nklee's library 309 articles Export

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	Factors influencing the identification of transcription factor binding sites by cross-species comparison. [My Copy] Genome Res, Vol. 12, No. 10. (October 2002), pp. 1523-1532. by L. A. McCue, W. Thompson, C. S. Carmack, C. E. Lawrence posted to cross-species by nklee on 2007-09-30 23:52:11 as along with 2 people kaarsinogen dquest
	Evolution of transcription factor DNA binding sites. [My Copy] Gene, Vol. 347, No. 2. (14 March 2005), pp. 255-263. by E. A. Kotelnikova, V. J. Makeev, M. S. Gelfand posted to binding consensus energy matrix position weight by nklee on 2007-09-30 23:47:15 as along with 4 people and 1 group balajis gpalidwor cisevol yevishere cis-regulatory-evolution
	Raising the estimate of functional human sequences. [My Copy] Genome Res (9 August 2007) by Michael Pheasant, John S S. Mattick posted to functional genome signal by nklee on 2007-09-19 23:35:06 as along with 11 people and 1 group galka8_diploma hdopazo guhjy jfr andersbj djkt grahamc lp2 cabbagezs ljs mimulus_99 microRNA
	Enumerating and Ranking Discrete Motifs [My Copy] pp. 202-209. by Craig, Komal S. Sethi, Thomas D. Wu, Douglas L. Brutlag posted to important by nklee on 2007-07-27 03:09:11 as
	Insights from genomic profiling of transcription factors [My Copy] Nat Rev Genet, 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 16 people and 2 groups inesdesantiago fenghezi samanthacooper fpattyn druvus frohike stubrown qayub megraw TRHvidsten mkiyer ericrpaquet ilyashl jbhiatt idonaldson danmaclean Journal picks Chinnaiyan 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
	Incorporating background frequency improves entropy-based residue conservation measures [My Copy] BMC Bioinformatics, Vol. 7 (17 August 2006), 385. by Kai Wang, Ram Samudrala posted to analysis conservation entropy by nklee on 2008-02-13 06:01:31 as along with 2 people marti bicko
	Large-Scale Discovery of Promoter Motifs in Drosophila melanogaster [My Copy] PLoS Comput Biol, Vol. 3, No. 1. (19 January 2007), e7. by Thomas A. Down, Casey M. Bergman, Jing Su, Tim J. P. Hubbard posted to drosophila melanogaster by nklee on 2008-02-01 06:11:17 as along with 11 people and 1 group daveGerrard ychromosome timhubbard lusk wowalz indigoviolet dpollard dquest SeungjoonOh emptyhb isimpson EisenLab
	A novel approach to identifying regulatory motifs in distantly related genomes [My Copy] Genome Biology, Vol. 6, No. 13. (2005) by Ruth Van Hellemont, Pieter Monsieurs, Gert Thijs, Bart De Moor, Yves Van de Peer, Kathleen Marchal posted to clustering comparative footprinting genomic by nklee on 2008-01-31 04:19:31 as along with 1 person wowalz
	Rank order metrics for quantifying the association of sequence features with gene regulation. [My Copy] Bioinformatics, Vol. 19, No. 2. (22 January 2003), pp. 212-218. by N. D. Clarke, J. A. Granek posted to hypergeometric significance statistical by nklee on 2008-01-28 00:09:55 as along with 2 people and 1 group kaspermunch xili03 Bioinformatics
	Transcriptional Regulatory Networks in Saccharomyces cerevisiae [My Copy] Science, Vol. 298, No. 5594. (25 October 2002), pp. 799-804. by Tong I. Lee, Nicola J. Rinaldi, Francois Robert, et al.Duncan T. Odom, Ziv Bar-Joseph, Georg K. Gerber, Nancy M. Hannett, Christopher T. Harbison, Craig M. Thompson, Itamar Simon, Julia Zeitlinger, Ezra G. Jennings, Heather L. Murray, D. Benjamin Gordon, Bing Ren, John J. Wyrick, Jean-Bosco Tagne, Thomas L. Volkert, Ernest Fraenkel, David K. Gifford, Richard A. Young posted to genomic yeast by nklee on 2008-01-01 23:51:40 as along with 31 people and 2 groups mjoach kmdaily kinop junehlee lillo80 camster snuppepuppan icases forluvoft ggrot alokm opheliav samal sameetmehta cconboy koller jguinney franklin timflutre jpoyatos lusk karfunkel mimulus_99 roys njcitulike brant kristallreiner Borelli Takayuki dquest siebert dbk-lab TNT
	Data clustering: a review [My Copy] ACM Computing Surveys, Vol. 31, No. 3. (1999), pp. 264-323. by A. K. Jain, M. N. Murty, P. J. Flynn posted to algorithm clustering review survey by nklee on 2008-01-01 04:15:05 as along with 24 people and 3 groups marquisdesade jmenche doitian radical V pdlug stanley jelsas sona gangli macowell mhaller ali grimm numata carueda microserf rahul aviad_work rchauhan sugarexpletive stewi2 MortMan shinichi3 tulip SRL BUiGEM
	Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions [My Copy] BMC Bioinformatics, Vol. 8, No. 1. (2007) by Victor Levitsky, Elena Ignatieva, Elena Ananko, et al.Igor Turnaev, Tatyana Merkulova, Nikolay Kolchanov, T. Hodgman posted to algorithm genetic by nklee on 2007-12-20 03:31:47 as along with 5 people druvus maximilianh yevishere csdhwang xili03
	Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome [My Copy] Genome Biology, Vol. 3, No. 12. (2002) by Casey Bergman, Barret Pfeiffer, Diego R. Limas, et al.Roger Hoskins, Andreas Gnirke, Chris Mungall, Adrienne Wang, Brent Kronmiller, Joanne Pacleb, Soo Park, Mark Stapleton, Kenneth Wan, Reed George, Pieter de Jong, Juan Botas, Gerald Rubin, Susan Celniker posted to comparative drosophila genome by nklee on 2007-12-19 01:54:54 as along with 5 people and 2 groups hrogers indigoviolet dpollard cisevol brant EisenLab cis-regulatory-evolution
	Position dependencies in transcription factor binding sites. [My Copy] Bioinformatics, Vol. 23, No. 8. (15 April 2007), pp. 933-941. by A. Tomovic, E. J. Oakeley posted to dependency position by nklee on 2007-11-29 21:56:11 as along with 2 people aalibes yevishere
	Sequencing and comparison of yeast species to identify genes and regulatory elements [My Copy] Nature, Vol. 423, No. 6937. (15 May 2003), pp. 241-254. by Manolis Kellis, Nick Patterson, Matthew Endrizzi, Bruce Birren, Eric S. Lander posted to comparative motif yeast by nklee on 2007-11-27 06:30:25 as along with 4 people Dulce kaarsinogen lyongu kmdaily
	Finding coevolving amino acid residues using row and column weighting of mutual information and multi-dimensional amino acid representation [My Copy] Algorithms for Molecular Biology, Vol. 2 (03 October 2007), 12. by Rodrigo Gouveia-Oliveira, Anders G. Pedersen posted to entropy information mutual by nklee on 2007-11-27 06:14:51 as along with 3 people bicko IrinaMoreira ca3295
	Unifying cost and information in information-theoretic competitive learning [My Copy] Neural Networks In IJCNN 2005, Vol. 18, No. 5-6. ( 2005), pp. 711-718. by Ryotaro Kamimura posted to entropy information learning network neural by nklee on 2007-11-15 20:45:06 as
	Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. [My Copy] Nature, Vol. 450, No. 7167. (8 November 2007), pp. 219-232. by A. Stark, M. F. Lin, P. Kheradpour, et al.J. S. Pedersen, L. Parts, J. W. Carlson, M. A. Crosby, M. D. Rasmussen, S. Roy, A. N. Deoras, J. G. Ruby, J. Brennecke, , , E. Hodges, A. S. Hinrichs, A. Caspi, B. Paten, S. W. Park, M. V. Han, M. L. Maeder, B. J. Polansky, B. E. Robson, S. Aerts, J. van Helden, B. Hassan, D. G. Gilbert, D. A. Eastman, M. Rice, M. Weir, M. W. Hahn, Y. Park, C. N. Dewey, L. Pachter, W. J. Kent, D. Haussler, E. C. Lai, D. P. Bartel, G. J. Hannon, T. C. Kaufman, M. B. Eisen, A. G. Clark, D. Smith, S. E. Celniker, W. M. Gelbart, M. Kellis posted to comparative genome by nklee on 2007-11-07 20:55:20 as along with 21 people and 3 groups heliopais anphony kieran101 Neeperando pradiptaray rouault druvus operon tmmurali djkt timflutre stajich lp2 cabbagezs hpaces roys caseybrown gjuggler shuzhens PetrovLab cisevol microRNA Mycology Drosophila-Genetics-Genomics-2008
	The Hierarchical Fast Learning Artificial Neural Network (HieFLANN)--An Autonomous Platform for Hierarchical Neural Network Construction [My Copy] Neural Networks, IEEE Transactions on In Neural Networks, IEEE Transactions on, Vol. 18, No. 6. (2007), pp. 1645-1657. by A. L. P. Tay, J. M. Zurada, L. P. Wong, J. Xu posted to heirarchical network neural by nklee on 2007-11-06 21:37:31 as
	Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data. [My Copy] BMC bioinformatics, Vol. 7 (2006) by Bertrand R. Huber, Martha L. Bulyk posted to filtering merging motifs by nklee on 2007-10-26 01:34:10 as along with 4 people and 2 groups Stew bryankr indigoviolet gpalidwor Bioinformatics - CRUK EisenLab
	Automated derivation and refinement of sequence length patterns for protein sequences using evolutionary computation [My Copy] Biosystems, Vol. 81, No. 3. (September 2005), pp. 247-254. by M. I. Sadowski, J. H. Parish, D. R. Westhead posted to algorithm computing evolutionary genetic by nklee on 2007-10-16 04:47:04 as
	Comparative analysis of regulatory motif discovery tools for transcription factor binding sites. [My Copy] Genomics Proteomics Bioinformatics, Vol. 5, No. 2. (May 2007), pp. 131-142. by W. Wei, X. D. Yu posted to discovery motif survey tools by nklee on 2007-10-08 00:00:39 as along with 3 people natstreet maximilianh heliopais
	A Study of Statistical Methods for Function Prediction of Protein Motifs [My Copy] Applied Bioinformatics, Vol. 3, No. 2-3. (2004), pp. 115-124. by Tao Tao, Cheng X. Zhai, Xinghua Lu, Hui Fang posted to motifs scoring statistical function by nklee on 2007-10-01 06:05:16 as
	Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. [My Copy] Genome Biol, Vol. 5, No. 9. (2004) by B. P. Berman, B. D. Pfeiffer, T. R. Laverty, et al.S. L. Salzberg, G. M. Rubin, M. B. Eisen, S. E. Celniker posted to enhancers by nklee on 2007-09-30 23:50:43 as along with 9 people and 3 groups emptyhb cajunsushi mbeisen indigoviolet adepace Stew cisevol maximilianh Auger EisenLab cis-regulatory-evolution Dead 60's
	Measuring similarities between transcription factor binding sites [My Copy] BMC Bioinformatics, Vol. 6, No. 1. (2005) by Szymon Kielbasa, Didier Gonze, Hanspeter Herzel posted to metric similarity by nklee on 2007-09-30 23:49:23 as along with 1 person aalibes
	The design of transcription-factor binding sites is affected by combinatorial regulation. [My Copy] Genome Biol, Vol. 6, No. 12. (2005) by Y. Bilu, N. Barkai posted to combinatorial regulation by nklee on 2007-09-30 23:46:30 as along with 7 people and 1 group chrn dpollard tabu samal adepace lewbin xili03 EisenLab
	MotifCombinator: a web-based tool to search for combinations of cis-regulatory motifs [My Copy] BMC Bioinformatics, Vol. 8 (22 March 2007), 100. by Mamoru Kato, Tatsuhiko Tsunoda posted to algorithm genetic by nklee on 2007-09-28 08:21:00 as along with 3 people and 1 group cwbrown idonaldson isimpson EisenLab
	Comparative Genomic [My Copy] Annu. Rev. Genomics Hum. Genet, Vol. 5 (2004), pp. 15-56. by Webb Miller, Kateryna D. Makova, Anton Nekrutenko, Ross C. Hardison posted to comparative genomic by nklee on 2007-09-26 09:24:02 as
	Multiple sequence alignment with user-defined anchor points [My Copy] Algorithms for Molecular Biology, Vol. 1 (19 April 2006), 6. by Burkhard Morgenstern, Sonja J. Prohaska, Dirk Pöhler, Peter F. Stadler posted to alignment anchored multiple by nklee on 2007-09-20 00:40:03 as
	Analysis of computational approaches for motif discovery [My Copy] Algorithms for Molecular Biology, Vol. 1, No. 1. (19 May 2006), 8. by Nan Li, Martin Tompa posted to analysis discovery motif tools by nklee on 2007-09-19 07:03:30 as along with 11 people and 2 groups wowalz yevishere ana barry tuck chad_davis dquest lusk maximilianh xi03 csdhwang structural_bioinformatics Bioinformatics
	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 (1 October 2009), btp570. 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 1 person 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
	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, 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 11 people and 1 group 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

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comparative	30
clustering	29
motif	25
genomic	17
algorithm	15
genome	14
yeast	14
discovery	13
network	13
neural	13
review	11
survey	11
dependency	10
genetic	10
statistics	10
analysis	7
chip	7
conservation	7
detection	7
footprinting	7
information	7
alignment	6
mixture	6
position	6
scale	6
entropy	5
hierarchical	5
large	5
model	5
similarity	5
binding	4
database	4
map	4
multiple	4
mutual	4
nucleosome	4
organizing	4
protein	4
self	4
statistical	4
computing	3
dataset	3
drosophila	3
evaluation	3
evolutionary	3
feature	3
function	3
gibbs	3
human	3
likelihood	3
matrix	3
maximum	3
prediction	3
promoter	3
regulatory	3
sequence	3
significance	3
statistic	3
tools	3
arabidopsis	2
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benchmarking	2
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dna	2
elements	2
energy	2
evolution	2
familial	2
genomics	2
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melanogaster	2
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of	2
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roc	2
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dropsophila	1
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theoretical	1
threshold	1
transition	1
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two	1
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up	1
web	1
xxx	1
yeasts	1

nklee's library 309 articles Export

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