Tag motif-discovery [at least 200 articles] Export

Recent papers classified by the tag motif-discovery.

	Motif-Blind, Genome-Wide Discovery of cis-Regulatory Modules in Drosophila and Mouse [My Copy] Vol. 17, No. 4. (20 October 2009), pp. 568-579. by Miriam R. Kantorovitz, Majid Kazemian, Sarah Kinston, et al.Diego Miranda-Saavedra, Qiyun Zhu, Gene E. Robinson, Berthold Göttgens, Marc S. Halfon, Saurabh Sinha posted to tools tfbs prediction motifs motif-discovery algorithm by isimpson on 2009-10-27 14:16:21 as along with 1 person and 1 group daveGerrard BergmanLab
	Discovering multiple realistic TFBS motifs based on a generalized model. [My Copy] BMC bioinformatics, Vol. 10, No. 1. (7 October 2009), 321. by Tak-Ming M. Chan, Gang Li, Kwong-Sak S. Leung, Kin-Hong H. Lee posted to tool motif-discovery by idonaldson on 2009-10-12 12:05:29 as along with 2 people maximilianh ashishanand
	Uncovering a Macrophage Transcriptional Program by Integrating Evidence from Motif Scanning and Expression Dynamics [My Copy] PLoS Comput Biol, Vol. 4, No. 3. (21 March 2008), e1000021. by Stephen A. Ramsey, Sandy L. Klemm, Daniel E. Zak, et al.Kathleen A. Kennedy, Vesteinn Thorsson, Bin Li, Mark Gilchrist, Elizabeth S. Gold, Carrie D. Johnson, Vladimir Litvak, Garnet Navarro, Jared C. Roach, Carrie M. Rosenberger, Alistair G. Rust, Natalya Yudkovsky, Alan Aderem, Ilya Shmulevich posted to tfbs must-read motifs motif-discovery bayesian by isimpson to the group Jarman Lab on 2009-08-26 16:53:14 as along with 3 people nicholasflann talponer ptrobajo
	A data integration framework for prediction of transcription factor targets. [My Copy] Annals of the New York Academy of Sciences, Vol. 1158 (March 2009), pp. 205-214. by Matti Nykter, Harri Lähdesmäki, Alistair Rust, Vesteinn Thorsson, Ilya Shmulevich posted to tfbs must-read motifs motif-discovery bayesian by isimpson to the group Jarman Lab on 2009-08-26 16:53:14 as
	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 tfbs software must-read motifs motif-discovery bayesian by isimpson to the group Jarman Lab on 2009-08-26 16:49:30 as along with 4 people nklee dolchan druvus guhjy
	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 transcription-factor tfbs software phylogenetics must-read motif-discovery by isimpson on 2009-08-13 22:25:40 as along with 4 people idonaldson maximilianh maralena guhjy
	A Hybrid Model for Robust Detection of Transcription Factor Binding Sites. [My Copy] Bioinformatics (9 January 2008) by Sumedha Gunewardena, Zhaolei Zhang posted to transcription-factor tfbs must-read motif-discovery by isimpson on 2009-08-13 22:24:01 as along with 3 people guhjy maximilianh idonaldson
	Hybrid Gibbs-sampling algorithm for challenging motif discovery: GibbsDST. [My Copy] Genome informatics. International Conference on Genome Informatics, Vol. 17, No. 2. (2006), pp. 3-13. by K. Shida posted to motif-discovery by wowalz on 2009-07-08 18:39:12 as
	FR3D: finding local and composite recurrent structural motifs in RNA 3D structures. [My Copy] Journal of mathematical biology, Vol. 56, No. 1-2. (January 2008), pp. 215-252. by M. Sarver, C. L. Zirbel, J. Stombaugh, A. Mokdad, N. B. Leontis posted to motif-discovery unsure by wowalz on 2009-07-08 18:37:54 as along with 2 people reyez jarasch
	An efficient, versatile and scalable pattern growth approach to mine frequent patterns in unaligned protein sequences. [My Copy] Bioinformatics (Oxford, England), Vol. 23, No. 6. (15 March 2007), pp. 687-693. by K. Ye, W. A. Kosters, A. P. Ijzerman posted to motif-discovery unsure by wowalz on 2009-07-08 18:33:17 as along with 2 people thaliana birzele
	A sequential method for discovering probabilistic motifs in proteins. [My Copy] Methods of information in medicine, Vol. 43, No. 1. (2004), pp. 9-12. by K. Blekas, D. I. Fotiadis, A. Likas posted to motif-discovery by wowalz on 2009-07-08 18:32:20 as
	Finding subtle motifs by branching from sample strings. [My Copy] Bioinformatics (Oxford, England), Vol. 19 Suppl 2 (October 2003) by A. Price, S. Ramabhadran, P. A. Pevzner posted to motif-discovery by wowalz on 2009-07-08 18:03:32 as along with 2 people dquest Evangelia
	iGibbs: improving Gibbs motif sampler for proteins by sequence clustering and iterative pattern sampling. [My Copy] Proteins, Vol. 66, No. 3. (15 February 2007), pp. 671-681. by S. Kim, Z. Wang, M. Dalkilic posted to cluster motif-discovery by wowalz on 2009-07-08 18:02:51 as along with 1 person nklee
	Discovering motif pairs at interaction sites from protein sequences on a proteome-wide scale. [My Copy] Bioinformatics (Oxford, England), Vol. 22, No. 8. (15 April 2006), pp. 989-996. by H. Li, J. Li, L. Wong posted to motif-discovery unsure by wowalz on 2009-07-08 18:01:39 as along with 1 person and 2 groups bsmagic Bioinformatics bioinplant
	RNAProfile: an algorithm for finding conserved secondary structure motifs in unaligned RNA sequences. [My Copy] Nucleic acids research, Vol. 32, No. 10. (2004), pp. 3258-3269. by G. Pavesi, G. Mauri, M. Stefani, G. Pesole posted to motif-discovery by wowalz on 2009-07-08 18:00:11 as along with 4 people Glires evaf eckart_bindewald dquest
	A structure-based flexible search method for motifs in RNA. [My Copy] Journal of computational biology : a journal of computational molecular cell biology, Vol. 14, No. 7. (September 2007), pp. 908-926. by I. Veksler-Lublinsky, M. Ziv-Ukelson, D. Barash, K. Kedem posted to motif-discovery by wowalz on 2009-07-08 17:59:23 as along with 1 person eskay
	RNAMotif, an RNA secondary structure definition and search algorithm [My Copy] Nucl. Acids Res., Vol. 29, No. 22. (15 November 2001), pp. 4724-4735. by Thomas J. Macke, David J. Ecker, Robin R. Gutell, Daniel Gautheret, David A. Case, Rangarajan Sampath posted to motif-discovery by wowalz on 2009-07-08 17:56:33 as along with 2 people evaf dquest
	Searching for statistically significant regulatory modules. [My Copy] Bioinformatics (Oxford, England), Vol. 19 Suppl 2 (October 2003) by T. L. Bailey, W. S. Noble posted to motif-discovery by wowalz on 2009-07-08 17:55:15 as along with 4 people and 2 groups maximilianh indigoviolet stajich xili03 EisenLab Mycology
	A string pattern regression algorithm and its application to pattern discovery in long introns. [My Copy] Genome informatics. International Conference on Genome Informatics, Vol. 13 (2002), pp. 3-11. by H. Bannai, S. Inenaga, A. Shinohara, M. Takeda, S. Miyano posted to motif-discovery unsure by wowalz on 2009-07-08 17:54:10 as
	Finding motifs with insufficient number of strong binding sites. [My Copy] Journal of computational biology : a journal of computational molecular cell biology, Vol. 12, No. 6. (g 2005), pp. 686-701. by H. C. Leung, F. Y. Chin, S. M. Yiu, R. Rosenfeld, W. W. Tsang posted to motif-discovery by wowalz on 2009-07-08 17:52:35 as along with 1 person dquest
	Finding linear motif pairs from protein interaction networks: a probabilistic approach. [My Copy] Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference, Vol. 6 (2007), pp. 111-119. by H. C. Leung, M. H. Siu, S. M. Yiu, F. Y. Chin, K. W. Sung posted to motif-discovery by wowalz on 2009-07-08 17:50:59 as
	Finding motifs from all sequences with and without binding sites. [My Copy] Bioinformatics (Oxford, England), Vol. 22, No. 18. (15 September 2006), pp. 2217-2223. by H. C. Leung, F. Y. Chin posted to motif-discovery by wowalz on 2009-07-08 17:48:21 as along with 3 people eckart_bindewald dquest nuin
	ARCS-Motif: discovering correlated motifs from unaligned biological sequences. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 2. (15 January 2009), pp. 183-189. by S. Zhang, W. Su, J. Yang posted to motif-discovery unsure by wowalz on 2009-07-08 17:46:44 as along with 2 people djkt nuin
	Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm [published erratum appears in Bioinformatics 1998;14(2):229] [My Copy] Bioinformatics, Vol. 14, No. 1. (1 February 1998), pp. 55-67. by I. Rigoutsos, A. Floratos posted to motif-discovery by wowalz on 2009-07-08 17:42:34 as along with 6 people and 1 group stharward windman83 thaliana okarsligil dquest heliopais Bioinformatics
	On counting position weight matrix matches in a sequence, with application to discriminative motif finding. [My Copy] Bioinformatics (Oxford, England), Vol. 22, No. 14. (15 July 2006) by S. Sinha posted to motif-discovery by wowalz on 2009-07-08 17:39:18 as along with 3 people eckart_bindewald samal xili03
	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 evo-alg motif-discovery nolocalpdf unsure by wowalz on 2009-07-08 17:24:32 as along with 1 person nklee
	Counting of oligomers in sequences generated by markov chains for DNA motif discovery. [My Copy] Journal of bioinformatics and computational biology, Vol. 7, No. 1. (February 2009), pp. 39-54. by G. Shan, W. M. Zheng posted to markov motif-discovery by wowalz on 2009-07-08 17:14:23 as along with 1 person maximilianh
	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 by wowalz on 2009-07-08 17:12:41 as along with 7 people and 1 group tmarscha dpollard cjeans nklee niallhaslam maximilianh idonaldson EisenLab
	SMOTIF: efficient structured pattern and profile motif search. [My Copy] Algorithms for molecular biology : AMB, Vol. 1 (21 November 2006), 22. by Y. Zhang, M. J. Zaki posted to motif-discovery by wowalz on 2009-07-08 17:11:18 as along with 2 people beete kmdaily
	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 motif-discovery by wowalz on 2009-07-08 17:09:30 as along with 1 person nklee
	Computing the P-value of the information content from an alignment of multiple sequences. [My Copy] Bioinformatics (Oxford, England), Vol. 21 Suppl 1 (June 2005) by N. Nagarajan, N. Jones, U. Keich posted to motif-discovery unsure by wowalz on 2009-07-08 17:00:22 as along with 3 people treangen rabio nedwards
	Finding exact optimal motifs in matrix representation by partitioning. [My Copy] Bioinformatics (Oxford, England), Vol. 21 Suppl 2 (1 September 2005) by H. C. Leung, F. Y. Chin posted to motif-discovery unsure by wowalz on 2009-07-08 16:59:10 as along with 1 person dquest
	Efficient exact motif discovery. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 12. (15 June 2009), pp. i356-364. by T. Marschall, S. Rahmann posted to motif-discovery by wowalz on 2009-07-08 16:57:53 as along with 4 people dquest nuin idonaldson maximilianh
	Studying statistical properties of regulatory DNA sequences, and their use in predicting regulatory regions in the eukaryotic genomes [My Copy] Brief Bioinform, Vol. 7, No. 1. (1 March 2006), pp. 48-54. by Irina Abnizova, Walter R. Gilks posted to bioinformatics motif-discovery regulatory by akshayk on 2009-06-16 20:24:28 as
	Allegro: Analyzing expression and sequence in concert to discover regulatory programs [My Copy] Nucl. Acids Res. (16 January 2009), gkn1064. by Yonit Halperin, Chaim Linhart, Igor Ulitsky, Ron Shamir posted to bioinformatics mirna motif-discovery tau by akshayk on 2009-06-15 09:16:02 as along with 2 people rdiaz nuin
	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 bioinformatics mirna motif-discovery sysbio tau by akshayk on 2009-06-15 09:12:56 as along with 12 people and 1 group dolchan wowalz natstreet valeriehilgers jfr ealloza idonaldson maralena fpattyn isimpson tmmurali maximilianh BergmanLab
	Identifying short motifs by means of extreme value analysis [My Copy] EPL (Europhysics Letters), Vol. 84, No. 1. (2008), 18001. by D. Bianchi, B. Tirozzi posted to motif-discovery by wowalz on 2009-06-12 15:04:34 as
	Explicit equilibrium modeling of transcription-factor binding and gene regulation. [My Copy] Genome biology, Vol. 6, No. 10. (2005) by J. A. Granek, N. D. Clarke posted to motif-discovery tool yeast by idonaldson on 2009-06-09 14:52:13 as along with 2 people provero emptyhb
	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 motif-discovery motifs prediction software tfbs transcription-factor by isimpson on 2009-06-04 12:11:40 as along with 5 people druvus natstreet idonaldson nklee nuin
	MEME SUITE: tools for motif discovery and searching [My Copy] Nucl. Acids Res., Vol. 37, No. suppl_2. (1 July 2009), pp. W202-208. by Timothy L. Bailey, Mikael Boden, Fabian A. Buske, et al.Martin Frith, Charles E. Grant, Luca Clementi, Jingyuan Ren, Wilfred W. Li, William S. Noble posted to motif-discovery tool by idonaldson on 2009-05-26 10:29:19 as along with 6 people suizifish jlike maximilianh natstreet nuin cassj
	Pattern Discovery from Biosequences [My Copy] (2002) by Jaak Vilo, Jaak Vilo, Jaak Vilo posted to motif-discovery by wowalz on 2009-05-06 15:56:35 as
	Weeder Web: a Web-Based Tool for the Discovery of Transcription Factor Binding Sites [My Copy] by Giulio Pavesi, Giancarlo Mauri, Graziano Pesole posted to motif-discovery weeder by wowalz on 2009-05-06 15:45:22 as
	Pattern Detection and Discovery [My Copy] Pattern Detection and Discovery (2002), pp. 161-173. by David Hand posted to motif-discovery unsure by wowalz on 2009-05-06 15:44:25 as
	Pattern Discovery in Sequences under a Markov Assumption [My Copy] (2002) by Darya Chudova, Padhraic Smyth posted to markov motif-discovery by wowalz on 2009-05-06 15:42:04 as
	iMoMi (interactive Motif Mining)- a database and utilities to assist the discovery of new regulatory patterns [My Copy] by Nicolas Pons, Jean-Michel Batto, Dusko S. Ehrlich, Pierre Renault posted to motif-discovery by wowalz on 2009-05-06 15:40:32 as
	A Bayesian Hidden Markov Model for Motif Discovery Through Joint Modeling of Genomic Sequence and ChIP-Chip Data [My Copy] Biometrics, Vol. 9999, No. 9999. (2009) by Jonathan A. L. Gelfond, Mayetri Gupta, Joseph G. Ibrahim posted to bayesian motif-discovery unsure by wowalz on 2009-05-06 15:39:21 as along with 2 people maximilianh idonaldson
	Protein Sequence Motif Discovery on Distributed Supercomputer [My Copy] Advances in Grid and Pervasive Computing (2008), pp. 232-243. by Santan Challa, Parimala Thulasiraman posted to motif-discovery by wowalz on 2009-05-06 15:35:32 as
	Graphical approach for motif recognition in DNA sequences [My Copy] Computational Intelligence in Bioinformatics and Computational Biology, 2004. CIBCB '04. Proceedings of the 2004 IEEE Symposium on In Computational Intelligence in Bioinformatics and Computational Biology, 2004. CIBCB '04. Proceedings of the 2004 IEEE Symposium on (2004), pp. 147-152. by X. Yang, J. C. Rajapakse posted to motif-discovery by wowalz on 2009-05-06 15:33:03 as
	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 unsure by wowalz on 2009-05-06 15:28:55 as along with 5 people GustavoLacerda maximilianh idonaldson csdhwang isimpson
	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 unsure by wowalz on 2009-05-06 15:28:01 as along with 5 people druvus nuin chad_davis maximilianh idonaldson

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printout-exists	130
unsure	117
nolocalpdf	40
evo-alg	31
tfbs	25
tool	25
bayesian	21
motifs	17
must-read	14
bioinformatics	6
transcription-factor	6
transcription-regulation	6
cis-regulation	5
microarray	5
database	4
ea	4
functional-network	4
fuzzy	4
markov	4
mouse	4
prediction	4
review	4
software	4
time-series	4
weeder	4
model	3
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chip-chip	2
cis-regulatory-element	2
cluster	2
crm	2
enhancer	2
fish	2
gibbs-sampling	2
gpu	2
mammal	2
mirna	2
motif	2
parallel	2
tau	2
transcription-factor-binding-site	2
wtg09	2
affix-tree	1
algorithm	1
analysis	1
chromatin-immunoprecipitation	1
clustering	1
comparative	1
conservation	1
conserved	1
discovery	1
dna	1
genome-wide	1
heuristic	1
me	1
motif-statistics	1
now	1
phylogenetic-footprinting	1
phylogenetics	1
ppi-database	1
primer	1
protein	1
protein-networks	1
regulatory	1
rna	1
spacing	1
statistics	1
structural	1
structure	1
sysbio	1
tissue-specific	1
tools	1
trawler	1
yeast	1
zebrafish	1

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