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idonaldsons library [104 articles]

Senaste artiklarna i idonaldsons bibliotek.
  • Nucleosome positioning from tiling microarray data
    Bioinformatics, Vol. 24, No. 13. (1 July 2008), pp. i139-146.
    by Moran Yassour, Tommy Kaplan, Ariel Jaimovich, Nir Friedman
    posted to position nucleosome by idonaldson on 2008-06-27 11:37:55 as **
  • 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
  • ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species
    Nucl. Acids Res. (3 May 2008), gkn195.
    by Bart Hooghe, Paco Hulpiau, Frans van Roy, Pieter De Bleser
    posted to transcription-factor tool promoter conserved by idonaldson on 2008-05-13 10:38:49 as *** along with 3 people jyuh maralena maximilianh
  • Inferring the role of transcription factors in regulatory networks
    BMC Bioinformatics, Vol. 9 (06 May 2008), 228.
    by Philippe Veber, Carito Guziolowski, Michel Le Borgne, Ovidiu Radulescu, Anne Siegel
    posted to transcription-factor regulation networks by idonaldson on 2008-05-12 10:00:21 as ** along with 4 people isimpson maralena heliopais renatomilani
  • The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site
    Nucl. Acids Res. (26 March 2008), gkn137.
    by Kannan Tharakaraman, Olivier Bodenreider, David Landsman, John L Spouge, Leonardo Marino-Ramirez
    posted to tss motif by idonaldson on 2008-05-07 10:10:13 as *** along with 2 people fpattyn maximilianh
  • Detecting cis-regulatory binding sites for cooperatively binding proteins
    Nucl. Acids Res., Vol. 36, No. 8. (1 May 2008), e46.
    by Liesbeth van Oeffelen, Pierre Cornelis, Wouter Van Delm, Fedor De Ridder, Bart De Moor, Yves Moreau
    posted to motif combinatorial co cis-regulation by idonaldson on 2008-05-07 09:59:14 as ** along with 3 people isimpson maximilianh tmmurali
  • W-AlignACE: An improved Gibbs sampling algorithm based on more accurate position weight matrices learned from sequence and gene expression/ChIP-chip data.
    Bioinformatics (5 March 2008)
    by Xin Chen, Lingqiong Guo, Zhaocheng Fan, Tao Jiang
    posted to tool motif-discovery chip-on-chip chip-chip by idonaldson on 2008-04-25 14:11:01 as ** along with 2 people isimpson maximilianh
  • How many human genes can be defined as housekeeping with current expression data?
    BMC Genomics, Vol. 9, No. 1. (2008)
    by Jiang Zhu, Fuhong He, Shuhui Song, Jing Wang, Jun Yu
    posted to housekeeping by idonaldson on 2008-04-23 10:02:25 as ** along with 2 people jyuh cisevol
  • Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets.
    Genome research (14 April 2008)
    by Chaim Linhart, Yonit Halperin, Ron Shamir
    posted to motif-discovery tfbs tool by idonaldson on 2008-04-22 09:26:03 as *** along with 6 people and 1 group tmmurali isimpson fpattyn maximilianh ealloza maralena BergmanLab
  • Transposable elements and the evolution of regulatory networks.
    Nat Rev Genet (27 March 2008)
    by Cédric Feschotte
    posted to networks regulation review te by idonaldson on 2008-04-21 10:24:26 as *** along with 8 people and 1 group pradiptaray smbe2008 eskay roys cmzmasek jonsta247 djkt bootsy BergmanLab
  • Chromhome: A rich internet application for accessing comparative chromosome homology maps
    BMC Bioinformatics, Vol. 9 (26 March 2008), 168.
    by Sridevi Nagarajan, Willem Rens, James Stalker, Tony Cox, Malcolm A Ferguson-Smith
    posted to chromosome comparison tool by idonaldson on 2008-03-31 09:50:58 as *** along with 1 person jyuh
  • Dynamic Regulation of Nucleosome Positioning in the Human Genome
    Cell, Vol. 132, No. 5. (7 March 2008), pp. 887-898.
    by Dustin E Schones, Kairong Cui, Suresh Cuddapah, Tae-Young Roh, Artem Barski, Zhibin Wang, Gang Wei, Keji Zhao
    posted to nucleosome by idonaldson on 2008-03-28 16:36:56 as ** along with 7 people mikaelhuss vega sameetmehta aalibes dchughes sleepingcell oelemento
  • Motif discovery in tissue-specific regulatory sequences using directed information.
    EURASIP J Bioinform Syst Biol (2007)
    by A Rao, AO Hero Iii, DJ States, JD Engel
    posted to motif-discovery tissue-specific by idonaldson on 2008-03-17 11:03:58 as *** along with 2 people isimpson maximilianh
  • An efficient method for statistical significance calculation of transcription factor binding sites.
    Bioinformation, Vol. 2, No. 5. (2007), pp. 169-174.
    by Z Qian, L Lu, L Qi, Y Li
    posted to statistics tfbs by idonaldson on 2008-03-03 09:44:21 as ** along with 3 people and 1 group isimpson nklee maximilianh Motif Discovery
  • Assessment of composite motif discovery methods
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Kjetil Klepper, Geir Sandve, Osman Abul, Jostein Johansen, Finn Drablos
    posted to analysis motif-discovery tool by idonaldson on 2008-03-03 09:19:03 as *** along with 6 people and 1 group isimpson chad_davis nklee maximilianh xili03 csdhwang Motif Discovery
  • fdrMotif: Identifying cis-elements by an EM Algorithm Coupled with False Discovery Rate Control.
    Bioinformatics (22 February 2008)
    by Leping Li, Robert L L Bass, Yu Liang
    posted to motif-discovery tool by idonaldson on 2008-02-28 16:05:34 as *** along with 3 people isimpson maximilianh csdhwang
  • 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 modification review by idonaldson on 2008-02-26 14:27:28 as ** along with 7 people jyuh tmmurali dchughes vega zwang cabbagezs faion
  • 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
  • Transposable elements as drivers of genomic and biological diversity in vertebrates.
    Chromosome Res, Vol. 16, No. 1. (2008), pp. 203-215.
    by A Böhne, F Brunet, D Galiana-Arnoux, C Schultheis, JN Volff
    posted to te by idonaldson on 2008-02-25 10:08:33 as ** along with 1 person and 1 group dchughes BergmanLab
  • DNA sequence and structural properties as predictors of human and mouse promoters
    Gene, Vol. 410, No. 1. (29 February 2008), pp. 165-176.
    by Pelin Akan, Panos Deloukas
    posted to human mouse prediction promoter by idonaldson on 2008-02-21 08:36:50 as **
  • Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies
    Genome Res., Vol. 17, No. 6. (1 June 2007), pp. 898-909.
    by Ghia M Euskirchen, Joel S Rozowsky, Chia-Lin Wei, Wah H Lee, Zhengdong D Zhang, Stephen Hartman, Olof Emanuelsson, Viktor Stolc, Sherman Weissman, Mark B Gerstein, Yijun Ruan, Michael Snyder
    posted to chip-on-chip chip-seq comparison by idonaldson on 2008-02-20 14:32:15 as ** along with 6 people and 4 groups isimpson kengg jtaylor ghattem epigenetics blobbybirdman Bioinformatics Plantandetc UH - Computational Biology 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-regulation motif promoter by idonaldson on 2008-02-20 08:58:19 as *** along with 7 people isimpson ihpark gracio ealloza lp2 cabbagezs emptyhb
  • An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance
    BMC Bioinformatics, Vol. 9 (07 February 2008), 89.
    by Ana C Casimiro, Susana Vinga, Ana T Freitas, Arlindo L Oliveira
    posted to distribution motif promoter tfbs by idonaldson on 2008-02-15 09:30:51 as ** along with 3 people isimpson chad_davis xili03
  • Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors
    BMC Bioinformatics, Vol. 8 (09 November 2007), 437.
    by Xueping Yu, Jimmy Lin, Donald J Zack, Jiang Qian
    posted to crm tfbs tissue-specific by idonaldson on 2008-02-15 09:28:41 as *** along with 7 people bootsy jyuh chad_davis mikaelhuss nklee maximilianh njcitulike
  • Text-mining assisted regulatory annotation
    Genome Biology, Vol. 9, No. 2. (2008)
    by Stein Aerts, Maximilian Haeussler, Steven van Vooren, Obi Griffith, Paco Hulpiau, Steven Jones, Stephen Montgomery, Casey Bergman, The
    posted to annotation regulation text-mining by idonaldson on 2008-02-14 12:58:31 as *** along with 5 people isimpson dullhunk maximilianh mircea jsjoly
  • Jane: Suggesting Journals, Finding Experts.
    Bioinformatics (28 January 2008)
    by Martijn J J Schuemie, Jan A A Kors
    posted to journal tool by idonaldson on 2008-02-13 16:19:18 as ** along with 7 people merj jyuh chad_davis dullhunk farhat renatomilani Barend
  • A novel genome-scale repeat finder geared towards transposons
    Bioinformatics, Vol. 24, No. 4. (15 February 2008), pp. 468-476.
    by Xuehui Li, Tamer Kahveci, Mark A Settles
    posted to te tool by idonaldson on 2008-02-13 13:40:40 as ** along with 1 person and 1 group GustavoLacerda BergmanLab
  • Genome-scale ChIP-chip analysis using 10,000 human cells.
    Biotechniques, Vol. 43, No. 6. (December 2007), pp. 791-797.
    by LG Acevedo, AL Iniguez, HL Holster, X Zhang, R Green, PJ Farnham
    posted to chip-on-chip method by idonaldson on 2008-02-12 17:08:47 as ** along with 1 person jyuh
  • 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-on-chip comparison by idonaldson on 2008-02-12 17:07:30 as *** along with 10 people and 2 groups gracio stajich lp2 magusina jfr kengg djkt xiaobeizhao cabbagezs caseybrown Berkeley Mycology BergmanLab
  • GSE: a comprehensive database system for the representation, retrieval, and analysis of microarray data.
    Pac Symp Biocomput (2008), pp. 539-550.
    by T Danford, A Rolfe, D Gifford
    posted to database microarray by idonaldson on 2008-02-04 13:19:31 as ** along with 2 people jyuh jfr
  • CMARRT: a tool for the analysis of ChIP-chip data from tiling arrays by incorporating the correlation structure.
    Pac Symp Biocomput (2008), pp. 515-526.
    by PF Kuan, H Chun, S Keleş
    posted to chip-on-chip tool by idonaldson on 2008-02-04 13:14:00 as *** along with 1 person jfr
  • Model-based deconvolution of genome-wide DNA binding.
    Bioinformatics (1 December 2007)
    by David J J Reiss, Marc T T Facciotti, Nitin S S Baliga
    posted to chip-on-chip deconvolution tfbs by idonaldson on 2008-01-31 11:10:21 as *** along with 5 people isimpson vega jyuh djkt yevishere
  • TFBS Identification Based on Genetic Algorithm with Combined Representations and Adaptive Post-processing.
    Bioinformatics (6 December 2007)
    by Tak-Ming M Chan, Kwong-Sak S Leung, Kin-Hong H Lee
    posted to motif-discovery tfbs tool by idonaldson on 2008-01-31 11:07:05 as *** along with 5 people isimpson nklee maximilianh xili03 csdhwang
  • Predicting expression patterns from regulatory sequence in Drosophila segmentation
    Nature (02 January 2008)
    by Eran Segal, Tali Raveh-Sadka, Mark Schroeder, Ulrich Unnerstall, Ulrike Gaul
    posted to expression prediction by idonaldson on 2008-01-31 09:39:38 as *** along with 11 people tresch tmmurali eckart_bindewald djkt bootsy biomcgary roys emptyhb pkharchenko meiklej jrest
  • NestedMICA as an ab initio protein motif discovery tool
    BMC Bioinformatics, Vol. 9 (14 January 2008), 19.
    by Mutlu Dogruel, Thomas A Down, Tim JP Hubbard
    posted to motif-discovery protein tool by idonaldson on 2008-01-21 10:44:04 as **
  • Gene expression profiling by massively parallel sequencing
    Genome Res. (21 November 2007), gr.6984908.
    by Tatiana T Torres, Muralidhar Metta, Birgit Ottenwalder, Christian Schlotterer
    posted to expression mps by idonaldson on 2008-01-17 09:36:58 as ** along with 9 people gracio jyuh jfr dchughes stsaft echinotrix giovanni ghattem ohara
  • Functional evolution of the p53 regulatory network through its target response elements
    Proceedings of the National Academy of Sciences (10 January 2008), 0704694105.
    by Anil G Jegga, Alberto Inga, Daniel Menendez, Bruce J Aronow, Michael A Resnick
    posted to evolution networks p53 by idonaldson on 2008-01-14 09:51:08 as *** along with 5 people and 1 group brant cjeans zwang cisevol renatomilani cis-regulatory-evolution
  • Runx genes are direct targets of Scl/Tal1 in the yolk sac and fetal liver.
    Blood (9 January 2008)
    by Josette-Renee R Landry, Sarah Kinston, Kathy Knezevic, Marella F T R F de Bruijn, Nicola Wilson, Wade T T Nottingham, Michael Peitz, Frank Edenhofer, John E E Pimanda, Katrin Ottersbach, Berthold Gottgens
    posted to gottgens by idonaldson on 2008-01-14 09:45:16 as ***
  • A novel method for high accuracy sumoylation site prediction from protein sequences
    BMC Bioinformatics, Vol. 9 (08 January 2008), 8.
    by Jialin Xu, Yun He, Boqin Qiang, Jiangang Yuan, Xiaozhong Peng, Xian-Ming Pan
    posted to prediction sumoylation tool by idonaldson on 2008-01-14 09:35:35 as **
  • BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks
    Bioinformatics (16 November 2007), btm553.
    by Andrei Zinovyev, Eric Viara, Laurence Calzone, Emmanuel Barillot
    posted to networks tool by idonaldson on 2008-01-14 09:33:16 as ** along with 5 people jyuh jfr dullhunk grahamc sgoetz
  • A Hybrid Model for Robust Detection of Transcription Factor Binding Sites.
    Bioinformatics (9 January 2008)
    by Sumedha Gunewardena, Zhaolei Zhang
    posted to motif-discovery tfbs tool by idonaldson on 2008-01-14 09:30:49 as *** along with 2 people jyuh maximilianh
  • OrthoMaM: A database of orthologous genomic markers for placental mammal phylogenetics
    BMC Evolutionary Biology, Vol. 7 (30 November 2007), 241.
    by Vincent Ranwez, Frederic Delsuc, Sylvie Ranwez, Khalid Belkir, Marie-Ka Tilak, Emmanuel JP Douzery
    posted to orthologues phylogenetic tool by idonaldson on 2008-01-10 12:35:15 as *** along with 1 person aprasad
  • Maintenance of transposon-free regions throughout vertebrate evolution
    BMC Genomics, Vol. 8 (20 December 2007), 470.
    by Cas Simons, Igor V Makunin, Michael Pheasant, John S Mattick
    posted to transposon-free-regions by idonaldson on 2008-01-08 09:59:53 as *** along with 2 people and 2 groups blobbybirdman cisevol cis-regulatory-evolution BergmanLab
  • Housekeeping and tissue-specific genes differ in simple sequence repeats in the 5'-UTR region
    Gene, Vol. 407, No. 1-2. (15 January 2008), pp. 54-62.
    by Mark J Lawson, Liqing Zhang
    posted to 5utr gene ssr by idonaldson on 2008-01-04 09:40:19 as ** along with 1 person yoonk
  • Lyl1 Interacts with CREB1 and Alters Expression of CREB1 Target Genes.
    Biochim Biophys Acta (7 December 2007)
    by Serban San-Marina, Youqi Han, Fernando Suarez Saiz, Michael R R Trus, Mark D D Minden
    posted to chip-on-chip creb lyl by idonaldson on 2008-01-03 12:01:49 as **
  • Genome-wide analysis reveals regulatory role of G4 DNA in gene transcription
    Genome Res. (20 December 2007), gr.6905408.
    by Zhuo Du, Yiqiang Zhao, Ning Li
    posted to g4 regulation by idonaldson on 2007-12-21 10:26:10 as ** along with 3 people and 1 group bpagano jmrivort fpattyn G-quadruplex
  • 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 prediction promoter structural by idonaldson on 2007-12-21 10:22:56 as *** along with 3 people cjeans cabbagezs maximilianh
  • Predicting and understanding transcription factor interactions based on sequence level determinants of combinatorial control
    Bioinformatics, Vol. 24, No. 1. (1 January 2008), pp. 26-33.
    by ADJ van Dijk, Ter, RG Immink, GC Angenent, RCHJ van Ham
    posted to combinatorial interaction tfbs by idonaldson on 2007-12-20 12:33:25 as ** along with 2 people isimpson maximilianh
  • Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting
    Bioinformatics, Vol. 24, No. 1. (1 January 2008), pp. 18-25.
    by Kai Ye, Anton, Jaap Heringa, Adriaan P Ijzerman, Elena Marchiori
    posted to alignment multiple tool by idonaldson on 2007-12-20 12:28:20 as *** along with 1 person h-chi
  • 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 prediction tss by idonaldson on 2007-11-28 08:48:13 as *** along with 7 people dchughes cabbagezs maximilianh oelemento gjuggler ohara gracio
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