Group: EisenLab - with tag method [39 articles] Export

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

	Gene network inference via structural equation modeling in genetical genomics experiments. [My Copy] Genetics, Vol. 178, No. 3. (3 March 2008), pp. 1763-1776. by B. Liu, A. de la Fuente, I. Hoeschele posted to eqtl method network system by dpollard to the group EisenLab on 2008-02-12 23:12:26 as along with 8 people roys Scis0000002 orzenil raiyar xingxu caseybrown smgomez guhjy
	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
	The effect of the guide tree on multiple sequence alignments and subsequent phylogenetic analyses. [My Copy] Pac Symp Biocomput (2008), pp. 25-36. by S. Nelesen, K. Liu, D. Zhao, C. R. Linder, T. Warnow posted to accuracy alignment alignment_accuracy method multiple_alignment phylogeny reconstruction by dpollard to the group EisenLab on 2008-02-01 06:14:52 as along with 2 people sriesenfeld treangen
	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
	The cost of inbreeding in Arabidopsis. [My Copy] Nature, Vol. 416, No. 6880. (4 April 2002), pp. 531-534. by C. D. Bustamante, R. Nielsen, S. A. Sawyer, K. M. Olsen, M. D. Purugganan, D. L. Hartl posted to method population_genetics test_for_selection by dpollard to the group EisenLab on 2007-11-19 07:32:25 as along with 2 people emptyhb djkt
	MORPH: Probabilistic Alignment Combined with Hidden Markov Models of cis-Regulatory Modules [My Copy] PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e216. by Saurabh Sinha, Xin He posted to alignment alignment_accuracy binding_site_alignment brant_presented cis_regulatory_elements eisen_journal_club method round_robin by dpollard to the group EisenLab on 2007-11-16 23:53:34 as along with 7 people and 1 group ana cjeans zwang maximilianh hpaces Ema uwe cis-regulatory-evolution
	Bayesian estimation of concordance among gene trees. [My Copy] Mol Biol Evol, Vol. 24, No. 2. (February 2007), pp. 412-426. by C. Ané, B. Larget, D. A. Baum, S. D. Smith, A. Rokas posted to concordance gene_tree gene_vs_species_tree method phylogeny speciation by dpollard to the group EisenLab on 2007-11-06 22:35:21 as along with 2 people aprasad AaronDarling
	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
	Enhancing the quality of phylogenetic analysis using fuzzy hidden Markov model alignments. [My Copy] Medinfo, Vol. 12, No. Pt 2. (2007), pp. 1245-1249. by C. Collyda, S. Diplaris, P. Mitkas, N. Maglaveras, C. Pappas posted to alignment alignment_accuracy method phylogeny by dpollard to the group EisenLab on 2007-10-25 02:23:23 as
	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
	Computational and experimental approaches for modeling gene regulatory networks. [My Copy] Curr Pharm Des, Vol. 13, No. 14. (2007), pp. 1415-1436. by J. Goutsias, N. H. Lee posted to review regulatory_network modeling method experimental computational by dpollard to the group EisenLab on 2007-06-14 23:48:35 as along with 1 person bertelsen
	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
	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
	Imputation-based analysis of association studies: candidate regions and quantitative traits [My Copy] PLoS Genetics, Vol. preprint, No. 2007. (1 May 2007), e114.eor. by Bertrand Servin, Matthew Stephens posted to method association_mapping by dpollard to the group EisenLab on 2007-05-31 22:45:19 as
	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
	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
	RE-MuSiC: a tool for multiple sequence alignment with regular expression constraints. [My Copy] Nucleic Acids Res (8 May 2007) by Yun-Sheng S. Chung, Wei-Hsun H. Lee, Chuan Yi Y. Tang, Chin Lung L. Lu posted to regular_expressions multiple_alignment method by dpollard to the group EisenLab on 2007-05-23 00:25:21 as
	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
	ChIP-on-chip protocol for genome-wide analysis of transcription factor binding in Drosophila melanogaster embryos. [My Copy] Nat Protoc, Vol. 1, No. 6. (2006), pp. 2839-2855. by T. Sandmann, J. S. Jakobsen, E. E. Furlong posted to transcription_factor method drosophila chip_chip binding by dpollard to the group EisenLab on 2007-04-09 17:24:28 as along with 1 person johncumbers
	Quantifying DNA-protein binding specificities by using oligonucleotide mass tags and mass spectroscopy [My Copy] PNAS, Vol. 104, No. 9. (27 February 2007), pp. 3061-3066. by Lingang Zhang, Simon Kasif, And C. Cantor posted to transcription_factor method mass_spec dna_binding by cwbrown to the group EisenLab on 2007-03-29 22:07:00 as along with 2 people guhjy zwang
	Quantifying similarity between motifs [My Copy] Genome Biology, Vol. 8, No. 2. (26 February 2007), R24. by Shobhit Gupta, John Stamatoyannopoulos, Timothy Bailey, William Noble posted to motif_finding motif_comparison method by cwbrown to the group EisenLab on 2007-03-29 21:08:57 as along with 6 people jlike Dulce maximilianh grahamc nklee gracio
	DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies [My Copy] PLoS Computational Biology, Vol. preprint, No. 2007. (1 February 2007), e61.eor. by Shaun Mahony, Philip Auron, Panayiotis Benos posted to transcription_factor motifs method dna_binding by cwbrown to the group EisenLab on 2007-03-29 20:45:40 as
	In vitro analysis of DNA-protein interactions by proximity ligation. [My Copy] Proc Natl Acad Sci U S A, Vol. 104, No. 9. (27 February 2007), pp. 3067-3072. by S. M. Gustafsdottir, J. Schlingemann, A. Rada-Iglesias, et al.E. Schallmeiner, M. Kamali-Moghaddam, C. Wadelius, U. Landegren posted to transcription_factor round_robin method eisen_journal_club colin_presented binding by dpollard to the group EisenLab on 2007-03-23 19:28:14 as along with 2 people guhjy zwang
	Global Discriminative Learning for Higher-Accuracy Computational Gene Prediction [My Copy] PLoS Computational Biology, Vol. 3, No. 3. (1 March 2007), e54. by Axel Bernal, Koby Crammer, Artemis Hatzigeorgiou, Fernando Pereira posted to method gene_prediction ab_initio by dpollard to the group EisenLab on 2007-03-23 00:33:15 as along with 1 person GustavoLacerda
	Multiple Hypothesis Testing to Detect Lineages Under Positive Selection that Affects Only a Few Sites. [My Copy] Mol Biol Evol (5 March 2007) by Maria Anisimova, Ziheng Yang posted to multiple_testing method evolution adaptive by dpollard to the group EisenLab on 2007-03-22 23:51:26 as along with 3 people and 1 group stevanspringer operon gjuggler FAB-lab
	Incorporating indel information into phylogeny estimation for rapidly emerging pathogens [My Copy] BMC Evolutionary Biology, Vol. 7, No. 1. (14 March 2007), 40. by Benjamin Redelings, Marc Suchard posted to phylogeny method indels gene alignment by dpollard to the group EisenLab on 2007-03-22 22:56:37 as along with 5 people timflutre druvus operon aprasad stajich
	Global Discriminative Learning for Higher-Accuracy Computational Gene Prediction [My Copy] PLoS Computational Biology, Vol. 3, No. 3. (1 March 2007), e54. by Axel Bernal, Koby Crammer, Artemis Hatzigeorgiou, Fernando Pereira posted to ab_initio gene_prediction method by dpollard to the group EisenLab on 2007-03-16 21:10:40 as along with 5 people and 1 group dakelley wenhan zwang acarbo alexl Bioinformatics
	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
	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
	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
	Multiple alignment by sequence annealing. [My Copy] Bioinformatics, Vol. 23, No. 2. (15 January 2007) by A. S. Schwartz, L. Pachter posted to protein method alignment by dpollard to the group EisenLab on 2007-02-01 19:47:22 as
	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
	Exogean: a framework for annotating protein-coding genes in eukaryotic genomic DNA. [My Copy] Genome Biol, Vol. 7 Suppl 1 (2006) by S. Djebali, F. Delaplace, H. R. Crollius posted to annotation eukaryote gene method by dpollard to the group EisenLab on 2006-09-30 00:21:18 as along with 1 person indigoviolet
	Quantification of the variation in percentage identity for protein sequence alignments [My Copy] BMC Bioinformatics, Vol. 7 (19 September 2006), 415. by Ps G. Raghava, Geoffrey J. Barton posted to accuracy alignment gene method protein by dpollard to the group EisenLab on 2006-09-30 00:20:09 as along with 7 people thegoose sgoetz pansapiens bicko rabio medic0747 sujaikumar
	Estimating Selection Pressures from Limited Comparative Data. [My Copy] Mol Biol Evol (5 June 2006) by Joshua B B. Plotkin, Jonathan Dushoff, Michael M M. Desai, Hunter B B. Fraser posted to evolution gene method selection variation by dpollard to the group EisenLab on 2006-07-13 19:10:38 as along with 4 people bnchakraborty djkt BioNica friendpine
	Comparing gene expression networks in a multi-dimensional space to extract similarities and differences between organisms. [My Copy] Bioinformatics (9 March 2006) by Gaëlle Lelandais, Pierre Vincens, Anne Badel-Chagnon, Stéphane Vialette, Claude Jacq, Serge Hazout posted to evolution expression gene method network by dpollard to the group EisenLab on 2006-03-21 18:55:30 as along with 1 person wnpx

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Group: EisenLab - with tag method [39 articles] Export

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