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Tag promotors [39 articles]

Recent papers classified by the tag promotors.
  • oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes.
    Nucleic Acids Res, Vol. 33, No. 10. (2005), pp. 3154-3164.
    by Ho JH Sui, JR Mortimer, DJ Arenillas, J Brumm, CJ Walsh, BP Kennedy, WW Wasserman
    posted to promotors by tmmurali on 2005-06-17 19:05:26 as ** along with 2 people heliopais gpalidwor
  • Systematic discovery of regulatory motifs in human promoters and 3[prime] UTRs by comparison of several mammals
    Nature, Vol. aop, No. current. (27 February 2005)
    by Xiaohui Xie, Jun Lu, EJ Kulbokas, Todd R Golub, Vamsi Mootha, Kerstin Lindblad-Toh, Eric S Lander, Manolis Kellis
    posted to microrna_targets promotors by tmmurali on 2005-06-10 23:57:28 as *** along with 23 people and 4 groups kieran101 snuppepuppan BioGeek briann jtextori okarsligil jfr balajis lyongu eckart_bindewald mtagaya adepace fisherp nickluscombe panetebrother smiddha franklin oscarluoinau heliopais ale emptyhb maralena mariakmejia Bioinformatics EisenLab microRNA EBI-regulation
  • TAMO: a flexible, object-oriented framework for analyzing transcriptional regulation using DNA-sequence motifs.
    Bioinformatics (19 May 2005)
    by D Benjamin B Gordon, Lena Nekludova, Scott McCallum, Ernest Fraenkel
    posted to promotors by tmmurali on 2005-06-23 21:29:07 as ****
  • 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 learning_one_class promotors by tmmurali on 2007-11-17 18:22:44 as ** along with 6 people and 1 group cassj chad_davis cabbagezs maximilianh idonaldson isimpson csb_journal_club_public
  • Predicting expression patterns from regulatory sequence in Drosophila segmentation
    Nature (02 January 2008)
    by Eran Segal, Tali Raveh-Sadka, Mark Schroeder, Ulrich Unnerstall, Ulrike Gaul
    posted to promotors by tmmurali on 2008-01-30 21:30:49 as **** along with 15 people ptrobajo isimpson dakelley eckart_bindewald djkt bootsy biomcgary idonaldson roys emptyhb pkharchenko meiklej jrest tresch siebert
  • Subtle motifs: defining the limits of motif finding algorithms.
    Bioinformatics, Vol. 18, No. 10. (October 2002), pp. 1382-1390.
    by U Keich, PA Pevzner
    posted to promotors by tmmurali on 2005-06-17 17:11:52 as ** along with 3 people and 1 group okarsligil dquest nedwards Bioinformatics
  • Computational identification of transcriptional regulatory elements in DNA sequence
    Nucl. Acids Res., Vol. 34, No. 12. (19 July 2006), pp. 3585-3598.
    by Debraj Guhathakurta
    posted to promotors by tmmurali on 2006-07-26 18:01:51 as **** along with 10 people and 1 group aprasad isimpson jfr johncumbers reidy giovanni cabbagezs ankur_iitg vietanh0 xili03 GeschwindLab
  • Identifying the conserved network of cis-regulatory sites of a eukaryotic genome
    PNAS, Vol. 102, No. 48. (29 November 2005), pp. 17400-17405.
    by Ting Wang, Gary D Stormo
    posted to promotors by tmmurali on 2005-11-29 22:11:55 as **** along with 4 people and 2 groups indigoviolet kaspermunch emilyhare sconlan Bioinformatics EisenLab
  • DNA methylation immediately adjacent to active histone marking does not silence transcription.
    Nucleic Acids Res (3 January 2007)
    by Arie B B Brinkman, Sebastiaan W C W Pennings, Georgia G G Braliou, Luc E G E Rietveld, Hendrik G G Stunnenberg
    posted to active dna epigenetics histones methylation promotors silencing by kjglennie on 2008-08-28 16:37:32 as ** along with 1 person Anders
  • Evolution and Selection in Yeast Promoters: Analyzing the Combined Effect of Diverse Transcription Factor Binding Sites
    PLoS Computational Biology, Vol. 4, No. 1. (1 January 2008), e7.
    by Daniela Raijman, Ron Shamir, Amos Tanay
    posted to evolution promotors by Garamonfok to the group BioinfoCIPF on 2008-01-25 20:03:47 as ***** along with 8 people marck xili03 aalibes sebastien_vigneau lusk nklee maximilianh emptyhb
  • Clusters of Co-expressed Genes in Mammalian Genomes Are Conserved by Natural Selection
    Molecular Biology and Evolution, Vol. 22, No. 3. (March 2005), pp. 767-775.
    by Gregory AC Singer, Andrew T Lloyd, Lukasz B Huminiecki, Kenneth H Wolfe
    posted to coevolution coexpression evolution expression genome promotors by Garamonfok on 2007-11-09 17:17:18 as ***** along with 2 people jeremymiller JeffR100
  • Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments
    BMC Bioinformatics, Vol. 7 (14 August 2006), 376.
    by Daniel A Pollard, Alan M Moses, Venky N Iyer, Michael B Eisen
    posted to evolution promotors statistics by Garamonfok on 2007-09-24 14:48:30 as read along with 6 people and 2 groups aprasad dpollard lusk lilou cisevol emptyhb EisenLab cis-regulatory-evolution
  • ABS: a database of Annotated regulatory Binding Sites from orthologous promoters.
    Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006)
    by E Blanco, D Farré, MM Albà, X Messeguer, R Guigó
    posted to evolution promotors tools by Garamonfok on 2007-09-24 18:31:58 as **** along with 3 people Schmidtc treangen guhjy
  • MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model.
    Genome Biol, Vol. 5, No. 12. (2004)
    by AM Moses, DY Chiang, DA Pollard, VN Iyer, MB Eisen
    posted to evolution promotors statistics tools by Garamonfok on 2007-09-24 14:23:37 as read along with 4 people and 2 groups tuck indigoviolet lusk cisevol EisenLab cis-regulatory-evolution
  • Evolvability and hierarchy in rewired bacterial gene networks
    Nature, Vol. 452, No. 7189. (17 April 2008), pp. 840-845.
    by Mark Isalan, Caroline Lemerle, Konstantinos Michalodimitrakis, Carsten Horn, Pedro Beltrao, Emanuele Raineri, Mireia Garriga-Canut, Luis Serrano
    posted to bacteria evolution expression promotors by Garamonfok on 2008-04-25 11:23:09 as ** along with 19 people and 4 groups kaarsinogen aalibes tmmurali dullhunk neils cmzmasek AbnerCYH josedavid biehl caseybrown austin hryk dbikard cactus margaritis chad_davis michaelbarton aheilbut zwang GEB Centre de Recherches Interdisciplinaires SynBioSys BergmanLab
  • Functional Architecture and Evolution of Transcriptional Elements That Drive Gene Coexpression
    Science, Vol. 317, No. 5844. (14 September 2007), pp. 1557-1560.
    by Christopher D Brown, David S Johnson, Arend Sidow
    posted to evolution expression project_coexcoev promotors by Garamonfok on 2007-10-24 12:40:19 as read along with 9 people and 2 groups dpollard djkt joepickrell zwang Stew mimulus_99 maximilianh cisevol emptyhb EisenLab cis-regulatory-evolution
  • Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene
    Nature, Vol. 440, No. 7087., pp. 1050-1053.
    by Benjamin Prud'homme, Nicolas Gompel, Antonis Rokas, Victoria A Kassner, Thomas M Williams, Shu-Dan Yeh, John R True, Sean B Carroll
    posted to promotors by Garamonfok on 2007-09-24 14:56:10 as *** along with 9 people and 1 group carlfulp RMGraze dpollard balicea tny adepace ranb blobbybirdman emptyhb EisenLab
  • Genes involved in complex adaptive processes tend to have highly conserved upstream regions in mammalian genomes.
    BMC Genomics, Vol. 6 (27 November 2005)
    by S Lee, I Kohane, S Kasif
    posted to evolution promotors by Garamonfok on 2007-09-04 12:38:39 as read along with 2 people and 1 group dpollard balicea EisenLab
  • The gene regulatory logic of transcription factor evolution.
    Trends in ecology & evolution (Personal edition) (21 May 2008)
    by Günter P P Wagner, Vincent J J Lynch
    posted to evolution promotors by Garamonfok on 2008-07-20 10:59:49 as ** along with 2 people Stew bpcusack
  • Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome
    Genome Res., Vol. 17, No. 6. (1 June 2007), pp. 720-731.
    by Nathan D Trinklein, Ulas Karaoz, Jiaqian Wu, Anason Halees, Force, Patrick J Collins, Deyou Zheng, Zhengdong D Zhang, Mark B Gerstein, Michael Snyder, Richard M Myers, Zhiping Weng
    posted to encode evolution promotors by Garamonfok on 2007-09-24 18:20:35 as **** along with 5 people guhjy djkt olympos cjeans jasonflannick
  • Housekeeping genes tend to show reduced upstream sequence conservation
    Genome Biology, Vol. 8 (13 July 2007), R140.
    by Domenec Farré, Nicolas Bellora, Loris Mularoni, Xavier Messeguer, Mar
    posted to evolution promotors by Garamonfok on 2007-09-03 15:08:40 as read along with 4 people and 3 groups treangen djkt cisevol gjuggler Bioinformatics cis-regulatory-evolution BergmanLab
  • Natural selection on human microRNA binding sites inferred from SNP data.
    Nat Genet (29 October 2006)
    by Kevin Chen, Nikolaus Rajewsky
    posted to evolution mirna promotors snp by Garamonfok on 2007-10-05 13:12:34 as read along with 11 people and 3 groups capitall lp2 jfr tardigrade andersbj mtagaya ealloza plofje heliopais bpcusack ramensky Bioinformatics microRNA BioinfoCIPF
  • Enhancer sequence conservation between vertebrates is favoured in developmental regulator genes
    Trends in Genetics, Vol. 21, No. 4. (April 2005), pp. 207-210.
    by Charles Plessy, Thomas Dickmeis, Frederic Chalmel, Uwe Strahle
    posted to evolution promotors by Garamonfok on 2008-03-11 10:42:27 as **
  • How microRNAs choose their targets
    Nat Genet, Vol. 39, No. 10. (October 2007), pp. 1191-1192.
    by Ivo L Hofacker
    posted to mirna mrna-structure promotors by Garamonfok on 2007-10-11 14:54:19 as read along with 7 people and 2 groups jfr dchughes rdiaz ealloza epigenetics heliopais yavanna microRNA BioinfoCIPF
  • Adaptive evolution of Hox-gene homeodomains after cluster duplications
    BMC Evolutionary Biology, Vol. 6 (01 November 2006), 86.
    by Vincent J Lynch, Jutta J Roth, Gunter P Wagner
    posted to evolution promotors by Garamonfok on 2007-10-04 16:17:12 as read
  • Phylogenetic Simulation of Promoter Evolution: Estimation and Modeling of Binding Site Turnover Events and Assessing Their Impact on Alignment Tools
    Genome Biology, Vol. 8 (24 October 2007), R225.
    by Weichun Huang, Joseph R Nevins, Uwe Ohler
    posted to evolution genome promotors tools by Garamonfok on 2007-10-26 10:37:37 as **** along with 4 people and 2 groups dpollard djkt stajich maximilianh EisenLab cis-regulatory-evolution
  • Finding cis-regulatory elements using comparative genomics: Some lessons from ENCODE data.
    Genome Res, Vol. 17, No. 6. (June 2007), pp. 775-786.
    by DC King, J Taylor, Y Zhang, Y Cheng, HA Lawson, J Martin, , F Chiaromonte, W Miller, RC Hardison
    posted to encode evolution promotors by Garamonfok on 2007-09-24 18:27:23 as **** along with 2 people and 2 groups ghattem Stew Bioinformatics UH - Computational Biology
  • Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution
    Nat Genet, Vol. 39, No. 9. (2007), pp. 1140-1144.
    by Ralph Haygood, Olivier Fedrigo, Brian Hanson, Ken-Daigoro Yokoyama, Gregory A Wray
    posted to evolution genome promotors by Garamonfok on 2007-10-23 16:19:05 as read along with 6 people and 4 groups dchughes djkt mimulus_99 cisevol candypmcg mjoach G4ID Genetics-of-Gambling cis-regulatory-evolution Fasting, food and evolution
  • Genomic regulatory regions: insights from comparative sequence analysis
    Current Opinion in Genetics & Development, Vol. 13, No. 6. (December 2003), pp. 604-610.
    by Gregory M Cooper, Arend Sidow
    posted to evolution promotors statistics tools by Garamonfok on 2007-09-10 15:09:15 as ***
  • Transcription Factor Map Alignment of Promoter Regions
    PLoS Computational Biology, Vol. 2, No. 5. (1 May 2006), e49.
    by Enrique Blanco, Xavier Messeguer, Temple F Smith, Roderic Guigó
    posted to evolution promotors by Garamonfok on 2007-09-24 18:34:45 as **** along with 2 people reidy GustavoLacerda
  • Revealing posttranscriptional regulatory elements through network-level conservation.
    PLoS Comput Biol, Vol. 1, No. 7. (December 2005)
    by CS Chan, O Elemento, S Tavazoie
    posted to evolution mirna promotors by Garamonfok on 2007-10-16 17:37:20 as **** along with 4 people and 2 groups tharris balicea koller grahamc C. elegans / WormBase ParkinsonLab_at_MaRS
  • The evolution of gene regulation by transcription factors and microRNAs
    Nat Rev Genet, Vol. 8, No. 2. (February 2007), pp. 93-103.
    by Kevin Chen, Nikolaus Rajewsky
    posted to evolution mirna promotors by Garamonfok on 2007-10-01 19:26:17 as read along with 20 people and 4 groups aprasad jfr indigoviolet tardigrade andersbj dchughes emilyhare penka cdawson aswin plofje dbikard joepickrell EeHawk3 jayster4 dandaman maralena heliopais bootsy robertkofler EisenLab microRNA Nie GIG
  • notes Distribution and intensity of constraint in mammalian genomic sequence.
    Genome Res, Vol. 15, No. 7. (July 2005), pp. 901-913.
    by GM Cooper, EA Stone, G Asimenos, ED Green, S Batzoglou, A Sidow
    posted to evolution genome promotors statistics tools by Garamonfok on 2007-09-10 16:59:27 as ***** along with 5 people operon aprasad nirfriedman JeffR100 tale
  • Spatial preferences of microRNA targets in 3' untranslated regions
    BMC Genomics, Vol. 8 (07 June 2007), 152.
    by William H Majoros, Uwe Ohler
    posted to genome mirna promotors by Garamonfok on 2007-10-11 11:21:59 as read along with 3 people and 1 group andersbj heliopais jfr microRNA
  • Inference of miRNA targets using evolutionary conservation and pathway analysis
    BMC Bioinformatics, Vol. 8 (01 March 2007), 69.
    by Dimos Gaidatzis, Erik van Nimwegen, Jean Hausser, Mihaela Zavolan
    posted to evolution method mirna promotors statistics by Garamonfok on 2007-10-11 11:02:51 as read along with 7 people and 1 group jfr Lauren_Jones tardigrade andersbj dquest heliopais maralena microRNA
  • microRNA target predictions in animals.
    Nat Genet, Vol. 38 Suppl 1, No. 6s. (June 2006)
    by Nikolaus Rajewsky
    posted to evolution mirna promotors tools by Garamonfok on 2007-10-05 13:06:13 as read along with 9 people and 4 groups jfr marcius balicea andersbj mtagaya chenlc03 physics heliopais maralena Bioinformatics microRNA BioinfoCIPF SGU-CIPF
  • Intronic microRNA precursors that bypass Drosha processing
    Nature (24 June 2007)
    by Graham J Ruby, Calvin H Jan, David P Bartel
    posted to mirna promotors by Garamonfok on 2007-10-10 12:59:37 as **** along with 8 people and 5 groups GustavoLacerda tharris dpollard gpalidwor andersbj stajich ale tolot27 C. elegans / WormBase Bioinformatics EisenLab microRNA Berkeley Mycology
  • Prediction and validation of microRNAs and their targets.
    FEBS Lett, Vol. 579, No. 26. (31 October 2005), pp. 5904-5910.
    by I Bentwich
    posted to method mirna promotors statistics by Garamonfok on 2007-10-16 15:34:07 as read along with 5 people and 2 groups heliopais jfr mortenlindow mtagaya cdawson microRNA GIG
  • Retrotransposition as a Source of New Promoters.
    Mol Biol Evol (25 March 2008)
    by Kohji Okamura, Kenta Nakai
    posted to promotors retrogenes by clearbluespring on 2008-07-11 14:26:18 as ** along with 4 people and 1 group Glires rschulz cisevol inesdesantiago cis-regulatory-evolution
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