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Tag cis-regulatory [265 articles]

Articoli recentemente classificati sotto il tag cis-regulatory.
  • Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene
    Nature, Vol. 440, No. 7087., pp. 1050-1053.
    by Benjamin Prud'homme, Nicolas Gompel, Antonis Rokas, Victoria A Kassner, Thomas M Williams, Shu-Dan Yeh, John R True, Sean B Carroll
    posted to cis-regulatory fly by tny on 2006-04-27 07:18:09 as ** along with 9 people and 1 group carlfulp RMGraze dpollard balicea adepace ranb Garamonfok blobbybirdman emptyhb EisenLab
  • EVOLUTION: An Embarrassment of Switches
    Science, Vol. 317, No. 5839. (10 August 2007), pp. 758-759.
    by Leonid Kruglyak, David L Stern
    posted to alignment cis-regulatory cne identity by sujaikumar on 2007-08-17 09:00:42 as **
  • Prediction of cis-regulatory elements using binding site matrices--the successes, the failures and the reasons for both.
    Curr Opin Genet Dev, Vol. 15, No. 4. (August 2005), pp. 395-402.
    by T Vavouri, G Elgar
    posted to cis-regulatory elgar modules prediction review by Stew on 2007-07-27 22:18:57 as read along with 6 people and 2 groups troels_marstrand kaspermunch dpollard adepace lusk brant Bioinformatics EisenLab
  • Computational prediction of transcription-factor binding site locations.
    Genome Biol, Vol. 5, No. 1. (2003)
    by ML Bulyk
    posted to cis-regulatory clustering prediction review by Stew on 2007-09-17 20:40:18 as ** along with 6 people and 1 group kaarsinogen lusk nklee yevishere xili03 aalibes 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
  • 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 **
  • 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
  • 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 dpollard maximilianh cisevol isimpson EisenLab cis-regulatory-evolution
  • 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 **
  • 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
  • Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo.
    BMC Bioinformatics, Vol. 3 (24 October 2002)
    by N Rajewsky, M Vergassola, U Gaul, ED Siggia
    posted to cis-regulatory drosophila prediction by Stew on 2007-09-17 20:42:09 as ** along with 6 people and 1 group isimpson ansobol indigoviolet adepace koller csdhwang EisenLab
  • 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
  • CONDOR: a database resource of developmentally associated conserved non-coding elements
    BMC Developmental Biology, Vol. 7 (30 August 2007), 100.
    by Adam Woolfe, Debbie K Goode, Julie Cooke, Heather Callaway, Sarah Smith, Phil Snell, Gayle K Mcewen, Greg Elgar
    posted to cis-regulatory conserved elgar evolution non-coding by Stew on 2007-09-04 16:17:41 as ***** along with 1 person and 1 group maximilianh EisenLab
  • Adaptive Evolution of Conserved Noncoding Elements in Mammals
    PLoS Genetics, Vol. 3, No. 9. (1 September 2007), e147.
    by Su Y Kim, Jonathan K Pritchard
    posted to cis-regulatory conserved evolution mammals non-coding by Stew on 2007-09-18 01:09:01 as ** along with 9 people and 5 groups mattjb livingthingdan djkt stajich Garamonfok cabbagezs cisevol rrhudson bpcusack EisenLab ComplexAdaptiveSystems DSTO-CAS livingthing cis-regulatory-evolution
  • 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
  • (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
  • Different words, same meaning: understanding the languages of the genome.
    Trends Genet (27 September 2006)
    by Greg Elgar
    posted to cis-regulatory elgar prediction review by Stew on 2007-07-27 22:32:32 as read along with 2 people and 5 groups nickluscombe WJST EisenLab EBI-regulation asthma humangenetics SNP
  • 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
  • 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 **
  • Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome.
    Proc Natl Acad Sci U S A, Vol. 99, No. 2. (22 January 2002), pp. 757-762.
    by BP Berman, Y Nibu, BD Pfeiffer, P Tomancak, SE Celniker, M Levine, GM Rubin, MB Eisen
    posted to cis-regulatory clustering drosophila modules prediction by Stew on 2007-09-17 20:14:51 as read along with 3 people and 1 group indigoviolet emptyhb csdhwang EisenLab
  • 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
  • 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 16 people and 8 groups icases ana chad_davis moborg gpalidwor dchughes nickluscombe johncumbers giovanni xiaobeizhao bertelsen nklee jdiezperezj ArtemPankin mariakmejia isimpson structural_bioinformatics Bioinformatics EisenLab G4ID EBI-regulation GeschwindLab TNT Genetics-of-Gambling
  • Levers and fulcrums: progress in cis-regulatory motif models
    Nature Methods, Vol. 5, No. 4., pp. 297-298.
    by Ewan Birney
    posted to cis-regulatory comparative_genomics methods motif prediction by stajich on 2008-04-07 16:11:40 as ** along with 3 people and 3 groups emptyhb pradiptaray isimpson EisenLab Berkeley Mycology Jarman Lab
  • Searching for statistically significant regulatory modules.
    Bioinformatics, Vol. 19 Suppl 2 (October 2003)
    by TL Bailey, WS Noble
    posted to cis-regulatory methods module motif by stajich on 2007-12-05 18:30:08 as ** along with 2 people and 2 groups indigoviolet xili03 EisenLab Berkeley Mycology
  • Independent effects of cis- and trans-regulatory variation on gene expression in Drosophila melanogaster
    Genetics (3 February 2008), genetics.107.082032.
    by Patricia J Wittkopp, Belinda K Haerum, Andrew G Clark
    posted to cis-regulatory transcription by stajich on 2008-02-04 08:13:01 as ***** along with 5 people and 3 groups brant djkt mimulus_99 dpollard caseybrown EisenLab cis-regulatory-evolution RockmanLab
  • Identifying cis-regulatory modules by combining comparative and compositional analysis of DNA.
    Bioinformatics (10 October 2006)
    by Nora Pierstorff, Casey M M Bergman, Thomas Wiehe
    posted to cis-regulatory elements by SeungjoonOh on 2007-02-20 06:42:22 as ** along with 3 people and 1 group dpollard plofje csdhwang EisenLab
  • Tissue-specific regulatory elements in mammalian promoters
    Mol Syst Biol, Vol. 3 (16 January 2007)
    by Andrew D Smith, Pavel Sumazin, Michael Q Zhang
    posted to cis-regulatory elements by SeungjoonOh on 2007-02-20 06:36:53 as ** along with 3 people and 2 groups dchughes heliopais roys G4ID Genetics-of-Gambling
  • Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques.
    Genome Res (19 October 2006)
    by Laura Elnitski, Victor X X Jin, Peggy J J Farnham, Steven J M J Jones
    posted to cis-regulatory elements by SeungjoonOh on 2007-02-20 06:40:02 as ** along with 7 people and 1 group dquest bryankr giovanni lusk cabbagezs maximilianh gdb GeschwindLab
  • 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 cis-regulatory elements by SeungjoonOh on 2007-02-20 06:42:07 as ** along with 8 people and 2 groups bais miguel tuck eckart_bindewald djkt blobbybirdman inesdesantiago xingxu Bioinformatics UH - Computational Biology
  • EDGEdb: a transcription factor-DNA interaction database for the analysis of C. elegans differential gene expression
    BMC Genomics, Vol. 8 (18 January 2007), 21.
    by Inmaculada M Barrasa, Philippe Vaglio, Fabien Cavasino, Laurent Jacotot, Albertha JM Walhout
    posted to cis-regulatory elements by SeungjoonOh on 2007-02-20 06:35:42 as ** along with 2 people and 1 group tharris sujaikumar C. elegans / WormBase
  • Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae
    BMC Bioinformatics, Vol. 7 (28 October 2006), 478.
    by Illes J Farkas, Chuang Wu, Chakra Chennubhotla, Ivet Bahar, Zoltan N Oltvai
    posted to cis-regulatory elements by SeungjoonOh on 2007-02-20 06:39:45 as ** along with 1 person and 1 group icases TNT
  • Characterization of binding sites of eukaryotic transcription factors.
    Genomics Proteomics Bioinformatics, Vol. 4, No. 2. (May 2006), pp. 67-79.
    by J Qian, J Lin, DJ Zack
    posted to cis-regulatory elements by SeungjoonOh on 2007-02-20 06:42:35 as **
  • Statistical significance of cis-regulatory modules
    BMC Bioinformatics, Vol. 8, No. 1. (2007)
    by Dustin Schones, Andrew Smith, Michael Zhang
    posted to cis-regulatory elements by SeungjoonOh on 2007-02-20 06:33:31 as *** along with 9 people and 1 group indigoviolet dpollard dquest sebastien_vigneau shigepong GustavoLacerda nklee xili03 sconlan EisenLab
  • Analysis of promoter regions of co-expressed genes identified by microarray analysis
    BMC Bioinformatics, Vol. 7 (17 August 2006), 384.
    by Srinivas Veerla, Mattias Hoglund
    posted to cis-regulatory elements by SeungjoonOh on 2007-02-20 06:48:21 as ** along with 5 people and 1 group jfr gpalidwor giovanni heliopais nuin GeschwindLab
  • Reconstructing dynamic regulatory maps.
    Mol Syst Biol, Vol. 3 (2007)
    by J Ernst, O Vainas, CT Harbison, I Simon, Z Bar-Joseph
    posted to cis-regulatory elements by SeungjoonOh on 2007-02-20 06:36:05 as ** along with 6 people and 1 group okarsligil aswin mikaelhuss berthoums natstreet jo_davies Bioinformatics
  • Integrating transcription factor binding site information with gene expression datasets.
    Bioinformatics (24 November 2006)
    by Ian B B Jeffery, Stephen F F Madden, Paul A A McGettigan, Guy Perrière, Aedín C C Culhane, Desmond G G Higgins
    posted to cis-regulatory elements by SeungjoonOh on 2007-02-20 06:38:14 as ** along with 4 people and 1 group jyuh dpollard gpalidwor wnpx EisenLab
  • Large-Scale Discovery of Promoter Motifs in Drosophila melanogaster
    PLoS Computational Biology, Vol. 3, No. 1. (1 January 2007), e7.
    by Thomas A Down, Casey M Bergman, Jing Su, Tim J Hubbard
    posted to cis-regulatory elements by SeungjoonOh on 2007-02-20 06:34:53 as ** along with 6 people and 1 group indigoviolet dpollard dquest nklee emptyhb isimpson EisenLab
  • Beyond microarrays: Finding key transcription factors controlling signal transduction pathways
    BMC Bioinformatics, Vol. 7, No. Suppl 2. (2006)
    by Alexdander Kel, Nico Voss, Ruy Jauregui, Olga K Margoulis, Edgar Wingender
    posted to cis-regulatory elements by SeungjoonOh on 2007-02-20 06:38:01 as ** along with 2 people jfr gpalidwor
  • Advances in the Discovery of cis-Regulatory Elements
    Current Bioinformatics, Vol. 1, No. 3. (August 2006), pp. 321-336.
    by Pan, Youlian
    posted to cis-regulatory by nklee on 2007-09-26 09:16:00 as ** along with 1 person csdhwang
  • 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 architecture cis-regulatory elements by mimulus_99 on 2007-09-14 18:13:00 as ** along with 9 people and 2 groups dpollard djkt joepickrell zwang Garamonfok Stew maximilianh cisevol emptyhb EisenLab cis-regulatory-evolution
  • Possible involvement of SINEs in mammalian-specific brain formation.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 105, No. 11. (18 March 2008), pp. 4220-4225.
    by T Sasaki, H Nishihara, M Hirakawa, K Fujimura, M Tanaka, N Kokubo, C Kimura-Yoshida, I Matsuo, K Sumiyama, N Saitou, T Shimogori, N Okada
    posted to cis-regulatory mammals transposon by cisevol to the group BergmanLab on 2008-04-26 19:38:10 as ** along with 1 person and 1 group FMoncini cis-regulatory-evolution
  • The information coded in the yeast response elements accounts for most of the topological properties of its transcriptional regulation network.
    PLoS ONE, Vol. 2, No. 6. (2007)
    by D Balcan, A Kabakçioğlu, M Mungan, A Erzan
    posted to cis-regulatory flies by cisevol to the group BergmanLab on 2007-10-19 15:35:36 as ** along with 1 person thecolourblue
  • A novel mode of enhancer evolution: The Tal1 stem cell enhancer recruited a MIR element to specifically boost its activity.
    Genome research (7 August 2008)
    by Aileen M M Smith, Maria-Jose J Sanchez, George A A Follows, Sarah Kinston, Ian J J Donaldson, Anthony R R Green, Berthold Göttgens
    posted to cis-regulatory mammals transposon by cisevol to the group BergmanLab on 2008-08-11 19:50:59 as ** along with 1 person and 1 group maximilianh cis-regulatory-evolution
  • PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation
    Genome Biology, Vol. 8 (04 October 2007), R207.
    by Elodie Portales-Casamar, Stefan Kirov, Jonathan Lim, Stuart Lithwick, Magdalena I Swanson, Amy Ticoll, Jay Snoddy, Wyeth W Wasserman
    posted to cis-regulatory database by cisevol to the group BergmanLab on 2007-10-23 19:13:41 as ** along with 2 people and 2 groups dpollard pradiptaray EisenLab cis-regulatory-evolution
  • Links between core promoter and basic gene features influence gene expression
    BMC Genomics, Vol. 9 (25 February 2008), 92.
    by Sandra Moshonov, Rofa Elfakess, Michal Golan-Mashiach, Hadar Sinvani, Rivka Dikstein
    posted to cis-regulatory by cisevol to the group BergmanLab on 2008-02-29 09:36:38 as ** along with 1 group cis-regulatory-evolution
  • A transposable element inserted just 5' to a Drosophila glue protein gene alters gene expression and chromatin structure.
    Cell, Vol. 34, No. 1. (August 1983), pp. 75-84.
    by W McGinnis, AW Shermoen, SK Beckendorf
    posted to cis-regulatory flies transposon by cisevol to the group BergmanLab on 2007-12-01 16:48:38 as ** along with 1 group cis-regulatory-evolution
  • Repeated Recruitment of LTR Retrotransposons as Promoters by the Anti-Apoptotic Locus NAIP during Mammalian Evolution
    PLoS Genetics, Vol. 3, No. 1. (1 January 2007), e10.
    by Mark T Romanish, Wynne M Lock, Louie N de Lagemaat, Catherine A Dunn, Dixie L Mager
    posted to cis-regulatory mammals transposon by cisevol to the group BergmanLab on 2007-11-01 10:55:08 as ** along with 3 people and 3 groups dchughes Fei yoanjacquemin G4ID Genetics-of-Gambling cis-regulatory-evolution
  • Evolution of the mammalian transcription factor binding repertoire via transposable elements.
    Genome research (5 August 2008)
    by Guillaume Bourque, Bernard Leong, Vinsensius B B Vega, Xi Chen, Yen Ling L Lee, Kandhadayar G G Srinivasan, Joon-Lin L Chew, Yijun Ruan, Chia-Lin L Wei, Huck-Hui H Ng, Edison T T Liu
    posted to transposon mammals cis-regulatory by cisevol to the group BergmanLab on 2008-09-30 08:23:52 as ** along with 1 person and 1 group carlfulp cis-regulatory-evolution
  • Genome-wide B1 retrotransposon binds the transcription factors dioxin receptor and Slug and regulates gene expression in vivo.
    Proc Natl Acad Sci U S A (25 January 2008)
    by Angel Carlos C Roman, Dixan A A Benitez, Jose M M Carvajal-Gonzalez, Pedro M M Fernandez-Salguero
    posted to cis-regulatory mammals transposon by cisevol to the group BergmanLab on 2008-02-05 21:18:50 as ** along with 1 person and 1 group maximilianh cis-regulatory-evolution
  • ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation
    Bioinformatics, Vol. 22, No. 5. (1 March 2006), pp. 637-640.
    by SB Montgomery, OL Griffith, CM Bergman, M Bilenky, ED Pleasance, Y Prychyna, X Zhang, SJM Jones
    posted to cis-regulatory database by cisevol to the group BergmanLab on 2007-10-23 19:23:21 as ** along with 2 people and 2 groups yas fpattyn T_lab cis-regulatory-evolution
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