Group: EisenLab - with tag alignment [32 articles] Export Sort

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

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	Alignment Uncertainty and Genomic Analysis [My Copy] Science, Vol. 319, No. 5862. (25 January 2008), pp. 473-476. by Karen M. Wong, Marc A. Suchard, John P. Huelsenbeck posted to alignment alignment_accuracy by dpollard to the group EisenLab on 2008-02-01 06:16:51 as along with 33 people and 1 group Jporci operon walshtp darian ptrobajo friendpine skembel druvus treangen bpb aprasad dayjm pradiptaray tny djkt cjeans zwang lisa1 cactus biomcgary lilou dandaman gjuggler renatomilani mclarenv youdon bpcusack guhjy jdelcampo adacier gracio timflutre jfr microbiology_nijmegen
	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
	BLAT--the BLAST-like alignment tool. [My Copy] Genome research, Vol. 12, No. 4. (1 April 2002), pp. 656-664. by W. James Kent posted to algorithm alignment by indigoviolet to the group EisenLab on 2007-12-03 20:27:15 as along with 37 people and 2 groups azazello rshe dchughes rdowell gwallau druvus aprasad maria_hauser n00c sficklin Thaverkamp cpwardell daveGerrard coela daforerog pwais umit mmartin paszkows operon miguel pcahan1 Ayest mtagaya treangen michC djkt timflutre olympos cjeans wenhan natstreet antonkratz yoanjacquemin talponer bozdagd gpappas LabDros BergmanLab
	T-Coffee: A novel method for fast and accurate multiple sequence alignment. [My Copy] Journal of molecular biology, Vol. 302, No. 1. (8 September 2000), pp. 205-217. by C. Notredame, D. G. Higgins, J. Heringa posted to algorithm alignment by indigoviolet to the group EisenLab on 2007-12-03 18:04:40 as along with 17 people bratwurst viktor21614 tomjad robert laurabailey medic0747 BioNica sebk miguel dayjm ffranca treangen Haggan siebertm adijr marti newton1234
	Aligning multiple genomic sequences with the threaded blockset aligner. [My Copy] Genome research, Vol. 14, No. 4. (April 2004), pp. 708-715. by Mathieu Blanchette, W. James Kent, Cathy Riemer, et al.Laura Elnitski, Arian F. Smit, Krishna M. Roskin, Robert Baertsch, Kate Rosenbloom, Hiram Clawson, Eric D. Green, David Haussler, Webb Miller posted to algorithm alignment by indigoviolet to the group EisenLab on 2007-12-03 12:28:07 as along with 13 people roys emptyhb nuin aprasad APRegier operon ujh csardas djkt yylin Neeperando maralena AlexanderPico
	AVID: A Global Alignment Program [My Copy] Genome Research, Vol. 13, No. 1. (1 January 2003), pp. 97-102. by Nick Bray, Inna Dubchak, Lior Pachter posted to algorithm alignment by indigoviolet to the group EisenLab on 2007-12-03 12:24:42 as along with 5 people n00c mhiromi Neeperando adijr yoanjacquemin
	DIALIGN: finding local similarities by multiple sequence alignment [My Copy] Bioinformatics, Vol. 14, No. 3. (1 April 1998), pp. 290-294. by B. Morgenstern, K. Frech, A. Dress, T. Werner posted to algorithm alignment by indigoviolet to the group EisenLab on 2007-12-03 12:11:49 as along with 2 people BioNica adijr
	Human–Mouse Alignments with BLASTZ [My Copy] Genome Research, Vol. 13, No. 1. (1 January 2003), pp. 103-107. by Scott Schwartz, W. James Kent, Arian Smit, et al.Zheng Zhang, Robert Baertsch, Ross C. Hardison, David Haussler, Webb Miller posted to algorithm alignment by indigoviolet to the group EisenLab on 2007-12-03 12:10:51 as along with 6 people gdb daveGerrard druvus operon treangen nedwards
	Benchmarking tools for the alignment of functional noncoding DNA. [My Copy] BMC Bioinformatics, Vol. 5 (21 January 2004) by D. A. Pollard, C. M. Bergman, J. Stoye, S. E. Celniker, M. B. Eisen posted to algorithm alignment evaluation by indigoviolet to the group EisenLab on 2007-12-03 12:09:57 as along with 6 people cap1 lilou adijr idonaldson gjuggler nklee
	Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. [My Copy] Nucleic acids research, Vol. 25, No. 17. (1 September 1997), pp. 3389-3402. by S. F. Altschul, T. L. Madden, A. A. Schäffer, et al.J. Zhang, Z. Zhang, W. Miller, D. J. Lipman posted to algorithm alignment by indigoviolet to the group EisenLab on 2007-12-03 10:41:36 as along with 69 people and 4 groups saunders rshe niallhaslam ucbcjbm timhubbard parnell tfuji maria_hauser jbhiatt yylin mgomes BioNica idoerg pjcite swp09 kgutwin mcbla cpwardell johanviklund daforerog nlapalu sebk tjimenez shung pwais dakelley knaseanka setar iakes miguel kaarsinogen bjorns bicko jmeppley chad_davis balajis nuke2005 eweaver david_parsons dullhunk robert dgront happy_manatee caporaso treangen kengg manzanita CitoJam jdelcampo aengisch rabio massivemayhem mirzazadeh azazello sujaikumar beatrizfernandez GustavoLacerda siebertm adijr viktor21614 mijam grottenolm bandrewfox edvin newton1234 mariakmejia granujilla marti CharlesM References for 3DSim paper biomedical-nlp Microbial-Ecology Plantandetc
	Identification of protein coding regions by database similarity search. [My Copy] Nat Genet, Vol. 3, No. 3. (March 1993), pp. 266-272. by W. Gish, D. J. States posted to algorithm alignment computational by indigoviolet to the group EisenLab on 2007-12-03 10:39:38 as along with 2 people bluto wenhan
	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
	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
	Measuring the accuracy of genome-size multiple alignments [My Copy] Genome Biology, Vol. 8 (26 June 2007), R124. by Amol Prakash, Martin Tompa posted to alignment alignment_accuracy whole_genome by dpollard to the group EisenLab on 2007-10-25 01:39:42 as along with 5 people and 1 group druvus treangen AaronDarling stajich lilou Mycology
	Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments [My Copy] BMC Bioinformatics, Vol. 7 (14 August 2006), 376. by Daniel A. Pollard, Alan M. Moses, Venky N. Iyer, Michael B. Eisen posted to tree_topology divergence_estimation binding_site_alignment alignment_accuracy alignment by dpollard to the group EisenLab on 2007-08-02 01:13:48 as along with 6 people and 1 group aprasad lusk Garamonfok lilou cisevol emptyhb cis-regulatory-evolution
	Multiple sequence alignment accuracy and evolutionary distance estimation [My Copy] BMC Bioinformatics, Vol. 6, No. 1. (2005), 278. by Michael Rosenberg posted to divergence_estimation alignment_accuracy alignment by dpollard to the group EisenLab on 2007-08-02 01:09:41 as along with 4 people and 1 group gjuggler treangen aprasad cisevol cis-regulatory-evolution
	The many faces of sequence alignment [My Copy] Brief Bioinform, Vol. 6, No. 1. (1 January 2005), pp. 6-22. by Serafim Batzoglou posted to review alignment by dpollard to the group EisenLab on 2007-08-02 01:04:27 as along with 11 people and 1 group nuttpo druvus n00c pimmy timflutre BioNica treangen balajis sdvillal gjuggler yoanjacquemin Bioinformatics
	Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome [My Copy] Genome Res., Vol. 17, No. 6. (1 June 2007), pp. 760-774. by Elliott H. Margulies, Gregory M. Cooper, George Asimenos, et al.Daryl J. Thomas, Colin N. Dewey, Adam Siepel, Ewan Birney, Damian Keefe, Ariel S. Schwartz, Minmei Hou, James Taylor, Sergey Nikolaev, Juan I. Montoya-Burgos, Ari Loytynoja, Simon Whelan, Fabio Pardi, Tim Massingham, James B. Brown, Peter Bickel, Ian Holmes, James C. Mullikin, Abel Ureta-Vidal, Benedict Paten, Eric A. Stone, Kate R. Rosenbloom, James W. Kent, Gerard G. Bouffard, Xiaobin Guan, Nancy F. Hansen, Jacquelyn R. Idol, Valerie V. Maduro, Baishali Maskeri, Jennifer C. Mcdowell, Morgan Park, Pamela J. Thomas, Alice C. Young, Robert W. Blakesley, Donna M. Muzny, Erica Sodergren, David A. Wheeler, Kim C. Worley, Huaiyang Jiang, George M. Weinstock, Richard A. Gibbs, Tina Graves, Robert Fulton, Elaine R. Mardis, Richard K. Wilson, Michele Clamp, James Cuff, Sante Gnerre, David B. Jaffe, Jean L. Chang, Kerstin Lindblad-Toh, Eric S. Lander, Angie Hinrichs, Heather Trumbower, Hiram Clawson, Ann Zweig, Robert M. Kuhn, Galt Barber, Rachel Harte, Donna Karolchik, Matthew A. Field, Richard A. Moore, Carrie A. Matthewson, Jacqueline E. Schein, Marco A. Marra, Stylianos E. Antonarakis, Serafim Batzoglou, Nick Goldman, Ross Hardison, David Haussler, Webb Miller, Lior Pachter, Eric D. Green, Arend Sidow posted to mammal encode constraint alignment by dpollard to the group EisenLab on 2007-06-29 05:54:18 as along with 11 people and 4 groups daveGerrard polivares timflutre aprasad dchughes AaronDarling djkt ghattem Garamonfok gjuggler elfar BergmanLab Bioinformatics G4ID Genetics-of-Gambling
	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
	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
	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
	Logarithmic gap costs decrease alignment accuracy [My Copy] BMC Bioinformatics, Vol. 7 (05 December 2006), 527. by Reed A. Cartwright posted to indels alignment accuracy by dpollard to the group EisenLab on 2007-01-19 16:35:28 as along with 4 people timflutre druvus treangen groepl
	LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. [My Copy] Genome Res, Vol. 13, No. 4. (April 2003), pp. 721-731. by M. Brudno, C. B. Do, G. M. Cooper, et al.M. F. Kim, E. Davydov, E. D. Green, A. Sidow, S. Batzoglou, posted to alignment noncoding by dpollard to the group EisenLab on 2006-11-07 01:53:28 as along with 14 people treangen operon balajis xwbcn dquest adepace hdopazo lusk Garamonfok adijr natstreet nklee Neeperando kcrawlik
	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
	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
	MACO: A gapped-alignment scoring tool for comparing transcription factor binding sites. [My Copy] In Silico Biol, Vol. 6, No. 4. (29 May 2006) by Gang Su, Binchen Mao, Jin Wang posted to alignment matrix pwm similarity by dpollard to the group EisenLab on 2006-08-25 17:56:58 as
	Parametric Alignment of Drosophila Genomes [My Copy] PLoS Computational Biology, Vol. 2, No. 6. (1 June 2006), e73. by Colin N. Dewey, Peter M. Huggins, Kevin Woods, Bernd Sturmfels, Lior Pachter posted to algorithm alignment by emilyhare to the group EisenLab on 2006-06-24 00:43:28 as along with 3 people treangen dquest joshuashen
	MCALIGN2: Faster, accurate global pairwise alignment of non-coding DNA sequences based on explicit models of indel evolution [My Copy] BMC Bioinformatics, Vol. 7, No. 1. (08 June 2006), 292. by Jun Wang, Peter Keightley, Toby Johnson posted to alignment evolution indel model by dpollard to the group EisenLab on 2006-06-16 20:34:32 as along with 6 people timflutre druvus gjuggler Ayest papamicd bozdagd
	Evolutionary turnover of mammalian transcription start sites. [My Copy] Genome Res (10 May 2006) by Martin C C. Frith, Jasmina Ponjavic, David Fredman, et al.Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayshizaki, Albin Sandelin posted to alignment conserved evolution gene mammal promoter transcription turnover vertebrate by dpollard to the group EisenLab on 2006-05-12 17:41:10 as along with 5 people and 2 groups galka8_diploma cmm jsnoddy cisevol gjuggler FAB-lab cis-regulatory-evolution
	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
	Sigma: multiple alignment of weakly-conserved non-coding DNA sequence. [My Copy] BMC Bioinformatics, Vol. 7, No. 1. (16 March 2006) by Rahul Siddharthan posted to alignment noncoding by dpollard to the group EisenLab on 2006-04-02 23:08:10 as along with 3 people and 1 group aprasad cisevol lilou cis-regulatory-evolution

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Group: EisenLab - with tag alignment [32 articles] Export Sort

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