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dquest library [322 articles]

Статьи, недавно добавленные в библиотеку dquest .
  • Discovering sequence motifs with arbitrary insertions and deletions.
    PLoS computational biology, Vol. 4, No. 4. (April 2008)
    by MC Frith, NF Saunders, B Kobe, TL Bailey
    posted to motifsampling motifpaper by dquest on 2008-05-14 19:38:39 as ** along with 4 people Stew gjuggler neils cabbagesofdoom
  • Implementing arithmetic and other analytic operations by transcriptional regulation.
    PLoS computational biology, Vol. 4, No. 4. (April 2008)
    by SM Cory, TJ Perkins
    posted to regulatorynetworks by dquest on 2008-05-14 19:35:15 as ** along with 1 person maximilianh
  • ELPH Manual from the Center for Bioinformatics and Computational Biology
    (2000)
    posted to motifsampling motifpaper by dquest on 2008-05-09 20:42:44 as **
  • A Parallel Architecture for Regulatory Motif Algorithm Assessment
    Hicomb (14 April 2008)
    by Daniel Quest, Kathryn Dempsey, Mohammad Shafiullah, Dhundy Bastola, Hesham Ali
    edited by Bertil Schmidt, Srinvas Aluru, David Bader
    posted to questpapers parallel by dquest on 2008-05-08 15:35:30 as read
  • notes Discovering transcriptional modules from motif, chip-chip and microarray data.
    Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (2005), pp. 483-494.
    by T De Bie, P Monsieurs, K Engelen, B De Moor, N Cristianini, K Marchal
    posted to motifsampling motifpaper by dquest on 2008-05-07 23:04:45 as read
  • H-NS: a universal regulator for a dynamic genome.
    Nature reviews. Microbiology, Vol. 2, No. 5. (May 2004), pp. 391-400.
    by CJ Dorman
    posted to regulatorynetworks by dquest on 2008-05-05 22:09:12 as **
  • Co-regulation of Salmonella enterica genes required for virulence and resistance to antimicrobial peptides by SlyA and PhoP/PhoQ
    Molecular Microbiology, Vol. 56, No. 2. (April 2005), pp. 492-508.
    by Navarre W Wiley, A Halsey, Walthers Don, Frye Jonathan, Mcclelland Michael, L Potter, J Kenney, S Gunn, C Fang, J Libby
    posted to regulatorynetworks by dquest on 2008-05-05 21:42:38 as **
  • Alternate SlyA and H-NS nucleoprotein complexes control hlyE expression in Escherichia coli K-12.
    Molecular microbiology, Vol. 66, No. 3. (November 2007), pp. 685-698.
    by JK Lithgow, F Haider, IS Roberts, J Green
    posted to regulatorynetworks by dquest on 2008-05-05 21:38:52 as **
  • Histone H2A monoubiquitination represses transcription by inhibiting RNA polymerase II transcriptional elongation.
    Molecular cell, Vol. 29, No. 1. (18 January 2008), pp. 69-80.
    by W Zhou, P Zhu, J Wang, G Pascual, KA Ohgi, J Lozach, CK Glass, MG Rosenfeld
    posted to histones by dquest on 2008-05-02 20:34:24 as **
  • Nuclear Receptor-Enhanced Transcription Requires Motor- and LSD1-Dependent Gene Networking in Interchromatin Granules
    Cell, Vol. 132, No. 6. (21 March 2008), pp. 996-1010.
    by Esperanza Nunez, Young-Soo Kwon, Kasey R Hutt, Qidong Hu, Maria D Cardamone, Kenneth A Ohgi, Ivan Garcia-Bassets, David W Rose, Christopher K Glass, Michael G Rosenfeld, Xiang-Dong Fu
    posted to histones by dquest on 2008-05-02 20:30:38 as ** along with 1 person jjray
  • FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription.
    Cell, Vol. 132, No. 6. (21 March 2008), pp. 958-970.
    by M Lupien, J Eeckhoute, CA Meyer, Q Wang, Y Zhang, W Li, JS Carroll, XS Liu, M Brown
    posted to histones by dquest on 2008-05-02 19:48:31 as **
  • In vivo study of the nucleosome assembly functions of ASF1 histone chaperones in human cells.
    Molecular and cellular biology (31 March 2008)
    by Angélique Galvani, Régis Courbeyrette, Morgane Agez, Françoise Ochsenbein, Carl Mann, Jean-Yves Y Thuret
    posted to histones by dquest on 2008-05-02 19:42:23 as read
  • On the optimality of the neighbor-joining algorithm
    Algorithms for Molecular Biology, Vol. 3 (30 April 2008), 5.
    by Kord Eickmeyer, Peter Huggins, Lior Pachter, Ruriko Yoshida
    posted to phylogenetics by dquest on 2008-05-02 18:57:05 as read along with 2 people joaocarrico cmzmasek
  • Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Yuji Zhang, Jianhua Xuan, Benildo, Robert Clarke, Habtom Ressom
    posted to motifsampling motifpaper by dquest on 2008-04-23 15:14:39 as ** along with 4 people bertelsen bootsy kengg robertvandenberg
  • Eukaryotic transcriptional control
    Trends in Cell Biology, Vol. 9, No. 12. (1 December 1999), pp. M46-M49.
    by Roger D Kornberg
    posted to bioregulationoverview by dquest on 2008-04-17 22:03:27 as **
  • Physical constraints and functional characteristics of transcription factor-DNA interaction.
    Proc Natl Acad Sci U S A, Vol. 99, No. 19. (17 September 2002), pp. 12015-12020.
    by U Gerland, JD Moroz, T Hwa
    posted to bioregulationoverview by dquest on 2008-04-17 20:56:47 as ** along with 1 person jstajic
  • Ab initio prediction of transcription factor targets using structural knowledge.
    PLoS Comput Biol, Vol. 1, No. 1. (June 2005)
    by T Kaplan, N Friedman, H Margalit
    posted to motifpaper motifsampling by dquest on 2008-04-17 16:48:46 as ** along with 1 person bpb
  • Dual-function regulators: the cAMP receptor protein and the CytR regulator can act either to repress or to activate transcription depending on the context.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 93, No. 19. (17 September 1996), pp. 10151-10155.
    by PB Rasmussen, B Holst, P Valentin-Hansen
    posted to bioregulationoverview by dquest on 2008-04-11 19:08:36 as **
  • Large-scale identification of protein-protein interaction of Escherichia coli K-12.
    Genome Res (10 April 2006)
    by Mohammad Arifuzzaman, Maki Maeda, Aya Itoh, Kensaku Nishikata, Chiharu Takita, Rintaro Saito, Takeshi Ara, Kenji Nakahigashi, Hsuan-Cheng C Huang, Aki Hirai, Kohei Tsuzuki, Seira Nakamura, Mohammad Altaf-Ul-Amin, Taku Oshima, Tomoya Baba, Natsuko Yamamoto, Tomoyo Kawamura, Tomoko Ioka-Nakamichi, Masanari Kitagawa, Masaru Tomita, Shigehiko Kanaya, Chieko Wada, Hirotada Mori
    posted to bioregulationoverview by dquest on 2008-04-11 18:52:13 as ** along with 5 people and 1 group tny nickluscombe aswin lpfernandes hevol EBI-regulation
  • Integration of Horizontally Transferred Genes into Regulatory Interaction Networks Takes Many Million Years
    Mol Biol Evol (24 December 2007), msm283.
    by Martin J Lercher, Csaba Pal
    posted to bioregulationoverview regulatorynetworks by dquest on 2008-04-11 18:47:20 as ** along with 1 person cjeans
  • Studies of the distribution of Escherichia coli cAMP-receptor protein and RNA polymerase along the E. coli chromosome.
    Proc Natl Acad Sci U S A, Vol. 102, No. 49. (6 December 2005), pp. 17693-17698.
    by DC Grainger, D Hurd, M Harrison, J Holdstock, SJ Busby
    posted to bioregulationoverview by dquest on 2008-04-11 18:08:43 as ** along with 1 person and 1 group nickluscombe EBI-regulation
  • Expression of glnA in Escherichia coli is regulated at tandem promoters.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 82, No. 7. (April 1985), pp. 1979-1983.
    by LJ Reitzer, B Magasanik
    posted to bioregulationoverview by dquest on 2008-04-11 13:57:23 as **
  • Competition among seven Escherichia coli sigma subunits: relative binding affinities to the core RNA polymerase.
    Nucleic acids research, Vol. 28, No. 18. (15 September 2000), pp. 3497-3503.
    by H Maeda, N Fujita, A Ishihama
    posted to bioregulationoverview by dquest on 2008-04-11 13:33:08 as read
  • Nitrogen assimilation and global regulation in Escherichia coli.
    Annual review of microbiology, Vol. 57 (2003), pp. 155-176.
    by L Reitzer
    posted to bioregulationoverview by dquest on 2008-04-11 13:32:12 as read
  • A scoring matrix approach to detecting miRNA target sites
    Algorithms for Molecular Biology, Vol. 3 (31 March 2008), 3.
    by Simon Moxon, Vincent Moulton, Jan T Kim
    posted to rnafolding rnastructure sirna by dquest on 2008-04-01 17:18:10 as read along with 1 person and 1 group heliopais microRNA
  • DNAAlignEditor: DNA Alignment editor tool
    BMC Bioinformatics, Vol. 9 (19 March 2008), 154.
    by Hector Sanchez-Villeda, Steven Schroeder, Sherry Flint-Garcia, Katherine E Guill, Masanori Yamasaki, Michael D Mcmullen
    posted to bioinformaticscoursematerial_sequences by dquest on 2008-03-21 17:45:39 as read along with 3 people jyuh silverak renatomilani
  • BioSAVE: Display of scored annotation within a sequence context
    BMC Bioinformatics, Vol. 9 (20 March 2008), 157.
    by Richard F Pollock, Boris Adryan
    posted to visualization by dquest on 2008-03-21 17:43:08 as read along with 1 person jyuh
  • Shape based indexing for faster search of RNA family databases
    BMC Bioinformatics, Vol. 9 (29 February 2008), 131.
    by Stefan Janssen, Jens Reeder, Robert Giegerich
    posted to rnastructure by dquest on 2008-03-10 15:17:52 as read
  • Transcriptional regulation by the numbers: applications.
    Curr Opin Genet Dev, Vol. 15, No. 2. (April 2005), pp. 125-135.
    by L Bintu, NE Buchler, HG Garcia, U Gerland, T Hwa, J Kondev, T Kuhlman, R Phillips
    posted to transcriptregulation by dquest on 2008-02-14 15:55:51 as read along with 4 people and 1 group imouthesmp dpollard madhadron discreteonyxorb EisenLab
  • Transcriptional regulation by the numbers: models.
    Curr Opin Genet Dev, Vol. 15, No. 2. (April 2005), pp. 116-124.
    by L Bintu, NE Buchler, HG Garcia, U Gerland, T Hwa, J Kondev, R Phillips
    posted to transcriptregulation by dquest on 2008-02-14 15:54:57 as ** along with 3 people imouthesmp madhadron discreteonyxorb
  • Pfam: clans, web tools and services
    Nucleic Acids Research, Vol. 34, No. Database Issue. (2006), pp. 247-251.
    by Robert D Finn, Jaina Mistry, Benjamin Schuster-Böckler, Sam Griffiths-Jones, Volker Hollich1, Timo Lassmann, Simon Moxon, Mhairi Marshall, Ajay Khanna, Richard Durbin, Sean R Eddy, Erik L Sonnhammer, Alex Bateman
    posted to databases proteinstructure by dquest on 2008-02-14 02:54:44 as **
  • Evolutionary approaches for the reverse-engineering of gene regulatory networks: a study on a biologically realistic dataset
    BMC Bioinformatics, Vol. 9 (08 February 2008), 91.
    by Cedric Auliac, Vincent Frouin, Xavier Gidrol, Florence D'alche-Buc
    posted to baysian motifpaper motifsampling regulatorynetworks by dquest on 2008-02-11 18:38:01 as read along with 1 person thomaskelder
  • Ori-Finder: a web-based system for finding oriCs in unannotated bacterial genomes
    BMC Bioinformatics, Vol. 9 (01 February 2008), 79.
    by Feng Gao, Chun-Ting Zhang
    posted to bacteriainfoandalgs by dquest on 2008-02-05 16:03:02 as read
  • SIGffRid: a tool to search for sigma factor binding sites in bacterial genomes using comparative approach and biologically driven statistics
    BMC Bioinformatics, Vol. 9 (31 January 2008), 73.
    by Fabrice Touzain, Sophie Schbath, Isabelle Debled-Rennesson, Bertrand Aigle, Gregory Kucherov, Pierre Leblond
    posted to motifpaper motifsampling by dquest on 2008-02-01 15:23:42 as ** along with 2 people chad_davis xili03
  • Identification of DNA-binding proteins using support vector machines and evolutionary profiles
    BMC Bioinformatics, Vol. 8 (27 November 2007), 463.
    by Manish Kumar, Michael M Gromiha, Gajendra PS Raghava
    posted to motifpaper motifsampling proteinmotiffinding by dquest on 2007-11-28 17:59:06 as read
  • Detecting putative orthologs.
    Bioinformatics, Vol. 19, No. 13. (1 September 2003), pp. 1710-1711.
    by DP Wall, HB Fraser, AE Hirsh
    posted to motifpaper orthalog by dquest on 2007-11-23 21:06:21 as ** along with 3 people and 3 groups ana indigoviolet ninch structural_bioinformatics Bioinformatics EisenLab
  • Orthologous Transcription Factors in Bacteria Have Different Functions and Regulate Different Genes
    PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e175.
    by Morgan N Price, Paramvir S Dehal, Adam P Arkin
    posted to motifpaper by dquest on 2007-11-23 21:02:52 as ** along with 6 people and 3 groups dpollard djkt zwang cabbagezs heliopais blobbybirdman EisenLab cis-regulatory-evolution Myxo group
  • LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA.
    Genome Res, Vol. 13, No. 4. (April 2003), pp. 721-731.
    by M Brudno, CB Do, GM Cooper, MF Kim, E Davydov, ED Green, A Sidow, S Batzoglou,
    posted to motifpaper by dquest on 2007-11-23 20:55:06 as ** along with 11 people and 1 group operon balajis dpollard xwbcn adepace hdopazo lusk Garamonfok adijr natstreet nklee EisenLab
  • KEGG: kyoto encyclopedia of genes and genomes.
    Nucleic Acids Res, Vol. 28, No. 1. (1 January 2000), pp. 27-30.
    by M Kanehisa, S Goto
    posted to motifpaper by dquest on 2007-11-23 20:49:45 as ** along with 8 people Evangelia j3xucite fisherp koerner ruvido noby naegele katerinakal
  • Improved benchmarks for computational motif discovery
    BMC Bioinformatics, Vol. 8 (08 June 2007), 193.
    by Geir K Sandve, Osman Abul, Vegard Walseng, Finn Drablos
    posted to motifpaper motifsampling by dquest on 2007-11-23 15:52:44 as read
  • REDUCE: An online tool for inferring cis-regulatory elements and transcriptional module activities from microarray data.
    Nucleic Acids Res, Vol. 31, No. 13. (1 July 2003), pp. 3487-3490.
    by C Roven, HJ Bussemaker
    posted to motifpaper motifsampling by dquest on 2007-11-23 14:25:46 as ** along with 3 people and 1 group mariakmejia nickluscombe heliopais 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 motifpaper motifsampling by dquest on 2007-11-23 13:58:08 as ** along with 2 people and 1 group dpollard yevishere EisenLab
  • Approaches to the automatic discovery of patterns in biosequences.
    J Comput Biol, Vol. 5, No. 2. (1998), pp. 279-305.
    by A Brazma, I Jonassen, I Eidhammer, D Gilbert
    posted to motifpaper motifsampling by dquest on 2007-11-23 13:48:37 as ** along with 1 person treangen
  • Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP-chip data
    BMC Bioinformatics, Vol. 8 (03 August 2007), 283.
    by Xiangdong Liu, Walter J Jessen, Siva Sivaganesan, Bruce J Aronow, Mario Medvedovic
    posted to motifpaper motifsampling by dquest on 2007-11-22 13:59:46 as ** along with 2 people and 1 group nklee naegele ic4
  • A survey of DNA motif finding algorithms
    BMC Bioinformatics, Vol. 8, No. Suppl 7. (2007)
    by Modan Das, Ho K Dai
    posted to motifpaper motifsampling by dquest on 2007-11-22 13:55:32 as ** along with 6 people xili03 brant nklee maximilianh yevishere csdhwang
  • Structure-Templated Predictions of Novel Protein Interactions from Sequence Information
    PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e182.
    by Doron Betel, Kevin E Breitkreuz, Ruth Isserlin, Danielle Dewar-Darch, Mike Tyers, Christopher W Hogue
    posted to proteinnetworks by dquest on 2007-11-14 15:21:22 as read along with 3 people bicko chad_davis zwang
  • MotifViz: an analysis and visualization tool for motif discovery.
    Nucleic Acids Res, Vol. 32, No. Web Server issue. (1 July 2004)
    by Y Fu, MC Frith, PM Haverty, Z Weng
    posted to motifpaper motifsampling visualization by dquest on 2007-11-11 20:34:10 as **
  • CoMoDis: composite motif discovery in mammalian genomes
    Nucleic Acids Research, Vol. 35, No. 1. (January 2007), pp. e1-e1.
    by Donaldson, J Ian, Gottgens, Berthold
    posted to motifpaper motifsampling by dquest on 2007-11-11 20:32:00 as **
  • BRAGI: linking and visualization of database information in a 3D viewer and modeling tool
    Bioinformatics, Vol. 21, No. 7. (01 April 2005), pp. 1291-1293.
    by Reichelt Joachim, Dieterich Guido, Kvesic Marsel, Schomburg Dietmar, W Heinz
    posted to 3d visualization by dquest on 2007-09-19 19:08:49 as **
  • notes Informative priors based on transcription factor structural class improve de novo motif discovery
    Bioinformatics, Vol. 22, No. 14. (15 July 2006), pp. e384-392.
    by Leelavati Narlikar, Raluca Gordan, Uwe Ohler, Alexander J Hartemink
    posted to motifpaper by dquest on 2007-08-17 07:25:41 as ** along with 3 people nklee idonaldson yevishere
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