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idonaldsons library [120 articles]

Neue Artikel in idonaldsons Bibliothek.
  • Uncovering mechanisms of transcriptional regulations by systematic mining of cis regulatory elements with gene expression profiles.
    BioData mining, Vol. 1, No. 1. (2008)
    by Q Ma, GW Chirn, JD Szustakowski, A Bakhtiarova, PA Kosinski, D Kemp, N Nirmala
    posted to tool microarray by idonaldson on 2008-10-06 09:12:26 as **
  • GIMSAN: a Gibbs motif finder with significance analysis
    Bioinformatics, Vol. 24, No. 19. (1 October 2008), pp. 2256-2257.
    by Patrick Ng, Uri Keich
    posted to tool motif-discovery by idonaldson on 2008-09-29 09:48:40 as *** along with 2 people nuin GeeSharpMinor
  • Model-based Analysis of ChIP-Seq (MACS)
    Genome Biology, Vol. 9, No. 9. (2008)
    by Yong Zhang, Tao Liu, Clifford Meyer, Jerome Eeckhoute, David Johnson, Bradley Bernstein, Chad Nussbaum, Richard Myers, Myles Brown, Wei Li, Xiaole Liu
    posted to tool chip-seq by idonaldson on 2008-09-22 11:37:23 as *** along with 7 people and 1 group djkt stajich mdperry fpattyn bcondon caseybrown kengg Berkeley Mycology
  • A deterministic motif finding algorithm with application to the human genome
    Bioinformatics, Vol. 22, No. 9. (1 May 2006), pp. 1047-1054.
    by Lawrence S Hon, Ajay N Jain
    posted to tool motif discovery by idonaldson on 2008-09-09 11:34:45 as ** along with 3 people and 1 group dquest nklee maximilianh Motif Discovery
  • Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data.
    Nature methods (17 August 2008)
    by Anton Valouev, David S S Johnson, Andreas Sundquist, Catherine Medina, Elizabeth Anton, Serafim Batzoglou, Richard M M Myers, Arend Sidow
    posted to tool chip-seq by idonaldson on 2008-09-09 11:33:03 as ** along with 9 people mdperry gdb megraw kengg alhufton jyuh kjglennie bryankr maximilianh
  • A functional genome-wide RNAi screen identifies TAF1 as a regulator for apoptosis in response to genotoxic stress
    Nucl. Acids Res., Vol. 36, No. 16. (1 September 2008), pp. 5250-5259.
    by Junko Kimura, Su T Nguyen, Hanshao Liu, Naoe Taira, Yoshio Miki, Kiyotsugu Yoshida
    posted to apoptosis by idonaldson on 2008-09-09 11:30:35 as **
  • Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data
    Nucl. Acids Res. (6 August 2008), gkn488.
    by Raja Jothi, Suresh Cuddapah, Artem Barski, Kairong Cui, Keji Zhao
    posted to tool chip-seq by idonaldson on 2008-09-09 11:23:42 as ** along with 3 people inesdesantiago mdperry sebastien_vigneau
  • Parameter estimation for robust HMM analysis of ChIP-chip data
    BMC Bioinformatics, Vol. 9 (18 August 2008), 343.
    by Peter Humburg, David Bulger, Glenn Stone
    posted to chip-chip by idonaldson on 2008-08-28 09:46:40 as ** along with 1 person dakelley
  • Seeder: Discriminative Seeding DNA Motif Discovery.
    Bioinformatics (Oxford, England) (21 August 2008)
    by François Fauteux, Mathieu Blanchette, Martina V V Strömvik
    posted to motif-discovery tool by idonaldson on 2008-08-26 10:37:49 as ** along with 4 people nuin brant maximilianh isimpson
  • 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
    posted to polymerase promoter by idonaldson on 2008-08-18 14:30:04 as ** along with 7 people and 3 groups agustinarce dchughes xiaobeizhao zwang cabbagezs cisevol GeeSharpMinor G4ID Genetics-of-Gambling cis-regulatory-evolution
  • Ripples from neighbouring transcription.
    Nature cell biology (10 August 2008)
    by Miki Ebisuya, Takuya Yamamoto, May Nakajima, Eisuke Nishida
    posted to neighbouring transcription by idonaldson on 2008-08-18 14:28:06 as ** along with 3 people catcremona GeeSharpMinor megraw
  • MotifVoter: a novel ensemble method for fine-grained integration of generic motif finders.
    Bioinformatics (Oxford, England) (12 August 2008)
    by Edward Wijaya, Siu-Ming M Yiu, Ngo Thanh T Son, Rajaraman Kanagasabai, Wing-Kin K Sung
    posted to motif-discovery tool by idonaldson on 2008-08-18 14:20:17 as *** along with 3 people nuin chad_davis maximilianh
  • ChIPping away at gene regulation.
    EMBO reports, Vol. 9, No. 4. (April 2008), pp. 337-343.
    by CE Massie, IG Mills
    posted to chip-chip chip-on-chip review by idonaldson on 2008-07-08 10:53:50 as *** along with 1 person yoonk
  • DiRE: identifying distant regulatory elements of co-expressed genes
    Nucl. Acids Res., Vol. 36, No. suppl_2. (1 July 2008), pp. W133-139.
    by Valer Gotea, Ivan Ovcharenko
    posted to crm tool by idonaldson on 2008-07-08 09:08:50 as ** along with 2 people heliopais Borelli
  • A survey of motif discovery methods in an integrated framework
    Biology Direct, Vol. 1, No. 1. (06 April 2006), 11.
    by Geir K Sandve, Finn Drabløs
    posted to motif-discovery review tools by idonaldson on 2008-07-08 09:03:38 as *** along with 6 people and 1 group aprasad dpollard samal yevishere csdhwang yoonk EisenLab
  • Retroviral promoters in the human genome
    Bioinformatics, Vol. 24, No. 14. (15 July 2008), pp. 1563-1567.
    by Andrew B Conley, Jittima Piriyapongsa, King I Jordan
    posted to promoter te by idonaldson on 2008-07-07 10:54:07 as ** along with 2 people and 2 groups maximilianh cisevol BergmanLab cis-regulatory-evolution
  • 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 nucleosome position by idonaldson on 2008-06-27 11:37:55 as ** along with 1 person mdperry
  • 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 cis-regulation crm motif-discovery tool by idonaldson on 2008-05-27 09:53:11 as *** along with 5 people maximilianh isimpson GustavoLacerda phoenixzxl yoonk
  • 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 conserved promoter tool transcription-factor by idonaldson on 2008-05-13 10:38:49 as *** along with 3 people maximilianh maralena jyuh
  • 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 networks regulation transcription-factor by idonaldson on 2008-05-12 10:00:21 as ** along with 4 people renatomilani heliopais maralena isimpson
  • 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 motif tss by idonaldson on 2008-05-07 10:10:13 as *** along with 3 people maximilianh fpattyn inesdesantiago
  • 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 cis-regulation co combinatorial motif by idonaldson on 2008-05-07 09:59:14 as ** along with 3 people tmmurali maximilianh isimpson
  • 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 chip-chip chip-on-chip motif-discovery tool by idonaldson on 2008-04-25 14:11:01 as ** along with 2 people maximilianh isimpson
  • 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 4 people jfr cisevol jyuh yoonk
  • 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 7 people and 1 group jfr ealloza maralena fpattyn isimpson tmmurali maximilianh 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 djkt bootsy cmzmasek smbe2008 eskay roys pradiptaray timflutre 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 10 people natstreet aalibes dchughes sleepingcell oelemento sameetmehta mikaelhuss vega kengg sonjadaniela
  • 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 maximilianh isimpson
  • 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 nklee maximilianh isimpson 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 7 people and 1 group chad_davis nklee maximilianh xili03 csdhwang isimpson yoonk 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 maximilianh csdhwang isimpson
  • 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 8 people tmmurali dchughes vega zwang cabbagezs faion bpcusack jyuh
  • 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 brant natstreet heliopais boudinot isimpson
  • 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 kengg jtaylor ghattem epigenetics blobbybirdman isimpson 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 6 people and 1 group ealloza lp2 cabbagezs emptyhb gracio isimpson Jarman Lab
  • 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 chad_davis xili03 isimpson
  • 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 8 people jyuh chad_davis mikaelhuss nklee maximilianh njcitulike bootsy snow_dragon
  • 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 8 people yas dullhunk maximilianh mircea jsjoly isimpson bpcusack jyuh
  • 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 jyuh chad_davis dullhunk farhat renatomilani Barend merj
  • 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 11 people and 2 groups jfr kengg djkt xiaobeizhao cabbagezs caseybrown magusina lp2 stajich gracio gdb BergmanLab Berkeley Mycology
  • 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 djkt yevishere jyuh vega isimpson
  • 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 nklee maximilianh xili03 csdhwang isimpson
  • 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 14 people and 1 group isimpson dakelley tmmurali eckart_bindewald djkt bootsy biomcgary roys emptyhb pkharchenko meiklej jrest tresch siebert Jarman Lab
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