmmurali Bioinformatics SynBioSys
	Enhancing the prediction of transcription factor binding sites by incorporating structural properties and nucleotide covariations. [My Copy] J Comput Biol, Vol. 13, No. 4. (May 2006), pp. 929-945. by S. Gunewardena, P. Jeavons, Z. Zhang posted to no-tag by nklee on 2007-10-10 23:25:03 as along with 2 people and 1 group dpollard samal EisenLab
	Semi-supervised clustering by seeding [My Copy] (2002) by S. Basu, A. Banerjee, R. Mooney posted to no-tag by nklee on 2007-10-10 23:24:05 as along with 4 people sona samal anon_pl jread82
	Integrated analysis of yeast regulatory sequences for biologically linked clusters of genes. [My Copy] Funct Integr Genomics, Vol. 3, No. 3. (July 2003), pp. 125-134. by A. Sandelin, A. Höglund, B. Lenhard, W. W. Wasserman posted to no-tag by nklee on 2007-10-08 00:59:06 as along with 2 people aalibes xili03
	Cooperative co-evolutionary algorithm-how to evaluate a module? [My Copy] Combinations of Evolutionary Computation and Neural Networks, 2000 IEEE Symposium on (2000), pp. 150-157. by Q. F. Zhao, O. Hammami, K. Kuroda, K. Saito posted to no-tag by nklee on 2007-10-08 00:01:57 as along with 2 people nsamways cwoodward
	Computer-assisted identification of cell cycle-related genes: new targets for E2F transcription factors, [My Copy] Journal of Molecular Biology, Vol. 309, No. 1. (25 May 2001), pp. 99-120. by Alexander E. Kel, Olga V. Kel-Margoulis, Peggy J. Farnham, Stephanie M. Bartley, Edgar Wingender, Michael Q. Zhang posted to no-tag by nklee on 2007-09-30 23:46:04 as along with 1 person tuck
	Statistical significance of cis-regulatory modules [My Copy] BMC Bioinformatics, Vol. 8, No. 1. (2007) by Dustin Schones, Andrew Smith, Michael Zhang posted to no-tag by nklee on 2007-09-28 08:16:02 as along with 10 people and 1 group druvus indigoviolet dpollard dquest sebastien_vigneau shigepong SeungjoonOh GustavoLacerda xili03 sconlan EisenLab
	Support Vector Machine-based method for predicting subcellular localization of mycobacterial proteins using evolutionary information and motifs [My Copy] BMC Bioinformatics, Vol. 8 (13 September 2007), 337. by Mamoon Rashid, Sudipto Saha, Gajendra P. S. Raghava posted to no-tag by nklee on 2007-09-28 08:09:17 as
	CLUSS: Clustering of protein sequences based on a new similarity measure [My Copy] BMC Bioinformatics, Vol. 8 (04 August 2007), 286. by Abdellali Kelil, Shengrui Wang, Ryszard Brzezinski, Alain Fleury posted to no-tag by nklee on 2007-09-28 08:07:27 as along with 4 people druvus grahamc ninch bobychan
	Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP-chip data [My Copy] BMC Bioinformatics, Vol. 8 (03 August 2007), 283. by Xiangdong Liu, Walter J. Jessen, Siva Sivaganesan, Bruce J. Aronow, Mario Medvedovic posted to no-tag by nklee on 2007-09-28 08:05:40 as along with 3 people and 1 group bais dquest naegele ic4
	Comparative analysis of long DNA sequences by per element information content using different contexts [My Copy] BMC Bioinformatics, Vol. 8, No. Suppl 2. (2007) by Trevor Dix, David Powell, Lloyd Allison, Julie Bernal, Samira Jaeger, Linda Stern posted to no-tag by nklee on 2007-09-28 08:04:38 as along with 1 person jengeldk
	Transcriptional Regulation by Competing Transcription Factor Modules [My Copy] PLoS Computational Biology, Vol. 2, No. 12. (1 December 2006), e164. by Rutger Hermsen, Sander Tans, Ten posted to no-tag by nklee on 2007-09-26 23:38:06 as along with 3 people wnpx nirfriedman zwang

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nklee's no-tag [52 articles] Export Sort

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