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maximilianhs library [779 articles]

Senaste artiklarna i maximilianhs bibliotek.
  • A genome-wide view of the spectrum of spontaneous mutations in yeast.
    Proceedings of the National Academy of Sciences of the United States of America (26 June 2008)
    by Michael Lynch, Way Sung, Krystalynne Morris, Nicole Coffey, Christian R R Landry, Erik B B Dopman, W Joseph J Dickinson, Kazufusa Okamoto, Shilpa Kulkarni, Daniel L L Hartl, W Kelley K Thomas
    posted to tandem mutations geneorder duplicates by maximilianh on 2008-07-03 11:09:59 as **
  • Reconstructing ordinal relationships in the Demospongiae using mitochondrial genomic data.
    Molecular phylogenetics and evolution (16 May 2008)
    by Dennis V V Lavrov, Xiujuan Wang, Michelle Kelly
    posted to syntenypaper geneorder by maximilianh on 2008-06-30 09:08:20 as **
  • Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences
    Bioinformatics, Vol. 24, No. 13. (1 July 2008), pp. i165-171.
    by Lucas D Ward, Harmen J Bussemaker
    posted to noalignment by maximilianh on 2008-06-27 15:59:14 as **
  • The GlxR regulon of the amino acid producer Corynebacterium glutamicum: In silico and in vitro detection of DNA binding sites of a global transcription regulator.
    Journal of biotechnology (3 June 2008)
    by Thomas A A Kohl, Jan Baumbach, Britta Jungwirth, Alfred Pühler, Andreas Tauch
    posted to application by maximilianh on 2008-06-26 16:32:01 as **
  • Non-random retention of protein-coding overlapping genes in Metazoa
    BMC Genomics, Vol. 9 (16 April 2008), 174.
    by Giulia Solda', Mikita Suyama, Paride Pelucchi, Silvia Boi, Alessandro Guffanti, Ermanno Rizzi, Peer Bork, Maria L Tenchini, Francesca D Ciccarelli
    posted to syntenyorientation synteny genes geneorder genecoregulation by maximilianh on 2008-06-23 23:59:43 as ** along with 1 person and 1 group cisevol BergmanLab
  • Discovering sequence motifs.
    Methods in molecular biology (Clifton, N.J.), Vol. 452 (2008), pp. 231-251.
    by TL Bailey
    posted to review motif by maximilianh on 2008-06-22 21:36:09 as **
  • Mapping and sequencing of structural variation from eight human genomes
    Nature, Vol. 453, No. 7191., pp. 56-64.
    by Jeffrey M Kidd, Gregory M Cooper, William F Donahue, Hillary S Hayden, Nick Sampas, Tina Graves, Nancy Hansen, Brian Teague, Can Alkan, Francesca Antonacci, Eric Haugen, Troy Zerr, Alice N Yamada, Peter Tsang, Tera L Newman, Eray Tüzün, Ze Cheng, Heather M Ebling, Nadeem Tusneem, Robert David, Will Gillett, Karen A Phelps, Molly Weaver, David Saranga, Adrianne Brand, Wei Tao, Erik Gustafson, Kevin Mckernan, Lin Chen, Maika Malig, Joshua D Smith, Joshua M Korn, Steven A Mccarroll, David A Altshuler, Daniel A Peiffer, Michael Dorschner, John Stamatoyannopoulos, David Schwartz, Deborah A Nickerson, James C Mullikin, Richard K Wilson, Laurakay Bruhn, Maynard V Olson, Rajinder Kaul, Douglas R Smith, Evan E Eichler
    posted to copy-number-variation by maximilianh on 2008-06-21 08:22:30 as ** along with 14 people and 1 group chrisamiller vplagnol kintoki chad_davis Ema hpaces aprasad kaniko psique shikin balicea djkt dchughes bpb GeneGo
  • A regulatory code for neurogenic gene expression in the Drosophila embryo.
    Development, Vol. 131, No. 10. (May 2004), pp. 2387-2394.
    by M Markstein, R Zinzen, P Markstein, KP Yee, A Erives, A Stathopoulos, M Levine
    posted to validated rennes enhancerprediction by maximilianh on 2008-06-16 23:41:37 as ** along with 2 people dquest blobbybirdman
  • Expression-Guided In Silico Evaluation of Candidate Cis Regulatory Codes for Drosophila Muscle Founder Cells
    PLoS Computational Biology, Vol. 2, No. 5. (1 May 2006), e53.
    by Anthony A Philippakis, Brian W Busser, Stephen S Gisselbrecht, Fangxue S He, Beatriz Estrada, Alan M Michelson, Martha L Bulyk
    posted to enhancerprediction combination by maximilianh on 2008-06-16 23:40:34 as ** along with 1 person and 1 group emilyhare EisenLab
  • Cis-regulatory modules in the mammalian liver: composition depends on strength of Foxa2 consensus site
    Nucl. Acids Res. (13 June 2008), gkn366.
    by Geetu Tuteja, Shane T Jensen, Peter White, Klaus H Kaestner
    posted to strengthofmatch cns-ranking by maximilianh on 2008-06-16 23:32:27 as **
  • Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura.
    Genome Biol, Vol. 5, No. 9. (2004)
    by BP Berman, BD Pfeiffer, TR Laverty, SL Salzberg, GM Rubin, MB Eisen, SE Celniker
    posted to enhancerprediction by maximilianh on 2008-06-12 12:17:31 as ** along with 6 people and 2 groups mbeisen indigoviolet adepace Stew nklee cisevol EisenLab cis-regulatory-evolution
  • Specific DNA-binding by Apicomplexan AP2 transcription factors
    Proceedings of the National Academy of Sciences (9 June 2008), 0801993105.
    by Erandi K De Silva, Andrew R Gehrke, Kellen Olszewski, Ilsa Leon, Jasdave S Chahal, Martha L Bulyk, Manuel Llinas
    posted to factors by maximilianh on 2008-06-12 09:12:15 as ** along with 1 person aalibes
  • Associating transcription factor-binding site motifs with target GO terms and target genes
    Nucl. Acids Res. (10 June 2008), gkn374.
    by Mikael Boden, Timothy L Bailey
    posted to motif go discovery by maximilianh on 2008-06-11 15:28:01 as ** along with 2 people mikaelboden ihpark
  • Systematic identification of cell cycle regulated transcription factors from microarray time series data
    BMC Genomics, Vol. 9 (03 March 2008), 116.
    by Chao Cheng, Lei M Li
    posted to rennes motif discovery application by maximilianh on 2008-06-06 23:38:57 as **
  • Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites
    BMC Bioinformatics, Vol. 9 (04 June 2008), 262.
    by Nak-Kyeong Kim, Kannan Tharakaraman, Leonardo Marino-Ramirez, John L Spouge
    posted to motif discovery by maximilianh on 2008-06-06 23:38:01 as ** along with 1 person xili03
  • Subfunctionalization of Duplicated Zebrafish pax6 Genes by cis-Regulatory Divergence
    PLoS Genetics, Vol. 4, No. 2. (1 February 2008), e29.
    by Dirk A Kleinjan, Ruth M Bancewicz, Philippe Gautier, Ralf Dahm, Helia B Schonthaler, Giuseppe Damante, Anne Seawright, Ann M Hever, Patricia L Yeyati, Veronica van Heyningen, Pedro Coutinho
    posted to tandem synteny duplicates cns-differences by maximilianh on 2008-06-05 23:41:15 as ** along with 4 people Stew brant gjuggler emptyhb
  • CTCF Genomic Binding Sites in Drosophila and the Organisation of the Bithorax Complex.
    PLoS Genet, Vol. 3, No. 7. (6 July 2007)
    by Eimear E E Holohan, Camilla Kwong, Boris Adryan, Marek Bartkuhn, Martin Herold, Rainer Renkawitz, Steven Russell, Robert White
    posted to insulator by maximilianh on 2008-06-05 23:39:42 as ** along with 1 person sebastien_vigneau
  • NcDNAlign: Plausible multiple alignments of non-protein-coding genomic sequences.
    Genomics (27 May 2008)
    by Dominic Rose, Jana Hertel, Kristin Reiche, Peter F F Stadler, Jörg Hackermüller
    posted to alignment by maximilianh on 2008-06-03 11:00:37 as **
  • Uncovering cis regulatory codes using synthetic promoter shuffling.
    PLoS ONE, Vol. 3, No. 4. (2008)
    by A Kinkhabwala, CC Guet
    posted to transcription generalregulation factors by maximilianh on 2008-05-30 15:24:56 as **
  • RSAT: regulatory sequence analysis tools
    Nucl. Acids Res. (21 May 2008), gkn304.
    by Morgane Thomas-Chollier, Olivier Sand, Jean-Valery Turatsinze, Rekin's Janky, Matthieu Defrance, Eric Vervisch, Sylvain Brohee, Jacques van Helden
    posted to review motif discovery comparison application by maximilianh on 2008-05-23 14:55:45 as ** along with 1 person jyuh
  • Transfer of a large gene regulatory apparatus to a new developmental address in echinoid evolution
    Proceedings of the National Academy of Sciences, Vol. 105, No. 16. (22 April 2008), pp. 6091-6096.
    by Feng Gao, Eric H Davidson
    posted to grn by maximilianh on 2008-05-19 14:45:18 as **
  • Convergent evolution of clustering of Iroquois homeobox genes across metazoans.
    Molecular biology and evolution (9 May 2008)
    by Manuel Irimia, Ignacio Maeso, Jordi Garcia-Fernàndez
    posted to tandem synteny duplicates copy-number-variation by maximilianh on 2008-05-17 10:01:23 as **
  • Interchromosomal associations between alternatively expressed loci
    Nature (08 May 2005)
    by Charalampos G Spilianakis, Maria D Lalioti, Terrence Town, Gap R Lee, Richard A Flavell
    posted to interchromosomal by maximilianh on 2008-05-16 17:22:29 as ** along with 2 people lingchong JeffR100
  • Interchromosomal Interactions and Olfactory Receptor Choice
    Cell, Vol. 126, No. 2. (28 July 2006), pp. 403-413.
    by Stavros Lomvardas, Gilad Barnea, David J Pisapia, Monica Mendelsohn, Jennifer Kirkland, Richard Axel
    posted to interchromosomal by maximilianh on 2008-05-16 17:21:38 as ** along with 2 people davfre margaritis
  • A transcriptional enhancer from the coding region of ADAMTS5.
    PLoS ONE, Vol. 3, No. 5. (2008)
    by KK Barthel, X Liu
    posted to enhancerincodingregion by maximilianh on 2008-05-16 12:38:11 as **
  • A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning
    Genome Res. (13 May 2008), gr.076463.108.
    by Anton Valouev, Jeffrey Ichikawa, Thaisan Tonthat, Jeremy Stuart, Swati Ranade, Heather Peckham, Kathy Zeng, Joel A Malek, Gina Costa, Kevin Mckernan, Arend Sidow, Andrew Fire, Steven M Johnson
    posted to nucleosome nomotif motif chromatin by maximilianh on 2008-05-16 12:23:42 as ** along with 5 people and 1 group caseybrown vega aalibes Stew dpollard RockmanLab
  • Multigene Analyses of Bilaterian Animals Corroborate the Monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia
    Molecular Biology and Evolution, Vol. 22, No. 5. (15 May 2005), pp. 1246-1253.
    by Herve Philippe, Nicolas Lartillot, Henner Brinkmann
    posted to phylogeny ascidians by maximilianh on 2008-05-13 13:52:21 as **
  • OGtree: a tool for creating genome trees of prokaryotes based on overlapping genes.
    Nucleic acids research (2 May 2008)
    by Li-Wei W Jiang, Kuang-Lun L Lin, Chin Lung L Lu
    posted to syntenytools syntenypaper synteny by maximilianh on 2008-05-11 22:20:19 as **
  • 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 by maximilianh on 2008-05-09 16:05:47 as ** along with 6 people and 1 group tmmurali isimpson fpattyn ealloza idonaldson maralena BergmanLab
  • The Otx binding site is required for the activation of HpOtxL mRNA expression in the sea urchin, Hemicentrotus pulcherrimus.
    Development, growth & differentiation, Vol. 46, No. 1. (February 2004), pp. 61-67.
    by Y Hayashibara, K Mitsunaga-Nakatsubo, N Sakamoto, T Shimotori, K Akasaka, T Yamamoto
    posted to enhancer-vertebrate-invertebrate cross-species-enhancer by maximilianh on 2008-05-09 16:02:38 as **
  • Acetylated YY1 regulates Otx2 expression in anterior neuroectoderm at two cis-sites 90 kb apart
    The EMBO Journal, Vol. aop, No. current. (01 March 2007)
    by Nobuyoshi Takasaki, Daisuke Kurokawa, Rika Nakayama, Jun-Ichi Nakayama, Shinichi Aizawa
    posted to enhancer-vertebrate-invertebrate cross-species-enhancer by maximilianh on 2008-05-09 15:58:56 as **
  • An evaluation of information content as a metric for the inference of putative conserved noncoding regions in DNA sequences using a genetic algorithms approach.
    IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM, Vol. 5, No. 1. (r 2008), pp. 1-14.
    by CB Congdon, JC Aman, GM Nava, HR Gaskins, CJ Mattingly
    posted to motif discovery by maximilianh on 2008-05-07 18:36:26 as **
  • Lifting the veil on the transcriptome
    Genome Biology, Vol. 9 (24 April 2008), 218.
    by Kevin P Callahan, Scott J Butler
    posted to ncrna mirna by maximilianh on 2008-05-07 18:13:20 as **
  • Global chromatin domain organization of the Drosophila genome.
    PLoS genetics, Vol. 4, No. 3. (March 2008)
    by E de Wit, U Braunschweig, F Greil, HJ Bussemaker, B van Steensel
    posted to dna chromatin 3dstructure by maximilianh on 2008-05-07 15:55:50 as **
  • CompariMotif: quick and easy comparisons of sequence motifs
    Bioinformatics, Vol. 24, No. 10. (15 May 2008), pp. 1307-1309.
    by Richard J Edwards, Norman E Davey, Denis C Shields
    posted to pwmcomparison motif by maximilianh on 2008-05-07 15:30:59 as ** along with 2 people GustavoLacerda jyuh
  • Combining Statistical Alignment and Phylogenetic Footprinting to Detect Regulatory Elements.
    Bioinformatics (18 March 2008)
    by R Satija, L Pachter, J Hein
    posted to noalignment footprinting alignment by maximilianh on 2008-05-07 15:29:24 as ** along with 4 people Stew Ema gjuggler eckart_bindewald
  • The words of the regulatory code are arranged in a variable manner in highly conserved enhancers.
    Developmental biology (4 April 2008)
    by Sepand Rastegar, Isabell Hess, Thomas Dickmeis, Jean Christophe C Nicod, Raymond Ertzer, Yavor Hadzhiev, Wolf-Gerolf G Thies, Gerd Scherer, Uwe Strähle
    posted to notconserved core cns-similarity cns-enhancer-screen cns-differences by maximilianh on 2008-05-06 23:57:24 as ** along with 2 people and 1 group cisevol brant cis-regulatory-evolution
  • 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 promoter motif conserved alignment by maximilianh on 2008-05-06 15:56:53 as ** along with 3 people idonaldson jyuh maralena
  • 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 scanning motif combination by maximilianh on 2008-05-06 15:27:19 as ** along with 3 people isimpson idonaldson tmmurali
  • Determinants of a transcriptionally competent environment at the GM-CSF promoter
    Nucl. Acids Res., Vol. 36, No. 8. (1 May 2008), pp. 2639-2653.
    by KH Brettingham-Moore, OR Sprod, X Chen, P Oakford, MF Shannon, AF Holloway
    posted to promoter histones chromatin 3dstructure by maximilianh on 2008-05-06 15:25:04 as **
  • MicroRNAs and the advent of vertebrate morphological complexity
    Proceedings of the National Academy of Sciences (14 February 2008), 0712259105.
    by Alysha M Heimberg, Lorenzo F Sempere, Vanessa N Moy, Philip C Donoghue, Kevin J Peterson
    posted to ncrna mirna by maximilianh on 2008-05-06 13:23:48 as ** along with 6 people and 2 groups djkt stajich heliopais maralena zhanglab prabhubpatil microRNA Berkeley Mycology
  • Computational intelligence approaches for pattern discovery in biological systems
    Brief Bioinform (5 May 2008), bbn021.
    by Gary B Fogel
    posted to review motif by maximilianh on 2008-05-06 13:22:16 as ** along with 1 person renatomilani
  • Genome-wide transcription and the implications for genomic organization.
    Nat Rev Genet (8 May 2007)
    by Philipp Kapranov, Aarron T T Willingham, Thomas R R Gingeras
    posted to ncrna-long ncrna by maximilianh on 2008-05-01 10:10:40 as ** along with 13 people and 5 groups jyuh balicea xico dchughes kengg sebastien_vigneau zwang ajgentles asddd hanansh antonkratz vietanh0 inesdesantiago Bioinformatics WetBiology G4ID Plantandetc Genetics-of-Gambling
  • Identification of active transcriptional regulatory modules by the functional assay of DNA from nucleosome-free regions.
    Genome research (25 April 2008)
    by Mahesh Yaragatti, Claudio Basilico, Lisa Dailey
    posted to assayscisregwetlab by maximilianh on 2008-05-01 10:03:17 as ** along with 1 person djkt
  • Nuclear Dvl, c-Jun, beta-catenin, and TCF form a complex leading to stabilization of beta-catenin-TCF interaction.
    The Journal of cell biology, Vol. 180, No. 6. (24 March 2008), pp. 1087-1100.
    by XQ Gan, JY Wang, Y Xi, ZL Wu, YP Li, L Li
    posted to factors factorinteractions combination by maximilianh on 2008-05-01 09:25:57 as **
  • Studying the functional conservation of cis-regulatory modules and their transcriptional output
    BMC Bioinformatics, Vol. 9 (29 April 2008), 220.
    by Denis C Bauer, Timothy L Bailey
    posted to notconserved noalignment enhancerprediction by maximilianh on 2008-05-01 09:16:32 as ** along with 2 people and 1 group xili03 cisevol cis-regulatory-evolution
  • Promoter analysis of MADS-box genes in eudicots through phylogenetic footprinting.
    Molecular biology and evolution, Vol. 23, No. 6. (June 2006), pp. 1293-1303.
    by S De Bodt, G Theissen, Y Van de Peer
    posted to promoter noalignment composition comparison by maximilianh on 2008-04-30 15:54:45 as **
  • Highly similar noncoding genomic DNA sequences: ultraconserved, or merely widespread?
    Genome / National Research Council Canada = Génome / Conseil national de recherches Canada, Vol. 51, No. 5. (May 2008), pp. 396-397.
    by DA Hickey
    posted to whyconserved ultraconserved by maximilianh on 2008-04-30 13:01:09 as **
  • Detection and characterization of silencers and enhancer-blockers in the greater CFTR locus.
    Genome research (24 April 2008)
    by Hanna Petrykowska, Christopher Vockley, Laura Elnitski
    posted to silencer insulator enhancer cns-enhancer-screen by maximilianh on 2008-04-28 18:10:00 as **
  • 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 transcription factors combination by maximilianh on 2008-04-28 18:07:18 as ** along with 4 people and 1 group dbikard jjray eskay dquest SynBioSys
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