idonaldson's library 265 articles Export

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	A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data--A case study using E2F1. [My Copy] Genome Res (19 October 2006) by Victor X X. Jin, Alina Rabinovich, Sharon L L. Squazzo, Roland Green, Peggy J J. Farnham posted to chip-chip crm tfbs tool by idonaldson on 2007-11-08 08:50:56 as along with 2 people aprasad jfr
	Discovering motifs with transcription factor domain knowledge. [My Copy] Pac Symp Biocomput (2007), pp. 472-483. by H. C. Leung, F. Y. Chin, B. M. Chan posted to motif-discovery tfbs tool by idonaldson on 2007-11-12 08:50:57 as along with 1 person maximilianh
	Mining Biological Networks for Unknown Pathways. [My Copy] Bioinformatics (30 August 2007) by Ali Cakmak, Gultekin Ozsoyoglu posted to go networks by idonaldson on 2007-11-06 09:38:08 as along with 8 people cswinburne guhjy tmmurali bluto shigepong cabbagezs acakmak mdstobbe
	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 cis-regulation crm tool by idonaldson on 2007-11-06 09:15:33 as along with 3 people and 1 group cwbrown nklee isimpson EisenLab
	Regulatory motif discovery using a population clustering evolutionary algorithm. [My Copy] IEEE/ACM Trans Comput Biol Bioinform, Vol. 4, No. 3. (p 2007), pp. 403-414. by M. A. Lones, A. M. Tyrrell posted to motif-discovery tool by idonaldson on 2007-10-22 09:26:24 as along with 6 people Dulce wowalz nklee xili03 csdhwang isimpson
	Discriminative motif discovery in DNA and protein sequences using the DEME algorithm. [My Copy] BMC bioinformatics, Vol. 8, No. 1. (2007) by E. Redhead, T. L. Bailey posted to motif-discovery tool by idonaldson on 2007-10-22 09:25:28 as along with 7 people and 1 group wowalz tmarscha dpollard cjeans nklee niallhaslam maximilianh EisenLab
	DBTSS: database of transcription start sites, progress report 2008 [My Copy] Nucl. Acids Res. (16 October 2007), gkm901. by Hiroyuki Wakaguri, Riu Yamashita, Yutaka Suzuki, Sumio Sugano, Kenta Nakai posted to promoter tool tss by idonaldson on 2007-10-22 09:22:09 as along with 2 people megraw guhjy
	Retrieve-ensembl-seq: user-friendly and large-scale retrieval of single or multi-genome sequences from Ensembl [My Copy] Bioinformatics, Vol. 25, No. 20. (15 October 2009), pp. 2739-2740. by Olivier Sand, Morgane Thomas-Chollier, Jacques van Helden posted to tool sequence retrieve ensembl by idonaldson on 2009-10-09 08:53:57 as along with 4 people druvus inesdesantiago natstreet sebastien_vigneau
	ChIP-seq accurately predicts tissue-specific activity of enhancers [My Copy] Nature, Vol. 457, No. 7231. (12 February 2009), pp. 854-858. by Axel Visel, Matthew J. Blow, Zirong Li, et al.Tao Zhang, Jennifer A. Akiyama, Amy Holt, Ingrid Plajzer-Frick, Malak Shoukry, Crystal Wright, Feng Chen, Veena Afzal, Bing Ren, Edward M. Rubin, Len A. Pennacchio posted to chip-seq tissue-specific by idonaldson on 2009-02-12 09:32:17 as along with 22 people and 2 groups tonamswish ewilban1 samanthacooper ashkelon13 isimpson gdb dnewburger jochenG bertelsen oelemento rpatward cajunsushi WanderingAengus absterga provero cassj anphony dpollard caseybrown biomcgary xingxu djkt RockmanLab cis-regulatory-evolution
	RSAT: regulatory sequence analysis tools [My Copy] Nucl. Acids Res. (21 May 2008), gkn304. by Morgane Thomas-Chollier, Olivier Sand, Jean-Valery Turatsinze, et al.Rekin's Janky, Matthieu Defrance, Eric Vervisch, Sylvain Brohee, Jacques van Helden posted to analysis sequence tool by idonaldson on 2009-02-06 10:19:02 as along with 6 people cassj natstreet druvus maximilianh guhjy dullhunk
	Extracting transcription factor binding sites from unaligned gene sequences with statistical models. [My Copy] BMC bioinformatics, Vol. 9 Suppl 12 (2008) by C. C. Lu, W. H. Yuan, T. M. Chen posted to chip-chip tfbs tool by idonaldson on 2009-01-15 09:56:34 as along with 3 people and 1 group stajich kristallreiner maximilianh Mycology
	RNA-Seq: a revolutionary tool for transcriptomics [My Copy] Nature Reviews Genetics, Vol. 10, No. 1. (01 January 2009), pp. 57-63. by Zhong Wang, Mark Gerstein, Michael Snyder posted to review rna-seq by idonaldson on 2009-01-13 13:15:22 as along with 38 people sandfire maren jwfoley urgi RNA-protein cthachuk heliopais GustavoLacerda rdiaz TRHvidsten dswan roys woodson8 jonilaserson gdb n00c ThomasDOtto burak natstreet athma druvus tonamswish fishtank daed JohnBallam jmcq dandaman cassj xingxu raiyar inesdesantiago vplagnol jbhiatt giovanni orzenil nuin guhjy GeeSharpMinor
	Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. [My Copy] Nature protocols, Vol. 4, No. 1. (18 December 2009), pp. 44-57. by Da Wei a. . W. Huang, Brad T. Sherman, Richard A. Lempicki posted to go pathway procedure tool by idonaldson on 2009-01-08 09:44:53 as along with 15 people and 2 groups rschulz jperkins tonamswish operon VGreiff jfr Stew bertelsen Sonix dswan guhjy wimufi brianb mrochman daforerog Bioinformatics - CRUK Bioinformatics
	Molecular Hallmarks of Endogenous Chromatin Complexes Containing Master Regulators of Hematopoiesis [My Copy] Mol. Cell. Biol., Vol. 28, No. 21. (1 November 2008), pp. 6681-6694. by Ryan J. Wozniak, Sunduz Keles, Jesse J. Lugus, et al.Ken H. Young, Meghan E. Boyer, Tuan M. Tran, Kyunghee Choi, Emery H. Bresnick posted to crm haematopoiesis by idonaldson on 2008-11-25 10:06:35 as
	PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale. [My Copy] Genes & development, Vol. 22, No. 21. (1 November 2008), pp. 2941-2952. by M. I. Lefterova, Y. Zhang, D. J. Steger, et al.M. Schupp, J. Schug, A. Cristancho, D. Feng, D. Zhuo, C. J. Stoeckert, X. S. Liu, M. A. Lazar posted to chip-chip by idonaldson on 2008-11-07 10:20:38 as
	Positional distribution of human transcription factor binding sites. [My Copy] Nucleic acids research (25 October 2008) by Mark Koudritsky, Eytan Domany posted to distribution tfbs tss by idonaldson on 2008-11-03 09:11:41 as along with 9 people and 2 groups daforerog jfr jforman ghattem barriot fpattyn nklee maximilianh nuin SIMR bioinformatics BenosLab
	GIMSAN: a Gibbs motif finder with significance analysis [My Copy] Bioinformatics, Vol. 24, No. 19. (1 October 2008), pp. 2256-2257. by Patrick Ng, Uri Keich posted to motif-discovery tool by idonaldson on 2008-09-29 09:48:40 as along with 3 people tmarscha nuin GeeSharpMinor
	Model-based Analysis of ChIP-Seq (MACS) [My Copy] Genome Biology, Vol. 9, No. 9. (2008), R137. by Yong Zhang, Tao Liu, Clifford Meyer, et al.Jerome Eeckhoute, David Johnson, Bradley Bernstein, Chad Nussbaum, Richard Myers, Myles Brown, Wei Li, X. Shirley Liu posted to chip-seq tool by idonaldson on 2008-09-22 11:37:23 as along with 23 people and 2 groups Vincent_Rouilly darian stubrown mkiyer humburg cassj floatingpoint WanderingAengus bryankr jfr rschulz mcm polivares gdb ghattem yadadi djkt stajich mdperry fpattyn bcondon caseybrown kengg SIMR bioinformatics Mycology
	MotifVoter: a novel ensemble method for fine-grained integration of generic motif finders. [My Copy] Bioinformatics (Oxford, England) (12 August 2008) by Edward Wijaya, Siu-Ming M. Yiu, Ngo Thanh T. Son, Rajaraman Kanagasabai, Wing-Kin K. Sung posted to motif-discovery tool by idonaldson on 2008-08-18 14:20:17 as along with 5 people wowalz druvus nuin chad_davis maximilianh
	ChIPping away at gene regulation. [My Copy] EMBO reports, Vol. 9, No. 4. (April 2008), pp. 337-343. by C. E. Massie, I. G. Mills posted to chip-chip review by idonaldson on 2008-07-08 10:53:50 as along with 1 person yoonk
	A survey of motif discovery methods in an integrated framework [My Copy] Biology Direct, Vol. 1, No. 1. (06 April 2006), 11. by Geir K. Sandve, Finn Drabløs posted to motif-discovery review tool by idonaldson on 2008-07-08 09:03:38 as along with 11 people and 1 group tomhebbron Scis0000002 maximilianh wowalz AbnerCYH aprasad dpollard samal yevishere csdhwang yoonk EisenLab
	Cross-species de novo identification of cis-regulatory modules with GibbsModule: application to gene regulation in embryonic stem cells [My Copy] Genome Res. (15 May 2008), gr.072769.107. by Dan Xie, Jun Cai, Na-Yu Chia, Huck Ng, Sheng Zhong posted to cis-regulation crm motif-discovery tool by idonaldson on 2008-05-27 09:53:11 as along with 7 people lusk dandaman maximilianh isimpson GustavoLacerda phoenixzxl yoonk
	ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species [My Copy] Nucl. Acids Res. (3 May 2008), gkn195. by Bart Hooghe, Paco Hulpiau, Frans van Roy, Pieter De Bleser posted to conserved promoter tool transcription-factor by idonaldson on 2008-05-13 10:38:49 as along with 4 people isimpson maximilianh maralena guhjy
	The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site. [My Copy] Nucleic acids research, Vol. 36, No. 8. (26 May 2008), pp. 2777-2786. by Kannan Tharakaraman, Olivier Bodenreider, David Landsman, John L. Spouge, Leonardo Mariño-Ramírez posted to motif tss by idonaldson on 2008-05-07 10:10:13 as along with 4 people daforerog maximilianh fpattyn inesdesantiago
	Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets. [My Copy] Genome research (14 April 2008) by Chaim Linhart, Yonit Halperin, Ron Shamir posted to motif-discovery tfbs tool by idonaldson on 2008-04-22 09:26:03 as along with 13 people and 1 group roys dolchan akshayk wowalz natstreet valeriehilgers jfr ealloza maralena fpattyn isimpson tmmurali maximilianh BergmanLab
	Transposable elements and the evolution of regulatory networks [My Copy] Nat Rev Genet, Vol. 9, No. 5. (27 May 2008), pp. 397-405. by Cedric Feschotte posted to networks regulation review te by idonaldson on 2008-04-21 10:24:26 as along with 12 people and 1 group robfsouza fhalbrit balicea gwallau djkt bootsy cmzmasek smbe2008 eskay roys pradiptaray timflutre BergmanLab
	Chromhome: A rich internet application for accessing comparative chromosome homology maps [My Copy] BMC Bioinformatics, Vol. 9 (26 March 2008), 168. by Sridevi Nagarajan, Willem Rens, James Stalker, Tony Cox, Malcolm A. Ferguson-Smith posted to chromosome comparison tool by idonaldson on 2008-03-31 09:50:58 as along with 1 person guhjy
	Motif discovery in tissue-specific regulatory sequences using directed information. [My Copy] EURASIP J Bioinform Syst Biol (2007) by A. Rao, A. O. Hero Iii, D. J. States, J. D. Engel posted to motif-discovery tissue-specific by idonaldson on 2008-03-17 11:03:58 as along with 3 people wowalz maximilianh isimpson
	Assessment of composite motif discovery methods. [My Copy] BMC bioinformatics, Vol. 9, No. 1. (2008) by K. Klepper, G. K. Sandve, O. Abul, J. Johansen, F. Drablos posted to analysis motif-discovery tool by idonaldson on 2008-03-03 09:19:03 as along with 8 people and 1 group wowalz chad_davis nklee maximilianh xili03 csdhwang isimpson yoonk Motif Discovery
	fdrMotif: identifying cis-elements by an EM algorithm coupled with false discovery rate control. [My Copy] Bioinformatics (Oxford, England), Vol. 24, No. 5. (1 March 2008), pp. 629-636. by L. Li, R. L. Bass, Y. Liang posted to motif-discovery tool by idonaldson on 2008-02-28 16:05:34 as along with 5 people wowalz GustavoLacerda maximilianh csdhwang isimpson
	Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes [My Copy] Genome Biology, Vol. 9 (15 February 2008), R34. by Par G. Engstrom, David Fredman, Boris Lenhard posted to cis-regulation conserved tool by idonaldson on 2008-02-25 10:25:05 as along with 5 people brant natstreet heliopais boudinot isimpson
	Systematic functional characterization of cis-regulatory motifs in human core promoters [My Copy] Genome Research, Vol. 18, No. 3. (6 March 2008), pp. 477-488. by Saurabh Sinha, Adam S. Adler, Yair Field, Howard Y. Chang, Eran Segal posted to cis-regulation motif promoter by idonaldson on 2008-02-20 08:58:19 as along with 8 people ptrobajo heliopais ealloza lp2 cabbagezs emptyhb gracio isimpson
	Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors [My Copy] BMC Bioinformatics, Vol. 8 (09 November 2007), 437. by Xueping Yu, Jimmy Lin, Donald J. Zack, Jiang Qian posted to crm tfbs tissue-specific by idonaldson on 2008-02-15 09:28:41 as along with 9 people isimpson guhjy chad_davis mikaelhuss nklee maximilianh njcitulike bootsy snow_dragon
	Text-mining assisted regulatory annotation [My Copy] Genome Biology, Vol. 9, No. 2. (2008) by Stein Aerts, Maximilian Haeussler, Steven van Vooren, et al.Obi Griffith, Paco Hulpiau, Steven Jones, Stephen Montgomery, Casey Bergman, The posted to annotation regulation text-mining by idonaldson on 2008-02-14 12:58:31 as along with 13 people and 2 groups artaban421 henk-cul daforerog daveGerrard cisevol yas dullhunk maximilianh mircea jsjoly isimpson bpcusack guhjy dbmi-nlp BergmanLab
	Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets [My Copy] Genome Research, Vol. 18, No. 3. (7 March 2008), pp. 393-403. by David S. Johnson, Wei Li, D. Benjamin Gordon, et al.Arindam Bhattacharjee, Bo Curry, Jayati Ghosh, Leonardo Brizuela, Jason S. Carroll, Myles Brown, Paul Flicek, Christoph M. Koch, Ian Dunham, Mark Bieda, Xiaoqin Xu, Peggy J. Farnham, Philipp Kapranov, David A. Nix, Thomas R. Gingeras, Xinmin Zhang, Heather Holster, Nan Jiang, Roland D. Green, Jun S. Song, Scott A. Mccuine, Elizabeth Anton, Loan Nguyen, Nathan D. Trinklein, Zhen Ye, Keith Ching, David Hawkins, Bing Ren, Peter C. Scacheri, Joel Rozowsky, Alexander Karpikov, Ghia Euskirchen, Sherman Weissman, Mark Gerstein, Michael Snyder, Annie Yang, Zarmik Moqtaderi, Heather Hirsch, Hennady P. Shulha, Yutao Fu, Zhiping Weng, Kevin Struhl, Richard M. Myers, Jason D. Lieb, X. Shirley Liu posted to chip-chip comparison by idonaldson on 2008-02-12 17:07:30 as along with 12 people and 2 groups fenghezi jfr kengg djkt xiaobeizhao cabbagezs caseybrown magusina lp2 stajich gracio gdb BergmanLab Mycology
	CMARRT: a tool for the analysis of ChIP-chip data from tiling arrays by incorporating the correlation structure. [My Copy] Pac Symp Biocomput (2008), pp. 515-526. by P. F. Kuan, H. Chun, S. Keleş posted to chip-chip tool by idonaldson on 2008-02-04 13:14:00 as along with 1 person jfr
	Model-based deconvolution of genome-wide DNA binding. [My Copy] Bioinformatics (1 December 2007) by David J J. Reiss, Marc T T. Facciotti, Nitin S S. Baliga posted to chip-chip deconvolution tfbs by idonaldson on 2008-01-31 11:10:21 as along with 5 people djkt yevishere guhjy vega isimpson
	TFBS Identification Based on Genetic Algorithm with Combined Representations and Adaptive Post-processing. [My Copy] Bioinformatics (6 December 2007) by Tak-Ming M. Chan, Kwong-Sak S. Leung, Kin-Hong H. Lee posted to motif-discovery tfbs tool by idonaldson on 2008-01-31 11:07:05 as along with 6 people wowalz nklee maximilianh xili03 csdhwang isimpson
	Predicting expression patterns from regulatory sequence in Drosophila segmentation [My Copy] Nature, Vol. 451, No. 7178. (02 January 2008), pp. 535-540. by Eran Segal, Tali Raveh-Sadka, Mark Schroeder, Ulrich Unnerstall, Ulrike Gaul posted to expression prediction by idonaldson on 2008-01-31 09:39:38 as along with 19 people and 2 groups TRHvidsten daveGerrard koller dlmace ptrobajo isimpson dakelley tmmurali eckart_bindewald djkt bootsy biomcgary roys emptyhb pkharchenko meiklej jrest tresch siebert BergmanLab TranscriptionalRegulationWithThermodynamicModels
	Functional evolution of the p53 regulatory network through its target response elements. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 105, No. 3. (22 January 2008), pp. 944-949. by A. G. Jegga, A. Inga, D. Menendez, B. J. Aronow, M. A. Resnick posted to evolution networks p53 by idonaldson on 2008-01-14 09:51:08 as along with 7 people and 1 group danaiancu brant cjeans zwang cisevol renatomilani guhjy cis-regulatory-evolution
	Runx genes are direct targets of Scl/Tal1 in the yolk sac and fetal liver. [My Copy] Blood (9 January 2008) by Josette-Renee R. Landry, Sarah Kinston, Kathy Knezevic, et al.Marella F T R F. de Bruijn, Nicola Wilson, Wade T T. Nottingham, Michael Peitz, Frank Edenhofer, John E E. Pimanda, Katrin Ottersbach, Berthold Gottgens posted to gottgens by idonaldson on 2008-01-14 09:45:16 as
	A Hybrid Model for Robust Detection of Transcription Factor Binding Sites. [My Copy] Bioinformatics (9 January 2008) by Sumedha Gunewardena, Zhaolei Zhang posted to motif-discovery tfbs tool by idonaldson on 2008-01-14 09:30:49 as along with 3 people isimpson guhjy maximilianh
	OrthoMaM: A database of orthologous genomic markers for placental mammal phylogenetics [My Copy] BMC Evolutionary Biology, Vol. 7, No. 1. (30 November 2007), 241. by Vincent Ranwez, Frederic Delsuc, Sylvie Ranwez, Khalid Belkhir, Marie K. Tilak, Emmanuel Douzery posted to orthologues phylogenetic tool by idonaldson on 2008-01-10 12:35:15 as along with 4 people and 1 group avilella gjuggler bpcusack aprasad Ensembl Compara citations
	Maintenance of transposon-free regions throughout vertebrate evolution [My Copy] BMC Genomics, Vol. 8 (20 December 2007), 470. by Cas Simons, Igor V. Makunin, Michael Pheasant, John S. Mattick posted to transposon-free-regions by idonaldson on 2008-01-08 09:59:53 as along with 2 people and 2 groups blobbybirdman cisevol cis-regulatory-evolution BergmanLab
	Generic eukaryotic core promoter prediction using structural features of DNA [My Copy] Genome Research, Vol. 18, No. 2. (20 February 2008), pp. 310-323. by Thomas Abeel, Yvan Saeys, Eric Bonnet, Pierre RouzÃ©, Yves Van de Peer posted to prediction promoter structural by idonaldson on 2007-12-21 10:22:56 as along with 8 people timflutre chvlyl hagechouchin443 rsaito tonamswish cjeans cabbagezs maximilianh
	Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting [My Copy] Bioinformatics, Vol. 24, No. 1. (1 January 2008), pp. 18-25. by Kai Ye, Anton, Jaap Heringa, Adriaan P. Ijzerman, Elena Marchiori posted to alignment multiple tool by idonaldson on 2007-12-20 12:28:20 as along with 2 people jameswasmuth h-chi
	A code for transcription initiation in mammalian genomes. [My Copy] Genome research, Vol. 18, No. 1. (21 January 2008), pp. 1-12. by M. C. Frith, E. Valen, A. Krogh, Y. Hayashizaki, P. Carninci, A. Sandelin posted to prediction tss by idonaldson on 2007-11-28 08:48:13 as along with 12 people megraw guhjy rpatward inesdesantiago myrtilus dchughes cabbagezs maximilianh oelemento gjuggler ohara gracio
	OSCAR: One-class SVM for Accurate Recognition of Cis-elements [My Copy] Bioinformatics (5 October 2007), btm473. by Bo Jiang, Michael Q. Zhang, Xuegong Zhang posted to cis-regulation tfbs tool by idonaldson on 2007-11-27 14:42:52 as along with 7 people suizifish cassj tmmurali chad_davis cabbagezs maximilianh isimpson
	Ab initio prediction of transcription factor binding sites. [My Copy] Pac Symp Biocomput (2007), pp. 484-495. by L. A. Liu, J. S. Bader posted to prediction tfbs by idonaldson on 2007-11-12 09:14:45 as along with 1 person aalibes
	A systems biology approach for pathway level analysis [My Copy] Genome Research, Vol. 17, No. 10. (4 October 2007), pp. 1537-1545. by Sorin Draghici, Purvesh Khatri, Adi L. Tarca, et al.Kashyap Amin, Arina Done, Calin Voichita, Constantin Georgescu, Roberto Romero posted to networks tool by idonaldson on 2007-11-01 08:47:00 as along with 22 people and 2 groups zufar bertelsen tonamswish gbloeb cgaugain ptrobajo pengchy tmmurali dragonrez jfr gurkanbebek grahamc shigepong zwang cabbagezs cerami xingxu shikin Pao-Yang thomaskelder heliopais AlexanderPico Bioinformatics OPIG

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tool	108
tfbs	53
motif-discovery	29
chip-chip	26
cis-regulation	24
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sumoylation	1
topology	1
transcription	1
transgenic	1
transposon-free-regions	1
ucsc	1
yy1	1

idonaldson's library 265 articles Export

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