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isimpson no-tag [92 articles]

Recent papers added to isimpson library classified by the tag no-tag. You can also see everyone's no-tag.
  • Drosophila DLMO is a positive regulator of transcription during thoracic bristle development.
    Genetics (9 August 2008)
    by Shamir Zenvirt, Yael Nevo-Caspi, Sigal Rencus-Lazar, Daniel Segal
    posted to no-tag by isimpson on 2008-08-19 16:57:54 as ** along with 1 group Jarman Lab
  • Hox and Senseless Antagonism Functions as a Molecular Switch to Regulate EGF Secretion in the Drosophila PNS
    Developmental Cell, Vol. 15, No. 2. (12 August 2008), pp. 298-308.
    by David Li-Kroeger, Lorraine M Witt, Leighton H Grimes, Tiffany A Cook, Brian Gebelein
    posted to no-tag by isimpson on 2008-08-13 10:44:07 as *** along with 1 group Jarman Lab
  • Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks.
    Mol Biol Evol, Vol. 21, No. 1. (January 2004), pp. 36-44.
    by K Tamura, S Subramanian, S Kumar
    posted to no-tag by isimpson on 2008-08-11 10:51:41 as read along with 1 person and 1 group indigoviolet EisenLab
  • Specificity of Atonal and Scute bHLH factors: analysis of cognate E box binding sites and the influence of Senseless.
    Genes to cells : devoted to molecular & cellular mechanisms (4 August 2008)
    by Lynn M M Powell, Aimée M M Deaton, Martin A A Wear, Andrew P P Jarman
    posted to no-tag by isimpson on 2008-08-08 10:03:37 as ***** along with 1 group Jarman Lab
  • The genetics of early telencephalon patterning: some assembly required.
    Nature reviews. Neuroscience (6 August 2008)
    by Jean M M Hébert, Gord Fishell
    posted to no-tag by isimpson on 2008-08-08 09:46:34 as **
  • Inferring genome-scale rearrangement phylogeny and ancestral gene order: A Drosophila case study
    Genome Biology, Vol. 8 (08 November 2007), R236.
    by Arjun Bhutkar, William M Gelbart, Temple F Smith
    posted to no-tag by isimpson on 2008-07-21 14:01:19 as ** along with 5 people and 1 group indigoviolet dpollard balicea maximilianh hpaces EisenLab
  • Polytene Chromosomal Maps of 11 Drosophila species: The order of genomic scaffolds inferred from genetic and physical maps.
    Genetics (13 July 2008)
    by Stephen W W Schaeffer, Arjun Bhutkar, Bryant F F McAllister, Muneo Matsuda, Luciano M M Matzkin, Patrick M M O'Grady, Claudia Rohde, Vera L S L Valente, Montserrat Aguadé, Wyatt W W Anderson, Kevin Edwards, Ana C L C Garcia, Josh Goodman, James Hartigan, Eiko Kataoka, Richard T T Lapoint, Elena R R Lozovsky, Carlos A A Machado, Mohamed A F A Noor, Montserrat Papaceit, Laura K K Reed, Stephen Richards, Tania T T Rieger, Susan M M Russo, Hajime Sato, Carmen Segarra, Douglas R R Smith, Temple F F Smith, Victor Strelets, Yoshiko N N Tobari, Yoshihiko Tomimura, Marvin Wasserman, Thomas Watts, Robert Wilson, Kiyohito Yoshida, Therese A A Markow, William M M Gelbart, Thomas C C Kaufman
    posted to no-tag by isimpson on 2008-07-21 14:01:05 as ** along with 1 group Notre Dame Bioinformatics
  • Chromosomal rearrangement inferred from comparisons of twelve Drosophila genomes.
    Genetics (13 July 2008)
    by Arjun Bhutkar, Stephen W W Schaeffer, Susan M M Russo, Mu Xu, Temple F F Smith, William M M Gelbart
    posted to no-tag by isimpson on 2008-07-21 14:00:54 as ****
  • Evolution of genes and genomes on the Drosophila phylogeny
    Nature, Vol. 450, No. 7167. (November 2007), pp. 203-218.
    posted to no-tag by isimpson on 2008-07-21 12:50:44 as ***** along with 19 people and 6 groups hdopazo cisevol balicea CharlesM PetrovLab operon tmmurali indigoviolet djkt timflutre stajich zwang Garamonfok lp2 hpaces caseybrown emptyhb urgi noor Drosophila-Genetics-Genomics-2008 BergmanLab Bioinformatics EisenLab csb_journal_club_public Berkeley Mycology
  • Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm
    PLoS Biology, Vol. 6, No. 2. (1 February 2008), e27.
    by Xiao-Yong Li, Stewart Macarthur, Richard Bourgon, David Nix, Daniel A Pollard, Venky N Iyer, Aaron Hechmer, Lisa Simirenko, Mark Stapleton, Cris L Hendriks, Hou C Chu, Nobuo Ogawa, William Inwood, Victor Sementchenko, Amy Beaton, Richard Weiszmann, Susan E Celniker, David W Knowles, Tom Gingeras, Terence P Speed, Michael B Eisen, Mark D Biggin
    posted to no-tag by isimpson on 2008-07-21 12:16:28 as ***** along with 7 people and 1 group gdb Stew brant kengg maximilianh caseybrown emptyhb Jarman Lab
  • Trim11 modulates the function of neurogenic transcription factor Pax6 through ubiquitin-proteosome system.
    Genes & development, Vol. 22, No. 14. (15 July 2008), pp. 1972-1986.
    by TC Tuoc, A Stoykova
    posted to no-tag by isimpson on 2008-07-18 09:53:53 as **
  • Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences.
    Cell, Vol. 133, No. 7. (27 June 2008), pp. 1266-1276.
    by MF Berger, G Badis, AR Gehrke, S Talukder, AA Philippakis, L Peña-Castillo, TM Alleyne, S Mnaimneh, OB Botvinnik, ET Chan, F Khalid, W Zhang, D Newburger, SA Jaeger, QD Morris, ML Bulyk, TR Hughes
    posted to no-tag by isimpson on 2008-07-09 14:51:18 as ***** along with 1 person icq242500260
  • Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites.
    Cell, Vol. 133, No. 7. (27 June 2008), pp. 1277-1289.
    by MB Noyes, RG Christensen, A Wakabayashi, GD Stormo, MH Brodsky, SA Wolfe
    posted to no-tag by isimpson on 2008-07-09 14:50:27 as ***** along with 1 person and 1 group icq242500260 Jarman Lab
  • A lexicon for homeodomain-DNA recognition.
    Cell, Vol. 133, No. 7. (27 June 2008), pp. 1133-1135.
    by M Affolter, M Slattery, RS Mann
    posted to no-tag by isimpson on 2008-07-09 14:49:34 as ***** along with 2 people inesdesantiago icq242500260
  • Systematic determination of genetic network architecture.
    Nat Genet, Vol. 22, No. 3. (July 1999), pp. 281-285.
    by S Tavazoie, JD Hughes, MJ Campbell, RJ Cho, GM Church
    posted to no-tag by isimpson on 2008-07-03 00:37:45 as ***** along with 6 people and 2 groups jo_davies ellakat adepace nickluscombe karfunkel maralena EisenLab EBI-regulation
  • Regulatory element detection using correlation with expression.
    Nat Genet, Vol. 27, No. 2. (February 2001), pp. 167-171.
    by HJ Bussemaker, H Li, ED Siggia
    posted to no-tag by isimpson on 2008-07-02 16:02:36 as ***** along with 4 people and 2 groups tvdbulck dpollard nickluscombe heliopais EisenLab EBI-regulation
  • MEME: discovering and analyzing DNA and protein sequence motifs.
    Nucleic Acids Res, Vol. 34, No. Web Server issue. (1 July 2006)
    by TL Bailey, N Williams, C Misleh, WW Li
    posted to no-tag by isimpson on 2008-07-02 14:42:12 as ***** along with 1 person dquest
  • What are DNA sequence motifs?
    Nature Biotechnology, Vol. 24, No. 4., pp. 423-425.
    by Patrik D'Haeseleer
    posted to no-tag by isimpson on 2008-07-02 14:41:33 as ***** along with 3 people and 1 group okarsligil rlhsiao ekoenig Bioinformatics
  • Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes.
    BMC bioinformatics, Vol. 3 (2002)
    by M Caselle, F Di Cunto, P Provero
    posted to no-tag by isimpson on 2008-07-02 14:16:55 as *****
  • Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation.
    Nat Biotechnol, Vol. 16, No. 10. (October 1998), pp. 939-945.
    by FP Roth, JD Hughes, PW Estep, GM Church
    posted to no-tag by isimpson on 2008-07-02 14:16:42 as ***** along with 2 people and 1 group dquest kengg Plantandetc
  • An introduction to ROC analysis
    Pattern Recognition Letters, Vol. 27, No. 8. (June 2006), pp. 861-874.
    by Tom Fawcett
    posted to no-tag by isimpson on 2008-07-02 14:12:41 as ** along with 22 people and 6 groups nherveg jyuh AbnerCYH ldietz vavi dquest sdvillal xiaoyan2006 dwf camu schlauchi vmoa drivard nklee imrchen kmdaily gsiwo tgyork idonaldson napvasconcelos cdeane haiyeong Bioinformatics Crypto VT_DLRL Randomness LIVIA BergmanLab
  • Statistical power of phylo-HMM for evolutionarily conserved element detection
    BMC Bioinformatics, Vol. 8 (05 October 2007), 374.
    by Xiaodan Fan, Jun Zhu, Eric E Schadt, Jun S Liu
    posted to no-tag by isimpson on 2008-07-02 14:12:36 as ** along with 2 people and 1 group pradiptaray idonaldson BergmanLab
  • A Primer on Learning in Bayesian Networks for Computational Biology
    PLoS Computational Biology, Vol. 3, No. 8. (1 August 2007), e129.
    by Chris J Needham, James R Bradford, Andrew J Bulpitt, David R Westhead
    posted to no-tag by isimpson on 2008-07-02 14:12:33 as ** along with 11 people and 2 groups jyuh brian jfr balicea grahamc zwang bertelsen cabbagezs groepl ppark idonaldson Bioinformatics 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 no-tag by isimpson on 2008-07-02 14:12:29 as ** along with 4 people nklee idonaldson xili03 csdhwang
  • MATLIGN: a motif clustering, comparison and matching tool
    BMC Bioinformatics, Vol. 8 (08 June 2007), 189.
    by Matti Kankainen, Ari Loytynoja
    posted to no-tag by isimpson on 2008-07-02 14:12:26 as ** along with 3 people and 1 group xili03 smbe2008 idonaldson BergmanLab
  • How does DNA sequence motif discovery work?
    Nature Biotechnology, Vol. 24, No. 8., pp. 959-961.
    by Patrik D'Haeseleer
    posted to no-tag by isimpson on 2008-07-02 14:12:22 as ** along with 5 people and 1 group Evangelia okarsligil antonkratz xi03 idonaldson Bioinformatics
  • 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 no-tag by isimpson on 2008-07-02 14:12:19 as ** along with 3 people maximilianh idonaldson annacarina07
  • 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 no-tag by isimpson on 2008-07-02 14:12:14 as ** along with 6 people eckart_bindewald zwang GeeSharpMinor ppark idonaldson hpaces
  • 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 no-tag by isimpson on 2008-07-02 14:12:09 as ** along with 11 people and 3 groups ana postrational dquest AaronDarling nickluscombe noano adsmitty lusk lilou idonaldson yevishere structural_bioinformatics Bioinformatics EBI-regulation
  • 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 no-tag by isimpson on 2008-07-02 14:12:05 as ** along with 3 people nuin maximilianh idonaldson
  • Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules
    Algorithms for Molecular Biology, Vol. 2 (10 October 2007), 13.
    by Valentina Boeva, Julien Clement, Mireille Regnier, Mikhail A Roytberg, Vsevolod J Makeev
    posted to no-tag by isimpson on 2008-07-02 14:12:01 as ** along with 2 people and 1 group idonaldson guos csb_journal_club_public
  • 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 no-tag by isimpson on 2008-07-02 14:11:56 as ** along with 3 people and 1 group cwbrown nklee idonaldson EisenLab
  • Fine-Tuning Enhancer Models to Predict Transcriptional Targets across Multiple Genomes.
    PLoS ONE, Vol. 2, No. 11. (2007)
    by S Aerts, J van Helden, O Sand, BA Hassan
    posted to no-tag by isimpson on 2008-07-02 14:11:50 as ** along with 4 people and 1 group brant maximilianh idonaldson barwil cis-regulatory-evolution
  • 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 no-tag by isimpson on 2008-07-02 14:11:45 as ** along with 2 people maximilianh idonaldson
  • 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 no-tag by isimpson on 2008-07-02 14:11:40 as ** along with 6 people and 1 group cassj tmmurali chad_davis cabbagezs maximilianh idonaldson csb_journal_club_public
  • 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 no-tag by isimpson on 2008-07-02 14:11:36 as ** along with 5 people and 1 group grahamc cjeans nklee maximilianh idonaldson Motif Discovery
  • 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 no-tag by isimpson on 2008-07-02 14:11:32 as ** along with 2 people maximilianh idonaldson
  • 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 no-tag by isimpson on 2008-07-02 14:11:27 as ** along with 5 people nklee maximilianh idonaldson xili03 csdhwang
  • 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 no-tag by isimpson on 2008-07-02 14:11:22 as ** along with 5 people vega jyuh djkt idonaldson yevishere
  • 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 no-tag by isimpson on 2008-07-02 14:11:17 as ** along with 7 people jyuh bpcusack dullhunk maximilianh idonaldson mircea jsjoly
  • 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 no-tag by isimpson on 2008-07-02 14:11:13 as ** along with 3 people chad_davis idonaldson xili03
  • 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 no-tag by isimpson on 2008-07-02 14:11:08 as ** along with 6 people and 4 groups kengg jtaylor ghattem epigenetics blobbybirdman idonaldson Bioinformatics Plantandetc UH - Computational Biology BergmanLab
  • 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 no-tag by isimpson on 2008-07-02 14:11:04 as ** along with 5 people boudinot brant natstreet heliopais idonaldson
  • 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 no-tag by isimpson on 2008-07-02 14:11:00 as ** along with 3 people maximilianh idonaldson csdhwang
  • 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 no-tag by isimpson on 2008-07-02 14:10:56 as ** along with 7 people and 1 group yoonk chad_davis nklee maximilianh idonaldson xili03 csdhwang Motif Discovery
  • 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 no-tag by isimpson on 2008-07-02 14:10:52 as ** along with 3 people and 1 group nklee maximilianh idonaldson Motif Discovery
  • 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 no-tag by isimpson on 2008-07-02 14:10:48 as ** along with 2 people maximilianh idonaldson
  • 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 no-tag by isimpson on 2008-07-02 14:10:44 as ** along with 2 people idonaldson 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 no-tag by isimpson on 2008-07-02 14:10:40 as ** along with 3 people idonaldson maximilianh tmmurali
  • 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 no-tag by isimpson on 2008-07-02 14:10:31 as ** along with 5 people yoonk phoenixzxl GustavoLacerda ihpark idonaldson
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