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cabbagezs's library [163 articles]

Recent papers added to cabbagezs's library.
  • Single-Molecule DNA Sequencing of a Viral Genome
    Science, Vol. 320, No. 5872. (4 April 2008), pp. 106-109.
    by Timothy D Harris, Phillip R Buzby, Hazen Babcock, Eric Beer, Jayson Bowers, Ido Braslavsky, Marie Causey, Jennifer Colonell, James Dimeo, William J Efcavitch, Eldar Giladi, Jaime Gill, John Healy, Mirna Jarosz, Dan Lapen, Keith Moulton, Stephen R Quake, Kathleen Steinmann, Edward Thayer, Anastasia Tyurina, Rebecca Ward, Howard Weiss, Zheng Xie
    posted to genome genomics by cabbagezs on 2008-04-11 07:49:07 as ** along with 14 people and 3 groups jyuh vmarshal ilyaf austin operon dchughes samjlord neils zwang kinestetika benlin caseybrown kjglennie melting moernerlab Microbial-Ecology microbiology_nijmegen
  • The regulatory activity of microRNA(*) species has substantial influence on microRNA and 3' UTR evolution.
    Nature structural & molecular biology (30 March 2008)
    by Katsutomo Okamura, Michael D D Phillips, David M M Tyler, Hong Duan, Yu-Ting T Chou, Eric C C Lai
    posted to evolution mirna by cabbagezs on 2008-04-08 06:18:07 as ** along with 4 people and 1 group heliopais elfar maralena mdphillips microRNA
  • Potent effect of target structure on microRNA function.
    Nat Struct Mol Biol (1 April 2007)
    by Dang Long, Rosalind Lee, Peter Williams, Chi Yu Y Chan, Victor Ambros, Ye Ding
    posted to mirna mirna_target by cabbagezs on 2008-03-30 17:18:10 as read along with 6 people and 2 groups tardigrade andersbj cdawson Garamonfok physics lp2 microRNA GIG
  • 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
    posted to chromatin genome review by cabbagezs on 2008-03-10 00:26:14 as ** along with 8 people bpcusack jyuh tmmurali dchughes vega zwang idonaldson faion
  • Excess of microRNAs in large and very 5' biased introns
    Biochemical and Biophysical Research Communications, Vol. In Press, Corrected Proof
    by Hongjun Zhou, Kui Lin
    posted to intronic_mirna mirna by cabbagezs on 2008-02-20 13:54:36 as ***** along with 2 people maralena bootsy
  • Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions
    Genome Res., Vol. 18, No. 2. (1 February 2008), pp. 242-251.
    by Elfar Torarinsson, Zizhen Yao, Eric D Wiklund, Jesper B Bramsen, Claus Hansen, Jorgen Kjems, Niels Tommerup, Walter L Ruzzo, Jan Gorodkin
    posted to encode rna_structure by cabbagezs on 2008-02-19 14:07:33 as ** along with 2 people djkt xingxu
  • Understanding biological functions through molecular networks
    Cell Res, Vol. 18, No. 2. (0000), pp. 224-237.
    by Jing-Dong J Han
    posted to network review by cabbagezs on 2008-02-19 14:05:48 as ** along with 8 people and 1 group jyuh cmmorel jo_davies shikin mingzhi giorgiofotia maralena phoenixzxl GeneGo
  • Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets
    Genome Res. (7 February 2008), gr.7080508.
    by David S Johnson, Wei Li, Benjamin D Gordon, Arindam Bhattacharjee, Bo Curry, Jayati Ghosh, Leonardo Brizuela, Jason S Carroll, Myles Brown, Paul Flicek, Christopher M Koch, Ian Dunham, Mark Bieda, Xiaoqin Xu, Peggy J Farnham, Philipp Kapranov, David A Nix, Thomas R Gingeras, Xinmin Zhang, Heather Holster, Nan Jiang, Roland Green, Jun S Song, Scott A Mccuine, Elizabeth Anton, Loan Nguyen, Nathan D Trinklein, Zhen Ye, Keith Ching, David Hawkins, Bing Ren, Peter C Scacheri, Joel Rozowsky, Alexander Karpikov, Ghia Euskirchen, Sherman Weissman, Mark Gerstein, Michael Snyder, Annie Yang, Zarmik Moqtaderi, Heather Hirsch, Hennady P Shulha, Yutao Fu, Zhiping Weng, Kevin Struhl, Richard M Myers, Jason D Lieb, Shirley X Liu
    posted to chip-chip by cabbagezs on 2008-02-19 12:56:19 as ** along with 10 people and 2 groups gracio stajich lp2 magusina jfr kengg djkt xiaobeizhao idonaldson caseybrown Berkeley Mycology BergmanLab
  • 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-regulatory genomics motif promoter by cabbagezs on 2008-02-19 12:55:45 as ** along with 7 people isimpson ihpark gracio ealloza lp2 idonaldson emptyhb
  • Diversity of preferred nucleotide sequences around the translation initiation codon in eukaryote genomes
    Nucl. Acids Res., Vol. 36, No. 3. (11 February 2008), pp. 861-871.
    by So Nakagawa, Yoshihito Niimura, Takashi Gojobori, Hiroshi Tanaka, Kin-Ichiro Miura
    posted to genomic genomics translation_initiation by cabbagezs on 2008-02-18 03:28:42 as **
  • Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method
    Mol Syst Biol, Vol. 4 (12 February 2008)
    by Lukas Burger, Erik van Nimwegen
    posted to alignment bayesian ppi prediction by cabbagezs on 2008-02-18 03:20:52 as ** along with 10 people pansapiens kengg grahamc laughcry zwang biomcgary roys cdeane gjuggler phoenixzxl
  • Predicting synthetic rescues in metabolic networks
    Mol Syst Biol, Vol. 4 (12 February 2008)
    by Adilson E Motter, Natali Gulbahce, Eivind Almaas, Albert-Laszlo Barabasi
    posted to metabolic_network prediction by cabbagezs on 2008-02-18 03:20:25 as ** along with 9 people tmmurali debasis kentsis zwang bootsy biomcgary westoll shikin shung
  • What are artificial neural networks?
    Nature Biotechnology, Vol. 26, No. 2., pp. 195-197.
    by Anders Krogh
    posted to neural_network tutorial by cabbagezs on 2008-02-18 03:16:16 as **** along with 8 people adacier jfr Yanno jyuh dullhunk zwang asddd sci91078
  • Non-coding RNA.
    Hum Mol Genet, Vol. 15, No. suppl_1. (15 April 2006)
    by John S S Mattick, Igor V V Makunin
    posted to noncoding_rna review by cabbagezs on 2008-01-02 11:44:27 as ** along with 10 people and 7 groups bertelsen tuck marcius eckart_bindewald tardigrade andersbj dchughes mtagaya scroft bsmagic Bioinformatics microRNA G4ID BioinfoCIPF bioinplant SGU-CIPF Genetics-of-Gambling
  • Generic eukaryotic core promoter prediction using structural features of DNA
    Genome Res. (20 December 2007), gr.6991408.
    by Thomas Abeel, Yvan Saeys, Eric Bonnet, Pierre Rouze, Yves Van de Peer
    posted to genomics prediction promoter by cabbagezs on 2007-12-21 02:54:12 as read along with 3 people cjeans maximilianh idonaldson
  • Computational Epigenetics.
    Bioinformatics (17 November 2007)
    by Christoph Bock, Thomas Lengauer
    posted to epigenetics review by cabbagezs on 2007-12-20 01:12:14 as ** along with 11 people and 1 group jyuh Thomasah Ema sebastien_vigneau ealloza djkt frohike timflutre cjeans epigenetics barriot Bioinformatics
  • Coupling and coordination in gene expression processes: a systems biology view.
    Nat Rev Genet (11 December 2007)
    by Suzanne Komili, Pamela A A Silver
    posted to expression regulatory review by cabbagezs on 2007-12-19 15:56:26 as read along with 6 people jyuh tmmurali margaritis bootsy Ema renatomilani
  • Getting Started in Probabilistic Graphical Models
    PLoS Computational Biology, Vol. 3, No. 12. (1 December 2007), e252.
    by Edoardo M Airoldi
    posted to general graph network tutorial by cabbagezs on 2007-12-10 08:57:36 as *** along with 12 people and 1 group jfr jyuh balicea AbnerCYH stajich cjeans GustavoLacerda GeeSharpMinor sobolevnrm nklee biehl softsimu baker-group
  • Putative promoter regions of miRNA genes involved in evolutionarily conserved regulatory systems among vertebrates.
    Bioinformatics (30 November 2007)
    by Shuji Fujita, Hideo Iba
    posted to mirna mirna_precursor promoter by cabbagezs on 2007-12-10 08:18:01 as read along with 2 people maralena bootsy
  • 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
    posted to drosophila functional_elements genome by cabbagezs on 2007-11-27 08:52:09 as ** along with 13 people and 2 groups shuzhens PetrovLab operon tmmurali djkt timflutre stajich lp2 nklee hpaces roys caseybrown gjuggler csb_journal_club_public Berkeley Mycology
  • Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes
    Genome Res. (7 November 2007), gr.6593807.
    by Alexander Stark, Pouya Kheradpour, Leopold Parts, Julius Brennecke, Emily Hodges, Gregory J Hannon, Manolis Kellis
    posted to drosophila mirna by cabbagezs on 2007-11-27 08:48:51 as **** along with 4 people and 2 groups stajich lp2 heliopais maralena microRNA Berkeley Mycology
  • Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs
    Genome Res. (7 November 2007), gr.6597907.
    by Graham J Ruby, Alexander Stark, Wendy K Johnston, Manolis Kellis, David P Bartel, Eric C Lai
    posted to drosophila mirna mirna_biogenesis mirna_target by cabbagezs on 2007-11-27 08:48:21 as ** along with 5 people and 2 groups stajich lp2 heliopais urgi Alexander_Kanitz microRNA Berkeley Mycology
  • Xenbase: a Xenopus biology and genomics resource
    Nucl. Acids Res. (4 November 2007), gkm826.
    by Jeff B Bowes, Kevin A Snyder, Erik Segerdell, Ross Gibb, Chris Jarabek, Etienne Noumen, Nicolas Pollet, Peter D Vize
    posted to database genomics xenopus by cabbagezs on 2007-11-27 08:44:47 as ** along with 1 person lisa1
  • miRBase: tools for microRNA genomics.
    Nucleic Acids Res (8 November 2007)
    by Sam Griffiths-Jones, Harpreet Kaur K Saini, Stijn van V Dongen, Anton J J Enright
    posted to database genomics mirna by cabbagezs on 2007-11-27 08:44:04 as ** along with 2 people jyuh jfr
  • Programming gene expression with combinatorial promoters
    Mol Syst Biol, Vol. 3 (13 November 2007)
    by Robert S Cox, Michael G Surette, Michael B Elowitz
    posted to expression promoter by cabbagezs on 2007-11-27 08:42:24 as ** along with 14 people and 2 groups tresch Retchless tmmurali austin dpollard balicea kengg dbikard margaritis lusk cjeans zwang discreteonyxorb Ema EisenLab SynBioSys
  • The Genomic Landscapes of Human Breast and Colorectal Cancers.
    Science (11 October 2007)
    by Laura D D Wood, D Williams W Parsons, Siân Jones, Jimmy Lin, Tobias Sjöblom, Rebecca J J Leary, Dong Shen, Simina M M Boca, Thomas Barber, Janine Ptak, Natalie Silliman, Steve Szabo, Zoltan Dezso, Vadim Ustyanksky, Tatiana Nikolskaya, Yuri Nikolsky, Rachel Karchin, Paul A A Wilson, Joshua S S Kaminker, Zemin Zhang, Randal Croshaw, Joseph Willis, Dawn Dawson, Michail Shipitsin, James K V K Willson, Saraswati Sukumar, Kornelia Polyak, Ben Ho H Park, Charit L L Pethiyagoda, P V Krishna V Pant, Dennis G G Ballinger, Andrew B B Sparks, James Hartigan, Douglas R R Smith, Erick Suh, Nickolas Papadopoulos, Phillip Buckhaults, Sanford D D Markowitz, Giovanni Parmigiani, Kenneth W W Kinzler, Victor E E Velculescu, Bert Vogelstein
    posted to cancer genomic by cabbagezs on 2007-11-27 08:37:42 as ** along with 13 people and 1 group cerami gwenknight jyuh tmmurali jfr rdiaz eisei ramensky massivemayhem bioyang xingxu shikin renatomilani VUMCGenomics
  • Genomics: Decoding the regulatory genome
    Nature Reviews Genetics, Vol. 8, No. 12., pp. 908-909.
    by Louisa Flintoft
    posted to genome genomics regulatory by cabbagezs on 2007-11-27 08:35:42 as **
  • Inferring Transcriptional Regulatory Networks from High-throughput Data.
    Bioinformatics (22 September 2007)
    by Rui-Sheng S Wang, Yong Wang, Xiang-Sun S Zhang, Luonan Chen
    posted to network transcription by cabbagezs on 2007-11-27 08:33:35 as ** along with 4 people wnpx rdiaz sebastien_vigneau shigepong
  • NONCODE v2.0: decoding the non-coding
    Nucl. Acids Res. (13 November 2007), gkm1011.
    by Shunmin He, Changning Liu, Geir Skogerbo, Haitao Zhao, Jie Wang, Tao Liu, Baoyan Bai, Yi Zhao, Runsheng Chen
    posted to database noncoding_rna by cabbagezs on 2007-11-27 08:30:50 as **
  • A code for transcription initiation in mammalian genomes
    Genome Res. (21 November 2007), gr.6831208.
    by Martin C Frith, Eivind Valen, Anders Krogh, Yoshihide Hayashizaki, Piero Carninci, Albin Sandelin
    posted to genome genomics transcription transcription_initiation by cabbagezs on 2007-11-27 08:09:09 as **** along with 7 people dchughes maximilianh idonaldson oelemento gjuggler ohara gracio
  • Hubs with network motifs organize modularity dynamically in the protein-protein interaction network of yeast.
    PLoS ONE, Vol. 2, No. 11. (2007)
    by G Jin, S Zhang, XS Zhang, L Chen
    posted to hub modular network ppi by cabbagezs on 2007-11-27 07:57:28 as ** along with 2 people lpfernandes cdeane
  • miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes
    Nucl. Acids Res. (19 November 2007), gkm1012.
    by Sheng-Da Hsu, Chia-Huei Chu, Ann-Ping Tsou, Shu-Jen Chen, Hua-Chien Chen, Paul W Hsu, Yung-Hao Wong, Yi-Hsuan Chen, Gian-Hung Chen, Hsien-Da Huang
    posted to databse genome genomics mirna by cabbagezs on 2007-11-27 07:52:36 as **** along with 3 people and 1 group heliopais jdiezperezj maralena microRNA
  • 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
    posted to genome genomic sequence_analysis by cabbagezs on 2007-11-27 07:49:58 as **** along with 15 people and 3 groups Ema tmmurali rvosa balicea sebastien_vigneau giovanni neils stajich cjeans maximilianh oelemento gjuggler slroberd renatomilani gracio EisenLab FAB-lab Berkeley Mycology
  • Computational Analysis of Mouse piRNA Sequence and Biogenesis
    PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e222.
    by Doron Betel, Robert Sheridan, Debora S Marks, Chris Sander
    posted to sequence sequence_analysis pirna by cabbagezs on 2007-11-14 05:47:14 as read along with 4 people cjeans oelemento fpattyn altotor
  • Regulation of gene expression by small non-coding RNAs: a quantitative view
    Mol Syst Biol, Vol. 3 (2007)
    by Yishai Shimoni, Gilgi Friedlander, Guy Hetzroni, Gali Niv, Shoshy Altuvia, Ofer Biham, Hanah Margalit
    posted to expression noncoding_rna review by cabbagezs on 2007-11-05 12:01:17 as *** along with 5 people heliopais margaritis afenley vietanh0 Ema
  • Specialization and evolution of endogenous small RNA pathways
    Nat Rev Genet, Vol. 8, No. 11. (November 2007), pp. 884-896.
    by Elisabeth J Chapman, James C Carrington
    posted to mirna by cabbagezs on 2007-11-05 11:57:17 as *** along with 5 people Einat dchughes alwinpremanand dandaman maralena
  • A Universal Framework for Regulatory Element Discovery across All Genomes and Data Types.
    Mol Cell, Vol. 28, No. 2. (26 October 2007), pp. 337-350.
    by O Elemento, N Slonim, S Tavazoie
    posted to regulatory review sequence by cabbagezs on 2007-11-05 11:49:39 as ** along with 12 people and 2 groups ana brant cwbrown aswin cjeans zwang nklee maximilianh idonaldson sb_journal_club kristen barwil EisenLab Motif Discovery
  • Getting started in tiling microarray analysis.
    PLoS Comput Biol, Vol. 3, No. 10. (26 October 2007), pp. 1842-1844.
    by XS Liu
    posted to general microarray review by cabbagezs on 2007-11-05 11:45:54 as ***** along with 4 people cassj jfr waszak yevishere
  • Ten Simple Rules for Doing Your Best Research, According to Hamming
    PLoS Computational Biology, Vol. 3, No. 10. (1 October 2007), e213.
    by Thomas C Erren, Paul Cullen, Michael Erren, Philip E Bourne
    posted to general by cabbagezs on 2007-11-05 11:45:39 as ***** along with 6 people eckart_bindewald leonardo dullhunk zwang suizan closure
  • Global Analysis of Posttranslational Protein Arginylation
    PLoS Biology, Vol. 5, No. 10. (1 October 2007), e258.
    by Catherine C Wong, Tao Xu, Reena Rai, Aaron O Bailey, John R Yates, Yuri I Wolf, Henry Zebroski, Anna Kashina
    posted to protein translation by cabbagezs on 2007-11-05 11:41:23 as *****
  • A New Human Genome Sequence Paves the Way for Individualized Genomics
    PLoS Biology, Vol. 5, No. 10. (1 October 2007), e266.
    by Liza Gross
    posted to genome review sequence by cabbagezs on 2007-11-05 11:38:40 as ** along with 1 person dullhunk
  • The Piwi-piRNA Pathway Provides an Adaptive Defense in the Transposon Arms Race
    Science, Vol. 318, No. 5851. (2 November 2007), pp. 761-764.
    by Alexei A Aravin, Gregory J Hannon, Julius Brennecke
    posted to pirna by cabbagezs on 2007-11-05 11:20:15 as ** along with 3 people zhanghuiqiong dchughes heliopais
  • Genetics: Networks uncover new cancer susceptibility suspect
    Nature Reviews Cancer, Vol. 7, No. 11., pp. 816-817.
    by Patrick Goymer
    posted to cancer network by cabbagezs on 2007-11-05 11:18:57 as **
  • Evolutionary models for formation of network motifs and modularity in the Saccharomyces transcription factor network.
    PLoS Comput Biol, Vol. 3, No. 10. (26 October 2007), pp. 1993-2002.
    by JJ Ward, JM Thornton
    posted to motif network by cabbagezs on 2007-11-05 11:12:51 as ** along with 2 people zwang grottenolm
  • Genomic analysis of human microRNA transcripts.
    Proc Natl Acad Sci U S A (26 October 2007)
    by Harpreet Kaur K Saini, Sam Griffiths-Jones, Anton James J Enright
    posted to genomic mirna mirna_biogenesis mirna_precursor sequence_analysis by cabbagezs on 2007-11-05 07:52:37 as read along with 11 people and 1 group jyuh tmmurali dchughes AbnerCYH ealloza bootsy lp2 maximilianh RedmondSmyth gracio maralena csb_journal_club_public
  • Mammalian mirtron genes.
    Mol Cell, Vol. 28, No. 2. (26 October 2007), pp. 328-336.
    by E Berezikov, WJ Chung, J Willis, E Cuppen, EC Lai
    posted to intronic_mirna mirna mirna_precursor mirtron by cabbagezs on 2007-11-02 07:00:42 as read along with 3 people hpaces ale dchughes
  • Genome-wide Prediction of Mammalian Enhancers Based on Analysis of Transcription-Factor Binding Affinity
    Cell, Vol. 124, No. 1. (13 January 2006), pp. 47-59.
    by Outi Hallikas, Kimmo Palin, Natalia Sinjushina, Reetta Rautiainen, Juha Partanen, Esko Ukkonen, Jussi Taipale
    posted to genomic sequence_analysis transcription_factor by cabbagezs on 2007-11-02 06:53:27 as **** along with 12 people and 5 groups Terkko kaarsinogen tuck brant xwbcn dchughes nickluscombe olympos karfunkel maximilianh heliopais oelemento Bioinformatics EisenLab G4ID EBI-regulation Genetics-of-Gambling
  • The role of site accessibility in microRNA target recognition
    Nat Genet, Vol. 39, No. 10. (October 2007), pp. 1278-1284.
    by Michael Kertesz, Nicola Iovino, Ulrich Unnerstall, Ulrike Gaul, Eran Segal
    posted to mirna mirna_target by cabbagezs on 2007-10-17 03:44:12 as read along with 13 people and 1 group mtagaya rdiaz Hosna djkt Garamonfok physics bootsy epigenetics lp2 heliopais uwe yavanna maralena microRNA
  • 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-regulatory machine_learning by cabbagezs on 2007-10-15 08:02:05 as ***** along with 6 people and 1 group isimpson cassj tmmurali chad_davis maximilianh idonaldson csb_journal_club_public
  • CG dinucleotide clustering is a species-specific property of the genome.
    Nucleic Acids Res (10 October 2007)
    by Jacob L L Glass, Reid F F Thompson, Batbayar Khulan, Maria E E Figueroa, Emmanuel N N Olivier, Erin J J Oakley, Gary Van Zant, Eric E E Bouhassira, Ari Melnick, Aaron Golden, Melissa J J Fazzari, John M M Greally
    posted to genomic by cabbagezs on 2007-10-15 08:00:59 as ** along with 2 people operon fpattyn
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