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Stew's library [101 articles]

Recent papers added to Stew's library.
  • Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution
    Cell, Vol. 134, No. 1. (11 July 2008), pp. 25-36.
    by Sean B Carroll
    posted to sean morphology evolution evo-devo carroll by Stew on 2008-07-18 09:19:14 as ***** along with 3 people icq242500260 djkt dchughes
  • Evolution of Evolvability in Gene Regulatory Networks
    PLoS Comput Biol, Vol. 4, No. 7. (11 July 2008), e1000112.
    by Anton Crombach, Paulien Hogeweg
    posted to regulatory networks gene evolvability evolution by Stew on 2008-07-15 12:12:20 as *** along with 7 people and 1 group jdiezperezj erel10 djkt dquest dlobo bootsy Ema GEB
  • An efficient method to identify differentially expressed genes in microarray experiments.
    Bioinformatics (Oxford, England) (3 May 2008)
    by Huaizhen Qin, Tao Feng, Scott A A Harding, Chung-Jui J Tsai, Shuanglin Zhang
    posted to microarray genes expressed differentially by Stew on 2008-07-07 08:46:20 as **** along with 2 people natstreet shigepong
  • Calibrating the Performance of SNP Arrays for Whole-Genome Association Studies
    PLoS Genet, Vol. 4, No. 6. (27 June 2008), e1000109.
    by Ke Hao, Eric E Schadt, John D Storey
    posted to snp association arrays affy by Stew on 2008-07-07 08:45:06 as **** along with 3 people jyuh balicea caseybrown
  • A novel, evolutionary conserved enhancer of cone photoreceptor-specific expression.
    J Biol Chem (13 February 2008)
    by Vincent A A Smyth, David Di Lorenzo, Breandán N N Kennedy
    posted to photoreceptor evolution enhancer conserved cone by Stew on 2008-06-14 14:45:26 as **
  • CSMET: Comparative Genomic Motif Detection via Multi-Resolution Phylogenetic Shadowing
    PLoS Comput Biol, Vol. 4, No. 6. (6 June 2008), e1000090.
    by Pradipta Ray, Suyash Shringarpure, Mladen Kolar, Eric P Xing
    posted to phylogenetic motif genomics footprinting detection comparative by Stew on 2008-06-14 14:43:13 as ***** along with 3 people and 1 group Ema cisevol djkt cis-regulatory-evolution
  • Combining Statistical Alignment and Phylogenetic Footprinting to Detect Regulatory Elements.
    Bioinformatics (18 March 2008)
    by R Satija, L Pachter, J Hein
    posted to regulatory prediction phylogenetic footprinting drosophila cis-regulatory alignment by Stew on 2008-06-06 08:24:29 as **** along with 4 people Ema gjuggler maximilianh eckart_bindewald
  • Subfunctionalization of Duplicated Zebrafish pax6 Genes by cis-Regulatory Divergence
    PLoS Genetics, Vol. 4, No. 2. (1 February 2008), e29.
    by Dirk A Kleinjan, Ruth M Bancewicz, Philippe Gautier, Ralf Dahm, Helia B Schonthaler, Giuseppe Damante, Anne Seawright, Ann M Hever, Patricia L Yeyati, Veronica van Heyningen, Pedro Coutinho
    posted to zebrafish subfunctionalization divergence cis-regulatory by Stew on 2008-06-06 08:20:04 as ** along with 4 people maximilianh brant gjuggler emptyhb
  • Tinker where the tinkering's good.
    Trends in genetics : TIG (29 May 2008)
    by Matthew V V Rockman, David L L Stern
    posted to pleiotropy pigmentation phenotype evolution drosophila cis-regulatory by Stew on 2008-06-06 08:19:22 as **** along with 1 person and 1 group stajich Berkeley Mycology
  • SEARCHING FOR FUNCTIONAL GENETIC VARIANTS IN NON-CODING DNA
    Clinical and Experimental Pharmacology and Physiology, Vol. 35, No. 4. (April 2008), pp. 372-375.
    by Cobb, Joanna, Busst, Cara, Petrou, Steven, Harrap, Stephen, Ellis, Justine
    posted to variation non-coding functional by Stew on 2008-06-02 10:54:59 as ***
  • The gene regulatory logic of transcription factor evolution.
    Trends in ecology & evolution (Personal edition) (21 May 2008)
    by Günter P P Wagner, Vincent J J Lynch
    posted to transcription logic factor evolution by Stew on 2008-06-02 10:53:58 as **** along with 1 person Garamonfok
  • Non-neutral processes drive the nucleotide composition of non-coding sequences in Drosophila.
    Biology letters (27 May 2008)
    by Penelope R R Haddrill, Brian Charlesworth
    posted to nucleotide non-neutral non-coding drosophila composition base by Stew on 2008-06-02 10:52:39 as **
  • A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning
    Genome Res. (13 May 2008), gr.076463.108.
    by Anton Valouev, Jeffrey Ichikawa, Thaisan Tonthat, Jeremy Stuart, Swati Ranade, Heather Peckham, Kathy Zeng, Joel A Malek, Gina Costa, Kevin Mckernan, Arend Sidow, Andrew Fire, Steven M Johnson
    posted to nucleosome celegans by Stew on 2008-05-27 13:45:27 as ** along with 5 people and 1 group caseybrown vega aalibes dpollard maximilianh RockmanLab
  • The atypical mammalian ligand Delta-like1 (Dlk1) can regulate Notch signalling in Drosophila
    BMC Developmental Biology, Vol. 8 (31 January 2008), 11.
    by Sarah J Bray, Shuji Takada, Emma Harrison, Shing-Chuan Shen, Anne Ferguson-Smith
    posted to notch drosophila delta by Stew on 2008-05-16 09:20:22 as **
  • NELF and GAGA factor are linked to promoter-proximal pausing at many genes in Drosophila.
    Molecular and cellular biology, Vol. 28, No. 10. (May 2008), pp. 3290-3300.
    by C Lee, X Li, A Hechmer, M Eisen, MD Biggin, BJ Venters, C Jiang, J Li, BF Pugh, DS Gilmour
    posted to promoter pausing nelf gaga drosophila by Stew on 2008-05-16 08:55:57 as **
  • Fast Evolution of Core Promoters in Primate Genomes
    Mol Biol Evol, Vol. 25, No. 6. (1 June 2008), pp. 1239-1244.
    by Han Liang, Yeong-Shin Lin, Wen-Hsiung Li
    posted to promoter primate genome evolution by Stew on 2008-05-13 17:24:34 as ** along with 2 people and 1 group aprasad cisevol cis-regulatory-evolution
  • Evolution of Gene Expression in the Drosophila Olfactory System
    Mol Biol Evol, Vol. 25, No. 6. (1 June 2008), pp. 1081-1092.
    by Artyom Kopp, Olga Barmina, Andrew M Hamilton, Laura Higgins, Lauren M Mcintyre, Corbin D Jones
    posted to olfactory gene expression evolution drosophila by Stew on 2008-05-13 17:23:32 as *****
  • The McDonald-Kreitman Test and Slightly Deleterious Mutations
    Mol Biol Evol, Vol. 25, No. 6. (1 June 2008), pp. 1007-1015.
    by Jane Charlesworth, Adam Eyre-Walker
    posted to mutation mcdonald kreitman deleterious by Stew on 2008-05-13 17:22:27 as ** along with 4 people and 1 group gjuggler cabbagesofdoom stajich stevanspringer Berkeley Mycology
  • Discovering sequence motifs with arbitrary insertions and deletions.
    PLoS computational biology, Vol. 4, No. 4. (April 2008)
    by MC Frith, NF Saunders, B Kobe, TL Bailey
    posted to motif indel detection de-novo by Stew on 2008-05-13 10:24:59 as ** along with 5 people Ema dquest gjuggler neils cabbagesofdoom
  • DNA motif representation with nucleotide dependency.
    IEEE/ACM Trans Comput Biol Bioinform, Vol. 5, No. 1. (r 2008), pp. 110-119.
    by F Chin, HC Leung
    posted to motif dna detection de-novo by Stew on 2008-05-12 15:58:42 as ** along with 3 people AbnerCYH maximilianh xili03
  • Differential Evolution of the Thirteen Atlantic Salmon Hox Clusters.
    Molecular biology and evolution (18 April 2008)
    by Sutada Mungpakdee, Hee-Chan C Seo, Anna Rita R Angotzi, Xianjun Dong, Altuna Akalin, Daniel Chourrout
    posted to hox evolution by Stew on 2008-04-25 13:36:18 as **
  • Evolution of metal hyperaccumulation required cis-regulatory changes and triplication of HMA4
    Nature (20 April 2008)
    by Marc Hanikenne, Ina N Talke, Michael J Haydon, Christa Lanz, Andrea Nolte, Patrick Motte, Juergen Kroymann, Detlef Weigel, Ute Krämer
    posted to evolution cis-regulatory by Stew on 2008-04-25 13:35:15 as **
  • The origin of subfunctions and modular gene regulation.
    Genetics, Vol. 170, No. 1. (May 2005), pp. 433-446.
    by A Force, WA Cresko, FB Pickett, SR Proulx, C Amemiya, M Lynch
    posted to gene lynch regulation subfunctionalization by Stew on 2008-04-22 07:21:49 as **** along with 3 people lusk brant bluto
  • The evolution of genetic networks by non-adaptive processes
    Nature Reviews Genetics, Vol. 8, No. 10., pp. 803-813.
    by Michael Lynch
    posted to evolution lynch networks non-adaptive by Stew on 2008-04-22 07:20:07 as ***** along with 10 people and 2 groups lusk brant balicea dchughes aswin stajich margaritis zwang nosada17 lilith G4ID Genetics-of-Gambling
  • O fly, where art thou?
    Journal of the Royal Society, Interface / the Royal Society (26 March 2008)
    by Dhruv Grover, John Tower, Simon Tavaré
    posted to behaviour drosophila by Stew on 2008-04-14 09:18:43 as **
  • The Evolution of Gene Regulation Underlies a Morphological Difference between Two Drosophila Sister Species.
    Cell, Vol. 132, No. 5. (7 March 2008), pp. 783-793.
    by S Jeong, M Rebeiz, P Andolfatto, T Werner, J True, SB Carroll
    posted to drosophila evolution gene morphology regulation by Stew on 2008-04-14 09:03:17 as ***** along with 1 person and 1 group cisevol cis-regulatory-evolution
  • Ultraconservation identifies a small subset of extremely constrained developmental enhancers.
    Nat Genet (6 January 2008)
    by Axel Visel, Shyam Prabhakar, Jennifer A A Akiyama, Malak Shoukry, Keith D D Lewis, Amy Holt, Ingrid Plajzer-Frick, Veena Afzal, Edward M M Rubin, Len A A Pennacchio
    posted to no-tag by Stew on 2008-02-29 12:21:51 as ** along with 4 people bpcusack maximilianh gjuggler emptyhb
  • RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo
    Nature Genetics, Vol. 39, No. 12. (11 November 2007), pp. 1512-1516.
    by Julia Zeitlinger, Alexander Stark, Manolis Kellis, Joung-Woo Hong, Sergei Nechaev, Karen Adelman, Michael Levine, Richard A Young
    posted to development drosophila embryo gene melanogaster polymerase rna stalling by Stew on 2007-12-14 00:13:07 as ** along with 4 people mikaelhuss caseybrown margaritis rschulz
  • Retroviral enhancer detection insertions in zebrafish combined with comparative genomics reveal genomic regulatory blocks - a fundamental feature of vertebrate genomes.
    Genome Biol, Vol. 8 Suppl 1 (2007)
    by H Kikuta, D Fredman, S Rinkwitz, B Lenhard, TS Becker
    posted to cis-regulatory comparative genomics regulatory zebrafish by Stew on 2007-12-07 16:30:39 as ** along with 1 person maximilianh
  • Association of cohesin and Nipped-B with transcriptionally active regions of the Drosophila melanogaster genome.
    Chromosoma (27 October 2007)
    by Ziva Misulovin, Yuri B Schwartz, Xiao-Yong Y Li, Tatyana G Kahn, Maria Gause, Stewart Macarthur, Justin C Fay, Michael B Eisen, Vincenzo Pirrotta, Mark D Biggin, Dale Dorsett
    posted to chip-chip chromatin drosophila nipped-b by Stew on 2007-12-03 18:20:44 as **
  • Conserved eukaryotic transposable elements and the evolution of gene regulation.
    Cell Mol Life Sci (20 November 2007)
    by J Jurka
    posted to no-tag by Stew on 2007-11-23 21:17:29 as ** along with 5 people and 2 groups gpappas dchughes maximilianh cisevol idonaldson cis-regulatory-evolution BergmanLab
  • DNA variations within the sea urchin Otx gene enhancer.
    FEBS Lett (16 October 2007)
    by Takashi Yamamoto, Rie Kawamoto, Takayoshi Fujii, Naoaki Sakamoto, Tatsuo Shibata
    posted to no-tag by Stew on 2007-11-01 23:18:50 as **
  • A New Retroposed Gene in Drosophila Heterochromatin Detected by Microarray-Based Comparative Genomic Hybridization
    Journal of Molecular Evolution, Vol. 64, No. 2. (February 2007), pp. 272-283.
    by Fan, Chuanzhu, Long, Manyuan
    posted to no-tag by Stew on 2007-11-01 23:18:30 as **
  • Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting.
    Proc Natl Acad Sci U S A (29 March 2007)
    by Alona Sosinsky, Barry Honig, Richard S S Mann, Andrea Califano
    posted to cis-regulatory drosophila footprinting phlyogenetic prediction by Stew on 2007-10-19 00:42:18 as ** along with 4 people and 2 groups isimpson dpollard maximilianh cisevol EisenLab cis-regulatory-evolution
  • The TAGteam DNA motif controls the timing of Drosophila pre-blastoderm transcription
    Development, Vol. 133, No. 10. (15 May 2006), pp. 1967-1977.
    by John R Bosch, Joseph A Benavides, Thomas W Cline
    posted to caggtag drosophila tagteam timing transcription by Stew on 2007-10-09 19:36:45 as ** along with 3 people and 2 groups emilyhare adepace wrowell EisenLab Cline_lab
  • Functional Architecture and Evolution of Transcriptional Elements That Drive Gene Coexpression
    Science, Vol. 317, No. 5844. (14 September 2007), pp. 1557-1560.
    by Christopher D Brown, David S Johnson, Arend Sidow
    posted to no-tag by Stew on 2007-10-04 23:31:41 as ***** along with 9 people and 2 groups emptyhb dpollard djkt joepickrell zwang Garamonfok mimulus_99 maximilianh cisevol EisenLab cis-regulatory-evolution
  • Temporal ChIP-on-chip reveals Biniou as a universal regulator of the visceral muscle transcriptional network.
    Genes Dev, Vol. 21, No. 19. (1 October 2007), pp. 2448-2460.
    by JS Jakobsen, M Braun, J Astorga, EH Gustafson, T Sandmann, M Karzynski, P Carlsson, EE Furlong
    posted to chip-chip by Stew on 2007-10-04 23:31:08 as ***** along with 1 person and 1 group dpollard EisenLab
  • A cis-regulatory sequence within the yellow locus of Drosophila melanogaster required for normal male mating success.
    Genetics, Vol. 172, No. 2. (February 2006), pp. 1009-1030.
    by MD Drapeau, SA Cyran, MM Viering, PK Geyer, AD Long
    posted to cis-regulatory drosophila mating success yellow by Stew on 2007-10-02 17:50:26 as **
  • Finding cis-regulatory elements using comparative genomics: Some lessons from ENCODE data.
    Genome Res, Vol. 17, No. 6. (June 2007), pp. 775-786.
    by DC King, J Taylor, Y Zhang, Y Cheng, HA Lawson, J Martin, , F Chiaromonte, W Miller, RC Hardison
    posted to cis-regulatory comparative encode by Stew on 2007-10-02 16:57:50 as **** along with 2 people and 2 groups ghattem Garamonfok Bioinformatics UH - Computational Biology
  • Adaptive protein evolution at the Adh locus in Drosophila
    Nature, Vol. 351, No. 6328. (20 June 1991), pp. 652-654.
    by John H Mcdonald, Martin Kreitman
    posted to kreitman mcdonald test by Stew on 2007-10-02 16:40:39 as read along with 5 people pradiptaray bpb RMGraze brant Garamonfok
  • GeneWise and Genomewise
    Genome Res., Vol. 14, No. 5. (1 May 2004), pp. 988-995.
    by Ewan Birney, Michele Clamp, Richard Durbin
    posted to gene prediction by Stew on 2007-10-02 08:16:21 as ** along with 4 people and 2 groups indigoviolet azazello alexl wenhan EisenLab MBLAB
  • The effects of multiple features of alternatively spliced exons on the K(A)/K(S) ratio test.
    BMC Bioinformatics, Vol. 7 (2006)
    by FC Chen, TJ Chuang
    posted to alternative exons kaks splicing test by Stew on 2007-09-28 23:27:22 as **
  • Biological function of unannotated transcription during the early development of Drosophila melanogaster
    Nature Genetics, Vol. 38, No. 10. (03 September 2006), pp. 1151-1158.
    by Robert J Manak, Sujit Dike, Victor Sementchenko, Philipp Kapranov, Frederic Biemar, Jeff Long, Jill Cheng, Ian Bell, Srinka Ghosh, Antonio Piccolboni, Thomas R Gingeras
    posted to affy development drosophila transcription by Stew on 2007-09-21 21:03:24 as read along with 5 people and 6 groups dpollard neveaire djkt wrowell xingxu Biostatistics Computational-Genomics Bioinformatics EisenLab Neuroscience Cline_lab
  • Ultraconserved elements in insect genomes: A highly conserved intronic sequence implicated in the control of homothorax mRNA splicing.
    Genome Res (17 May 2005)
    by Evgeny A A Glazov, Michael Pheasant, Elizabeth A A McGraw, Gill Bejerano, John S S Mattick
    posted to drosophila insect mrna splicing ultraconserved by Stew on 2007-09-19 18:41:01 as **** along with 2 people and 1 group ujh sujaikumar EisenLab
  • The Probability of Duplicate Gene Preservation by Subfunctionalization
    Genetics, Vol. 154, No. 1. (1 January 2000), pp. 459-473.
    by Michael Lynch, Allan Force
    posted to duplication neofunctionalization subfunctionalization by Stew on 2007-09-19 18:36:15 as read along with 2 people and 1 group BioNica bluto EisenLab
  • Applied bioinformatics for the identification of regulatory elements.
    Nat Rev Genet, Vol. 5, No. 4. (April 2004), pp. 276-287.
    by WW Wasserman, A Sandelin
    posted to cis-regulatory prediction review by Stew on 2007-09-18 18:26:40 as read along with 15 people and 8 groups mariakmejia icases ana chad_davis moborg gpalidwor dchughes nickluscombe johncumbers giovanni xiaobeizhao bertelsen nklee jdiezperezj ArtemPankin structural_bioinformatics Bioinformatics EisenLab G4ID EBI-regulation GeschwindLab TNT Genetics-of-Gambling
  • Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene.
    Nat Genet (17 September 2006)
    by Hilde Janssens, Shuling Hou, Johannes Jaeger, Ah-Ram R Kim, Ekaterina Myasnikova, David Sharp, John Reinitz
    posted to cis-regulatory drosophila model by Stew on 2007-09-18 05:22:10 as read along with 6 people and 2 groups okarsligil brant dpollard adepace allPowerde emptyhb Bioinformatics EisenLab
  • (Re)modeling the transcriptional enhancer
    Nature Genetics, Vol. 38, No. 10. (October 2006), pp. 1102-1103.
    by Marc S Halfon
    posted to cis-regulatory model by Stew on 2007-09-18 05:20:58 as ** along with 1 group EisenLab
  • Cracking the genome's second code: enhancer detection by combined phylogenetic footprinting and transgenic fish and frog embryos.
    Methods, Vol. 39, No. 3. (July 2006), pp. 212-219.
    by ML Allende, M Manzanares, JJ Tena, CG Feijóo, JL Gómez-Skarmeta
    posted to cis-regulatory fish footprinting frog phlyogenetic prediction by Stew on 2007-09-18 01:19:46 as read along with 1 group EisenLab
  • Parallel evolution of conserved noncoding elements that target a common set of developmental regulatory genes from worms to humans.
    Genome Biology, Vol. 8 (02 February 2007), R15.
    by Tanya Vavouri, Klaudia Walter, Walter R Gilks, Ben Lehner, Greg Elgar
    posted to conserved evolution human non-coding worm by Stew on 2007-09-18 01:17:38 as ** along with 7 people and 2 groups smbe2008 indigoviolet dpollard adepace djkt sujaikumar cisevol EisenLab cis-regulatory-evolution
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