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djkt's library [578 articles]

Recent papers added to djkt's library ordered by importance.
  • Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes
    Genome Research, Vol. 18, No. 9., 1393.
    by Studer
    posted to selection proteins duplication by djkt on 2008-09-01 19:03:24 as ***
  • Predicting Human Nucleosome Occupancy from Primary Sequence
    PLoS Comput Biol, Vol. 4, No. 8. (2008), e1000134.
    by Shobhit Gupta, Jonathan Dennis, Robert E Thurman, Robert Kingston, John A Stamatoyannopoulos, William S Noble
    posted to epigenetics nucleosome prediction by djkt on 2008-08-22 18:17:54 as *** along with 2 people Stew aalibes
  • Significant contribution of Archaea to extant biomass in marine subsurface sediments
    Nature (20 July 2008)
    by Julius S Lipp, Yuki Morono, Fumio Inagaki, Kai-Uwe Hinrichs
    posted to ecology metagenomics microbes by djkt on 2008-08-20 20:14:10 as *** along with 1 person and 1 group neils iSEEM
  • Direct Estimation of the Mitochondrial DNA Mutation Rate in Drosophila melanogaster
    PLoS Biology, Vol. 6, No. 8. (1 August 2008), e204.
    by Cathy Haag-Liautard, Nicole Coffey, David Houle, Michael Lynch, Brian Charlesworth, Peter D Keightley
    posted to evolution fly indel molclock snps by djkt on 2008-08-19 19:18:55 as *** along with 1 person aprasad
  • Reduced purifying selection prevails over positive selection in human copy number variant evolution
    Genome Research (2008)
    by Nguyen
    posted to evolution human selection sv by djkt on 2008-08-18 21:19:48 as ***
  • The Airborne Metagenome in an Indoor Urban Environment
    PLoS ONE, Vol. 3, No. 4. (2 April 2008), e1862.
    by Susannah G Tringe, Tao Zhang, Xuguo Liu, Yiting Yu, Wah H Lee, Jennifer Yap, Fei Yao, Sim T Suan, Seah K Ing, Matthew Haynes, Forest Rohwer, Chia L Wei, Patrick Tan, James Bristow, Edward M Rubin, Yijun Ruan
    posted to metagenomics microbes by djkt on 2008-08-15 17:55:03 as *** along with 1 person and 1 group semrich iSEEM
  • Genetic Variation in an Individual Human Exome
    PLoS Genet, Vol. 4, No. 8. (2008), e1000160.
    by Pauline C Ng, Samuel Levy, Jiaqi Huang, Timothy B Stockwell, Brian P Walenz, Kelvin Li, Nelson Axelrod, Dana A Busam, Robert L Strausberg, Craig J Venter
    posted to human popgen proteins sequencing snps by djkt on 2008-08-15 17:26:39 as *** along with 5 people bpcusack caseybrown Ema jyuh reyez
  • Counting the Uncountable: Statistical Approaches to Estimating Microbial Diversity
    Appl. Environ. Microbiol., Vol. 67, No. 10. (1 October 2001), pp. 4399-4406.
    by Jennifer B Hughes, Jessica J Hellmann, Taylor H Ricketts, Brendan J Bohannan
    posted to diversity metagenomics review by djkt on 2008-07-24 18:27:30 as *** along with 6 people and 2 groups jmeppley Stenuite andrewirwin vrich mcox Olaf_Ilzins Biological oceanography iSEEM
  • An Automated Phylogenetic Tree-Based Small Subunit rRNA Taxonomy and Alignment Pipeline (STAP)
    PLoS ONE, Vol. 3, No. 7. (2 July 2008), e2566.
    by Dongying Wu, Amber Hartman, Naomi Ward, Jonathan A Eisen
    posted to metagenomics rna by djkt on 2008-07-24 18:14:38 as *** along with 1 person and 1 group skato_toyaku iSEEM
  • Metagenomics: application of genomics to uncultured microorganisms.
    Microbiol Mol Biol Rev, Vol. 68, No. 4. (December 2004), pp. 669-685.
    by J Handelsman
    posted to metagenomics microbes review by djkt on 2008-07-24 18:00:33 as *** along with 5 people and 2 groups knaseanka vrich mcox orzenil jlgreen Green Lab iSEEM
  • No effect of recombination on the efficacy of natural selection in primates
    Genome Res. (16 January 2008), gr.071548.107.
    by Kevin L Bullaughey, Molly Przeworski, Graham Coop
    posted to primates recombination selection by djkt on 2008-01-18 01:41:08 as ***
  • Viral Evolution in the Genomic Age
    PLoS Biology, Vol. 5, No. 10. (1 October 2007), e278.
    by Edward C Holmes
    posted to acceleration ecology evolution phylogenetics virus by djkt on 2007-10-02 20:25:08 as *** along with 3 people dullhunk zwang dayjm
  • Deletion of Ultraconserved Elements Yields Viable Mice
    PLoS Biology, Vol. 5, No. 9. (1 September 2007), e234.
    by Nadav Ahituv, Yiwen Zhu, Axel Visel, Amy Holt, Veena Afzal, Len A Pennacchio, Edward M Rubin
    posted to conservation development expression rodents by djkt on 2007-09-05 17:57:49 as *** along with 8 people and 3 groups balicea dchughes cwbrown lp2 cabbagezs Stew gjuggler bpcusack EisenLab G4ID Genetics-of-Gambling
  • Human Genome Ultraconserved Elements Are Ultraselected
    Science, Vol. 317, No. 5840. (17 August 2007), 915.
    by Sol Katzman, Andrew D Kern, Gill Bejerano, Ginger Fewell, Lucinda Fulton, Richard K Wilson, Sofie R Salama, David Haussler
    posted to conservation selection by djkt on 2007-08-20 16:42:57 as *** along with 9 people and 1 group aprasad balicea lp2 cabbagezs cisevol Minty fpattyn gjuggler bpcusack cis-regulatory-evolution
  • Identification and Characterization of Cell Type–Specific and Ubiquitous Chromatin Regulatory Structures in the Human Genome
    posted to chromatin by djkt on 2007-08-18 00:01:07 as ***
  • Cis- and Trans-Acting Elements Regulate the Mouse Psmb9 Meiotic Recombination Hotspot
    posted to recombination rodents by djkt on 2007-06-22 19:48:45 as ***
  • New Approach for Using Genome Scans to Detect Recent Positive Selection in the Human Genome
    posted to acceleration evolution selection snps by djkt on 2007-06-19 21:04:09 as ***
  • Identification of the Imprinted KLF14 Transcription Factor Undergoing Human-Specific Accelerated Evolution
    posted to acceleration tf by djkt on 2007-05-06 06:56:47 as ***
  • Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates
    Genome Res., Vol. 17, No. 5. (1 May 2007), pp. 545-555.
    by Hiroshi Kikuta, Mary Laplante, Pavla Navratilova, Anna Z Komisarczuk, Par G Engstrom, David Fredman, Altuna Akalin, Mario Caccamo, Ian Sealy, Kerstin Howe, Julien Ghislain, Guillaume Pezeron, Philippe Mourrain, Staale Ellingsen, Andrew C Oates, Christine Thisse, Bernard Thisse, Isabelle Foucher, Birgit Adolf, Andrea Geling, Boris Lenhard, Thomas S Becker
    posted to evolution msa by djkt on 2007-05-03 19:30:18 as *** along with 3 people and 3 groups dchughes maximilianh boudinot Bioinformatics G4ID Genetics-of-Gambling
  • Evolutionary and Biomedical Insights from the Rhesus Macaque Genome
    Science, Vol. 316, No. 5822. (13 April 2007), pp. 222-234.
    by Rhesus, Richard A Gibbs, Jeffrey Rogers, Michael G Katze, Roger Bumgarner, George M Weinstock, Elaine R Mardis, Karin A Remington, Robert L Strausberg, Craig J Venter, Richard K Wilson, Mark A Batzer, Carlos D Bustamante, Evan E Eichler, Matthew W Hahn, Ross C Hardison, Kateryna D Makova, Webb Miller, Aleksandar Milosavljevic, Robert E Palermo, Adam Siepel, James M Sikela, Tony Attaway, Stephanie Bell, Kelly E Bernard, Christian J Buhay, Mimi N Chandrabose, Marvin Dao, Clay Davis, Kimberly D Delehaunty, Yan Ding, Huyen H Dinh, Shannon Dugan-Rocha, Lucinda A Fulton, Ramatu A Gabisi, Toni T Garner, Jennifer Godfrey, Alicia C Hawes, Judith Hernandez, Sandra Hines, Michael Holder, Jennifer Hume, Shalini N Jhangiani, Vandita Joshi, Ziad M Khan, Ewen F Kirkness, Andrew Cree, Gerald R Fowler, Sandra Lee, Lora R Lewis, Zhangwan Li, Yih-Shin Liu, Stephanie M Moore, Donna Muzny, Lynne V Nazareth, Dinh N Ngo, Geoffrey O Okwuonu, Grace Pai, David Parker, Heidie A Paul, Cynthia Pfannkoch, Craig S Pohl, Yu-Hui Rogers, San J Ruiz, Aniko Sabo, Jireh Santibanez, Brian W Schneider, Scott M Smith, Erica Sodergren, Amanda F Svatek, Teresa R Utterback, Selina Vattathil, Wesley Warren, Courtney S White, Asif T Chinwalla, Yucheng Feng, Aaron L Halpern, Ladeana W Hillier, Xiaoqiu Huang, Pat Minx, Joanne O Nelson, Kymberlie H Pepin, Xiang Qin, Granger G Sutton, Eli Venter, Brian P Walenz, John W Wallis, Kim C Worley, Shiaw-Pyng Yang, Steven M Jones, Marco A Marra, Mariano Rocchi, Jacqueline E Schein, Robert Baertsch, Laura Clarke, Miklos Csuros, Jarret Glasscock, Alan R Harris, Paul Havlak, Andrew R Jackson, Huaiyang Jiang, Yue Liu, David N Messina, Yufeng Shen, Henry X Song, Todd Wylie, Lan Zhang, Ewan Birney, Kyudong Han, Miriam K Konkel, Jungnam Lee, Arian F Smit, Brygg Ullmer, Hui Wang, Jinchuan Xing, Richard Burhans, Ze Cheng, John E Karro, Jian Ma, Brian Raney, Xinwei She, Michael J Cox, Jeffery P Demuth, Laura J Dumas, Sang-Gook Han, Janet Hopkins, Anis Karimpour-Fard, Young H Kim, Jonathan R Pollack, Tomas Vinar, Charles Addo-Quaye, Jeremiah Degenhardt, Alexandra Denby, Melissa J Hubisz, Amit Indap, Carolin Kosiol, Bruce T Lahn, Heather A Lawson, Alison Marklein, Rasmus Nielsen, Eric J Vallender, Andrew G Clark, Betsy Ferguson, Ryan D Hernandez, Kashif Hirani, Hildegard Kehrer-Sawatzki, Jessica Kolb, Shobha Patil, Ling-Ling Pu, Yanru Ren, David G Smith, David A Wheeler, Ian Schenck, Edward V Ball, Rui Chen, David N Cooper, Belinda Giardine, Fan Hsu, James W Kent, Arthur Lesk, David L Nelson, William E O'Brien, Kay Prufer, Peter D Stenson, James C Wallace, Hui Ke, Xiao-Ming Liu, Peng Wang, Andy P Xiang, Fan Yang, Galt P Barber, David Haussler, Donna Karolchik, Andy D Kern, Robert M Kuhn, Kayla E Smith, Ann S Zwieg
    posted to genome primates by djkt on 2007-04-13 18:30:18 as *** along with 4 people and 4 groups dchughes stajich hpaces Garamonfok Bioinformatics G4ID Genetics-of-Gambling Berkeley Mycology
  • Human-Specific Changes of Genome Structure Detected by Genomic Triangulation
    Science, Vol. 316, No. 5822. (13 April 2007), pp. 235-237.
    by RA Harris, J Rogers, A Milosavljevic
    posted to acceleration primates by djkt on 2007-04-13 18:29:44 as *** along with 1 person and 3 groups dchughes Bioinformatics G4ID Genetics-of-Gambling
  • Genomic sweeping for hypermethylated genes
    Bioinformatics, Vol. 23, No. 3. (1 February 2007), pp. 281-288.
    by Liang Goh, Susan K Murphy, Sayan Muhkerjee, Terrence S Furey
    posted to prediction imprinting by djkt on 2007-02-02 17:44:49 as *** along with 1 person and 1 group mgaldzic CHIP
  • Maximum likelihood inference of imprinting and allele-specific expression from EST data.
    Bioinformatics (11 October 2006)
    by Cathal Seoighe, Victoria Nembaware, Konrad Scheffler
    posted to imprinting by djkt on 2006-12-02 17:02:54 as *** along with 1 person Ayest
  • A supervised hidden Markov model framework for efficiently segmenting tiling array data in transcriptional and ChIP-chip experiments: systematically incorporating validated biological knowledge.
    Bioinformatics (12 October 2006)
    by Jiang Du, Joel S S Rozowsky, Jan O O Korbel, Zhengdong D D Zhang, Thomas E E Royce, Martin H H Schultz, Michael Snyder, Mark Gerstein
    posted to arrays chip-chip hmm prediction by djkt on 2006-12-02 16:49:13 as *** along with 7 people and 2 groups miguel tuck eckart_bindewald SeungjoonOh blobbybirdman inesdesantiago xingxu Bioinformatics UH - Computational Biology
  • Thrice out of Africa: ancient and recent expansions of the honey bee, Apis mellifera.
    Science, Vol. 314, No. 5799. (27 October 2006), pp. 642-645.
    by CW Whitfield, SK Behura, SH Berlocher, AG Clark, JS Johnston, WS Sheppard, DR Smith, AV Suarez, D Weaver, ND Tsutsui
    posted to evolution popgen by djkt on 2006-11-02 19:11:44 as ***
  • Genomic Selective Constraints in Murids
    PLoS Genetics, Vol. preprint, No. 2006. (1 October 2006)
    by Daniel Gaffney, Peter Keightley
    posted to conservation evolution msa rodents selection by djkt on 2006-10-20 20:27:57 as ***
  • Heterogeneous Genomic Molecular Clocks in Primates
    PLoS Genetics, Vol. 2, No. 10. (1 October 2006), e163.
    by Seong-Ho Kim, Navin Elango, Charles Warden, Eric Vigoda, Soojin V Yi
    posted to acceleration molclock primates by djkt on 2006-10-10 18:11:10 as *** along with 1 person and 2 groups dchughes G4ID Genetics-of-Gambling
  • Time ordering of gene coexpression
    Biostat, Vol. 7, No. 4. (1 October 2006), pp. 569-584.
    by Xiaoyan Leng, Hans-Georg Muller
    posted to arrays clustering expression by djkt on 2006-09-28 18:23:31 as ***
  • Genomic signatures of positive selection in humans and the limits of outlier approaches
    Genome Res., Vol. 16, No. 8. (1 August 2006), pp. 980-989.
    by Joanna L Kelley, Jennifer Madeoy, John C Calhoun, Willie Swanson, Joshua M Akey
    posted to evolution popgen proteins snps by djkt on 2006-08-07 18:18:20 as *** along with 1 person and 1 group hdopazo BioinfoCIPF
  • Copy number variation: New insights in genome diversity
    Genome Res., Vol. 16, No. 8. (1 August 2006), pp. 949-961.
    by Jennifer L Freeman, George H Perry, Lars Feuk, Richard Redon, Steven A Mccarroll, David M Altshuler, Hiroyuki Aburatani, Keith W Jones, Chris Tyler-Smith, Matthew E Hurles, Nigel P Carter, Stephen W Scherer, Charles Lee
    posted to indel popgen review by djkt on 2006-08-07 18:16:31 as *** along with 7 people and 3 groups bpb balicea dchughes jri bioguru2000 debasis jasonflannick Bioinformatics G4ID Genetics-of-Gambling
  • Heterozygous carriers of Nijmegen Breakage Syndrome have a distinct gene expression phenotype
    Genome Res., Vol. 16, No. 8. (1 August 2006), pp. 973-979.
    by Vivian G Cheung, Warren J Ewens
    posted to expression popgen snps by djkt on 2006-08-07 18:15:32 as ***
  • Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes
    Nature (20 July 2008)
    by Dacheng Tian, Qiang Wang, Pengfei Zhang, Hitoshi Araki, Sihai Yang, Martin Kreitman, Thomas Nagylaki, Richard Hudson, Joy Bergelson, Jian-Qun Chen
    posted to snps mutation indel by djkt on 2008-09-04 17:40:37 as ** along with 4 people psique caseybrown bpcusack gjuggler
  • The impact of microRNAs on protein output
    Nature (30 July 2008)
    by Daehyun Baek, Judit Villã©n, Chanseok Shin, Fernando D Camargo, Steven P Gygi, David P Bartel
    posted to rna expression by djkt on 2008-09-04 17:10:57 as ** along with 10 people giovenko mtagaya megraw brianb emptyhb erel10 maralena ajaymalik caizhiqiang gdb
  • A common sequence motif associated with recombination hot spots and genome instability in humans
    Nature Genetics, Vol. 40, No. 9. (24 August 2008), pp. 1124-1129.
    by Simon Myers, Colin Freeman, Adam Auton, Peter Donnelly, Gil Mcvean
    posted to recombination by djkt on 2008-09-02 18:59:17 as ** along with 1 person caseybrown
  • The Evolutionary Rate of Duplicated Genes under Concerted Evolution
    Genetics (30 August 2008), genetics.108.087676.
    by Shuhei Mano, Hideki Innan
    posted to selection evolution duplication bgc by djkt on 2008-09-01 20:06:17 as **
  • A Weighted-Holm Procedure accounting for allele frequencies in Genome-Wide Association Studies
    Genetics (24 August 2008), genetics.108.089839.
    by Cyril Dalmasso, Emmanuelle Genin, David-Alexandre Tregouet
    posted to popgen mtp association by djkt on 2008-09-01 19:59:34 as **
  • The Influence of Gene Conversion on Linkage Disequilibrium around a Selective Sweep
    Genetics (30 August 2008), genetics.108.092270.
    by Danielle A Jones, John Wakeley
    posted to selection recombination bgc by djkt on 2008-09-01 19:58:19 as **
  • Low duplicability and network fragility of cancer genes
    Trends in Genetics, Vol. 24, No. 9. (September 2008), pp. 427-430.
    by Davide Rambaldi, Federico M Giorgi, Fabrizio Capuani, Andrea Ciliberto, Francesca D Ciccarelli
    posted to duplication cancer by djkt on 2008-09-01 19:56:42 as ** along with 1 person tmmurali
  • Tracking the complex flow of chromosome rearrangements from the Hominoidea Ancestor to extant Hylobates and Nomascus Gibbons by high-resolution synteny mapping
    Genome Research, Vol. 18, No. 9., 1530.
    by Misceo
    posted to primates evolution duplication chromosome by djkt on 2008-09-01 19:12:56 as **
  • On the origin of new genes in Drosophila
    Genome Research, Vol. 18, No. 9., 1446.
    by Zhou
    posted to proteins fly evolution duplication by djkt on 2008-09-01 19:10:43 as **
  • A novel mode of enhancer evolution: The Tal1 stem cell enhancer recruited a MIR element to specifically boost its activity
    Genome Research, Vol. 18, No. 9., 1422.
    by Smith
    posted to tf evolution duplication by djkt on 2008-09-01 19:07:49 as **
  • Resolving Individuals Contributing Trace Amounts of DNA to Highly Complex Mixtures Using High-Density SNP Genotyping Microarrays
    PLoS Genet, Vol. 4, No. 8. (2008), e1000167.
    by Nils Homer, Szabolcs Szelinger, Margot Redman, David Duggan, Waibhav Tembe, Jill Muehling, John V Pearson, Dietrich A Stephan, Stanley F Nelson, David W Craig
    posted to snps metagenomics by djkt on 2008-09-01 18:55:00 as ** along with 3 people jasonbobe rs fpattyn
  • Modeling ChIP Sequencing In Silico with Applications
    PLoS Comput Biol, Vol. 4, No. 8. (2008), e1000158.
    by Zhengdong D Zhang, Joel Rozowsky, Michael Snyder, Joseph Chang, Mark Gerstein
    posted to chip-chip sequencing by djkt on 2008-08-22 18:20:29 as ** along with 4 people kengg Stew gdb caseybrown
  • Gene Dosage and Gene Duplicability
    Genetics, Vol. 179 (2008), pp. 2319-2324.
    by Wenfeng Qian, Jianzhi Zhang
    posted to duplication evolution proteins by djkt on 2008-08-19 02:15:55 as **
  • Integrating biological data - the Distributed Annotation System
    BMC Bioinformatics, Vol. 9, No. Suppl 8. (2008)
    by Andrew Jenkinson, Mario Albrecht, Ewan Birney, Hagen Blankenburg, Thomas Down, Robert Finn, Henning Hermjakob, Tim Hubbard, Rafael Jimenez, Philip Jones, Andreas Kahari, Eugene Kulesha, Jose Macias, Gabrielle Reeves, Andreas Prlic
    posted to db by djkt on 2008-08-18 21:16:46 as ** along with 3 people jyuh chad_davis aconesa
  • Genomic analysis of the relationship between gene expression variation and DNA polymorphism in Drosophila simulans
    Genome Biology, Vol. 9, No. 8. (2008)
    by Mara Lawniczak, Alisha Holloway, David Begun, Corbin Jones
    posted to expression fly popgen variation by djkt on 2008-08-18 21:15:41 as ** along with 3 people and 1 group APRegier caseybrown cisevol cis-regulatory-evolution
  • Computational Improvements Reveal Great Bacterial Diversity and High Metal Toxicity in Soil
    Science, Vol. 309, No. 5739. (26 August 2005), pp. 1387-1390.
    by Jason Gans, Murray Wolinsky, John Dunbar
    posted to diversity ecology metagenomics microbes by djkt on 2008-08-15 18:22:43 as ** along with 4 people and 1 group knaseanka jmeppley paleorthid jlgreen iSEEM
  • Binning sequences using very sparse labels within a metagenome
    BMC Bioinformatics, Vol. 9 (28 April 2008), 215.
    by Chon-Kit K Chan, Arthur L Hsu, Saman K Halgamuge, Sen-Lin Tang
    posted to metagenomics microbes by djkt on 2008-08-15 18:13:29 as ** along with 4 people and 2 groups alexl mjetten werwiesel jlgreen microbiology_nijmegen iSEEM
  • A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome
    Science (3 July 2008), 1160342.
    by Marc Sultan, Marcel H Schulz, Hugues Richard, Alon Magen, Andreas Klingenhoff, Matthias Scherf, Martin Seifert, Tatjana Borodina, Aleksey Soldatov, Dmitri Parkhomchuk, Dominic Schmidt, Sean O'Keeffe, Stefan Haas, Martin Vingron, Hans Lehrach, Marie-Laure Yaspo
    posted to expression sequencing by djkt on 2008-08-15 02:02:43 as ** along with 10 people and 1 group oelemento Ema reyez caseybrown kjglennie dh0000 GeeSharpMinor balicea ArtemPankin zwang Khavkin's lab
  • A discontinuous hammerhead ribozyme embedded in a mammalian messenger RNA
    Nature (09 July 2008)
    by Monika Martick, Lucas H Horan, Harry F Noller, William G Scott
    posted to mammals rna by djkt on 2008-08-13 21:09:09 as ** along with 1 person mtagaya
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