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idonaldsons tool [55 articles]

Neue Publikationen in idonaldsons Bibliothek eingetragen unter dem Bezeichner: tool. You can also see everyone's tool.
  • An annotation infrastructure for the analysis and interpretation of Affymetrix exon array data
    Genome Biology, Vol. 8 (11 May 2007), R79.
    by Michal J Okoniewski, Tim Yates, Sian Dibben, Crispin J Miller
    posted to tool exon-array browser by idonaldson on 2008-11-17 16:28:59 as ** along with 3 people jfr heliopais bertelsen
  • X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis
    Nucl. Acids Res. (11 October 2007), gkm779.
    by Tim Yates, Michal J Okoniewski, Crispin J Miller
    posted to tool exon-array browser by idonaldson on 2008-11-17 16:12:19 as **
  • An integrated software system for analyzing ChIP-chip and ChIP-seq data
    Nature Biotechnology, Vol. 26, No. 11. (02 November 2008), pp. 1293-1300.
    by Hongkai Ji, Hui Jiang, Wenxiu Ma, David S Johnson, Richard M Myers, Wing H Wong
    posted to tool chip-chip by idonaldson on 2008-11-10 09:21:39 as ** along with 5 people and 1 group jyuh inesdesantiago pengchy kengg bais BenosLab
  • 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 9 people and 1 group ghattem yadadi 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 10 people ptrobajo mdperry gdb megraw kengg alhufton jyuh kjglennie bryankr maximilianh
  • 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 4 people Eroslavochka inesdesantiago mdperry sebastien_vigneau
  • 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
  • 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
  • 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
  • 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
  • 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-chip by idonaldson on 2008-04-25 14:11:01 as ** along with 2 people maximilianh isimpson
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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 tool chip-chip by idonaldson on 2008-02-04 13:14:00 as *** along with 1 person jfr
  • 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
  • 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 **
  • 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
  • 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 Profile-Based Deterministic Sequential Monte Carlo Algorithm for Motif Discovery.
    Bioinformatics (17 November 2007)
    by Kuo-Ching C Liang, Xiaodong Wang, Dimitris Anastassiou
    posted to cis-regulation tfbs tool by idonaldson on 2007-11-27 14:46:52 as ** along with 5 people and 1 group grahamc cjeans nklee maximilianh isimpson Motif Discovery
  • 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-regulation tfbs tool by idonaldson on 2007-11-27 14:42:52 as *** along with 6 people and 1 group cassj tmmurali chad_davis cabbagezs maximilianh isimpson csb_journal_club_public
  • JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update.
    Nucleic Acids Res (15 November 2007)
    by Jan Christian C Bryne, Eivind Valen, Man-Hung Eric H Tang, Troels Marstrand, Ole Winther, Isabelle da Piedade, Anders Krogh, Boris Lenhard, Albin Sandelin
    posted to matrix tfbs tool by idonaldson on 2007-11-19 11:15:24 as read along with 6 people natstreet druvus jyuh dullhunk sci91078 jfr
  • Discovering motifs with transcription factor domain knowledge.
    Pac Symp Biocomput (2007), pp. 472-483.
    by HC Leung, FY Chin, BM Chan
    posted to motif-discovery tfbs tool by idonaldson on 2007-11-12 08:50:57 as **** along with 1 person maximilianh
  • A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data--A case study using E2F1.
    Genome Res (19 October 2006)
    by Victor X X Jin, Alina Rabinovich, Sharon L L Squazzo, Roland Green, Peggy J J Farnham
    posted to tool tfbs crm chip-chip by idonaldson on 2007-11-08 08:50:56 as ***** along with 2 people aprasad jfr
  • Comparative genome analysis across a kingdom of eukaryotic organisms: Specialization and diversification in the Fungi
    Genome Res. (5 November 2007), gr.6531807.
    by Michael J Cornell, Intikhab Alam, Darren M Soanes, Han M Wong, Cornelia Hedeler, Norman W Paton, Magnus Rattray, Simon J Hubbard, Nicholas J Talbot, Stephen G Oliver
    posted to comparison conserved fungi tool by idonaldson on 2007-11-08 08:46:47 as ** along with 6 people and 1 group stajich grahamc GustavoLacerda nklee seitentaisei alanrw Berkeley Mycology
  • HeliCis: a DNA motif discovery tool for colocalized motif pairs with periodic spacing
    BMC Bioinformatics, Vol. 8 (28 October 2007), 418.
    by Erik Larsson, Per Lindahl, Petter Mostad
    posted to motif-discovery spacing tfbs tool by idonaldson on 2007-11-06 09:18:26 as read along with 2 people maximilianh isimpson
  • MotifCombinator: a web-based tool to search for combinations of cis-regulatory motifs
    BMC Bioinformatics, Vol. 8 (22 March 2007), 100.
    by Mamoru Kato, Tatsuhiko Tsunoda
    posted to cis-regulation crm tool by idonaldson on 2007-11-06 09:15:33 as **** along with 3 people and 1 group cwbrown nklee isimpson EisenLab
  • A systems biology approach for pathway level analysis
    Genome Res. (4 September 2007), gr.6202607.
    by Sorin Draghici, Purvesh Khatri, Adi L Tarca, Kashyap Amin, Arina Done, Calin Voichita, Constantin Georgescu, Roberto Romero
    posted to networks tool by idonaldson on 2007-11-01 08:47:00 as *** along with 17 people and 3 groups ptrobajo pengchy tmmurali dragonrez jfr gurkanbebek grahamc shigepong zwang cabbagezs cerami xingxu shikin Pao-Yang thomaskelder heliopais AlexanderPico Bioinformatics ParkinsonLab_at_MaRS OPIG
  • dPattern: transcription factor binding site (TFBS) discovery in human genome using a discriminative pattern analysis
    Bioinformatics, Vol. 23, No. 19. (1 October 2007), pp. 2619-2621.
    by Seung-Hee Bae, Haixu Tang, Jing Wu, Jun Xie, Sun Kim
    posted to motif-discovery tfbs tool by idonaldson on 2007-10-29 11:42:16 as ** along with 3 people maximilianh isimpson nuin
  • PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny.
    PLoS Comput Biol, Vol. 1, No. 7. (December 2005)
    by R Siddharthan, ED Siggia, E van Nimwegen
    posted to conserved motif-discovery tfbs tool by idonaldson on 2007-10-29 10:39:49 as read along with 12 people and 3 groups druvus ana postrational dquest AaronDarling nickluscombe noano adsmitty lusk lilou yevishere isimpson structural_bioinformatics Bioinformatics EBI-regulation
  • Discovering Motifs in Ranked Lists of DNA Sequences
    PLoS Computational Biology, Vol. 3, No. 3. (1 March 2007), e39.
    by Eran Eden, Doron Lipson, Sivan Yogev, Zohar Yakhini
    posted to motif-discovery tool by idonaldson on 2007-10-29 10:38:59 as *** along with 6 people eckart_bindewald zwang GeeSharpMinor ppark hpaces isimpson
  • IEM: An Algorithm for Iterative Enhancement of Motifs Using Comparative Genomics Data.
    Comput Syst Bioinformatics Conf, Vol. 6 (2007), pp. 227-235.
    by E Zeng, K Mathee, G Narasimhan
    posted to cis-regulation conserved tfbs tool by idonaldson on 2007-10-29 10:04:48 as *** along with 3 people maximilianh annacarina07 isimpson
  • Identifying tissue-selective transcription factor binding sites in vertebrate promoters.
    Proc Natl Acad Sci U S A, Vol. 102, No. 5. (1 February 2005), pp. 1560-1565.
    by AD Smith, P Sumazin, MQ Zhang
    posted to cis-regulation promoter tfbs tool by idonaldson on 2007-10-24 09:14:11 as read along with 1 person heliopais
  • Benchmarking tools for the alignment of functional noncoding DNA.
    BMC Bioinformatics, Vol. 5 (21 January 2004)
    by DA Pollard, CM Bergman, J Stoye, SE Celniker, MB Eisen
    posted to alignment tool by idonaldson on 2007-10-23 15:58:35 as *** along with 6 people and 1 group cap1 indigoviolet lilou adijr gjuggler nklee EisenLab
  • MATLIGN: a motif clustering, comparison and matching tool
    BMC Bioinformatics, Vol. 8 (08 June 2007), 189.
    by Matti Kankainen, Ari Loytynoja
    posted to matrix tfbs tool by idonaldson on 2007-10-22 09:36:12 as read along with 3 people and 1 group smbe2008 isimpson xili03 BergmanLab
  • Regulatory motif discovery using a population clustering evolutionary algorithm.
    IEEE/ACM Trans Comput Biol Bioinform, Vol. 4, No. 3. (p 2007), pp. 403-414.
    by MA Lones, AM Tyrrell
    posted to motif-discovery tool by idonaldson on 2007-10-22 09:26:24 as **** along with 4 people nklee xili03 csdhwang isimpson
  • Discriminative motif discovery in DNA and protein sequences using the DEME Algorithm
    BMC Bioinformatics, Vol. 8, No. 1. (2007)
    by Emma Redhead, Timothy Bailey
    posted to motif-discovery tool by idonaldson on 2007-10-22 09:25:28 as **** along with 5 people and 1 group dpollard cjeans nklee niallhaslam maximilianh EisenLab
  • DBTSS: database of transcription start sites, progress report 2008
    Nucl. Acids Res. (16 October 2007), gkm901.
    by Hiroyuki Wakaguri, Riu Yamashita, Yutaka Suzuki, Sumio Sugano, Kenta Nakai
    posted to promoter tool tss by idonaldson on 2007-10-22 09:22:09 as **** along with 1 person jyuh
  • OrthoDB: the hierarchical catalog of eukaryotic orthologs.
    Nucleic Acids Res (18 October 2007)
    by Evgenia V V Kriventseva, Nazim Rahman, Octavio Espinosa, Evgeny M M Zdobnov
    posted to orthologues tool by idonaldson on 2007-10-22 09:21:23 as *** along with 1 person jyuh
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