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di Stew library [125 articles]

Articoli aggiunti di recente nella biblioteca di Stew .
  • Sepsid even-skipped Enhancers Are Functionally Conserved in Drosophila Despite Lack of Sequence Conservation
    PLoS Genet, Vol. 4, No. 6. (27 June 2008), e1000106.
    by Emily E Hare, Brant K Peterson, Venky N Iyer, Rudolf Meier, Michael B Eisen
    posted to sequence sepdid functional eve enhancer drosophila conserved by Stew on 2008-09-05 09:03:26 as ** along with 7 people and 2 groups maximilianh emptyhb djkt stajich pradiptaray cisevol caseybrown Berkeley Mycology cis-regulatory-evolution
  • Assessing computational tools for the discovery of transcription factor binding sites
    Nature Biotechnology, Vol. 23, No. 1. (06 January 2005), pp. 137-144.
    by Martin Tompa, Nan Li, Timothy L Bailey, George M Church, Bart D De Moor, Eleazar Eskin, Alexander V Favorov, Martin C Frith, Yutao Fu, James J Kent, Vsevolod J Makeev, Andrei A Mironov, William S Noble, Giulio Pavesi, Graziano Pesole, Mireille Régnier, Nicolas Simonis, Saurabh Sinha, Gert Thijs, Jacques v van Helden, Mathias Vandenbogaert, Zhiping Weng, Christopher Workman, Chun Ye, Zhou Zhu
    posted to de-novo motif by Stew on 2008-08-28 17:12:40 as ** along with 25 people and 6 groups bryankr icases ana barry aalibes aprasad jfr tuck chad_davis lyongu tabu dquest neveaire ranb johncumbers noano xiaobeizhao olympos GustavoLacerda nklee mdimon dandaman vietanh0 ep161302 nuin structural_bioinformatics Biostatistics Computational-Genomics Bioinformatics Neuroscience TNT
  • MTAP: The Motif Tool Assessment Platform
    BMC Bioinformatics, Vol. 9, No. Suppl 9. (2008)
    by Daniel Quest, Kathryn Dempsey, Mohammad Shafiullah, Dhundy Bastola, Hesham Ali
    posted to de-novo motif by Stew on 2008-08-28 17:06:06 as ** along with 1 person dquest
  • Positive and negative selection on noncoding DNA in Drosophila simulans.
    Molecular biology and evolution (29 May 2008)
    by Penelope R R Haddrill, Doris Bachtrog, Peter Andolfatto
    posted to drosophila negative non-coding positive selection by Stew on 2008-08-24 20:52:03 as ** along with 2 people emptyhb caseybrown
  • Confirming the Phylogeny of Mammals by Use of Large Comparative Sequence Datasets.
    Molecular biology and evolution (2 May 2008)
    by Arjun B B Prasad, Marc W W Allard, , Eric D D Green
    posted to comparative mammals phylogeny sequence by Stew on 2008-08-24 20:51:31 as ** along with 2 people aprasad dchughes
  • 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 in-silico model sequencing by Stew on 2008-08-24 20:49:38 as ** along with 5 people aramesh2 djkt kengg gdb caseybrown
  • A Feature-Based Approach to Modeling Protein–DNA Interactions
    PLoS Comput Biol, Vol. 4, No. 8. (2008), e1000154.
    by Eilon Sharon, Shai Lubliner, Eran Segal
    posted to dna interactions model protein segal by Stew on 2008-08-24 20:48:42 as ** along with 4 people dakelley emptyhb zwang aalibes
  • 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 human nucleosome occupancy primary sequence by Stew on 2008-08-24 20:47:42 as ** along with 2 people djkt aalibes
  • Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm
    PLoS Biology, Vol. 6, No. 2. (1 February 2008), e27.
    by Xiao-Yong Li, Stewart Macarthur, Richard Bourgon, David Nix, Daniel A Pollard, Venky N Iyer, Aaron Hechmer, Lisa Simirenko, Mark Stapleton, Cris L Hendriks, Hou C Chu, Nobuo Ogawa, William Inwood, Victor Sementchenko, Amy Beaton, Richard Weiszmann, Susan E Celniker, David W Knowles, Tom Gingeras, Terence P Speed, Michael B Eisen, Mark D Biggin
    posted to chip-chip drosophila by Stew on 2008-08-22 11:24:20 as ** along with 7 people and 1 group kengg maximilianh caseybrown emptyhb brant isimpson gdb Jarman Lab
  • Spike-in validation of an Illumina-specific variance-stabilizing transformation.
    BMC research notes, Vol. 1 (2008)
    by MJ Dunning, ME Ritchie, NL Barbosa-Morais, S Tavaré, AG Lynch
    posted to beadarray illumina microarray spike-in stabilization variance vst by Stew on 2008-08-22 09:11:39 as **
  • Hidden copy number variation in the HapMap population.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 105, No. 29. (22 July 2008), pp. 10067-10072.
    by JC Marioni, M White, S Tavaré, AG Lynch
    posted to cnv copy hapmap number tavare variation by Stew on 2008-08-18 09:40:13 as ** along with 2 people waszak jyuh
  • A comparison of background correctionm ethods for two-colour microarrays.
    Bioinformatics (25 August 2007)
    by Matthew E E Ritchie, Jeremy Silver, Alicia Oshlack, Melissa Holmes, Dileepa Diyagama, Andrew Holloway, Gordon K K Smyth
    posted to background correction microarray by Stew on 2008-08-18 09:39:05 as ** along with 6 people jyuh jfr shigepong GeeSharpMinor debasis caseybrown
  • Statistical issues in the analysis of Illumina data
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Mark Dunning, Nuno B Morais, Andy Lynch, Simon Tavare, Matthew Ritchie
    posted to analysis beadarray illumina statistics by Stew on 2008-08-18 09:37:58 as ** along with 6 people and 1 group neveaire RockHI thomaskelder stajich srp33 jyuh Berkeley Mycology
  • Defining the epithelial stem cell niche in skin.
    Science, Vol. 303, No. 5656. (16 January 2004), pp. 359-363.
    by T Tumbar, G Guasch, V Greco, C Blanpain, WE Lowry, M Rendl, E Fuchs
    posted to affy cells epithelial expression skin stem by Stew on 2008-08-14 13:59:06 as ** along with 1 person journal888
  • Efficient representation and P-value computation for high-order Markov motifs
    Bioinformatics, Vol. 24, No. 16. (15 August 2008), pp. i160-166.
    by Paulo G da Fonseca, Katia S Guimaraes, Marie-France Sagot
    posted to markov motif pssm p-value pwm by Stew on 2008-08-11 09:08:07 as ** along with 1 person Evangelia
  • Core transcriptional regulatory circuitry in human embryonic stem cells.
    Cell, Vol. 122, No. 6. (23 September 2005), pp. 947-956.
    by LA Boyer, TI Lee, MF Cole, SE Johnstone, SS Levine, JP Zucker, MG Guenther, RM Kumar, HL Murray, RG Jenner, DK Gifford, DA Melton, R Jaenisch, RA Young
    posted to microrna regulation stem transcription young by Stew on 2008-08-08 14:06:36 as ** along with 13 people rklancer kentsis tardigrade balicea tabu cconboy koller faisalm mikaelhuss tdmckee brant dquest kengg
  • ZOOM! Zillions Of Oligos Mapped
    Bioinformatics (6 August 2008), btn416.
    by Hao Lin, Zefeng Zhang, Michael Q Zhang, Bin Ma, Ming Li
    posted to illumina mapping oligos software solexa zoom by Stew on 2008-08-08 13:40:14 as ** along with 1 person Neeperando
  • High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi
    Nature Genetics, Vol. 40, No. 8. (27 July 2008), pp. 987-993.
    by Kathryn E Holt, Julian Parkhill, Camila J Mazzoni, Philippe Roumagnac, François-Xavier Weill, Ian Goodhead, Richard Rance, Stephen Baker, Duncan J Maskell, John Wain, Christiane Dolecek, Mark Achtman, Gordon Dougan
    posted to bacteria evolution genome high-throughput illumina sequencing solexa variation by Stew on 2008-08-07 09:19:20 as ** along with 1 person aconesa
  • RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
    Genome Res. (11 June 2008), gr.079558.108.
    by John Marioni, Cristopher Mason, Shrikant Mane, Matthew Stephens, Yoav Gilad
    posted to arrays comparison expression rna-seq by Stew on 2008-08-06 15:01:38 as ** along with 16 people and 1 group dakelley caseybrown Ema balicea vega lusk semrich vmarshal fpattyn stajich giovanni ela503 jyuh kengg shurjo GustavoLacerda Berkeley Mycology
  • Simultaneous Analysis of All SNPs in Genome-Wide and Re-Sequencing Association Studies
    PLoS Genet, Vol. 4, No. 7. (25 July 2008), e1000130.
    by Clive J Hoggart, John C Whittaker, Maria De Iorio, David J Balding
    posted to association genome-wide snps studies by Stew on 2008-08-06 10:45:45 as ** along with 3 people djkt jyuh Schmidtc
  • Illumina universal bead arrays.
    Methods Enzymol, Vol. 410 (2006), pp. 57-73.
    by JB Fan, KL Gunderson, M Bibikova, JM Yeakley, J Chen, E Wickham Garcia, LL Lebruska, M Laurent, R Shen, D Barker
    posted to beadarray illumina microarray by Stew on 2008-08-05 14:04:31 as ** along with 2 people and 1 group stsaft jeremymiller GeschwindLab
  • beadarray: R classes and methods for Illumina bead-based data
    Bioinformatics, Vol. 23, No. 16. (15 August 2007), pp. 2183-2184.
    by Mark J Dunning, Mike L Smith, Matthew E Ritchie, Simon Tavare
    posted to beadarray illumina r by Stew on 2008-08-04 17:27:25 as ** along with 3 people raylim srp33 jyuh
  • lumi: a pipeline for processing Illumina microarray.
    Bioinformatics (Oxford, England) (8 May 2008)
    by Pan Du, Warren A A Kibbe, Simon M M Lin
    posted to illumina lumi microarray by Stew on 2008-08-04 17:26:29 as ** along with 1 person jyuh
  • Maps of cis-Regulatory Nodes in Megabase Long Genome Segments are an Inevitable Intermediate Step Toward Whole Genome Functional Mapping.
    Current genomics, Vol. 8, No. 2. (April 2007), pp. 137-149.
    by LG Nikolaev, SB Akopov, IP Chernov, ED Sverdlov
    posted to cis-regulatory functional mapping by Stew on 2008-08-01 07:37:28 as **
  • 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 carroll evo-devo evolution morphology sean by Stew on 2008-07-18 09:19:14 as ***** along with 3 people icq242500260 dchughes djkt
  • 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 evolution evolvability gene networks regulatory by Stew on 2008-07-15 12:12:20 as *** along with 11 people and 1 group aramesh2 erel10 Ema jdiezperezj bootsy dlobo djkt dquest shoshin rebeccamancy Borelli 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 differentially expressed genes microarray by Stew on 2008-07-07 08:46:20 as **** along with 3 people natstreet shigepong GeeSharpMinor
  • 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 affy arrays association snp by Stew on 2008-07-07 08:45:06 as **** along with 3 people caseybrown balicea jyuh
  • 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 cone conserved enhancer evolution photoreceptor 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 comparative detection footprinting genomics motif phylogenetic by Stew on 2008-06-14 14:43:13 as ***** along with 3 people and 1 group djkt cisevol Ema 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 alignment cis-regulatory drosophila footprinting phylogenetic prediction regulatory by Stew on 2008-06-06 08:24:29 as **** along with 5 people druvus eckart_bindewald maximilianh gjuggler Ema
  • 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 cis-regulatory divergence subfunctionalization zebrafish by Stew on 2008-06-06 08:20:04 as ** along with 4 people brant gjuggler emptyhb maximilianh
  • Tinker where the tinkering's good.
    Trends in genetics : TIG (29 May 2008)
    by Matthew V V Rockman, David L L Stern
    posted to cis-regulatory drosophila evolution phenotype pigmentation pleiotropy 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 functional non-coding variation 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 evolution factor logic transcription by Stew on 2008-06-02 10:53:58 as **** along with 2 people Garamonfok bpcusack
  • 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 base composition drosophila non-coding non-neutral nucleotide 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 celegans nucleosome by Stew on 2008-05-27 13:45:27 as ** along with 5 people and 1 group maximilianh caseybrown vega dpollard aalibes 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 delta drosophila notch 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 drosophila gaga nelf pausing promoter 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 evolution genome primate promoter by Stew on 2008-05-13 17:24:34 as ** along with 2 people and 1 group cisevol aprasad 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 drosophila evolution expression gene olfactory 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 deleterious kreitman mcdonald mutation by Stew on 2008-05-13 17:22:27 as ** along with 5 people and 1 group cabbagesofdoom gjuggler stevanspringer stajich bpcusack 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 de-novo detection indel motif by Stew on 2008-05-13 10:24:59 as ** along with 6 people gjuggler dquest cabbagesofdoom neils Ema Evangelia
  • 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 de-novo detection dna motif 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 evolution hox 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 cis-regulatory evolution 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 brant bluto lusk
  • 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 brant balicea dchughes aswin stajich margaritis zwang nosada17 lilith lusk 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
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