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Tag cisreg [63 articles]

Recent papers classified by the tag cisreg.
  • Effect of polymorphisms within probe-target sequences on olignonucleotide microarray experiments
    Nucl. Acids Res., Vol. 36, No. 13. (1 August 2008), pp. 4417-4423.
    by David Benovoy, Tony Kwan, Jacek Majewski
  • A mutation accumulation assay reveals a broad capacity for rapid evolution of gene expression
    Nature, Vol. 438, No. 7065., pp. 220-223.
    by Scott A Rifkin, David Houle, Junhyong Kim, Kevin P White
  • Tissue-specific transcriptional regulation has diverged significantly between human and mouse
    Nature Genetics, Vol. 39, No. 6. (21 May 2007), pp. 730-732.
    by Duncan T Odom, Robin D Dowell, Elizabeth S Jacobsen, William Gordon, Timothy W Danford, Kenzie D Macisaac, Alexander P Rolfe, Caitlin M Conboy, David K Gifford, Ernest Fraenkel
  • Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease
    Nature Genetics, Vol. 37, No. 3. (13 February 2005), pp. 243-253.
    by Norbert Hubner, Caroline A Wallace, Heike Zimdahl, Enrico Petretto, Herbert Schulz, Fiona Maciver, Michael Mueller, Oliver Hummel, Jan Monti, Vaclav Zidek, Alena Musilova, Vladimir Kren, Helen Causton, Laurence Game, Gabriele Born, Sabine Schmidt, Anita Müller, Stuart A Cook, Theodore W Kurtz, John Whittaker, Michal Pravenec, Timothy J Aitman
  • The Widespread Impact of Mammalian MicroRNAs on mRNA Repression and Evolution.
    Science (24 November 2005)
    by Kyle Kai-How K Farh, Andrew Grimson, Calvin Jan, Benjamin P P Lewis, Wendy K K Johnston, Lee P P Lim, Christopher B B Burge, David P P Bartel
  • Genome-wide promoter extraction and analysis in human, mouse, and rat.
    Genome Biol, Vol. 6, No. 8. (2005)
    by Z Xuan, F Zhao, J Wang, G Chen, MQ Zhang
    posted to cisreg promoter by caseybrown on 2008-02-13 14:57:14 as ** along with 2 people nur77 uz_labu_laimi
  • The Regulation and Evolution of a Genetic Switch Controlling Sexually Dimorphic Traits in Drosophila
    Cell, Vol. 134, No. 4. (22 August 2008), pp. 610-623.
    by Thomas M Williams, Jane E Selegue, Thomas Werner, Nicolas Gompel, Artyom Kopp, Sean B Carroll
    posted to cisreg melanogaster molevol sex by caseybrown on 2008-08-23 03:22:14 as read along with 1 person brant
  • Model-based analysis of tiling-arrays for ChIP-chip.
    Proc Natl Acad Sci U S A, Vol. 103, No. 33. (15 August 2006), pp. 12457-12462.
    by WE Johnson, W Li, CA Meyer, R Gottardo, JS Carroll, M Brown, XS Liu
  • RNA polymerase is poised for activation across the genome
    Nature Genetics, Vol. 39, No. 12. (11 November 2007), pp. 1507-1511.
    by Ginger W Muse, Daniel A Gilchrist, Sergei Nechaev, Ruchir Shah, Joel S Parker, Sherry F Grissom, Julia Zeitlinger, Karen Adelman
  • Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease
    Nat Genet, Vol. 40, No. 9. (2008), pp. 1107-1112.
    by Steven A Mccarroll, Alan Huett, Petric Kuballa, Shannon D Chilewski, Aimee Landry, Philippe Goyette, Michael C Zody, Jennifer L Hall, Steven R Brant, Judy H Cho, Richard H Duerr, Mark S Silverberg, Kent D Taylor, John D Rioux, David Altshuler, Mark J Daly, Ramnik J Xavier
    posted to cisreg crohns by caseybrown on 2008-08-28 03:23:53 as ** along with 1 person vplagnol
  • 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
  • Human-Specific Gain of Function in a Developmental Enhancer
    Science, Vol. 321, No. 5894. (5 September 2008), pp. 1346-1350.
    by Shyam Prabhakar, Axel Visel, Jennifer A Akiyama, Malak Shoukry, Keith D Lewis, Amy Holt, Ingrid Plajzer-Frick, Harris Morrison, David R Fitzpatrick, Veena Afzal, Len A Pennacchio, Edward M Rubin, James P Noonan
  • 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
  • A survey of allelic imbalance in F1 mice
    Genome Res., Vol. 18, No. 4. (1 April 2008), pp. 555-563.
    by Catarina D Campbell, Andrew Kirby, James Nemesh, Mark J Daly, Joel N Hirschhorn
    posted to cisreg mouse transcription by caseybrown on 2008-04-01 22:31:47 as read along with 1 person mimulus_99
  • Dominance and the evolutionary accumulation of cis- and trans-effects on gene expression.
    Proceedings of the National Academy of Sciences of the United States of America (12 September 2008)
    by Bernardo Lemos, Luciana O O Araripe, Pierre Fontanillas, Daniel L L Hartl
  • Divergence of Transcription Factor Binding Sites Across Related Yeast Species
    Science, Vol. 317, No. 5839. (10 August 2007), pp. 815-819.
    by Anthony R Borneman, Tara A Gianoulis, Zhengdong D Zhang, Haiyuan Yu, Joel Rozowsky, Michael R Seringhaus, Lu Y Wang, Mark Gerstein, Michael Snyder
  • Gene Network Inference via Structural Equation Modeling in Genetical Genomics Experiments.
    Genetics (3 February 2008)
    by Bing Liu, Alberto de la Fuente, Ina Hoeschele
  • Widespread Monoallelic Expression on Human Autosomes
    Science, Vol. 318, No. 5853. (16 November 2007), pp. 1136-1140.
    by Alexander Gimelbrant, John N Hutchinson, Benjamin R Thompson, Andrew Chess
  • Using ChIP-chip technology to reveal common principles of transcriptional repression in normal and cancer cells
    Genome Res. (17 March 2008), gr.074609.107.
    by Vitalina M Komashko, Luis G Acevedo, Sharon L Squazzo, Sushma S Iyengar, Alina Rabinovich, Henriette O'Geen, Roland Green, Peggy J Farnham
    posted to chip cisreg expression_array by caseybrown on 2008-03-17 21:54:43 as **
  • Serum response factor binding sites differ in three human cell types
    Genome Res., Vol. 17, No. 2. (1 February 2007), pp. 136-144.
    by Sara J Cooper, Nathan D Trinklein, Loan Nguyen, Richard M Myers
  • Use of an evolutionary model to provide evidence for a wide heterogeneity of required affinities between transcription factors and their binding sites in yeast.
    Pac Symp Biocomput (2008), pp. 489-500.
    by RW Lusk, MB Eisen
  • Genome-wide allele-specific expression analysis using Massively Parallel Signature Sequencing (MPSS) reveals cis- and trans-effects on gene expression in maize hybrid meristem tissue.
    Plant molecular biology, Vol. 66, No. 5. (March 2008), pp. 551-563.
    by M Guo, S Yang, M Rupe, B Hu, DR Bickel, L Arthur, O Smith
  • Genome-Wide Mapping of in Vivo Protein-DNA Interactions
    Science (31 May 2007), 1141319.
    by David S Johnson, Ali Mortazavi, Richard M Myers, Barbara Wold
  • Evolvability and hierarchy in rewired bacterial gene networks
    Nature, Vol. 452, No. 7189. (17 April 2008), pp. 840-845.
    by Mark Isalan, Caroline Lemerle, Konstantinos Michalodimitrakis, Carsten Horn, Pedro Beltrao, Emanuele Raineri, Mireia Garriga-Canut, Luis Serrano
  • Fine mapping of regulatory loci for mammalian gene expression using radiation hybrids
    Nat Genet, Vol. 40, No. 4. (April 2008), pp. 421-429.
    by Christopher C Park, Sangtae Ahn, Joshua S Bloom, Andy Lin, Richard T Wang, Tongtong Wu, Aswin Sekar, Arshad H Khan, Christine J Farr, Aldons J Lusis, Richard M Leahy, Kenneth Lange, Desmond J Smith
    posted to cisreg eqtl mouse transcription by caseybrown on 2008-03-27 15:20:09 as read along with 1 person parkcc
  • 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
  • Genome wide prediction of HNF4alpha functional binding sites by the use of local and global sequence context
    Genome Biology, Vol. 9 (21 February 2008), R36.
    by Alexander E Kel, Monika Niehof, Volker Matys, Rudiger Zemlin, Jurgen Borlak
    posted to cisreg liver by caseybrown on 2008-03-12 18:46:16 as ** along with 2 people heliopais ptrobajo
  • Evolutionary plasticity of genetic interaction networks
    Nat Genet, Vol. 40, No. 4. (April 2008), pp. 390-391.
    by Julia Tischler, Ben Lehner, Andrew G Fraser
  • Concurrent Fast and Slow Cycling of a Transcriptional Activator at an Endogenous Promoter
    Science, Vol. 319, No. 5862. (25 January 2008), pp. 466-469.
    by Tatiana S Karpova, Min J Kim, Corentin Spriet, Kip Nalley, Timothy J Stasevich, Zoulika Kherrouche, Laurent Heliot, James G Mcnally
    posted to cisreg transcription by caseybrown on 2008-02-02 22:06:44 as read along with 3 people djkt margaritis cjeans
  • Evolution of gene expression in the Drosophila melanogaster subgroup.
    Nat Genet, Vol. 33, No. 2. (February 2003), pp. 138-144.
    by SA Rifkin, J Kim, KP White
  • Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing.
    Nat Methods (11 June 2007)
    by Gordon Robertson, Martin Hirst, Matthew Bainbridge, Misha Bilenky, Yongjun Zhao, Thomas Zeng, Ghia Euskirchen, Bridget Bernier, Richard Varhol, Allen Delaney, Nina Thiessen, Obi L L Griffith, Ann He, Marco Marra, Michael Snyder, Steven Jones
  • Reliable prediction of regulator targets using 12 Drosophila genomes.
    Genome Res (7 November 2007)
    by Alexander Stark, Pouya Kheradpour, Sushmita Roy, Manolis Kellis
  • The Role of Regulatory Genes During Maize Domestication: Evidence From Nucleotide Polymorphism and Gene Expression
    Genetics, Vol. 178, No. 4. (1 April 2008), pp. 2133-2143.
    by Qiong Zhao, Anne-Celine Thuillet, Nathan K Uhlmann, Allison Weber, Antoni J Rafalski, Stephen M Allen, Scott Tingey, John Doebley
    posted to cisreg maize polymorphism by caseybrown on 2008-04-26 14:27:05 as **
  • Integrative genetic analysis of transcription modules: towards filling the gap between genetic loci and inherited traits
    Human Molecular Genetics, Vol. 15, No. 3. (1 February 2006), pp. 481-492.
    by Hongqiang Li, Hao Chen, Kenneth F Manly, Elissa J Chesler, Lu Lu, Jintao Wang, Mi Zhou, Robert W Williams, Yan Cui
    posted to cisreg eqtl by caseybrown on 2008-03-17 14:49:18 as ** along with 1 person hms
  • Genetical genomics analysis of a yeast segregant population for transcription network inference.
    Genetics, Vol. 170, No. 2. (June 2005), pp. 533-542.
    by N Bing, I Hoeschele
  • Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome.
    Nat Genet (4 February 2007)
    by Nathaniel D D Heintzman, Rhona K K Stuart, Gary Hon, Yutao Fu, Christina W W Ching, R David D Hawkins, Leah O O Barrera, Sara Van Calcar, Chunxu Qu, Keith A A Ching, Wei Wang, Zhiping Weng, Roland D D Green, Gregory E E Crawford, Bing Ren
  • A gene atlas of the mouse and human protein-encoding transcriptomes.
    Proc Natl Acad Sci U S A, Vol. 101, No. 16. (20 April 2004), pp. 6062-6067.
    by AI Su, T Wiltshire, S Batalov, H Lapp, KA Ching, D Block, J Zhang, R Soden, M Hayakawa, G Kreiman, MP Cooke, JR Walker, JB Hogenesch
  • Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures
    Nature, Vol. 450, No. 7167., pp. 219-232.
    by Alexander Stark, Michael F Lin, Pouya Kheradpour, Jakob S Pedersen, Leopold Parts, Joseph W Carlson, Madeline A Crosby, Matthew D Rasmussen, Sushmita Roy, Ameya N Deoras, Graham J Ruby, Julius Brennecke, Harvard F Curators, Berkeley, Emily Hodges, Angie S Hinrichs, Anat Caspi, Benedict Paten, Seung-Won Park, Mira V Han, Morgan L Maeder, Benjamin J Polansky, Bryanne E Robson, Stein Aerts, Jacques van Helden, Bassem Hassan, Donald G Gilbert, Deborah A Eastman, Michael Rice, Michael Weir, Matthew W Hahn, Yongkyu Park, Colin N Dewey, Lior Pachter, James W Kent, David Haussler, Eric C Lai, David P Bartel, Gregory J Hannon, Thomas C Kaufman, Michael B Eisen, Andrew G Clark, Douglas Smith, Susan E Celniker, William M Gelbart, Manolis Kellis
  • Genetic regulation of gene expression during shoot development in Arabidopsis.
    Genetics, Vol. 172, No. 2. (February 2006), pp. 1155-1164.
    by R DeCook, S Lall, D Nettleton, SH Howell
    posted to arabidopsis cisreg eqtl by caseybrown on 2008-03-18 16:13:19 as ** along with 1 person fisherp
  • Regulatory network construction in Arabidopsis by using genome-wide gene expression quantitative trait loci
    PNAS, Vol. 104, No. 5. (30 January 2007), pp. 1708-1713.
    by Joost J Keurentjes, Jingyuan Fu, Inez R Terpstra, Juan M Garcia, Guido van den Ackerveken, Basten L Snoek, Anton J Peeters, Dick Vreugdenhil, Maarten Koornneef, Ritsert C Jansen
    posted to arabidopsis cisreg eqtl by caseybrown on 2008-03-17 18:46:27 as read along with 2 people natstreet jmjimenez
  • Cis and trans regulatory effects contribute to natural variation in transcriptome of Drosophila melanogaster
    Mol Biol Evol (12 November 2007), msm247.
    by Anne Genissel, Lauren M Mcintyre, Marta L Wayne, Sergey V Nuzhdin
  • Adaptive Gene Expression Divergence Inferred from Population Genomics
    PLoS Genetics, Vol. 3, No. 10. (1 October 2007), e187.
    by Alisha K Holloway, Mara K Lawniczak, Jason G Mezey, David J Begun, Corbin D Jones
  • Genetic Properties Influencing the Evolvability of Gene Expression.
    Science (24 May 2007)
    by Christian R R Landry, Bernardo Lemos, Scott A A Rifkin, W J J Dickinson, Daniel L L Hartl
  • Global eQTL Mapping Reveals the Complex Genetic Architecture of Transcript-Level Variation in Arabidopsis
    Genetics, Vol. 175, No. 3. (1 March 2007), pp. 1441-1450.
    by Marilyn A West, Kyunga Kim, Daniel J Kliebenstein, Hans van Leeuwen, Richard W Michelmore, RW Doerge, Dina A St. Clair
  • Shadow Enhancers as a Source of Evolutionary Novelty
    Science, Vol. 321, No. 5894. (5 September 2008), 1314.
    by Joung-Woo Hong, David A Hendrix, Michael S Levine
  • 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
  • DNA motifs in human and mouse proximal promoters predict tissue-specific expression.
    Proc Natl Acad Sci U S A (10 April 2006)
    by Andrew D D Smith, Pavel Sumazin, Zhenyu Xuan, Michael Q Q Zhang
    posted to cisreg transcription by caseybrown on 2008-02-13 14:44:02 as ** along with 2 people jfr postrational
  • Selection to minimise noise in living systems and its implications for the evolution of gene expression
    Mol Syst Biol, Vol. 4 (4 March 2008)
    by Ben Lehner
  • Mapping Determinants of Gene Expression Plasticity by Genetical Genomics in C. elegans
    PLoS Genetics, Vol. 2, No. 12. (1 December 2006), e222.
    by Yang Li, Olga A Álvarez, Evert W Gutteling, Marcel Tijsterman, Jingyuan Fu, Joost A Riksen, Esther Hazendonk, Pjotr Prins, Ronald H Plasterk, Ritsert C Jansen, Rainer Breitling, Jan E Kammenga
  • On the relation between promoter divergence and gene expression evolution
    Mol Syst Biol, Vol. 4 (15 January 2008)
    by Itay Tirosh, Adina Weinberger, Dana Bezalel, Mark Kaganovich, Naama Barkai
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