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dmc's library [58 articles]

Recent papers added to dmc's library.
  • Gene conversion tracts in Saccharomyces cerevisiae can be extremely short and highly directional
    Nucl. Acids Res., Vol. 31, No. 4. (15 February 2003), pp. 1164-1173.
    by Sean Palmer, Ezra Schildkraut, Raquel Lazarin, Jimmy Nguyen, Jac A Nickoloff
    posted to sgrp by dmc on 2008-03-17 16:43:50 as **
  • Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans
    PLoS Biology, Vol. 5, No. 11. (1 November 2007), e310.
    by David J Begun, Alisha K Holloway, Kristian Stevens, Ladeana W Hillier, Yu-Ping Poh, Matthew W Hahn, Phillip M Nista, Corbin D Jones, Andrew D Kern, Colin N Dewey, Lior Pachter, Eugene Myers, Charles H Langley
    posted to assembly indels by dmc on 2008-03-13 10:47:50 as *** along with 3 people pradiptaray bpb emptyhb
  • Phylogenomics and the reconstruction of the tree of life
    Nature Reviews Genetics, Vol. 6, No. 5. (01 May 2005), pp. 361-375.
    by Frederic Delsuc, Henner Brinkmann, Herve Philippe
    posted to phylogenetics by dmc on 2008-03-07 14:03:08 as ** along with 3 people maximilianh cmzmasek gjuggler
  • Molecular signatures of natural selection.
    Annu Rev Genet, Vol. 39 (2005), pp. 197-218.
    by R Nielsen
    posted to positiveselection by dmc on 2008-03-07 14:02:05 as ** along with 7 people pradiptaray BioNica jasonflannick operon bpb eckart_bindewald timflutre
  • Genomix: a method for combining gene-finders' predictions, which uses evolutionary conservation of sequence and intron-exon structure.
    Bioinformatics (5 May 2007)
    by Avril Coghlan, Richard Durbin
    posted to durbingrouppub genefinding by dmc on 2008-03-07 13:57:39 as read along with 3 people and 2 groups indigoviolet stajich GustavoLacerda EisenLab Durbin group
  • The phusion assembler.
    Genome Res, Vol. 13, No. 1. (2003), pp. 81-90.
    by JC Mullikin, Z Ning
    posted to assembly sgrp by dmc on 2008-03-07 13:56:39 as read along with 2 people bpb wenhan
  • Efficient algorithms and software for detection of full-length LTR retrotransposons.
    J Bioinform Comput Biol, Vol. 4, No. 2. (April 2006), pp. 197-216.
    by A Kalyanaraman, S Aluru
    posted to assembly transposons by dmc on 2008-03-07 13:55:51 as ** along with 1 person yoanjacquemin
  • A Dirichlet process model for detecting positive selection in protein-coding DNA sequences.
    Proc Natl Acad Sci U S A, Vol. 103, No. 16. (18 April 2006), pp. 6263-6268.
    by JP Huelsenbeck, S Jain, SW Frost, SL Pond
    posted to positiveselection by dmc on 2008-03-07 13:52:41 as ** along with 2 people kieran101 ejeffery
  • The Yeast Gene Order Browser: Combining curated homology and syntenic context reveals gene fate in polyploid species
    Genome Res., Vol. 15, No. 10. (1 October 2005), pp. 1456-1461.
    by Kevin P Byrne, Kenneth H Wolfe
    posted to sgrp by dmc on 2008-03-07 13:46:22 as **
  • Changing perspectives in yeast research nearly a decade after the genome sequence.
    Genome Res, Vol. 15, No. 12. (December 2005), pp. 1611-1619.
    by K Dolinski, D Botstein
    posted to sgrp by dmc on 2008-03-07 13:44:38 as ** along with 3 people and 1 group lfriedl nirfriedman fishtank kdl
  • Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.
    Genome Res, Vol. 15, No. 8. (August 2005), pp. 1034-1050.
    by A Siepel, G Bejerano, JS Pedersen, AS Hinrichs, M Hou, K Rosenbloom, H Clawson, J Spieth, LW Hillier, S Richards, GM Weinstock, RK Wilson, RA Gibbs, WJ Kent, W Miller, D Haussler
    posted to genefinding by dmc on 2008-03-07 13:41:41 as ** along with 14 people and 2 groups pradiptaray bpb aprasad balajis eckart_bindewald indigoviolet brant adepace djkt olympos sujaikumar Stew cisevol elfar EisenLab cis-regulatory-evolution
  • Copy correction and concerted evolution in the conservation of yeast genes.
    Genetics, Vol. 170, No. 4. (August 2005), pp. 1501-1513.
    by S Pyne, S Skiena, B Futcher
    posted to sgrp by dmc on 2008-03-07 13:40:09 as **
  • Genetic diversity in yeast assessed with whole-genome oligonucleotide arrays.
    Genetics, Vol. 163, No. 1. (January 2003), pp. 79-89.
    by EA Winzeler, CI Castillo-Davis, G Oshiro, D Liang, DR Richards, Y Zhou, DL Hartl
    posted to sgrp by dmc on 2008-03-07 13:37:27 as **
  • The genetics of human obesity
    Nature Reviews Genetics, Vol. 6, No. 3. (01 March 2005), pp. 221-234.
    by Christopher G Bell, Andrew J Walley, Philippe Froguel
    posted to human by dmc on 2008-03-07 13:36:34 as ** along with 1 person caldavis
  • Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies.
    Genetics, Vol. 164, No. 4. (August 2003), pp. 1567-1587.
    by D Falush, M Stephens, JK Pritchard
    posted to structure by dmc on 2008-03-07 13:34:41 as ** along with 3 people sriram_s hms Xavier
  • Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences in Populations
    Journal of Computational Biology, Vol. 14, No. 10. (2007), pp. 1273-1286.
    by Yun S Song, Zhihong Ding, Dan Gusfield, Charles H Langley, Yufeng Wu
    posted to imputation by dmc on 2008-03-07 13:28:15 as read
  • SSAHA: A fast search method for large DNA databases
    Genome Res., Vol. 11, No. 10. (2001), pp. 1725-1729.
    by Z Ning, AJ Cox, JC Mullikin
    posted to assembly imputation sgrp by dmc on 2008-03-07 13:19:47 as read along with 3 people bpb j3xucite lp2
  • Generalized analysis of molecular variance.
    PLoS Genet, Vol. 3, No. 4. (6 April 2007)
    by CM Nievergelt, O Libiger, NJ Schork
    posted to association human by dmc on 2008-03-07 13:18:22 as ** along with 4 people and 1 group jyuh stevanspringer bpb ryanraaum FAB-lab
  • Imputation-Based Analysis of Association Studies: Candidate Regions and Quantitative Traits
    PLoS Genetics, Vol. 3, No. 7. (1 July 2007), e114.
    by Bertrand Servin, Matthew Stephens
    posted to association imputation by dmc on 2008-03-07 13:17:12 as ** along with 2 people brant xingxu
  • Population genomics of human gene expression.
    Nat Genet (16 September 2007)
    by Barbara E E Stranger, Alexandra C C Nica, Matthew S S Forrest, Antigone Dimas, Christine P P Bird, Claude Beazley, Catherine E E Ingle, Mark Dunning, Paul Flicek, Daphne Koller, Stephen Montgomery, Simon Tavaré, Panos Deloukas, Emmanouil T T Dermitzakis
    posted to expression human by dmc on 2008-03-07 13:16:38 as ** along with 8 people and 1 group jyuh kentsis rdiaz lp2 jo_davies mimulus_99 cisevol annacarina07 cis-regulatory-evolution
  • Genetic Association Mapping via Evolution-Based Clustering of Haplotypes
    PLoS Genetics, Vol. 3, No. 7. (1 July 2007), e111.
    by Ioanna Tachmazidou, Claudio J Verzilli, Maria D Iorio
    posted to association imputation by dmc on 2008-03-07 13:15:48 as ** along with 2 people zwang xingxu
  • Highly efficient concerted evolution in the ribosomal DNA repeats: total rDNA repeat variation revealed by whole-genome shotgun sequence data.
    Genome Res, Vol. 17, No. 2. (February 2007), pp. 184-191.
    by AR Ganley, T Kobayashi
    posted to rdna sgrp by dmc on 2008-03-07 13:14:56 as read along with 2 people bjorns dandaman
  • Measurement of the human allele frequency spectrum demonstrates greater genetic drift in East Asians than in Europeans
    Nat Genet, Vol. 39, No. 10. (October 2007), pp. 1251-1255.
    by Alon Keinan, James C Mullikin, Nick Patterson, David Reich
    posted to human by dmc on 2008-03-07 13:13:51 as read along with 3 people and 1 group dchughes ryanraaum lh3 Durbin group
  • Population genetics of the wild yeast Saccharomyces paradoxus.
    Genetics, Vol. 166, No. 1. (January 2004), pp. 43-52.
    by LJ Johnson, V Koufopanou, MR Goddard, R Hetherington, SM Schäfer, A Burt
    posted to sgrp by dmc on 2008-03-07 13:12:05 as **
  • Homing endonuclease genes: the rise and fall and rise again of a selfish element.
    Curr Opin Genet Dev, Vol. 14, No. 6. (December 2004), pp. 609-615.
    by A Burt, V Koufopanou
    posted to sgrp by dmc on 2008-03-07 13:11:51 as **
  • The spatial scale of genetic differentiation in a model organism: the wild yeast Saccharomyces paradoxus.
    Philos Trans R Soc Lond B Biol Sci, Vol. 361, No. 1475. (29 November 2006), pp. 1941-1946.
    by V Koufopanou, J Hughes, G Bell, A Burt
    posted to sgrp by dmc on 2008-03-07 13:11:34 as **
  • Inferring missing genotypes in large SNP panels using fast nearest-neighbor searches over sliding windows.
    Bioinformatics, Vol. 23, No. 13. (1 July 2007)
    by A Roberts, L McMillan, W Wang, J Parker, I Rusyn, D Threadgill
    posted to imputation by dmc on 2008-03-07 13:10:13 as **
  • Automating resequencing-based detection of insertion-deletion polymorphisms
    Nature Genetics, Vol. 38, No. 12. (19 November 2006), pp. 1457-1462.
    by Tushar R Bhangale, Matthew Stephens, Deborah A Nickerson
    posted to indels sequencing by dmc on 2008-03-07 13:09:21 as **
  • Multiple Imputation of Missing Genotype Data for Unrelated Individuals
    Annals of Human Genetics, Vol. 70, No. 3. (May 2006), pp. 372-381.
    by OW Souverein, AH Zwinderman, MWT Tanck
    posted to imputation by dmc on 2008-03-07 13:08:09 as **
  • Imputation methods to improve inference in SNP association studies
    Genetic Epidemiology, Vol. 30 (2006), pp. 690-702.
    by JY Dai, I Ruczinski, M Leblanc, C Kooperberg
    posted to association imputation by dmc on 2008-03-07 13:07:08 as **
  • Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution
    Nature Genetics, Vol. 39, No. 11. (07 October 2007), pp. 1361-1368.
    by Zhaoshi Jiang, Haixu Tang, Mario Ventura, Maria F Cardone, Tomas Marques-Bonet, Xinwei She, Pavel A Pevzner, Evan E Eichler
    posted to assembly duplication by dmc on 2008-03-07 13:03:17 as ** along with 2 people timflutre urgi
  • Evolutionary trees from DNA sequences: a maximum likelihood approach.
    J Mol Evol, Vol. 17, No. 6. (1981), pp. 368-376.
    by J Felsenstein
    posted to imputation by dmc on 2008-03-07 13:01:29 as read along with 7 people and 1 group bpb chrn kaspermunch dquest djkt timflutre elfar Bioinformatics
  • A new multipoint method for genome-wide association studies by imputation of genotypes.
    Nat Genet (17 June 2007)
    by Jonathan Marchini, Bryan Howie, Simon Myers, Gil McVean, Peter Donnelly
    posted to association by dmc on 2008-03-07 12:59:49 as read along with 5 people jyuh balicea vplagnol hms mailund
  • Genome-wide strategies for detecting multiple loci that influence complex diseases
    Nature Genetics, Vol. 37, No. 4. (27 March 2005), pp. 413-417.
    by Jonathan Marchini, Peter Donnelly, Lon R Cardon
    posted to association by dmc on 2008-03-07 12:59:02 as read along with 2 people lp2 mailund
  • Genome-Wide Analysis of Nucleotide-Level Variation in Commonly Used Saccharomyces cerevisiae Strains.
    PLoS ONE, Vol. 2 (2007)
    by J Schacherer, DM Ruderfer, D Gresham, K Dolinski, D Botstein, L Kruglyak
    posted to sgrp by dmc on 2008-03-07 12:57:15 as ** along with 2 people and 1 group stajich michaelbarton Durbin group
  • A new approach to estimate parameters of speciation models with application to apes
    Genome Res. (21 August 2007), gr.6409707.
    by Celine Becquet, Molly Przeworski
    posted to speciation by dmc on 2008-03-07 12:55:45 as ** along with 2 people and 1 group ryanraaum mailund Durbin group
  • De novo repeat classification and fragment assembly.
    Genome Res, Vol. 14, No. 9. (September 2004), pp. 1786-1796.
    by PA Pevzner, H Tang, G Tesler
    posted to assembly by dmc on 2008-03-07 12:54:11 as ** along with 11 people Ema Neeperando brl briann operon timflutre azazello prajlondhe nedwards urgi yoanjacquemin
  • Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789
    PNAS, Vol. 104, No. 31. (31 July 2007), pp. 12825-12830.
    by Wu Wei, John H Mccusker, Richard W Hyman, Ted Jones, Ye Ning, Zhiwei Cao, Zhenglong Gu, Dan Bruno, Molly Miranda, Michelle Nguyen, Julie Wilhelmy, Caridad Komp, Raquel Tamse, Xiaojing Wang, Peilin Jia, Philippe Luedi, Peter J Oefner, Lior David, Fred S Dietrich, Yixue Li, Ronald W Davis, Lars M Steinmetz
    posted to sgrp by dmc on 2008-03-07 12:51:20 as ** along with 3 people and 2 groups lesander raiyar lp2 steinmetzlab Durbin group
  • 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 durbingrouppub genefinding by dmc on 2008-03-07 12:47:24 as read along with 2 people and 2 groups indigoviolet dpollard EisenLab Durbin group
  • Estimating the time since the fixation of a beneficial allele.
    Genetics, Vol. 164, No. 4. (August 2003), pp. 1667-1676.
    by M Przeworski
    posted to positiveselection by dmc on 2008-03-07 11:43:33 as ** along with 1 person and 1 group candypmcg Durbin group
  • SEQUENCE DIVERGENCE, FUNCTIONAL CONSTRAINT, AND SELECTION IN PROTEIN EVOLUTION
    Annual Review of Genomics and Human Genetics, Vol. 4, No. 1. (2003), pp. 213-235.
    by Justin C Fay, Chung I Wu
    posted to positiveselection by dmc on 2008-03-07 11:43:14 as ** along with 1 group Durbin group
  • A Map of Recent Positive Selection in the Human Genome.
    PLoS Biol, Vol. 4, No. 3. (7 March 2006)
    by Benjamin F F Voight, Sridhar Kudaravalli, Xiaoquan Wen, Jonathan K K Pritchard
    posted to positiveselection by dmc on 2008-03-07 11:42:54 as ** along with 20 people and 7 groups pradiptaray shoshin stevanspringer kentsis bpb balajis indigoviolet ejeffery madhadron breden tiago larios ashandanj hdopazo livingthingdan djkt mbeautru grahamc suizan iris42 Bioinformatics EisenLab FAB-lab SFUAntibodyResearch BioinfoCIPF livingthing Durbin group
  • How reliable are empirical genomic scans for selective sweeps?
    Genome Res, Vol. 16, No. 6. (June 2006), pp. 702-712.
    by KM Teshima, G Coop, M Przeworski
    posted to positiveselection by dmc on 2008-03-07 11:42:36 as ** along with 2 people and 2 groups indigoviolet hawksjohnd EisenLab Durbin group
  • Statistical Tests for Detecting Positive Selection by Utilizing High-Frequency Variants
    Genetics, Vol. 174, No. 3. (1 November 2006), pp. 1431-1439.
    by Kai Zeng, Yun-Xin Fu, Suhua Shi, Chung-I Wu
    posted to positiveselection by dmc on 2008-03-07 11:42:10 as ** along with 3 people and 2 groups stevanspringer operon ramensky FAB-lab Durbin group
  • Compound Tests for the Detection of Hitchhiking Under Positive Selection
    Mol Biol Evol (8 June 2007), msm119.
    by Kai Zeng, Suhua Shi, Chung-I Wu
    posted to positiveselection by dmc on 2008-03-07 11:40:41 as ** along with 1 person and 1 group cjeans Durbin group
  • The signature of positive selection on standing genetic variation.
    Evolution Int J Org Evolution, Vol. 59, No. 11. (November 2005), pp. 2312-2323.
    by M Przeworski, G Coop, JD Wall
    posted to positiveselection by dmc on 2008-03-07 11:40:06 as ** along with 1 person and 1 group ejeffery Durbin group
  • Simultaneous inference of selection and population growth from patterns of variation in the human genome.
    Proc Natl Acad Sci U S A, Vol. 102, No. 22. (31 May 2005), pp. 7882-7887.
    by SH Williamson, R Hernandez, A Fledel-Alon, L Zhu, R Nielsen, CD Bustamante
    posted to positiveselection by dmc on 2008-03-07 11:36:08 as ** along with 1 person and 1 group balajis Durbin group
  • Inferring Selection in Partially Sequenced Regions
    Mol Biol Evol (28 December 2007), msm273.
    by Jeffrey D Jensen, Kevin R Thornton, Charles F Aquadro
    posted to positiveselection by dmc on 2008-03-07 11:35:22 as ** along with 2 people and 1 group smbe2008 djkt Durbin group
  • Hitchhiking under positive Darwinian selection.
    Genetics, Vol. 155, No. 3. (July 2000), pp. 1405-1413.
    by JC Fay, CI Wu
    posted to positiveselection by dmc on 2008-03-07 11:33:17 as ** along with 2 people and 1 group operon ramensky Durbin group
  • The Hitchhiking Effect on Linkage Disequilibrium Between Linked Neutral Loci
    Genetics, Vol. 172, No. 4. (1 April 2006), pp. 2647-2663.
    by Wolfgang Stephan, Yun S Song, Charles H Langley
    posted to positiveselection by dmc on 2008-03-07 11:32:13 as ** along with 2 people and 1 group ccots balicea Durbin group
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