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Tag genome-wide [137 articles]

Recent papers classified by the tag genome-wide.
  • Genome-wide transcriptional plasticity underlies cellular adaptation to novel challenge
    Mol Syst Biol, Vol. 3 (24 April 2007)
    by Shay Stern, Tali Dror, Elad Stolovicki, Naama Brenner, Erez Braun
    posted to genome-wide transcription by zwang on 2007-04-24 16:59:02 as * along with 2 people Retchless kynn
  • An optimized split-ubiquitin cDNA-library screening system to identify novel interactors of the human Frizzled 1 receptor
    Nucl. Acids Res., Vol. 36, No. 6. (1 April 2008), e37.
    by Dietmar Dirnberger, Monika Messerschmid, Ralf Baumeister
    posted to interaction human genome-wide by zwang on 2008-05-14 12:10:35 as **
  • Mammalian RNA polymerase II core promoters: insights from genome-wide studies
    Nature Reviews Genetics, Vol. 8, No. 6. (08 May 2007), pp. 424-436.
    by Albin Sandelin, Piero Carninci, Boris Lenhard, Jasmina Ponjavic, Yoshihide Hayashizaki, David A Hume
  • Genome-wide transcription and the implications for genomic organization.
    Nat Rev Genet (8 May 2007)
    by Philipp Kapranov, Aarron T T Willingham, Thomas R R Gingeras
  • Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution
    Nature, Vol. 449, No. 7158., pp. 83-86.
    by Debbie Lindell, Jacob D Jaffe, Maureen L Coleman, Matthias E Futschik, Ilka M Axmann, Trent Rector, Gregory Kettler, Matthew B Sullivan, Robert Steen, Wolfgang R Hess, George M Church, Sallie W Chisholm
    posted to co-evolution genome-wide by zwang on 2007-09-06 15:07:45 as *** along with 2 people dayjm mellabee
  • Where have all the interactions gone? Estimating the coverage of two-hybrid protein interaction maps
    PLoS Computational Biology, Vol. preprint, No. 2007. (1 September 2007), e214.eor.
    by Hailiang Huang, Bruno Jedynak, Joel S Bader
    posted to genome-wide interaction protein y2h yeast by zwang on 2007-10-22 05:10:19 as **
  • Genome-wide mapping of allele-specific protein-DNA interactions in human cells
    Nature Methods, Vol. 5, No. 4. (16 March 2008), pp. 307-309.
    by Nathaniel D Maynard, Jing Chen, Rhona K Stuart, Jian-Bing Fan, Bing Ren
    posted to dna genome-wide interaction protein by zwang on 2008-04-02 07:26:10 as ** along with 1 person jyuh
  • Genome-wide profiling of DNA methylation reveals a class of normally methylated CpG island promoters.
    PLoS Genet, Vol. 3, No. 10. (26 October 2007), pp. 2023-2036.
    by L Shen, Y Kondo, Y Guo, J Zhang, L Zhang, S Ahmed, J Shu, X Chen, RA Waterland, JP Issa
  • Genome-wide prediction of matrix attachment regions that increase gene expression in mammalian cells
    Nat Meth, Vol. 4, No. 9. (2007), pp. 747-753.
    by Pierre-Alain Girod, Duc-Quang Nguyen, David Calabrese, Stefania Puttini, Melanie Grandjean, Danielle Martinet, Alexandre Regamey, Damien Saugy, Jacques S Beckmann, Philipp Bucher, Nicolas Mermod
  • Genome-Wide Profiling and Analysis of Arabidopsis siRNAs
    PLoS Biology, Vol. 5, No. 3. (1 March 2007), e57.
    by Kristin D Kasschau, Noah Fahlgren, Elisabeth J Chapman, Christopher M Sullivan, Jason S Cumbie, Scott A Givan, James C Carrington
    posted to genome-wide rna by zwang on 2007-04-19 15:08:21 as *
  • Using Phylogeny to Improve Genome-Wide Distant Homology Recognition
    PLoS Computational Biology, Vol. 3, No. 1. (1 January 2007), e3.
    by Sanne Abeln, Carlo Teubner, Charlotte M Deane
    posted to genome-wide homology phylogeny by zwang on 2007-04-12 10:35:42 as ****
  • The road to genome-wide association studies.
    Nat Rev Genet (19 February 2008)
    by Leonid Kruglyak
    posted to genome-wide by zwang on 2008-03-20 13:03:35 as ** along with 4 people jyuh mingzhi marpin ptrobajo
  • Estimating the size of the human interactome
    Proceedings of the National Academy of Sciences (12 May 2008), 0708078105.
    by Michael P Stumpf, Thomas Thorne, Eric de Silva, Ronald Stewart, Hyeong J An, Michael Lappe, Carsten Wiuf
  • A genome-scale computational study of the interplay between transcriptional regulation and metabolism
    Mol Syst Biol, Vol. 3 (17 April 2007)
    by Tomer Shlomi, Yariv Eisenberg, Roded Sharan, Eytan Ruppin
    posted to genome-wide regulation transcription by zwang on 2007-04-17 17:25:33 as ** along with 1 person dylan77
  • Genome-wide approaches to studying chromatin modifications
    Nat Rev Genet, Vol. 9, No. 3. (March 2008), pp. 179-191.
    by Dustin E Schones, Keji Zhao
  • Genome-wide analyses reveal properties of redundant and specific promoter occupancy within the ETS gene family
    Genes Dev., Vol. 21, No. 15. (1 August 2007), pp. 1882-1894.
    by Peter C Hollenhorst, Atul A Shah, Christopher Hopkins, Barbara J Graves
  • Toward simpler and faster genome-wide mutagenesis in mice
    Nature Genetics, Vol. 39, No. 7. (17 June 2007), pp. 922-930.
    by Sen Wu, Guoxin Ying, Qiang Wu, Mario R Capecchi
    posted to genome-wide mutation by zwang on 2007-08-28 03:54:37 as * along with 1 person zyfoo
  • Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation
    Science, Vol. 319, No. 5866. (22 February 2008), pp. 1100-1104.
    by Jun Z Li, Devin M Absher, Hua Tang, Audrey M Southwick, Amanda M Casto, Sohini Ramachandran, Howard M Cann, Gregory S Barsh, Marcus Feldman, Luigi L Cavalli-Sforza, Richard M Myers
  • Genome-wide analysis identifies a general requirement for polarity proteins in endocytic traffic
    Nature Cell Biology, Vol. 9, No. 9. (19 August 2007), pp. 1066-1073.
    by Zita Balklava, Saumya Pant, Hanna Fares, Barth D Grant
    posted to genome-wide protein by zwang on 2007-09-04 12:58:26 as *
  • A genome-wide analysis in Saccharomyces cerevisiae demonstrates the influence of chromatin modifiers on transcription
    Nature Genetics, Vol. 39, No. 3. (26 February 2007), pp. 303-309.
    by Israel Steinfeld, Ron Shamir, Martin Kupiec
    posted to chromatin genome-wide transcription yeast by zwang on 2007-03-19 13:32:22 as **
  • New models of collaboration in genome-wide association studies: the Genetic Association Information Network
    Nat Genet, Vol. 39, No. 9. (2007), pp. 1045-1051.
  • The past, present and future of genome-wide re-annotation.
    Genome Biol, Vol. 3, No. 2. (2002)
    by CA Ouzounis, PD Karp
    posted to bioinformatics genome-wide re-annotation by ziquje on 2005-02-08 17:48:44 as **
  • Origin of phenotypes: Genes and transcripts.
    Genome Res, Vol. 17, No. 6. (June 2007), pp. 682-690.
    by TR Gingeras
  • Statistical significance of cis-regulatory modules
    BMC Bioinformatics, Vol. 8, No. 1. (2007)
    by Dustin Schones, Andrew Smith, Michael Zhang
  • Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome.
    Cell, Vol. 128, No. 6. (23 March 2007), pp. 1231-1245.
    by TH Kim, ZK Abdullaev, AD Smith, KA Ching, DI Loukinov, RD Green, MQ Zhang, VV Lobanenkov, B Ren
  • Integrating physical and genetic maps: from genomes to interaction networks
    Nature Reviews Genetics, Vol. 8, No. 9., pp. 699-710.
    by Andreas Beyer, Sourav Bandyopadhyay, Trey Ideker
  • Large-scale, saturating insertional mutagenesis of the mouse genome.
    Proc Natl Acad Sci U S A (24 August 2007)
    by Alexander Gragerov, Kyoji Horie, Maria Pavlova, Linda Madisen, Hongkui Zeng, Galina Gragerova, Alex Rhode, Io Dolka, Patricia Roth, Amanda Ebbert, Stephanie Moe, Christopher Navas, Eric Finn, John Bergmann, Demetrios K K Vassilatis, George N N Pavlakis, George A A Gaitanaris
  • Direct isolation and identification of promoters in the human genome.
    Genome Res, Vol. 15, No. 6. (June 2005), pp. 830-839.
    by TH Kim, LO Barrera, C Qu, S Van Calcar, ND Trinklein, SJ Cooper, RM Luna, CK Glass, MG Rosenfeld, RM Myers, B Ren
    posted to genome-wide pic promoter by sebastien_vigneau on 2007-07-24 14:59:10 as ***
  • The Binding Sites for the Chromatin Insulator Protein CTCF Map to DNA Methylation-Free Domains Genome-Wide
    Genome Res., Vol. 14, No. 8. (1 August 2004), pp. 1594-1602.
    by Rituparna Mukhopadhyay, Wenqiang Yu, Joanne Whitehead, Junwang Xu, Magda Lezcano, Svetlana Pack, Chandrasekhar Kanduri, Meena Kanduri, Vasudeva Ginjala, Alexander Vostrov, Wolfgang Quitschke, Igor Chernukhin, Elena Klenova, Victor Lobanenkov, Rolf Ohlsson
  • Genome-Wide Analysis of Protein-DNA Interactions.
    Annu Rev Genomics Hum Genet, Vol. 7 (2006), pp. 81-102.
    by TH Kim, B Ren
  • Meiotic crossover hotspots contained in haplotype block boundaries of the mouse genome.
    Proc Natl Acad Sci U S A (9 August 2007)
    by Liisa Kauppi, Maria Jasin, Scott Keeney
  • Distinguishing protein-coding and noncoding genes in the human genome
    Proceedings of the National Academy of Sciences (26 November 2007), 0709013104.
    by Michele Clamp, Ben Fry, Mike Kamal, Xiaohui Xie, James Cuff, Michael F Lin, Manolis Kellis, Kerstin Lindblad-Toh, Eric S Lander
  • Prediction of Gene Expression in Embryonic Structures of Drosophila melanogaster
    PLoS Computational Biology, Vol. 3, No. 7. (1 July 2007), e144.
    by Anastasia A Samsonova, Mahesan Niranjan, Steven Russell, Alvis Brazma
  • Quantitative analysis of cell nucleus organisation.
    PLoS Comput Biol, Vol. 3, No. 7. (27 July 2007)
    by C Shiels, NM Adams, SA Islam, DA Stephens, PS Freemont
  • Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification.
    Nucleic Acids Res (7 August 2007)
    by Thomas E E Royce, Joel S S Rozowsky, Mark B B Gerstein
  • High-resolution profiling of histone methylations in the human genome.
    Cell, Vol. 129, No. 4. (18 May 2007), pp. 823-837.
    by A Barski, S Cuddapah, K Cui, TY Roh, DE Schones, Z Wang, G Wei, I Chepelev, K Zhao
  • A high-resolution map of active promoters in the human genome
    Nature (29 June 2005)
    by Tae H Kim, Leah O Barrera, Ming Zheng, Chunxu Qu, Michael A Singer, Todd A Richmond, Yingnian Wu, Roland D Green, Bing Ren
  • Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
    Nature (01 July 2007)
    by Tarjei S Mikkelsen, Manching Ku, David B Jaffe, Biju Issac, Erez Lieberman, Georgia Giannoukos, Pablo Alvarez, William Brockman, Tae-Kyung Kim, Richard P Koche, William Lee, Eric Mendenhall, Aisling O’donovan, Aviva Presser, Carsten Russ, Xiaohui Xie, Alexander Meissner, Marius Wernig, Rudolf Jaenisch, Chad Nusbaum, Eric S Lander, Bradley E Bernstein
  • Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites.
    Proc Natl Acad Sci U S A, Vol. 104, No. 17. (24 April 2007), pp. 7145-7150.
  • Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs.
    PLoS Genet, Vol. 2, No. 4. (April 2006)
    posted to annotation cdna genome-wide mouse transcriptome by raylim on 2008-03-08 23:22:51 as **
  • Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs
    Nature, Vol. 420 (December 2002), pp. 563-573.
    posted to annotation cdna genome-wide mouse transcriptome by raylim on 2008-03-08 23:20:00 as **
  • Integrative annotation of 21,037 human genes validated by full-length cDNA clones.
    PLoS Biol, Vol. 2, No. 6. (June 2004)
    by T Imanishi, T Itoh, Y Suzuki, C O'Donovan, S Fukuchi, KO Koyanagi, RA Barrero, T Tamura, Y Yamaguchi-Kabata, M Tanino, K Yura, S Miyazaki, K Ikeo, K Homma, A Kasprzyk, T Nishikawa, M Hirakawa, J Thierry-Mieg, D Thierry-Mieg, J Ashurst, L Jia, M Nakao, MA Thomas, N Mulder, Y Karavidopoulou, L Jin, S Kim, T Yasuda, B Lenhard, E Eveno, Y Suzuki, C Yamasaki, J Takeda, C Gough, P Hilton, Y Fujii, H Sakai, S Tanaka, C Amid, M Bellgard, Mde F Bonaldo, H Bono, SK Bromberg, AJ Brookes, E Bruford, P Carninci, C Chelala, C Couillault, SJ de Souza, MA Debily, MD Devignes, I Dubchak, T Endo, A Estreicher, E Eyras, K Fukami-Kobayashi, GR Gopinath, E Graudens, Y Hahn, M Han, ZG Han, K Hanada, H Hanaoka, E Harada, K Hashimoto, U Hinz, M Hirai, T Hishiki, I Hopkinson, S Imbeaud, H Inoko, A Kanapin, Y Kaneko, T Kasukawa, J Kelso, P Kersey, R Kikuno, K Kimura, B Korn, V Kuryshev, I Makalowska, T Makino, S Mano, R Mariage-Samson, J Mashima, H Matsuda, HW Mewes, S Minoshima, K Nagai, H Nagasaki, N Nagata, R Nigam, O Ogasawara, O Ohara, M Ohtsubo, N Okada, T Okido, S Oota, M Ota, T Ota, T Otsuki, D Piatier-Tonneau, A Poustka, SX Ren, N Saitou, K Sakai, S Sakamoto, R Sakate, I Schupp, F Servant, S Sherry, R Shiba, N Shimizu, M Shimoyama, AJ Simpson, B Soares, C Steward, M Suwa, M Suzuki, A Takahashi, G Tamiya, H Tanaka, T Taylor, JD Terwilliger, P Unneberg, V Veeramachaneni, S Watanabe, L Wilming, N Yasuda, HS Yoo, M Stodolsky, W Makalowski, M Go, K Nakai, T Takagi, M Kanehisa, Y Sakaki, J Quackenbush, Y Okazaki, Y Hayashizaki, W Hide, R Chakraborty, K Nishikawa, H Sugawara, Y Tateno, Z Chen, M Oishi, P Tonellato, R Apweiler, K Okubo, L Wagner, S Wiemann, RL Strausberg, T Isogai, C Auffray, N Nomura, T Gojobori, S Sugano
  • Identification and Classification of Conserved RNA Secondary Structures in the Human Genome.
    PLoS Comput Biol, Vol. 2, No. 4. (21 April 2006)
    by Jakob Skou S Pedersen, Gill Bejerano, Adam Siepel, Kate Rosenbloom, Kerstin Lindblad-Toh, Eric S S Lander, Jim Kent, Webb Miller, David Haussler
  • Local RNA base pairing probabilities in large sequences
    Bioinformatics, Vol. 22, No. 5. (1 March 2006), pp. 614-615.
    by Stephan H Bernhart, Ivo L Hofacker, Peter F Stadler
    posted to genome-wide rna_folding by raylim on 2008-03-08 23:03:02 as ** along with 1 person ilh
  • Prediction of locally stable RNA secondary structures for genome-wide surveys.
    Bioinformatics, Vol. 20, No. 2. (22 January 2004), pp. 186-190.
    posted to genome-wide rna_folding by raylim on 2008-03-08 23:00:33 as ** along with 2 people evaf ilh
  • Family-based vs. unrelated case-control designs for genetic associations
    PLoS Genetics, Vol. preprint, No. 2006. (1 June 2006), e123.eor.
    by Evangelos Evangelou, Thomas Trikalinos, Georgia Salanti, John P Ioannidis
    posted to association genome-wide mapping by oilcan on 2006-08-09 18:51:48 as ***
  • Genome-wide association studies for common diseases and complex traits
    Nature Reviews Genetics, Vol. 6, No. 2. (01 February 2005), pp. 95-108.
    by Joel N Hirschhorn, Mark J Daly
  • Genome-wide association studies: theoretical and practical concerns
    Nature Reviews Genetics, Vol. 6, No. 2. (01 February 2005), pp. 109-118.
    by William YS Wang, Bryan J Barratt, David G Clayton, John A Todd
  • The effects of human population structure on large genetic association studies
    Nat Genet, Vol. 36, No. 5. (May 2004), pp. 512-517.
    by Jonathan Marchini, Lon R Cardon, Michael S Phillips, Peter Donnelly
  • Family-based designs in the age of large-scale gene-association studies
    Nature Reviews Genetics, Vol. 7, No. 5., pp. 385-394.
    by Nan M Laird, Christoph Lange
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