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dpollards alignment [25 articles]

Neue Publikationen in dpollards Bibliothek eingetragen unter dem Bezeichner: alignment. You can also see everyone's alignment.
  • Alignment Uncertainty and Genomic Analysis
    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 on 2008-02-01 06:16:50 as *** along with 19 people and 2 groups adacier jyuh bpb aprasad dayjm tny djkt cjeans zwang lisa1 cactus biomcgary lilou kinestetika dandaman gjuggler renatomilani mclarenv youdon EisenLab microbiology_nijmegen
  • The effect of the guide tree on multiple sequence alignments and subsequent phylogenetic analyses.
    Pac Symp Biocomput (2008), pp. 25-36.
    by S Nelesen, K Liu, D Zhao, CR Linder, T Warnow
    posted to accuracy alignment alignment_accuracy method multiple_alignment phylogeny reconstruction by dpollard on 2008-02-01 06:14:51 as ** along with 1 group EisenLab
  • MORPH: Probabilistic Alignment Combined with Hidden Markov Models of cis-Regulatory Modules
    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 on 2007-11-16 23:53:34 as **** along with 7 people and 2 groups ana cjeans zwang maximilianh hpaces Ema uwe EisenLab cis-regulatory-evolution
  • Enhancing the quality of phylogenetic analysis using fuzzy hidden Markov model alignments.
    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 on 2007-10-25 02:23:22 as ** along with 1 group EisenLab
  • Incorporating evolution of transcription factor binding sites into annotated alignments.
    J Biosci, Vol. 32, No. 5. (August 2007), pp. 841-850.
    by AS Bais, S Grossmann, M Vingron
    posted to alignment binding_site conserved method prediction by dpollard on 2007-10-25 02:20:56 as ** along with 1 person and 2 groups maximilianh EisenLab cis-regulatory-evolution
  • Measuring the accuracy of genome-size multiple alignments
    Genome Biology, Vol. 8 (26 June 2007), R124.
    by Amol Prakash, Martin Tompa
    posted to alignment alignment_accuracy whole_genome by dpollard on 2007-10-25 01:39:42 as *** along with 3 people and 2 groups AaronDarling stajich lilou EisenLab Berkeley Mycology
  • Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments
    BMC Bioinformatics, Vol. 7 (14 August 2006), 376.
    by Daniel A Pollard, Alan M Moses, Venky N Iyer, Michael B Eisen
    posted to alignment alignment_accuracy binding_site_alignment divergence_estimation tree_topology by dpollard on 2007-08-02 01:13:48 as read along with 6 people and 2 groups emptyhb aprasad lusk Garamonfok lilou cisevol EisenLab cis-regulatory-evolution
  • Multiple sequence alignment accuracy and evolutionary distance estimation.
    BMC Bioinformatics, Vol. 6 (2005)
    by MS Rosenberg
    posted to alignment alignment_accuracy divergence_estimation by dpollard on 2007-08-02 01:09:41 as read along with 2 people and 2 groups aprasad cisevol EisenLab cis-regulatory-evolution
  • The many faces of sequence alignment.
    Brief Bioinform, Vol. 6, No. 1. (March 2005), pp. 6-22.
    by S Batzoglou
    posted to alignment review by dpollard on 2007-08-02 01:04:27 as read along with 4 people and 2 groups balajis sdvillal gjuggler yoanjacquemin Bioinformatics EisenLab
  • Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
    Genome Res., Vol. 17, No. 6. (1 June 2007), pp. 760-774.
    by Elliott H Margulies, Gregory M Cooper, George Asimenos, 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 alignment constraint encode mammal by dpollard on 2007-06-29 05:54:18 as *** along with 7 people and 4 groups dchughes AaronDarling djkt ghattem Garamonfok gjuggler elfar Bioinformatics EisenLab G4ID Genetics-of-Gambling
  • STAMP: a web tool for exploring DNA-binding motif similarities.
    Nucleic Acids Res (3 May 2007)
    by Shaun Mahony, Panayiotis V V Benos
    posted to alignment method motif pwm website by dpollard on 2007-05-23 00:40:45 as * along with 1 group EisenLab
  • Incorporating Indel Information into Phylogeny Estimation for Rapidly Emerging Pathogens
    BMC Evolutionary Biology, Vol. 7 (14 March 2007), 40.
    by Benjamin D Redelings, Marc A Suchard
    posted to alignment gene indels method phylogeny by dpollard on 2007-03-22 22:56:37 as ** along with 2 people and 1 group aprasad stajich EisenLab
  • Multiple alignment by sequence annealing.
    Bioinformatics, Vol. 23, No. 2. (15 January 2007)
    by AS Schwartz, L Pachter
    posted to protein method alignment by dpollard on 2007-02-01 19:47:22 as ** along with 1 group EisenLab
  • Simultaneous alignment and annotation of cis-regulatory regions.
    Bioinformatics, Vol. 23, No. 2. (15 January 2007)
    by AS Bais, S Grossmann, M Vingron
    posted to prediction binding_site alignment by dpollard on 2007-02-01 19:45:23 as ** along with 2 people and 1 group indigoviolet bluto EisenLab
  • Logarithmic gap costs decrease alignment accuracy
    BMC Bioinformatics, Vol. 7 (05 December 2006), 527.
    by Reed A Cartwright
    posted to indels alignment accuracy by dpollard on 2007-01-19 16:35:28 as ** along with 1 person and 1 group groepl EisenLab
  • LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA.
    Genome Res, Vol. 13, No. 4. (April 2003), pp. 721-731.
    by M Brudno, CB Do, GM Cooper, MF Kim, E Davydov, ED Green, A Sidow, S Batzoglou,
    posted to alignment noncoding by dpollard on 2006-11-07 01:53:28 as read along with 11 people and 1 group operon balajis xwbcn dquest adepace hdopazo lusk Garamonfok adijr natstreet nklee EisenLab
  • Vertebrate gene finding from multiple-species alignments using a two-level strategy.
    Genome Biol, Vol. 7 Suppl 1 (2006)
    by D Carter, R Durbin
    posted to alignment gene prediction by dpollard on 2006-09-30 00:22:15 as ** along with 2 people and 2 groups indigoviolet dmc EisenLab Durbin group
  • Quantification of the variation in percentage identity for protein sequence alignments
    BMC Bioinformatics, Vol. 7 (19 September 2006), 415.
    by Ps G Raghava, Geoffrey J Barton
    posted to accuracy alignment gene method protein by dpollard on 2006-09-30 00:20:09 as *** along with 5 people and 1 group pansapiens bicko rabio medic0747 sujaikumar EisenLab
  • MACO: A gapped-alignment scoring tool for comparing transcription factor binding sites.
    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 on 2006-08-25 17:56:58 as *** along with 1 group EisenLab
  • Close sequence comparisons are sufficient to identify human cis-regulatory elements.
    Genome Res (12 June 2006)
    by Shyam Prabhakar, Francis Poulin, Malak Shoukry, Veena Afzal, Edward M M Rubin, Olivier Couronne, Len A A Pennacchio
    posted to alignment annotation conserved constraint evolution human mammal prediction rate selection transcription turnover by dpollard on 2006-06-16 20:47:54 as ** along with 6 people and 2 groups mariakmejia indigoviolet samal nickluscombe olympos emptyhb EisenLab EBI-regulation
  • MCALIGN2: Faster, accurate global pairwise alignment of non-coding DNA sequences based on explicit models of indel evolution
    BMC Bioinformatics, Vol. 7 (08 June 2006), 292.
    by Jun Wang, Peter D Keightley, Toby Johnson
    posted to alignment evolution indel model by dpollard on 2006-06-16 20:34:32 as *** along with 2 people and 1 group Ayest papamicd EisenLab
  • Evolutionary turnover of mammalian transcription start sites.
    Genome Res (10 May 2006)
    by Martin C C Frith, Jasmina Ponjavic, David Fredman, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayshizaki, Albin Sandelin
    posted to alignment conserved evolution gene mammal promoter transcription turnover vertebrate by dpollard on 2006-05-12 17:41:10 as ** along with 4 people and 3 groups cmm jsnoddy cisevol gjuggler EisenLab FAB-lab cis-regulatory-evolution
  • Evaluating phylogenetic footprinting for human-rodent comparisons.
    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 on 2006-05-01 22:45:46 as ** along with 1 group EisenLab
  • Reference based annotation with GeneMapper.
    Genome Biol, Vol. 7, No. 4. (5 April 2006)
    by Sourav Chatterji, Lior Pachter
    posted to alignment annotation gene method by dpollard on 2006-04-08 23:24:07 as *** along with 3 people and 2 groups indigoviolet penka wenhan EisenLab Nie
  • Sigma: multiple alignment of weakly-conserved non-coding DNA sequence.
    BMC Bioinformatics, Vol. 7, No. 1. (16 March 2006)
    by Rahul Siddharthan
    posted to alignment noncoding by dpollard on 2006-04-02 23:08:10 as ** along with 1 person and 1 group lilou EisenLab
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