Group: EisenLab - with tag motif [27 articles] Export

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

	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
	Identifying DNA and protein patterns with statistically significant alignments of multiple sequences [My Copy] Bioinformatics, Vol. 15, No. 7. (1 July 1999), pp. 563-577. by G. Z. Hertz, G. D. Stormo posted to algorithm motif by indigoviolet to the group EisenLab on 2007-12-12 14:01:38 as along with 8 people megraw tonamswish wowalz yylin tuck dquest lusk chad_davis
	A computational genomics approach to the identification of gene networks [My Copy] Nucl. Acids Res., Vol. 25, No. 18. (15 September 1997), pp. 3594-3604. by A. Wagner posted to motif by indigoviolet to the group EisenLab on 2007-12-12 11:05:07 as
	A graph-based motif detection algorithm models complex nucleotide dependencies in transcription factor binding sites. [My Copy] Nucleic Acids Res, Vol. 34, No. 20. (2006), pp. 5730-5739. by B. T. Naughton, E. Fratkin, S. Batzoglou, D. L. Brutlag posted to motif by indigoviolet to the group EisenLab on 2007-12-12 11:00:03 as along with 4 people nklee yevishere xili03 GustavoLacerda
	Methods and statistics for combining motif match scores. [My Copy] J Comput Biol, Vol. 5, No. 2. (1998), pp. 211-221. by T. L. Bailey, M. Gribskov posted to motif by indigoviolet to the group EisenLab on 2007-12-12 10:56:53 as
	JASPAR: an open-access database for eukaryotic transcription factor binding profiles [My Copy] Nucl. Acids Res., Vol. 32, No. suppl_1. (1 January 2004), pp. D91-94. by Albin Sandelin, Wynand Alkema, Par Engstrom, Wyeth W. Wasserman, Boris Lenhard posted to database motif by indigoviolet to the group EisenLab on 2007-12-12 09:14:43 as along with 5 people and 1 group antonkratz aalibes jguinney nklee heliopais Motif Discovery
	MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes. [My Copy] BMC Bioinformatics, Vol. 6 (2005) by V. D. Marinescu, I. S. Kohane, A. Riva posted to algorithm motif by indigoviolet to the group EisenLab on 2007-12-12 05:44:21 as
	Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation [My Copy] Nature Methods, Vol. 4, No. 7. (24 June 2007), pp. 563-565. by Laurence Ettwiller, Benedict Paten, Mirana Ramialison, Ewan Birney, Joachim Wittbrodt posted to motif discovery chip-chip by brant to the group EisenLab on 2007-07-16 22:00:13 as along with 5 people wowalz cisstem zwang maximilianh fpattyn
	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 yeast venky_presented round_robin motif method eisen_journal_club binding_site ab_initio by dpollard to the group EisenLab on 2007-06-14 23:38:43 as along with 7 people pradiptaray nklee aalibes medic0747 GustavoLacerda mircea marti
	Determination of local statistical significance of patterns in Markov sequences with application to promoter element identification. [My Copy] J Comput Biol, Vol. 11, No. 1. (2004), pp. 1-14. by H. Huang, M. C. Kao, X. Zhou, J. S. Liu, W. H. Wong posted to stuart_presented round_robin motif method markov eisen_journal_club binding_site ab_initio by dpollard to the group EisenLab on 2007-06-04 22:47:45 as along with 1 person jguinney
	STAMP: a web tool for exploring DNA-binding motif similarities [My Copy] Nucleic acids research In Nucl. Acids Res., Vol. 35, No. suppl_2. (13 July 2007), pp. W253-258. by Shaun Mahony, Panayiotis V. Benos posted to website pwm motif method alignment by dpollard to the group EisenLab on 2007-05-23 00:40:45 as along with 4 people bsamal yuslinaz aalibes raylim
	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
	Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase. [My Copy] Genome Biology, Vol. 8 (22 February 2007), R23. by Alan M. Moses, Jean-Karim Heriche, Richard Durbin posted to protein motif clustering by dpollard to the group EisenLab on 2007-03-27 16:28:13 as along with 2 people hryk gjuggler
	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
	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
	Integrating transcription factor binding site information with gene expression datasets. [My Copy] Bioinformatics (24 November 2006) by Ian B B. Jeffery, Stephen F F. Madden, Paul A A. McGettigan, Guy Perrière, Aedín C C. Culhane, Desmond G G. Higgins posted to motif micro_array gene expression correlation by dpollard to the group EisenLab on 2007-01-19 16:12:50 as along with 4 people guhjy gpalidwor wnpx SeungjoonOh
	Identification of degenerate motifs using position restricted selection and hybrid ranking combination. [My Copy] Nucleic Acids Res, Vol. 34, No. 22. (2006), pp. 6379-6391. by C. H. Peng, J. T. Hsu, Y. S. Chung, et al.Y. J. Lin, W. Y. Chow, D. F. Hsu, C. Y. Tang posted to motif detection by dpollard to the group EisenLab on 2007-01-19 16:08:24 as
	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
	NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence. [My Copy] Nucleic acids research, Vol. 33, No. 5. (2005), pp. 1445-1453. by T. A. Down, T. J. Hubbard posted to dan_presented discovery eisen_journal_club motif round_robin by dpollard to the group EisenLab on 2006-12-13 22:14:20 as along with 5 people timhubbard emptyhb lyongu dquest waszak
	Single-Molecule Detection of Transcription Factor Binding to DNA in Real Time: Specificity, Equilibrium, and Kinetic Parameters. [My Copy] Biochemistry, Vol. 45, No. 46. (21 November 2006), pp. 13794-13806. by Eric A. Nalefski, Eugene Nebelitsky, Janice A. Lloyd, Steven R. Gullans posted to binding kenetics method motif by dpollard to the group EisenLab on 2006-11-17 13:00:37 as
	Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies. [My Copy] Mol Biol Evol, Vol. 15, No. 7. (July 1998), pp. 910-917. by A. L. Halpern, W. J. Bruno posted to constraint evolution model motif mutation phylogeny selection by dpollard to the group EisenLab on 2006-11-07 00:11:19 as along with 2 people emptyhb lusk
	Transcriptional repression in the Drosophila embryo. [My Copy] Philos Trans R Soc Lond B Biol Sci, Vol. 349, No. 1329. (29 September 1995), pp. 257-262. by S. Gray, H. Cai, S. Barolo, M. Levine posted to binding coactivator corepression development drosophila embryo expression grammar insulators mechanism model motif promoter range review short transcription by dpollard to the group EisenLab on 2006-10-11 18:29:07 as
	Regulation of the immunoglobulin heavy chain locus expression at the phylogenetic level of a bony fish: Transcription factor interaction with two variant octamer motifs. [My Copy] Gene (5 June 2006) by Jun-Ichi I. Hikima, Mara L L. Lennard, Melanie R R. Wilson, Norman W W. Miller, Gregory W W. Warr posted to binding grammar motif promoter spacing transcription by dpollard to the group EisenLab on 2006-06-16 20:44:19 as
	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
	Evaluating phylogenetic footprinting for human-rodent comparisons. [My Copy] Bioinformatics, Vol. 22, No. 4. (15 February 2006), pp. 430-437. by T. Sauer, E. Shelest, E. Wingender posted to alignment binding conserved evolution mammal motif rate transcription vertebrate by dpollard to the group EisenLab on 2006-05-01 22:45:46 as
	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 discovery motif review by dpollard to the group EisenLab on 2006-04-08 23:19:50 as along with 12 people bsamal tomhebbron Scis0000002 maximilianh wowalz AbnerCYH aprasad samal yevishere csdhwang idonaldson yoonk

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discovery	141
network	123
rna	62
bioinformatics	61
prediction	60
transcription	57
protein	52
tf	52
regulation	51
sequence	50
tfbs	48
promoter	47
structure	47
evolution	46
binding	44
algorithm	41
genome	41
review	38
expression	37
regulatory	35
conserved	31
yeast	27
targeting	25
genomics	24
pattern	22
search	22
software	21
alignment	20
dna	20
structural_biology	20
clustering	19
combination	19
database	19
detection	19
interaction	19
microarray	19
conservation	18
finding	16
biology	15
complex	15
human	15
pwm	15
scanning	15
somatodendritic	15
axon	14
chromatin	14
domain	14
function	14
gene	14
methods	13
ribosome	13
arabidopsis	12
de-novo	12
method	12
microrna	12
analysis	11
ctcf	11
factor	11
module	11
computational	10
dendrites	10
development	10
drosophila	10
eisen_journal_club	10
enhancers	10
ion-channels	10
ppi	10
round_robin	10
splicing	10
tools	10
algorithms	9
motifs	9
ncrna	9
peptide	9
prosite	9
tool	9
bayesian	8
chip	8
chip-chip	8
crm	8
functional	8
geneexp	8
mirna	8
mrna	8
pathway	8
phylogeny	8
signature	8
site	8
2004	7
ais	7
comparative	7
dynamics	7
elm	7
enhancerprediction	7
integration	7
mining	7
phosphorylation	7
projects	7
promotor	7
statistics	7

Group: EisenLab - with tag motif [27 articles] Export

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