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Tag cis-regulation [58 articles]

Recent papers classified by the tag cis-regulation.
  • Evolving Fractal Proteins
    Evolvable Systems: From Biology to Hardware, Vol. 2606 (2003), pp. 81-92.
    by Peter Bentley
    posted to gene-regulation gene-networks grn cis-regulation alife by mjoach on 2008-05-16 01:11:49 as read
  • Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution
    Nat Genet, Vol. 39, No. 9. (2007), pp. 1140-1144.
    by Ralph Haygood, Olivier Fedrigo, Brian Hanson, Ken-Daigoro Yokoyama, Gregory A Wray
    posted to evolution evo-devo cis-regulation by mjoach on 2008-05-14 10:55:16 as read along with 6 people and 4 groups candypmcg dchughes djkt Garamonfok mimulus_99 cisevol G4ID Genetics-of-Gambling cis-regulatory-evolution Fasting, food and evolution
  • The locus of evolution: evo devo and the genetics of adaptation
    Evolution, Vol. 61, No. 5. (2007), pp. 995-1016.
    by Hopi E Hoekstra, Jerry A Coyne
    posted to evo-devo criticism cis-regulation by mjoach on 2008-05-14 10:51:24 as read along with 8 people and 2 groups stevanspringer mcphee dpollard balicea TaqSys epigenetics jayster4 mimulus_99 EisenLab FAB-lab
  • Harnessing Morphogenesis
    Proceedings of Information Processing in Cells and Tissues (1995), pp. 29-41.
    by N Jakobi
    posted to gene-regulation gene-networks modelling grn cis-regulation ann alife by mjoach on 2008-05-16 00:39:27 as read along with 1 person and 1 group dlobo GEB
  • Structure and evolution of transcriptional regulatory networks.
    Curr Opin Struct Biol, Vol. 14, No. 3. (June 2004), pp. 283-291.
    by MM Babu, NM Luscombe, L Aravind, M Gerstein, SA Teichmann
    posted to cis-regulation evolution regulatory sequence_motif by koller on 2006-09-11 05:35:16 as ** along with 5 people and 2 groups tny kengg tvdbulck cjeans karfunkel Bioinformatics Plantandetc
  • Computational methods for transcriptional regulation.
    Curr Opin Genet Dev, Vol. 15, No. 2. (April 2005), pp. 214-221.
    by ED Siggia
    posted to cis-regulation reconstruction review sequence_motif by koller on 2006-08-25 22:26:16 as *** along with 3 people and 2 groups bertelsen barry dpollard Bioinformatics EisenLab
  • Inferring quantitative models of regulatory networks from expression data.
    Bioinformatics, Vol. 20 Suppl 1 (4 August 2004)
    by I Nachman, A Regev, N Friedman
    posted to cis-regulation dynamic network regulatory transcription by koller on 2006-08-24 01:18:10 as ** along with 4 people frohike brl wnpx apleite
  • 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-regulation crm reconstruction sequence_motif by koller on 2006-08-25 22:13:10 as *** along with 5 people and 1 group ansobol indigoviolet adepace Stew csdhwang EisenLab
  • Cis-acting expression quantitative trait loci in mice.
    Genome Res, Vol. 15, No. 5. (May 2005), pp. 681-691.
    by S Doss, EE Schadt, TA Drake, AJ Lusis
    posted to association cis-regulation network regulatory by koller on 2006-09-06 23:18:42 as ***
  • Multilevel modeling and inference of transcription regulation.
    J Comput Biol, Vol. 11, No. 2-3. (2004), pp. 357-375.
    by A Tanay, R Shamir
    posted to cis-regulation network reconstruction sequence_motif transcription by koller on 2006-08-25 21:40:09 as *** along with 1 person snuppepuppan
  • A Systems Approach to Mapping DNA Damage Response Pathways
    Science, Vol. 312, No. 5776. (19 May 2006), pp. 1054-1059.
    by Christopher T Workman, Craig H Mak, Scott Mccuine, Jean-Bosco Tagne, Maya Agarwal, Owen Ozier, Thomas J Begley, Leona D Samson, Trey Ideker
    posted to chip2 cis-regulation dna-repair reconstruction regulatory by koller on 2006-08-24 05:52:47 as **** along with 5 people tmmurali biozhang2001 jfr nirfriedman cconboy
  • Extensive low-affinity transcriptional interactions in the yeast genome.
    Genome Res (29 June 2006)
    by Amos Tanay
    posted to chip2 cis-regulation sequence_motif by koller on 2006-08-25 21:33:38 as ** along with 6 people and 1 group devin indigoviolet dpollard balicea lusk emptyhb EisenLab
  • Predicting gene expression from sequence.
    Cell, Vol. 117, No. 2. (16 April 2004), pp. 185-198.
    by MA Beer, S Tavazoie
    posted to bayesian cis-regulation reconstruction sequence_motif by koller on 2006-08-25 01:40:13 as **** along with 7 people and 4 groups ana xwbcn adepace nickluscombe noano jrest phoenixzxl structural_bioinformatics Bioinformatics EisenLab EBI-regulation
  • A global view of the selection forces in the evolution of yeast cis-regulation.
    Genome Res, Vol. 14, No. 5. (May 2004), pp. 829-834.
    by A Tanay, I Gat-Viks, R Shamir
    posted to cis-regulation evolution network by koller on 2006-08-25 21:25:12 as **** along with 2 people carlk briann
  • Transcriptional regulatory code of a eukaryotic genome
    Nature, Vol. 431, No. 7004. (2004), pp. 99-104.
    by Christopher T Harbison, Benjamin D Gordon, Tong I Lee, Nicola J Rinaldi, Kenzie D Macisaac, Timothy W Danford, Nancy M Hannett, Jean-Bosco Tagne, David B Reynolds, Jane Yoo, Ezra G Jennings, Julia Zeitlinger, Dmitry K Pokholok, Manolis Kellis, Alex P Rolfe, Ken T Takusagawa, Eric S Lander, David K Gifford, Ernest Fraenkel, Richard A Young
    posted to chip2 cis-regulation network regulatory transcription by koller on 2006-09-19 01:50:34 as ** along with 22 people and 8 groups kristallreiner mariakmejia brant alokm tuck chad_davis lyongu kaspermunch dpollard balicea kt dchughes nirfriedman cmm nickluscombe kengg gespim lusk nklee cisevol njcitulike xili03 Bioinformatics EisenLab FAB-lab G4ID EBI-regulation Plantandetc Genetics-of-Gambling BergmanLab
  • Histone acetylation and transcriptional regulation in the genome of Saccharomyces cerevisiae
    Bioinformatics, Vol. 22, No. 4. (15 February 2006), pp. 392-399.
    by Xiang Guo, Kay Tatsuoka, Rongxiang Liu
    posted to chromatin cis-regulation regulatory by koller on 2006-09-19 01:48:54 as ** along with 2 people and 1 group nirfriedman kengg Plantandetc
  • Deciphering principles of transcription regulation in eukaryotic genomes
    Mol Syst Biol, Vol. 2, No. 1. (11 April 2006), pp. msb4100054-E1-msb4100054-E10.
    by Dat H Nguyen, Patrik D'Haeseleer
    posted to regulatory sequence_motif transcription cis-regulation by koller on 2006-08-30 22:45:22 as ** along with 5 people and 2 groups isimpson okarsligil pau reidy mikaelhuss Bioinformatics RNAtransport
  • Core transcriptional regulatory circuitry in human hepatocytes.
    Mol Syst Biol, Vol. 2 (2006)
    by DT Odom, RD Dowell, ES Jacobsen, L Nekludova, PA Rolfe, TW Danford, DK Gifford, E Fraenkel, GI Bell, RA Young
    posted to cis-regulation network network_motif regulatory by koller on 2006-09-19 01:35:52 as ** along with 4 people and 1 group Schmidtc cconboy kengg jdiggans Plantandetc
  • 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 chip2 cis-regulation network network_motif reconstruction by koller on 2006-08-25 21:02:21 as *** along with 12 people dquest provero brant rklancer kentsis tardigrade balicea tabu cconboy faisalm mikaelhuss tdmckee
  • Identifying regulatory networks by combinatorial analysis of promoter elements.
    Nat Genet, Vol. 29, No. 2. (October 2001), pp. 153-159.
    by Y Pilpel, P Sudarsanam, GM Church
    posted to cis-regulation expression modules sequence_motif by koller on 2006-08-31 07:10:12 as ** along with 7 people and 1 group windman83 ihpark imouthesmp troels_marstrand xwbcn wnpx noano Bioinformatics
  • Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs.
    Genome Res, Vol. 14, No. 6. (June 2004), pp. 1107-1118.
    by H Yu, NM Luscombe, HX Lu, X Zhu, Y Xia, JD Han, N Bertin, S Chung, M Vidal, M Gerstein
    posted to cis-regulation evolution network p2p regulatory by koller on 2006-09-23 01:56:15 as ** along with 4 people dragonrez chad_davis balajis cjeans
  • Whole-Genome Discovery of Transcription Factor Binding Sites by Network-Level Conservation
    Genome Res., Vol. 14, No. 1. (1 January 2004), pp. 99-108.
    by Moshe Pritsker, Yir-Chung Liu, Michael A Beer, Saeed Tavazoie
    posted to cis-regulation evolution network reconstruction by koller on 2006-08-25 23:09:47 as ** along with 1 person kaarsinogen
  • Linking DNA-binding proteins to their recognition sequences by using protein microarrays.
    Proc Natl Acad Sci U S A (19 June 2006)
    by Su-Wen W Ho, Ghil Jona, Christina T L T Chen, Mark Johnston, Michael Snyder
    posted to chip2 cis-regulation sequence_motif transcription by koller on 2006-08-31 01:31:53 as ** along with 4 people and 3 groups emilyhare samal nickluscombe kengg EisenLab EBI-regulation Plantandetc
  • Computational discovery of gene modules and regulatory networks.
    Nat Biotechnol, Vol. 21, No. 11. (November 2003), pp. 1337-1342.
    by Z Bar-Joseph, GK Gerber, TI Lee, NJ Rinaldi, JY Yoo, F Robert, DB Gordon, E Fraenkel, TS Jaakkola, RA Young, DK Gifford
    posted to chip2 cis-regulation network reconstruction transcription by koller on 2006-08-26 02:17:54 as ** along with 12 people and 1 group balicea dquest carlk tvdbulck ggrot dragonrez bayesian wnpx nickluscombe frohike karfunkel roys EBI-regulation
  • Transcriptional regulatory networks in Saccharomyces cerevisiae.
    Science, Vol. 298, No. 5594. (25 October 2002), pp. 799-804.
    by TI Lee, NJ Rinaldi, F Robert, DT Odom, Z Bar-Joseph, GK Gerber, NM Hannett, CT Harbison, CM Thompson, I Simon, J Zeitlinger, EG Jennings, HL Murray, DB Gordon, B Ren, JJ Wyrick, JB Tagne, TL Volkert, E Fraenkel, DK Gifford, RA Young
    posted to chip2 cis-regulation network reconstruction transcription by koller on 2006-08-26 02:17:09 as *** along with 23 people and 2 groups Borelli kristallreiner brant camster snuppepuppan icases forluvoft ggrot alokm opheliav samal sameetmehta cconboy jguinney franklin timflutre jpoyatos lusk nklee karfunkel mimulus_99 roys njcitulike dbk-lab TNT
  • Genomic Regulatory Systems: Development and Evolution
    (15 February 2001)
    by Eric H Davidson
    posted to cis-regulation reference by indigoviolet on 2007-11-19 02:39:55 as ** along with 2 people and 1 group dpollard balicea EisenLab
  • Noncoding RNAs of Trithorax Response Elements Recruit Drosophila Ash1 to Ultrabithorax.
    Science, Vol. 311, No. 5764. (24 February 2006), pp. 1118-1123.
    by T Sanchez-Elsner, D Gou, E Kremmer, F Sauer
    posted to cis-regulation drosophila microrna transcription by indigoviolet on 2006-02-26 00:50:46 as **** along with 2 people and 1 group mtagaya gsrats EisenLab
  • Regulation of an intergenic transcript controls adjacent gene transcription in Saccharomyces cerevisiae
    Genes Dev., Vol. 19, No. 22. (15 November 2005), pp. 2695-2704.
    by Joseph A Martens, Pei-Yun J Wu, Fred Winston
    posted to cis-regulation enhancer intergenic transcription yeast by indigoviolet on 2005-11-16 22:58:58 as ** along with 1 person and 1 group dpollard EisenLab
  • A probabilistic method to detect regulatory modules.
    Bioinformatics, Vol. 19 Suppl 1 (2003)
    by S Sinha, E van Nimwegen, ED Siggia
    posted to algorithm cis-regulation clustering comparative computational by indigoviolet on 2007-11-19 03:27:58 as ** along with 3 people and 2 groups dquest lusk cisevol EisenLab cis-regulatory-evolution
  • Ancient and Recent Positive Selection Transformed Opioid cis-Regulation in Humans.
    PLoS Biol, Vol. 3, No. 12. (15 November 2005)
    by Matthew V V Rockman, Matthew W W Hahn, Nicole Soranzo, Fritz Zimprich, David B B Goldstein, Gregory A A Wray
    posted to cis-regulation constraint human positive selection by indigoviolet on 2005-11-14 19:51:17 as *** along with 8 people and 3 groups jphekman imouthesmp dpollard Archaeogenetics happy_manatee djkt mgaldzic cisevol EisenLab CHIP cis-regulatory-evolution
  • IEM: An Algorithm for Iterative Enhancement of Motifs Using Comparative Genomics Data.
    Comput Syst Bioinformatics Conf, Vol. 6 (2007), pp. 227-235.
    by E Zeng, K Mathee, G Narasimhan
    posted to cis-regulation conserved tfbs tool by idonaldson on 2007-10-29 10:04:48 as *** along with 3 people isimpson maximilianh annacarina07
  • The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells
    Nature Genetics, Vol. 38, No. 4. (05 March 2006), pp. 431-440.
    by Yuin-Han Loh, Qiang Wu, Joon-Lin Chew, Vinsensius B Vega, Weiwei Zhang, Xi Chen, Guillaume Bourque, Joshy George, Bernard Leong, Jun Liu, Kee-Yew Wong, Ken W Sung, Charlie WH Lee, Xiao-Dong Zhao, Kuo-Ping Chiu, Leonard Lipovich, Vladimir A Kuznetsov, Paul Robson, Lawrence W Stanton, Chia-Lin Wei, Yijun Ruan, Bing Lim, Huck-Hui Ng
    posted to tfbs cis-regulation mouse networks stem-cells by idonaldson on 2007-10-24 10:11:38 as *** along with 9 people MllePapillon jyuh cmmorel gpalidwor brixtonmc vega eukfn mikaelhuss tdmckee
  • Systematic functional characterization of cis-regulatory motifs in human core promoters
    Genome Res. (6 February 2008), gr.6828808.
    by Saurabh Sinha, Adam S Adler, Yair Field, Howard Y Chang, Eran Segal
    posted to cis-regulation motif promoter by idonaldson on 2008-02-20 08:58:19 as *** along with 7 people isimpson ihpark gracio ealloza lp2 cabbagezs emptyhb
  • Analysis of multiple genomic sequence alignments: a web resource, online tools, and lessons learned from analysis of mammalian SCL loci.
    Genome Res, Vol. 14, No. 2. (February 2004), pp. 313-318.
    by MA Chapman, IJ Donaldson, J Gilbert, D Grafham, J Rogers, AR Green, B Göttgens
    posted to alignment cis-regulation me tfbs tool by idonaldson on 2007-10-19 12:58:15 as read
  • Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication.
    Nucleic Acids Res, Vol. 34, No. 14. (2006), pp. 3862-3877.
    by R Johnson, RJ Gamblin, L Ooi, AW Bruce, IJ Donaldson, DR Westhead, IC Wood, RM Jackson, NJ Buckley
    posted to cis-regulation matrix re1 te by idonaldson on 2007-10-18 17:08:41 as read along with 2 people and 2 groups cisevol RaquelSL cis-regulatory-evolution BergmanLab
  • Genome-wide analysis of repressor element 1 silencing transcription factor/neuron-restrictive silencing factor (REST/NRSF) target genes.
    Proc Natl Acad Sci U S A, Vol. 101, No. 28. (13 July 2004), pp. 10458-10463.
    by AW Bruce, IJ Donaldson, IC Wood, SA Yerbury, MI Sadowski, M Chapman, B Göttgens, NJ Buckley
    posted to cis-regulation me tfbs tool by idonaldson on 2007-10-19 12:54:15 as read
  • Evolution of candidate transcriptional regulatory motifs since the human-chimpanzee divergence
    Genome Biology, Vol. 7 (29 June 2006), R52.
    by Ian J Donaldson, Berthold Göttgens
    posted to chimp cis-regulation evolution human me tfbs by idonaldson on 2007-10-18 15:58:36 as read along with 4 people and 2 groups indigoviolet ranb djkt cisevol EisenLab cis-regulatory-evolution
  • TFBScluster web server for the identification of mammalian composite regulatory elements.
    Nucleic Acids Res, Vol. 34, No. Web Server issue. (1 July 2006)
    by IJ Donaldson, B Göttgens
    posted to cis-regulation crm me tfbs tool by idonaldson on 2007-10-19 12:51:59 as read
  • A Profile-Based Deterministic Sequential Monte Carlo Algorithm for Motif Discovery.
    Bioinformatics (17 November 2007)
    by Kuo-Ching C Liang, Xiaodong Wang, Dimitris Anastassiou
    posted to cis-regulation tfbs tool by idonaldson on 2007-11-27 14:46:52 as ** along with 5 people and 1 group isimpson grahamc cjeans nklee maximilianh Motif Discovery
  • TFBScluster: a resource for the characterization of transcriptional regulatory networks.
    Bioinformatics, Vol. 21, No. 13. (1 July 2005), pp. 3058-3059.
    by IJ Donaldson, M Chapman, B Göttgens
    posted to cis-regulation crm me tfbs tool by idonaldson on 2007-10-19 12:48:27 as read along with 1 person dquest
  • OSCAR: One-class SVM for Accurate Recognition of Cis-elements
    Bioinformatics (5 October 2007), btm473.
    by Bo Jiang, Michael Q Zhang, Xuegong Zhang
    posted to cis-regulation tfbs tool by idonaldson on 2007-11-27 14:42:52 as *** along with 6 people and 1 group isimpson cassj tmmurali chad_davis cabbagezs maximilianh csb_journal_club_public
  • Identifying tissue-selective transcription factor binding sites in vertebrate promoters.
    Proc Natl Acad Sci U S A, Vol. 102, No. 5. (1 February 2005), pp. 1560-1565.
    by AD Smith, P Sumazin, MQ Zhang
    posted to cis-regulation promoter tfbs tool by idonaldson on 2007-10-24 09:14:11 as read along with 1 person heliopais
  • Cross-species de novo identification of cis-regulatory modules with GibbsModule: application to gene regulation in embryonic stem cells
    Genome Res. (15 May 2008), gr.072769.107.
    by Dan Xie, Jun Cai, Na-Yu Chia, Huck Ng, Sheng Zhong
    posted to tool motif-discovery crm cis-regulation by idonaldson on 2008-05-27 09:53:11 as *** along with 3 people isimpson GustavoLacerda ihpark
  • Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes
    Genome Biology, Vol. 9 (15 February 2008), R34.
    by Par G Engstrom, David Fredman, Boris Lenhard
    posted to cis-regulation conserved tool by idonaldson on 2008-02-25 10:25:05 as *** along with 5 people isimpson boudinot brant natstreet heliopais
  • CoMoDis: composite motif discovery in mammalian genomes.
    Nucleic Acids Res, Vol. 35, No. 1. (2007)
    by IJ Donaldson, B Göttgens
    posted to cis-regulation me motif-discovery tfbs tool by idonaldson on 2007-10-18 16:41:50 as read along with 1 person and 1 group csdhwang Bioinformatics
  • Genome-wide identification of cis-regulatory sequences controlling blood and endothelial development.
    Hum Mol Genet, Vol. 14, No. 5. (1 March 2005), pp. 595-601.
    by IJ Donaldson, M Chapman, S Kinston, JR Landry, K Knezevic, S Piltz, N Buckley, AR Green, B Göttgens
    posted to cis-regulation me tfbs transgenic by idonaldson on 2007-10-19 12:45:13 as read
  • Gata2, Fli1, and Scl form a recursively wired gene-regulatory circuit during early hematopoietic development.
    Proc Natl Acad Sci U S A (25 October 2007)
    by John E E Pimanda, Katrin Ottersbach, Kathy Knezevic, Sarah Kinston, Wan Y I Y Chan, Nicola K K Wilson, Josette-Renée R Landry, Andrew D D Wood, Anja Kolb-Kokocinski, Anthony R R Green, David Tannahill, Georges Lacaud, Valerie Kouskoff, Berthold Göttgens
    posted to cis-regulation crm gottgens haematopoiesis networks tfbs by idonaldson on 2007-10-29 10:30:29 as *** along with 2 people jjray maximilianh
  • MotifCombinator: a web-based tool to search for combinations of cis-regulatory motifs
    BMC Bioinformatics, Vol. 8 (22 March 2007), 100.
    by Mamoru Kato, Tatsuhiko Tsunoda
    posted to cis-regulation crm tool by idonaldson on 2007-11-06 09:15:33 as **** along with 3 people and 1 group isimpson cwbrown nklee EisenLab
  • MyoD uses overlapping but distinct elements to bind E-box and tetraplex structures of regulatory sequences of muscle-specific genes.
    Nucleic Acids Res (16 October 2007)
    by Jeny Shklover, Shulamit Etzioni, Pnina Weisman-Shomer, Anat Yafe, Eyal Bengal, Michael Fry
    posted to cis-regulation ebox muscle myod tfbs by idonaldson on 2007-10-22 09:23:27 as *** along with 1 person and 1 group jmrivort G-quadruplex
  • Statistical power of phylo-HMM for evolutionarily conserved element detection
    BMC Bioinformatics, Vol. 8 (05 October 2007), 374.
    by Xiaodan Fan, Jun Zhu, Eric E Schadt, Jun S Liu
    posted to cis-regulation conserved hmm by idonaldson on 2007-10-19 13:13:19 as *** along with 2 people and 1 group isimpson pradiptaray BergmanLab
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