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Group: BergmanLab - library [202 articles]

Neue Artikel von Mitliedern der Gruppe BergmanLab Gruppe
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  • GenomeGraphs: integrated genomic data visualization with R
    BMC Bioinformatics, Vol. 10, No. 1. (2009)
    by Steffen Durinck, James Bullard, Paul Spellman, Sandrine Dudoit
    posted to r genome_bioinformatics by cisevol to the group BergmanLab on 2009-01-07 19:29:16 as ** along with 3 people neils jmeppley GeeSharpMinor
  • BibGlimpse: The case for a light-weight reprint manager in distributed literature research
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Thomas Tuechler, Golda Velez, Alexandra Graf, David Kreil
    posted to text_mining by cisevol to the group BergmanLab on 2009-01-04 16:32:12 as ** along with 7 people guhjy nuin zimbo1 yas hpiwowar barriot dullhunk
  • Six senses in the literature. The bleak sensory landscape of biomedical texts.
    EMBO reports, Vol. 9, No. 3. (March 2008), pp. 212-215.
    by R Rodriguez-Esteban, A Rzhetsky
    posted to text_mining by cisevol to the group BergmanLab on 2009-01-03 12:25:15 as **
  • SPRINT: A new parallel framework for R
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Jon Hill, Matthew Hambley, Thorsten Forster, Muriel Mewissen, Terence Sloan, Florian Scharinger, Arthur Trew, Peter Ghazal
    posted to statistics r parallel_processing by cisevol to the group BergmanLab on 2008-12-31 14:03:06 as ** along with 9 people lptolik paszkows nuin irinamohorianu kvjanos kshameer jmeppley GeeSharpMinor pengchy
  • Annotation Sketch: a genome annotation drawing library
    Bioinformatics (23 December 2008), btn657.
    by Sascha Steinbiss, Gordon Gremme, Christin Scharfer, Malte Mader, Stefan Kurtz
    posted to visualization genome_bioinformatics by cisevol to the group BergmanLab on 2008-12-31 14:01:27 as ** along with 5 people and 1 group nuin Zephyrus jmeppley pkonings kshameer Roswell Cancer Crosstalk
  • A comprehensive collection of experimentally validated primers for Polymerase Chain Reaction quantitation of murine transcript abundance
    BMC Genomics, Vol. 9 (24 December 2008), 633.
    by Athanasia, Brian Seed
    posted to text_mining sequence_extraction by cisevol to the group BergmanLab on 2008-12-29 10:37:18 as ** along with 1 person maximilianh
  • Developmental Constraints on Vertebrate Genome Evolution
    PLoS Genet, Vol. 4, No. 12. (19 December 2008), e1000311.
    by Julien Roux, Marc Robinson-Rechavi
    posted to vertebrate hourglass_model by cisevol to the group BergmanLab on 2008-12-27 09:56:40 as ** along with 3 people JustinCrocker bpcusack djkt
  • Retroviral integration sites (RIS) mark cis-regulatory elements.
    Critical reviews in oncology/hematology (27 November 2008)
    by Cherry Ee Lin E Ng, Yoshiaki Ito, Motomi Osato
    posted to transposon cis-regulatory by cisevol to the group BergmanLab on 2008-12-09 20:03:28 as ** along with 1 group cis-regulatory-evolution
  • Assaying the regulatory potential of mammalian conserved non-coding sequences in human cells
    Genome Biology, Vol. 9 (02 December 2008), R168.
    by Catia, John A Stamatoyannopoulos
    posted to noncoding mammals by cisevol to the group BergmanLab on 2008-12-05 09:37:58 as ** along with 6 people and 2 groups djkt Zephyrus oelemento xianjun samgj maximilianh Roswell Cancer Crosstalk JacksonLab
  • Rapidly evolving human promoter regions
    Nat Genet, Vol. 40, No. 11. (November 2008), pp. 1262-1263.
    by Martin S Taylor, Tim Massingham, Yoshihide Hayashizaki, Piero Carninci, Nick Goldman, Colin A Semple
    posted to promoter mammals by cisevol to the group BergmanLab on 2008-12-04 22:33:30 as ** along with 3 people and 1 group Zephyrus caseybrown djkt R.E.A.D
  • Aggressive Assembly of Pyrosequencing Reads with Mates
    Bioinformatics (24 October 2008), btn548.
    by Arthur L Delcher, Sergey Koren, Jason R Miller, Eli Venter, Brian P Walenz, Anushka Brownley, Justin Johnson, Kelvin Li, Clark Mobarry, Granger Sutton
    posted to assembly 454 by cisevol to the group BergmanLab on 2008-12-04 21:32:37 as ** along with 4 people and 1 group jmeppley malcook Neeperando djkt SIMR bioinformatics
  • A fast algorithm for the multiple genome rearrangement problem with weighted reversals and transpositions
    BMC Bioinformatics, Vol. 9 (04 December 2008), 516.
    by Martin, Enno Ohlebusch
    posted to rearrangement by cisevol to the group BergmanLab on 2008-12-04 21:30:46 as ** along with 2 people nuin Neeperando
  • Enrichment or depletion of a GO category within a class of genes: which test?
    Bioinformatics (20 December 2006)
    by Isabelle Rivals, Léon Personnaz, Lieng Taing, Marie-Claude C Potier
    posted to review genome_bioinformatics gene_ontology by cisevol to the group BergmanLab on 2008-12-01 20:30:58 as ** along with 10 people and 2 groups cmzmasek paszkows winterschlaefer guhjy ealloza grahamc capitall zhouyu yas maralena BioinfoCIPF ParkinsonLab_at_MaRS
  • A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome.
    Nucleic Acids Res, Vol. 34, No. 8. (2006), pp. 2238-2246.
    by C Zhang, Z Xuan, S Otto, JR Hover, SR McCorkle, G Mandel, MQ Zhang
    posted to no-tag by polivares to the group BergmanLab on 2008-11-29 17:28:20 as ** along with 4 people and 1 group gpalidwor maximilianh emptyhb Auger Dead 60's
  • A Methodological Framework for the Reconstruction of Contiguous Regions of Ancestral Genomes and Its Application to Mammalian Genomes
    PLoS Comput Biol, Vol. 4, No. 11. (28 November 2008), e1000234.
    by Cedric Chauve, Eric Tannier
    posted to rearrangement mammals by cisevol to the group BergmanLab on 2008-11-29 09:34:39 as ** along with 2 people druvus djkt
  • BioLit: integrating biological literature with databases
    Nucl. Acids Res. (31 May 2008), gkn317.
    by Lynn J Fink, Sergey Kushch, Parker R Williams, Philip E Bourne
    posted to text_mining pubmedcentral by cisevol to the group BergmanLab on 2008-11-27 22:05:59 as ** along with 2 people ianturton neils
  • Fast Gene Ontology based clustering for microarray experiments.
    BioData mining, Vol. 1, No. 1. (21 November 2008)
    by Kristian Ovaska, Marko Laakso, Sampsa Hautaniemi
    posted to ontology microarray data-mining by michaelbarton to the group BergmanLab on 2008-11-27 10:59:37 as * along with 3 people guhjy renatomilani Terkko
  • Detecting influenza epidemics using search engine query data
    Nature (19 November 2008)
    by Jeremy Ginsberg, Matthew H Mohebbi, Rajan S Patel, Lynnette Brammer, Mark S Smolinski, Larry Brilliant
    posted to google flu by cisevol to the group BergmanLab on 2008-11-26 21:42:08 as ** along with 1 person rschulz
  • 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 text_mining cis-regulatory by cisevol to the group BergmanLab on 2008-11-25 16:02:01 as ** along with 9 people yas dullhunk maximilianh idonaldson mircea jsjoly isimpson bpcusack guhjy
  • Does Selection against Transcriptional Interference Shape Retroelement-Free Regions in Mammalian Genomes?
    PLoS ONE, Vol. 3, No. 11. (19 November 2008), e3760.
    by Tobias Mourier, Eske Willerslev
    posted to transposon mammals by cisevol to the group BergmanLab on 2008-11-25 08:41:30 as ** along with 2 people operon bpcusack
  • Intergenic and Genic Sequence Lengths Have Opposite Relationships with Respect to Gene Expression
    PLoS ONE, Vol. 3, No. 11. (7 November 2008), e3670.
    by Juliette Colinas, Scott C Schmidler, Gil Bohrer, Borislav Iordanov, Philip N Benfey
    posted to noncoding introns expression by cisevol to the group BergmanLab on 2008-11-18 09:17:35 as ** along with 2 people and 1 group druvus bpcusack cis-regulatory-evolution
  • Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web
    PLoS Comput Biol, Vol. 4, No. 10. (31 October 2008), e1000204.
    by Duncan Hull, Steve R Pettifer, Douglas B Kell
    posted to social citeulike bookmarking by cisevol to the group BergmanLab on 2008-11-10 21:58:56 as ** along with 82 people and 7 groups sirexkat Koh OriginalLurch sototozo akraemer thegoose kharke niallhaslam rdmagnuson JuanGiarrizzo pkonings jennialp lgibson rmasur GJNauta puchu rrbarb amarois mneeley dr_lee_xray IRTADOC zilvlan curthh mount_misery narroyo rdiaz treangen hpaces bumatic BerndBerndsen esterhasz phreeza dbk rempeljl teachingaging cs02 joseph_x_zhou continea Rosetta fletchad Betelgeuse60 tomroper 1971biblio timrwatkins rschulz ryan smithrise silberbauer natstreet pick600 xjlibod ukppdadsr robertlischke bookwormzz NIlz junwang4 taguchi tag barry kristgy caseybrown Gaetan bcondon lynnefox marekrud nuin sdgsilvana ckai1 guhjy neils carlfulp norris jago druvus alhoori emayorga GeeSharpMinor fgibson chad_davis Zephyrus leonardo dullhunk MEHTRadiology Département Hypermédia - Master NET JacksonLab McCammon kpa-resources structural_bioinformatics Roswell Cancer Crosstalk
  • PERSPECTIVE: RESURRECTING THE ROLE OF TRANSCRIPTION FACTOR CHANGE IN DEVELOPMENTAL EVOLUTION.
    Evolution; international journal of organic evolution (18 June 2008)
    by Vincent J J Lynch, Günter P P Wagner
    posted to cis-trans by maximilianh to the group BergmanLab on 2008-11-10 09:10:11 as ** along with 1 person bpcusack
  • Syntenator: Multiple gene order alignments with a gene-specific scoring function
    Algorithms for Molecular Biology, Vol. 3 (06 November 2008), 14.
    by Christian Rodelsperger, Christoph Dieterich
    posted to rearrangement by cisevol to the group BergmanLab on 2008-11-07 20:26:34 as ** along with 4 people Neeperando treangen maximilianh druvus
  • So much "junk" DNA in our genome.
    Brookhaven symposia in biology, Vol. 23 (1972), pp. 366-370.
    by S Ohno
    posted to junk_dna by cisevol to the group BergmanLab on 2008-11-05 20:13:43 as **
  • The safe-neighborhood hypothesis of junk DNA.
    Journal of theoretical biology, Vol. 90, No. 1. (7 May 1981), pp. 149-150.
    by B Grant
    posted to junk_dna by cisevol to the group BergmanLab on 2008-11-05 20:12:00 as **
  • What is "junk" DNA, and what is it worth?
    Scientific American, Vol. 296, No. 5. (May 2007)
    by A Khajavinia, W Makalowski
    posted to junk_dna by cisevol to the group BergmanLab on 2008-11-05 20:09:39 as **
  • Should scientists scrap the notion of junk DNA?
    J. Natl. Cancer Inst., Vol. 90, No. 14. (15 July 1998), pp. 1032-1033.
    by B Kuska
    posted to noncoding junk_dna by cisevol to the group BergmanLab on 2008-11-05 18:37:18 as ** along with 1 group cis-regulatory-evolution
  • fjoin: simple and efficient computation of feature overlaps.
    Journal of computational biology : a journal of computational molecular cell biology, Vol. 13, No. 8. (October 2006), pp. 1457-1464.
    by JE Richardson
    posted to overlap genome_bioinformatics by cisevol to the group BergmanLab on 2008-11-02 14:29:44 as **
  • The next generation of literature analysis: integration of genomic analysis into text mining.
    Brief Bioinform, Vol. 6, No. 3. (September 2005), pp. 287-297.
    by M Scherf, A Epple, T Werner
    posted to text_mining by cisevol to the group BergmanLab on 2008-11-02 12:54:19 as ** along with 7 people and 4 groups henk-cul daforerog irenas yas hpiwowar mroos loopback007 dbmi-nlp dbk-lab T_lab AID
  • A survey of current work in biomedical text mining.
    Brief Bioinform, Vol. 6, No. 1. (March 2005), pp. 57-71.
    by AM Cohen, WR Hersh
    posted to text_mining by cisevol to the group BergmanLab on 2008-11-02 12:53:59 as ** along with 22 people and 7 groups henk-cul lauras mitko vkwn irenas carlblesius route145 yas natsu t11 hpiwowar fisherp biblio24 bhaddow johnkork c061978 kkaiser benfqt farzanehs satre lillejul TheresaNiederberger dbk-lab Blog_and_Wiki_Research mgh-lcs hst-bmi T_lab Evidence-based-medicine IEG
  • Matching curated genome databases: a non trivial task
    BMC Genomics, Vol. 9 (24 October 2008), 501.
    by Stephane Descorps-Declere, Matthieu Barba, Bernard Labedan
    posted to genome_bioinformatics by cisevol to the group BergmanLab on 2008-10-31 19:08:53 as ** along with 4 people guhjy lptolik druvus neils
  • Promise and Pitfalls of Extending Google's PageRank Algorithm to Citation Networks
    J. Neurosci., Vol. 28, No. 44. (29 October 2008), pp. 11103-11105.
    by Sergei Maslov, Sidney Redner
    posted to page-rank citation-analysis by michaelbarton to the group BergmanLab on 2008-10-31 16:29:01 as **** along with 4 people Gaetan paulm fgibson psique
  • Seeking a New Biology through Text Mining
    Cell, Vol. 134, No. 1. (11 July 2008), pp. 9-13.
    by Andrey Rzhetsky, Michael Seringhaus, Mark Gerstein
    posted to text_mining review by cisevol to the group BergmanLab on 2008-10-28 13:09:50 as ** along with 10 people ajaymalik jfr yas icq242500260 pzoot guhjy bootsy fgibson dullhunk tharris
  • GENETICS: It's the Sequence, Stupid!
    Science, Vol. 322, No. 5900. (17 October 2008), pp. 380-381.
    by Hilary A Coller, Leonid Kruglyak
    posted to transformation mammals cis_vs_trans by cisevol to the group BergmanLab on 2008-10-25 22:08:28 as ** along with 9 people and 3 groups GustavoLacerda Zephyrus isimpson dlobo bpcusack reyez djkt ptrobajo marck Roswell Cancer Crosstalk cis-regulatory-evolution GEB
  • The Drosophila insulator proteins CTCF and CP190 link enhancer blocking to body patterning
    The EMBO Journal, Vol. aop, No. current. (06 September 2007)
    by Man Mohan, Marek Bartkuhn, Martin Herold, Angela Philippen, Nina Heinl, Imke Bardenhagen, Joerg Leers, Robert AH White, Renate Renkawitz-Pohl, Harald Saumweber, Rainer Renkawitz
    posted to gaga drosophila ctcf by cisevol to the group BergmanLab on 2008-10-21 11:24:12 as ** along with 1 person sebastien_vigneau
  • Novel approach for assessing performance of PCR cyclers used for diagnostic testing.
    Journal of clinical microbiology, Vol. 43, No. 6. (June 2005), pp. 2724-2728.
    by D Schoder, A Schmalwieser, G Schauberger, J Hoorfar, M Kuhn, M Wagner
    posted to thermal_cycler performance pcr by cisevol to the group BergmanLab on 2008-10-21 11:09:50 as **
  • Evading the annotation bottleneck: using sequence similarity to search non-sequence gene data.
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Michael Gilchrist, Mikkel Christensen, Richard Harland, Nicolas Pollet, James Smith, Naoto Ueno, Nancy Papalopulu
    posted to text_mining sequence image by cisevol to the group BergmanLab on 2008-10-17 23:39:46 as ** along with 4 people Keywan guhjy lptolik barriot
  • Caudal, a key developmental regulator, is a DPE-specific transcriptional factor.
    Genes & development, Vol. 22, No. 20. (15 October 2008), pp. 2823-2830.
    by T Juven-Gershon, JY Hsu, JT Kadonaga
    posted to promoter dpe by cisevol to the group BergmanLab on 2008-10-17 11:53:54 as **
  • BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams
    BMC Genomics, Vol. 9, No. 1. (2008)
    by Tim Hulsen, Jacob de Vlieg, Wynand Alkema
    posted to venn_diagrams by cisevol to the group BergmanLab on 2008-10-16 15:51:40 as ** along with 19 people and 1 group lscarafia jmeppley hessec GustavoLacerda stajich dswan polivares egonw ptrobajo guhjy jameswasmuth lptolik msampson pengchy natstreet druvus barriot Zephyrus thulsen Berkeley Mycology
  • ITFP: an integrated platform of mammalian transcription factors.
    Bioinformatics (Oxford, England) (19 August 2008)
    by Guangyong Zheng, Kang Tu, Qing Yang, Yun Xiong, Chaochun Wei, Lu Xie, Yangyong Zhu, Yixue Li
    posted to transcription_factor mammals by cisevol to the group BergmanLab on 2008-10-14 07:57:48 as ** along with 5 people jfr nuin pengchy druvus guhjy
  • MachiBase: a Drosophila melanogaster 5'-end mRNA transcription database.
    Nucleic acids research (8 October 2008)
    by Budrul Ahsan, Taro L L Saito, Shin-Ichi I Hashimoto, Keigo Muramatsu, Manabu Tsuda, Atsushi Sasaki, Kouji Matsushima, Toshiro Aigaki, Shinichi Morishita
    posted to core_promoter by RaquelSL to the group BergmanLab on 2008-10-13 15:42:37 as ** along with 1 person abizar
  • The Insulator Binding Protein CTCF Positions 20 Nucleosomes around Its Binding Sites across the Human Genome
    PLoS Genet, Vol. 4, No. 7. (25 July 2008), e1000138.
    by Yutao Fu, Manisha Sinha, Craig L Peterson, Zhiping Weng
    posted to genome_bioinformatics aggregator by cisevol to the group BergmanLab on 2008-10-13 15:08:25 as ** along with 5 people and 1 group madreach polivares djkt clearbluespring inesdesantiago JacksonLab
  • A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology
    Nat Biotech, Vol. 26, No. 10. (October 2008), pp. 1155-1160.
    by Markus J Herrgard, Neil Swainston, Paul Dobson, Warwick B Dunn, Yalcin K Arga, Mikko Arvas, Nils Buthgen, Simon Borger, Roeland Costenoble, Matthias Heinemann, Michael Hucka, Nicolas Le Novere, Peter Li, Wolfram Liebermeister, Monica L Mo, Ana P Oliveira, Dina Petranovic, Stephen Pettifer, Evangelos Simeonidis, Kieran Smallbone, Irena Spasie, Dieter Weichart, Roger Brent, David S Broomhead, Hans V Westerhoff, Betul Kurdar, Merja Penttila, Edda Klipp, Bernhard O Palsson, Uwe Sauer, Stephen G Oliver, Pedro Mendes, Jens Nielsen, Douglas B Kell
    posted to yeast flux-balance-analysis by michaelbarton to the group BergmanLab on 2008-10-10 14:19:56 as ***** along with 10 people alaninmcr allysonlister zwang guhjy dbk ptrobajo neils dullhunk pengchy tmmurali
  • Towards a paradigm shift in biology.
    Nature, Vol. 349, No. 6305. (10 January 1991)
    by W Gilbert
    posted to opinion genome_sequence by cisevol to the group BergmanLab on 2008-10-06 17:42:20 as ** along with 1 person polivares
  • Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairs.
    BMC Bioinformatics, Vol. 7 (2006)
    by VX Jin, GA Singer, FJ Agosto-Pérez, S Liyanarachchi, RV Davuluri
    posted to tss motif core_promoter by RaquelSL to the group BergmanLab on 2008-10-06 15:47:24 as ** along with 3 people guhjy olympos debasis
  • Advanced Genomic Data Mining
    PLoS Comput Biol, Vol. 4, No. 9. (2008), e1000121.
    by Xosé M Fernández-Suárez, Ewan Birney
    posted to tutorial r genome_browser by cisevol to the group BergmanLab on 2008-10-05 13:29:45 as ** along with 17 people daforerog kshameer jfr guhjy taguchi giovenko inesdesantiago usagi-kirin fgibson rdiaz aramesh2 sunhwan druvus mitko jandot jameswasmuth dullhunk
  • UCSC genome browser tutorial.
    Genomics (29 May 2008)
    by Ann S S Zweig, Donna Karolchik, Robert M M Kuhn, David Haussler, W James J Kent
    posted to tutorial genome_browser by cisevol to the group BergmanLab on 2008-10-04 14:27:55 as ** along with 6 people orzenil jfr ajaymalik niallhaslam dchughes guhjy
  • Automated Querying of Genome Databases
    PLoS Computational Biology, Vol. 3, No. 1. (1 January 2007), e1.
    by Peter Schattner
    posted to tutorial genome_browser by cisevol to the group BergmanLab on 2008-10-04 14:26:01 as ** along with 8 people daforerog polivares giovenko inesdesantiago druvus guhjy jfr Ayest
  • Databases, data tombs and dust in the wind
    Bioinformatics, Vol. 24, No. 19. (1 October 2008), pp. 2127-2128.
    by Jonathan D Wren, Alex Bateman
    posted to standards database by cisevol to the group BergmanLab on 2008-10-02 15:45:04 as ** along with 14 people Rosetta fgibson hpiwowar ajaymalik renatomilani sjcockell reyez Yanno druvus GeeSharpMinor neils mdstobbe dullhunk jandot
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