Group: EisenLab - with tag prediction [57 articles] Export

Recent papers posted by members of the EisenLab group with tag prediction

	Assessing phylogenetic motif models for predicting transcription factor binding sites [My Copy] Bioinformatics In Bioinformatics, Vol. 25, No. 12. (15 June 2009), pp. i339-347. by John Hawkins, Charles Grant, William S. Noble, Timothy L. Bailey posted to binding binding-sites factor motif phylogen prediction tfbs transcription by Stew to the group EisenLab on 2009-06-17 15:29:29 as along with 9 people and 2 groups bsamal dquest marti Lombardo_7 megraw operon nuin AlexBateman scjparker Bioinformatics - CRUK Journal picks
	Levers and fulcrums: progress in cis-regulatory motif models [My Copy] Nature Methods, Vol. 5, No. 4., pp. 297-298. by Ewan Birney posted to cis-regulatory comparative_genomics methods motif prediction by stajich to the group EisenLab on 2008-04-07 16:11:40 as along with 3 people and 1 group emptyhb pradiptaray isimpson Mycology
	Using DNA duplex stability information for transcription factor binding site discovery. [My Copy] Pac Symp Biocomput (2008), pp. 453-464. by R. Gordân, A. J. Hartemink posted to binding_site biophysical_model method motif_detection prediction transcription_factor by dpollard to the group EisenLab on 2008-02-01 06:21:42 as along with 1 person bootsy
	CisModule: De novo discovery of cis-regulatory modules by hierarchical mixture modeling [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 101, No. 33. (17 August 2004), pp. 12114-12119. by Qing Zhou, Wing H. Wong posted to ab_initio cis_regulatory_elements clustering method prediction by dpollard to the group EisenLab on 2007-12-05 22:46:33 as along with 4 people tonamswish isimpson indigoviolet ep161302
	Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes. [My Copy] Genome research, Vol. 17, No. 12. (7 December 2007), pp. 1932-1942. by Matthew D. Rasmussen, Manolis Kellis posted to drosophila method phylogeny prediction yeast by dpollard to the group EisenLab on 2007-11-21 02:56:16 as along with 6 people roys mmfonseca inquil druvus stajich caseybrown
	Reliable prediction of regulator targets using 12 Drosophila genomes [My Copy] Genome Research, Vol. 17, No. 12. (7 December 2007), pp. 1919-1931. by Pouya Kheradpour, Alexander Stark, Sushmita Roy, Manolis Kellis posted to cis_regulatory_elements drosophila eisen_journal_club matt_presented prediction round_robin by dpollard to the group EisenLab on 2007-11-17 00:01:35 as along with 9 people and 1 group heliopais valeriehilgers lp2 nklee maximilianh roys caseybrown emptyhb barwil cis-regulatory-evolution
	Discovery of Regulatory Elements by a Computational Method for Phylogenetic Footprinting [My Copy] Genome Res., Vol. 12, No. 5. (1 May 2002), pp. 739-748. by Mathieu Blanchette, Martin Tompa posted to ab_initio binding_site conservation method prediction by dpollard to the group EisenLab on 2007-11-01 00:41:11 as along with 7 people and 1 group wowalz coldmeadow chad_davis balajis lyongu dquest csdhwang cis-regulatory-evolution
	Regulatory element detection using correlation with expression [My Copy] Nature Genetics, Vol. 27, No. 2. (01 February 2001), pp. 167-174. by Harmen J. Bussemaker, Hao Li, Eric D. Siggia posted to ab_initio binding_site gene_expression prediction by dpollard to the group EisenLab on 2007-11-01 00:10:36 as along with 5 people and 1 group roys nickluscombe heliopais tvdbulck isimpson EBI-regulation
	Incorporating evolution of transcription factor binding sites into annotated alignments. [My Copy] J Biosci, Vol. 32, No. 5. (August 2007), pp. 841-850. by A. S. Bais, S. Grossmann, M. Vingron posted to alignment binding_site conserved method prediction by dpollard to the group EisenLab on 2007-10-25 02:20:56 as along with 1 person and 1 group maximilianh cis-regulatory-evolution
	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_detection prediction by dpollard to the group EisenLab on 2007-10-25 01:20:27 as along with 7 people wowalz tmarscha cjeans nklee niallhaslam maximilianh idonaldson
	Discovering and detecting transposable elements in genome sequences. [My Copy] Briefings in bioinformatics, Vol. 8, No. 6. (10 November 2007), pp. 382-392. by Casey M. Bergman, Hadi Quesneville posted to prediction te transposable_elements by dpollard to the group EisenLab on 2007-10-25 01:18:08 as along with 14 people and 1 group operon orzenil gwallau natstreet druvus gpappas timflutre GustavoLacerda cabbagezs maximilianh cisevol urgi yoanjacquemin pradiptaray BergmanLab
	Applied bioinformatics for the identification of regulatory elements. [My Copy] Nat Rev Genet, Vol. 5, No. 4. (April 2004), pp. 276-287. by W. W. Wasserman, A. Sandelin posted to review prediction cis-regulatory by Stew to the group EisenLab on 2007-09-18 18:26:40 as along with 19 people and 7 groups bsamal wowalz yas icases ana chad_davis moborg gpalidwor dchughes nickluscombe johncumbers giovanni xiaobeizhao bertelsen nklee jdiezperezj ArtemPankin mariakmejia isimpson structural_bioinformatics Bioinformatics G4ID EBI-regulation GeschwindLab TNT Genetics-of-Gambling
	Cracking the genome's second code: enhancer detection by combined phylogenetic footprinting and transgenic fish and frog embryos. [My Copy] Methods, Vol. 39, No. 3. (July 2006), pp. 212-219. by M. L. Allende, M. Manzanares, J. J. Tena, C. G. Feijóo, J. L. Gómez-Skarmeta posted to prediction phlyogenetic frog footprinting fish cis-regulatory by Stew to the group EisenLab on 2007-09-18 01:19:46 as
	Computational prediction of transcription-factor binding site locations [My Copy] Genome Biology, Vol. 5, No. 1. (2003), 201. by Martha Bulyk posted to review prediction clustering cis-regulatory by Stew to the group EisenLab on 2007-09-17 20:40:18 as along with 10 people xubeisi Baschl marti tkmaia kaarsinogen lusk nklee yevishere xili03 aalibes
	Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, No. 2. (22 January 2002), pp. 757-762. by Benjamin P. Berman, Yutaka Nibu, Barret D. Pfeiffer, et al.Pavel Tomancak, Susan E. Celniker, Michael Levine, Gerald M. Rubin, Michael B. Eisen posted to prediction modules drosophila clustering cis-regulatory by Stew to the group EisenLab on 2007-09-17 20:14:51 as along with 4 people farhat indigoviolet emptyhb csdhwang
	Different words, same meaning: understanding the languages of the genome. [My Copy] Trends Genet (27 September 2006) by Greg Elgar posted to review prediction elgar cis-regulatory by Stew to the group EisenLab on 2007-07-27 22:32:32 as along with 2 people and 4 groups nickluscombe WJST EBI-regulation asthma humangenetics SNP
	Stubb: a program for discovery and analysis of cis-regulatory modules. [My Copy] Nucleic Acids Res, Vol. 34, No. Web Server issue. (1 July 2006) by S. Sinha, Y. Liang, E. Siggia posted to regulatory prediction cis by Stew to the group EisenLab on 2007-07-27 22:17:11 as along with 2 people indigoviolet csdhwang
	Prediction of Gene Expression in Embryonic Structures of Drosophila melanogaster [My Copy] PLoS Computational Biology, Vol. 3, No. 7. (1 July 2007), e144. by Anastasia A. Samsonova, Mahesan Niranjan, Steven Russell, Alvis Brazma posted to tissue prediction expression drosophila by brant to the group EisenLab on 2007-07-24 19:58:38 as along with 3 people roys dpollard sebastien_vigneau
	Using multiple alignments to improve gene prediction. [My Copy] J Comput Biol, Vol. 13, No. 2. (March 2006), pp. 379-393. by S. S. Gross, M. R. Brent posted to prediction gene 12flies by indigoviolet to the group EisenLab on 2007-07-15 13:54:12 as along with 3 people jmartin49 druvus wenhan
	Prediction of gene structure. [My Copy] Journal of molecular biology, Vol. 226, No. 1. (5 July 1992), pp. 141-157. by R. Guigó, S. Knudsen, N. Drake, T. Smith posted to prediction gene 12flies by indigoviolet to the group EisenLab on 2007-07-15 13:52:20 as along with 2 people ajbattle wenhan
	Gene finding in novel genomes [My Copy] BMC Bioinformatics, Vol. 5, No. 1. (14 May 2004), 59. by Ian Korf posted to prediction gene 12flies by indigoviolet to the group EisenLab on 2007-07-15 13:51:00 as along with 7 people druvus jmartin49 LeightonP wenhan GustavoLacerda cmzmasek alexl
	A Survey of Genomic Properties for the Detection of Regulatory Polymorphisms [My Copy] PLoS Computational Biology, Vol. 3, No. 6. (1 June 2007), e106. by Stephen B. Montgomery, Obi L. Griffith, Johanna M. Schuetz, Angela Brooks-Wilson, Steven J. Jones posted to venky_presented snp sequence_properties round_robin regulatory_polymorphism prediction eisen_journal_club cis_regulatory_elements by dpollard to the group EisenLab on 2007-06-15 22:54:33 as along with 1 person and 2 groups cisevol Bioinformatics cis-regulatory-evolution
	Enhancer responses to similarly distributed antagonistic gradients in development. [My Copy] PLoS Comput Biol, Vol. 3, No. 5. (11 May 2007) by R. P. Zinzen, D. Papatsenko posted to prediction in_depth_suggestion experssion_pattern enhancer eisen_journal_club by dpollard to the group EisenLab on 2007-06-13 22:22:18 as
	Computational annotation of transcription factor binding sites in D. Melanogaster developmental genes. [My Copy] Genome Inform, Vol. 17, No. 2. (2006), pp. 14-24. by V. Narang, W. K. Sung, A. Mittal posted to prediction drosophila crm cis_regulatory_elements binding_site by dpollard to the group EisenLab on 2007-06-13 22:20:42 as
	Binding Site Graphs: A New Graph Theoretical Framework for Prediction of Transcription Factor Binding Sites [My Copy] PLoS Computational Biology, Vol. 3, No. 5. (1 May 2007), e90. by Timothy E. Reddy, Charles Delisi, Boris E. Shakhnovich posted to prediction method cis_regulatory_elements by dpollard to the group EisenLab on 2007-05-31 23:16:30 as along with 2 people adepace ajgentles
	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 A. Chakravarty, J. M. Carlson, R. S. Khetani, C. E. DeZiel, R. H. Gross posted to prediction method clustering cis_regulatory_elements binding_site by dpollard to the group EisenLab on 2007-05-23 01:10:50 as
	A phylogenetic Gibbs sampler that yields centroid solutions for cis-regulatory site prediction [My Copy] Bioinformatics, Vol. 23, No. 14. (15 July 2007), pp. 1718-1727. by Lee A. Newberg, William A. Thompson, Sean Conlan, Thomas M. Smith, Lee A. McCue, Charles E. Lawrence posted to prediction motif method discovery clustering cis_regulatory_elements by dpollard to the group EisenLab on 2007-05-23 00:29:25 as along with 7 people vingron operon Dulce Mehlhorn cjeans sconlan siebert
	Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting. [My Copy] Proc Natl Acad Sci U S A (29 March 2007) by Alona Sosinsky, Barry Honig, Richard S S. Mann, Andrea Califano posted to prediction method enhancer drosophila comparative clustering by dpollard to the group EisenLab on 2007-04-09 17:43:36 as along with 4 people and 1 group Stew maximilianh cisevol isimpson cis-regulatory-evolution
	Discovering Motifs in Ranked Lists of DNA Sequences [My Copy] PLoS Computational Biology, Vol. 3, No. 3. (1 March 2007), e39. by Eran Eden, Doron Lipson, Sivan Yogev, Zohar Yakhini posted to round_robin pwm prediction motif eisen_journal_club dan_presented chip_chip by dpollard to the group EisenLab on 2007-03-23 00:19:21 as along with 3 people heliopais dquest yevishere
	GAPWM: a genetic algorithm method for optimizing a position weight matrix [My Copy] Bioinformatics In Bioinformatics, Vol. 23, No. 10. (15 May 2007), pp. 1188-1194. by Leping Li, Yu Liang, Robert L. Bass posted to pwm prediction chip_chip by dpollard to the group EisenLab on 2007-03-22 23:37:15 as along with 6 people bsamal yevishere grahamc cjeans ghattem isimpson
	Computational methods for transcriptional regulation. [My Copy] Curr Opin Genet Dev, Vol. 15, No. 2. (April 2005), pp. 214-221. by E. D. Siggia posted to cis_regulatory_elements gene_expression method prediction by dpollard to the group EisenLab on 2007-03-15 00:30:41 as along with 7 people and 1 group barry koller bertelsen Borelli nklee balicea jjray Bioinformatics
	The identification and functional characterisation of conserved regulatory elements in developmental genes. [My Copy] Brief Funct Genomic Proteomic, Vol. 3, No. 4. (February 2005), pp. 332-350. by T. Dickmeis, F. Müller posted to cis_regulatory_elements conserved development prediction regulatory_sequence transcription_factor by dpollard to the group EisenLab on 2007-03-15 00:27:26 as along with 1 person brant
	Prediction of cis-regulatory elements using binding site matrices--the successes, the failures and the reasons for both. [My Copy] Curr Opin Genet Dev, Vol. 15, No. 4. (August 2005), pp. 395-402. by T. Vavouri, G. Elgar posted to binding_site cis_regulatory_elements method motif pattern prediction pwm regulatory_sequence by dpollard to the group EisenLab on 2007-03-15 00:24:34 as along with 6 people and 1 group troels_marstrand kaspermunch adepace lusk Stew brant Bioinformatics
	Good enhancer hunting. [My Copy] Nat Methods, Vol. 4, No. 1. (January 2007), pp. 8-9. by J. Potash posted to prediction enhancer by dpollard to the group EisenLab on 2007-02-09 01:57:00 as
	Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry. [My Copy] Nucleic Acids Res (30 January 2007) by Trevor W W. Siggers, Barry Honig posted to affinity binding_site dan_presented eisen_journal_club prediction round_robin structure transcription_factor by dpollard to the group EisenLab on 2007-02-09 01:34:13 as along with 1 person aalibes
	Statistical significance of cis-regulatory modules [My Copy] BMC Bioinformatics, Vol. 8, No. 1. (2007) by Dustin Schones, Andrew Smith, Michael Zhang posted to prediction method crm by dpollard to the group EisenLab on 2007-02-01 19:56:05 as along with 10 people druvus indigoviolet dquest sebastien_vigneau shigepong SeungjoonOh GustavoLacerda nklee xili03 sconlan
	PhyloScan: Identification of transcription factor binding sites using cross-species evidence [My Copy] Algorithms for Molecular Biology, Vol. 2 (23 January 2007), 1. by Steven C. Carmack, Lee A. Mccue, Lee A. Newberg, Charles E. Lawrence posted to prediction phylogeny comparative binding_site by dpollard to the group EisenLab on 2007-02-01 19:41:57 as along with 3 people dquest lusk nklee
	Large Scale Discovery of Promoter Motifs in Drosophila melanogaster [My Copy] PLoS Computational Biology, Vol. preprint, No. 2006. (1 December 2006), e7.eor. by Thomas A. Down, Casey M. Bergman, Jing Su, Tim J. Hubbard posted to drosophila eisen_journal_club emily_presented motif prediction promoter round_robin by dpollard to the group EisenLab on 2006-12-13 22:18:54 as
	Position specific variation in the rate of evolution in transcription factor binding sites. [My Copy] BMC Evol Biol, Vol. 3, No. 1. (28 August 2003) by A. M. Moses, D. Y. Chiang, M. Kellis, E. S. Lander, M. B. Eisen posted to binding conserved constraint evolution noncoding pattern phylogeny prediction pwm rate selection specific transcription by dpollard to the group EisenLab on 2006-11-07 00:22:07 as along with 6 people and 1 group briann adepace lusk nklee cisevol emptyhb cis-regulatory-evolution
	Large-Scale cis-Element Detection by Analysis of Correlated Expression and Sequence Conservation between Arabidopsis and Brassica oleracea [My Copy] Plant Physiol., Vol. 142, No. 4. (1 December 2006), pp. 1589-1602. by Georg Haberer, Michael T. Mader, Peter Kosarev, Manuel Spannagl, Li Yang, Klaus F. X. Mayer posted to coexpression conserved crm prediction by dpollard to the group EisenLab on 2006-10-18 20:12:50 as along with 5 people operon xwbcn kengg nklee xili03
	Identifying gene regulatory elements by genomic microarray mapping of DNaseI hypersensitive sites. [My Copy] Genome Res (8 September 2006) by George A A. Follows, Pawan Dhami, Berthold Göttgens, et al.Alexander W W. Bruce, Peter J J. Campbell, Shane C C. Dillon, Aileen M M. Smith, Christoph Koch, Ian J J. Donaldson, Mike A A. Scott, Ian Dunham, Mary E E. Janes, David Vetrie, Anthony R R. Green posted to array dnasei hypersensitive prediction by dpollard to the group EisenLab on 2006-09-30 00:26:22 as along with 2 people athma uz_labu_laimi
	Vertebrate gene finding from multiple-species alignments using a two-level strategy. [My Copy] Genome Biol, Vol. 7 Suppl 1 (2006) by D. Carter, R. Durbin posted to alignment gene prediction by dpollard to the group EisenLab on 2006-09-30 00:22:15 as along with 2 people and 1 group indigoviolet dmc Durbin group
	Predicting transcription factor binding sites using local overrepresentation and comparative genomics [My Copy] BMC Bioinformatics, Vol. 7 (31 August 2006), 396. by Matthieu Defrance, Helene Touzet posted to enhancer_finding prediction tools by brant to the group EisenLab on 2006-09-13 14:20:55 as along with 3 people dpollard gpalidwor natstreet
	Expression-Guided In Silico Evaluation of Candidate Cis Regulatory Codes for Drosophila Muscle Founder Cells [My Copy] PLoS Computational Biology, Vol. 2, No. 5. (1 May 2006), e53. by Anthony A. Philippakis, Brian W. Busser, Stephen S. Gisselbrecht, et al.Fangxue S. He, Beatriz Estrada, Alan M. Michelson, Martha L. Bulyk posted to enhancer prediction by emilyhare to the group EisenLab on 2006-07-06 01:26:10 as along with 2 people maximilianh_otx maximilianh
	Integrated assessment and prediction of transcription factor binding. [My Copy] PLoS computational biology, Vol. 2, No. 6. (16 June 2006), e70. by Andreas Beyer, Christopher Workman, Jens Hollunder, et al.Dörte Radke, Ulrich Möller, Thomas Wilhelm, Trey Ideker posted to prediction target tf by emilyhare to the group EisenLab on 2006-06-24 00:47:46 as along with 11 people marti vingron HawkinsJohnC ajbattle nklee jfr balajis wnpx samal reidy Ao_Li2007
	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 binding motif prediction structure transcription by dpollard to the group EisenLab on 2006-06-16 20:40:23 as along with 2 people samal nklee
	Computational Models for Neurogenic Gene Expression in the Drosophila Embryo. [My Copy] Curr Biol (1 June 2006) by Robert P P. Zinzen, Kate Senger, Mike Levine, Dmitri Papatsenko posted to drosophila expression network prediction transcription by dpollard to the group EisenLab on 2006-06-09 23:01:14 as along with 2 people and 1 group emilyhare klo TranscriptionalRegulationWithThermodynamicModels
	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 binding data genomic integration prediction transcription by dpollard to the group EisenLab on 2006-03-21 19:53:19 as along with 3 people and 1 group malcook adsmitty nklee SIMR bioinformatics
	Mapping Dmef2-binding regulatory modules by using a ChIP-enriched in silico targets approach [My Copy] PNAS, Vol. 102, No. 51. (20 December 2005), pp. 18479-18484. by Guillaume Junion, Teresa Jagla, Sebastien Duplant, Romain Tapin, Jean-Philippe Da Ponte, Krzysztof Jagla posted to chip-chip enhancer mef2 prediction by emilyhare to the group EisenLab on 2006-01-13 02:04:51 as along with 2 people and 1 group daveGerrard postrational BergmanLab
	Genome-wide Prediction of Mammalian Enhancers Based on Analysis of Transcription-Factor Binding Affinity [My Copy] Cell, Vol. 124, No. 1. (13 January 2006), pp. 47-59. by O. Hallikas, K. Palin, N. Sinjushina, et al.R. Rautiainen, J. Partanen, E. Ukkonen, J. Taipale posted to enhancer mammalian prediction by brant to the group EisenLab on 2006-01-13 01:55:31 as along with 16 people and 4 groups absterga xingxu cisstem Terkko kaarsinogen tuck xwbcn dchughes nickluscombe olympos cabbagezs karfunkel maximilianh heliopais oelemento emptyhb Bioinformatics G4ID EBI-regulation Genetics-of-Gambling

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protein	412
structure	401
bioinformatics	240
rna	199
interaction	137
network	135
function	122
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microrna	108
review	108
mirna	95
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gene	78
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markets	69
sequence	65
modeling	64
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ppi	62
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motif	60
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evolution	41
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methodspaper	32
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membrane	21
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peptide	21

Group: EisenLab - with tag prediction [57 articles] Export

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