nklee's library 315 articles Export

	Bioinformatics for the 'bench biologist': how to find regulatory regions in genomic DNA [My Copy] Nature Immunology, Vol. 5, No. 8. (01 August 2004), pp. 768-774. by Julie Nardone, Dong U. Lee, K. Mark Ansel, Anjana Rao posted to review by nklee on 2009-11-18 23:56:24 as along with 5 people idonaldson ziquje moborg kianpeng Jporci
	Diversity and Complexity in DNA Recognition by Transcription Factors [My Copy] Science, 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 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 22 people and 1 group 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 factorâDNA interactions [My Copy] Genome Research, Vol. 19, No. 11. (3 November 2009), pp. 2090-2100. by Raluca GordÃ¢n, Alexander J. Hartemink, Martha L. Bulyk posted to no-tag by nklee on 2009-11-18 04:54:37 as along with 11 people 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, 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 3 people and 2 groups sebastien_vigneau operon polivares CTCF BergmanLab
	Connecting protein structure with predictions of regulatory sites [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 17. (24 April 2007), pp. 7068-7073. by Alexandre V. Morozov, Eric D. Siggia posted to protein-dna interaction by nklee on 2009-11-13 06:23:47 as along with 6 people and 2 groups maximilianh ana aalibes kaarsinogen johncumbers lusk structural_bioinformatics Bioinformatics
	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
	Probabilistic Inference of Transcription Factor Binding from Multiple Data Sources [My Copy] PLoS ONE, Vol. 3, No. 3. (26 March 2008), e1820. by Harri Lähdesmäki, Alistair G. Rust, Ilya Shmulevich posted to multiple features by nklee on 2009-10-25 22:38:18 as along with 4 people and 1 group isimpson dolchan druvus guhjy Jarman Lab
	W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data [My Copy] Bioinformatics, Vol. 25, No. 23. (1 December 2009), pp. 3191-3193. by Victor X. Jin, Jeff Apostolos, Naga S. Nagisetty, Peggy J. Farnham posted to motif chip by nklee on 2009-10-08 10:06:32 as along with 3 people idonaldson farhat maximilianh
	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
	Insights from genomic profiling of transcription factors [My Copy] Nature Reviews Genetics, Vol. 10, No. 9. (11 August 2009), pp. 605-616. by Peggy J. Farnham posted to review by nklee on 2009-09-09 05:25:02 as along with 17 people and 2 groups heliopais inesdesantiago fenghezi samanthacooper fpattyn druvus frohike stubrown qayub megraw TRHvidsten mkiyer ericrpaquet ilyashl jbhiatt idonaldson danmaclean Journal picks Chinnaiyan Lab
	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 3 people roys xili03 eskay
	Asap: A Framework for Over-Representation Statistics for Transcription Factor Binding Sites [My Copy] PLoS ONE, Vol. 3, No. 2. (20 February 2008), e1623. by Troels T. Marstrand, Jes Frellsen, Ida Moltke, et al.Martin Thiim, Eivind Valen, Dorota Retelska, Anders Krogh posted to benchmark kmer overrepresentation by nklee on 2009-08-05 07:57:48 as along with 3 people natstreet druvus heliopais
	Finding regulatory elements and regulatory motifs: a general probabilistic framework [My Copy] BMC Bioinformatics, Vol. 8, No. Suppl 6. (2007), S4. by Erik van Nimwegen posted to statistic by nklee on 2009-07-21 04:43:05 as along with 2 people shigepong maximilianh
	Evolutionary computation for discovery of composite transcription factor binding sites [My Copy] Nucl. Acids Res., Vol. 36, No. 21. (1 December 2008), e142. by Gary B. Fogel, V. William Porto, Gabor Varga, et al.Ernst R. Dow, Andrew M. Craven, David M. Powers, Harry B. Harlow, Eric W. Su, Jude E. Onyia, Chen Su posted to algorithm genetic by nklee on 2009-07-21 04:40:07 as along with 5 people wowalz lptolik idonaldson davfre maximilianh
	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
	Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes [My Copy] Nucl. Acids Res., Vol. 37, No. suppl_2. (1 July 2009), pp. W247-252. by Federico Zambelli, Graziano Pesole, Giulio Pavesi posted to over-representation by nklee on 2009-07-03 02:50:26 as along with 5 people druvus natstreet idonaldson nuin isimpson
	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
	Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 14. (15 July 2009), pp. 1715-1721. by Hyungwon Choi, Alexey I. Nesvizhskii, Debashis Ghosh, Zhaohui S. Qin posted to chip-chip by nklee on 2009-07-03 02:47:49 as along with 12 people and 1 group jfr tonamswish rdiaz fpattyn jcbarret guhjy hendrik85 inesdesantiago polivares ewilban1 idonaldson humburg Journal picks
	SPACER: identification of cis-regulatory elements with non-contiguous critical residues [My Copy] 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 3 people 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 4 people and 2 groups guhjy TRHvidsten nuin cisevol cis-regulatory-evolution BergmanLab
	Computational methods for the detection of cis-regulatory modules [My Copy] Brief Bioinform, Vol. 10, No. 5. (1 September 2009), pp. 509-524. by Peter Van Loo, Peter Marynen posted to cis module regulatory survey by nklee on 2009-06-26 02:21:14 as along with 5 people and 1 group reyez idonaldson kshameer cisevol druvus BergmanLab
	Towards accurate human promoter recognition: a review of currently used sequence features and classification methods [My Copy] Brief Bioinform, Vol. 10, No. 5. (1 September 2009), pp. 498-508. by Jia Zeng, Shanfeng Zhu, Hong Yan posted to survey by nklee on 2009-06-26 02:19:53 as along with 1 person reyez
	BEST: Binding-site Estimation Suite of Tools [My Copy] Bioinformatics, Vol. 21, No. 12. (15 June 2005), pp. 2909-2911. by Dongsheng Che, Shane Jensen, Liming Cai, Jun S. Liu posted to tools by nklee on 2009-06-04 10:56:53 as along with 1 person dquest
	Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data [My Copy] Nature Methods, Vol. 5, No. 9. (17 August 2008), pp. 829-834. by Anton Valouev, David S. Johnson, Andreas Sundquist, et al.Catherine Medina, Elizabeth Anton, Serafim Batzoglou, Richard M. Myers, Arend Sidow posted to chip genome large scale by nklee on 2009-04-23 00:31:43 as along with 19 people and 1 group jwfoley ewilban1 bertelsen stajich smiddha clearbluespring WanderingAengus polivares ptrobajo mdperry idonaldson gdb megraw kengg alhufton guhjy kjglennie bryankr maximilianh Mycology
	Evolutionary Conserved Motif Finder (ECMFinder) for genome-wide identification of clustered YY1- and CTCF-binding sites [My Copy] Nucl. Acids Res. (10 February 2009), gkp077. by Keunsoo Kang, Jae H. Chung, Joomyeong Kim posted to detection motif by nklee on 2009-04-09 10:49:32 as along with 3 people idonaldson wowalz maximilianh
	Genome-wide promoter analysis of the SOX4 transcriptional network in prostate cancer cells. [My Copy] Cancer research, Vol. 69, No. 2. (15 January 2009), pp. 709-717. by Christopher D. Scharer, Colleen D. McCabe, Mohamed Ali-Seyed, Michael F. Berger, Martha L. Bulyk, Carlos S. Moreno posted to chip by nklee on 2009-04-09 09:34:15 as along with 1 person and 1 group Stew Bioinformatics - CRUK
	ChIP-chip comes of age for genome-wide functional analysis. [My Copy] Cancer research, Vol. 66, No. 14. (15 July 2006), pp. 6899-6902. by Jiejun Wu, Laura T. Smith, Christoph Plass, Tim H-M H. Huang posted to chip review by nklee on 2009-04-09 09:30:44 as along with 5 people and 1 group bertelsen guhjy imedina weimingzhe tvdbulck BioinfoCIPF
	GADEM: a genetic algorithm guided formation of spaced dyads coupled with an EM algorithm for motif discovery. [My Copy] Journal of computational biology : a journal of computational molecular cell biology, Vol. 16, No. 2. (February 2009), pp. 317-329. by L. Li posted to algorithm genetic by nklee on 2009-03-23 04:39:04 as along with 1 person wowalz
	MTAP: The Motif Tool Assessment Platform [My Copy] BMC Bioinformatics, Vol. 9, No. Suppl 9. (2008) by Daniel Quest, Kathryn Dempsey, Mohammad Shafiullah, Dhundy Bastola, Hesham Ali posted to review survey by nklee on 2009-02-28 09:19:51 as along with 5 people wowalz cassj YuvalTabach Stew dquest
	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
	Large scale hierarchical clustering of protein sequences [My Copy] BMC Bioinformatics, Vol. 6, No. 1. (2005) by Antje Krause, Jens Stoye, Martin Vingron posted to clustering hierarchical by nklee on 2008-12-31 03:14:29 as along with 3 people cmzmasek kgutwin lonshy
	Discriminative motifs. [My Copy] J Comput Biol, Vol. 10, No. 3-4. (2003), pp. 599-615. by S. Sinha posted to kmer significance statistic by nklee on 2008-12-12 08:13:04 as along with 2 people wowalz dquest
	Comparison of methods for estimating the nucleotide substitution matrix [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008) by Maribeth Oscamou, Daniel Mcdonald, Von B. Yap, Gavin Huttley, Manuel Lladser, Rob Knight posted to matrix nucleotide substitution by nklee on 2008-12-10 08:16:15 as along with 4 people sconlan nuin treangen druvus
	CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes. [My Copy] BMC bioinformatics, Vol. 9, No. 1. (2008), 495. by Matthew S. Hestand, Michiel van Galen, Michel P. Villerius, Gert-Jan J. van Ommen, Johan T. den Dunnen, Peter A. 't Hoen posted to detection motif by nklee on 2008-12-10 08:15:18 as along with 9 people and 1 group farhat avilella heliopais lptolik nuin GustavoLacerda natstreet maximilianh druvus Ensembl Compara citations
	Comparative analysis of regulatory patterns in bacterial genomes [My Copy] Brief Bioinform, Vol. 1, No. 4. (1 January 2000), pp. 357-371. by Mikhail S. Gelfand, Pavel S. Novichkov, Elena S. Novichkov, Andrey A. Mironov posted to review by nklee on 2008-12-05 05:29:55 as along with 1 person xili03
	Genome wide identification of regulatory motifs in Bacillus subtilis. [My Copy] BMC bioinformatics, Vol. 4 (16 May 2003) by M. M. Mwangi, E. D. Siggia posted to analysis genome large scale wide by nklee on 2008-12-05 05:26:02 as
	An approach to identify over-represented cis-elements in related sequences [My Copy] Nucl. Acids Res., Vol. 31, No. 7. (1 April 2003), pp. 1995-2005. by Jiashun Zheng, Jiajin Wu, Zhirong Sun posted to detection motif threshold by nklee on 2008-12-05 04:11:35 as
	Clustering DNA sequences by feature vectors [My Copy] Molecular Phylogenetics and Evolution, Vol. 41, No. 1. (October 2006), pp. 64-69. by Libin Liu, Yee-Kin Ho, Stephen Yau posted to clustering dna by nklee on 2008-12-03 23:45:57 as along with 1 person and 2 groups dchughes G4ID Genetics-of-Gambling
	MEME: discovering and analyzing DNA and protein sequence motifs [My Copy] Nucl. Acids Res., Vol. 34, No. suppl_2. (1 July 2006), pp. W369-373. by Timothy L. Bailey, Nadya Williams, Chris Misleh, Wilfred W. Li posted to discovery motif tool by nklee on 2008-12-03 23:34:01 as along with 8 people stharward wowalz coldmeadow yevishere pansapiens bryankr dquest isimpson
	Cluster-Buster: finding dense clusters of motifs in DNA sequences [My Copy] Nucl. Acids Res., Vol. 31, No. 13. (1 July 2003), pp. 3666-3668. by Martin C. Frith, Michael C. Li, Zhiping Weng posted to clustering dna by nklee on 2008-12-03 23:22:31 as along with 3 people and 1 group Dulce isimpson indigoviolet EisenLab
	Spectral clustering of protein sequences. [My Copy] Nucleic acids research, Vol. 34, No. 5. (2006), pp. 1571-1580. by Alberto Paccanaro, James A. Casbon, Mansoor A. Saqi posted to clustering protein by nklee on 2008-12-03 23:11:29 as along with 2 people and 1 group paccanarolab druvus Paccanaro Lab
	Clustering of DNA Sequences in Human Promoters [My Copy] Genome Res., Vol. 14, No. 8. (1 August 2004), pp. 1562-1574. by Peter C. Fitzgerald, Andrey Shlyakhtenko, Alain A. Mir, Charles Vinson posted to clustering human of promoter by nklee on 2008-12-03 23:04:48 as along with 3 people myrtilus smiddha ale
	Genome-wide analysis of mammalian promoter architecture and evolution. [My Copy] Nature genetics, Vol. 38, No. 6. (28 June 2006), pp. 626-635. by Piero Carninci, Albin Sandelin, Boris Lenhard, et al.Shintaro Katayama, Kazuro Shimokawa, Jasmina Ponjavic, Colin A. Semple, Martin S. Taylor, Pär G. Engström, Martin C. Frith, Alistair R. Forrest, Wynand B. Alkema, Sin Lam L. Tan, Charles Plessy, Rimantas Kodzius, Timothy Ravasi, Takeya Kasukawa, Shiro Fukuda, Mutsumi Kanamori-Katayama, Yayoi Kitazume, Hideya Kawaji, Chikatoshi Kai, Mari Nakamura, Hideaki Konno, Kenji Nakano, Salim Mottagui-Tabar, Peter Arner, Alessandra Chesi, Stefano Gustincich, Francesca Persichetti, Harukazu Suzuki, Sean M. Grimmond, Christine A. Wells, Valerio Orlando, Claes Wahlestedt, Edison T. Liu, Matthias Harbers, Jun Kawai, Vladimir B. Bajic, David A. Hume, Yoshihide Hayashizaki posted to analysis genome wide by nklee on 2008-12-02 06:30:11 as along with 19 people and 4 groups rsaito guhjy antonkratz athma inesdesantiago rpatward hagechouchin443 djkt jfr xwbcn dchughes tabu samal nickluscombe xiaobeizhao cisevol eviledv gjuggler jasonflannick G4ID EBI-regulation Genetics-of-Gambling cis-regulatory-evolution
	MotifMap: a human genome-wide map of candidate regulatory motif sites [My Copy] Bioinformatics, Vol. 25, No. 2. (15 January 2009), pp. 167-174. by Xiaohui Xie, Paul Rigor, Pierre Baldi posted to human motif by nklee on 2008-11-28 07:38:10 as along with 11 people jakebiesinger kmdaily guhjy wowalz ilyashl jfr abizar heliopais idonaldson nuin djkt
	Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world [My Copy] Nucl. Acids Res., Vol. 36, No. 21. (1 December 2008), pp. 6688-6719. by Eugene V. Koonin, Yuri I. Wolf posted to survey by nklee on 2008-11-28 07:15:35 as along with 10 people and 2 groups pkm skembel Huub_odc druvus johanviklund sbottani Katje barriot neils aramata Centre de Recherches Interdisciplinaires microbiology_nijmegen
	Ab initio identification of putative human transcription factor binding sites by comparative genomics. [My Copy] BMC bioinformatics, Vol. 6 (2005) by D. Corà, C. Herrmann, C. Dieterich, F. Di Cunto, P. Provero, M. Caselle posted to discovery integrated motif by nklee on 2008-11-27 07:56:39 as along with 1 person nuin
	Wide-scale analysis of human functional transcription factor binding reveals a strong bias towards the transcription start site. [My Copy] PLoS ONE, Vol. 2, No. 8. (2007) by Y. Tabach, R. Brosh, Y. Buganim, et al.A. Reiner, O. Zuk, A. Yitzhaky, M. Koudritsky, V. Rotter, E. Domany posted to detection motif promoter by nklee on 2008-11-24 06:15:09 as along with 1 person YuvalTabach
	Positional distribution of human transcription factor binding sites. [My Copy] Nucleic acids research (25 October 2008) by Mark Koudritsky, Eytan Domany posted to dataset distribution human position by nklee on 2008-11-24 06:12:11 as along with 9 people and 2 groups daforerog jfr jforman ghattem barriot fpattyn maximilianh idonaldson nuin SIMR bioinformatics BenosLab
	Motif Tool Manager: a web-based framework for motif discovery. [My Copy] Bioinformatics (Oxford, England), 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 5 people wowalz maximilianh nuin natstreet druvus

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nklee's library 315 articles Export

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