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Group: EisenLab - library [1110 articles]

Недавние статьи, отправленные по почте членами EisenLab группы
  • Levers and fulcrums: progress in cis-regulatory motif models
    Nature Methods, Vol. 5, No. 4., pp. 297-298.
    by Ewan Birney
    posted to cis-regulatory comparative_genomics methods motif prediction by stajich to the group EisenLab on 2008-04-07 16:11:40 as ** along with 1 person and 1 group emptyhb Berkeley Mycology
  • Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome
    Genome Res. (7 November 2007), gr.6691007.
    by Peter Andolfatto
    posted to drosophila hitchhiking positive_selection by dpollard to the group EisenLab on 2008-02-13 06:38:24 as *** along with 3 people djkt usagi-kirin mimulus_99
  • Gene Network Inference via Structural Equation Modeling in Genetical Genomics Experiments.
    Genetics (3 February 2008)
    by Bing Liu, Alberto de la Fuente, Ina Hoeschele
    posted to eqtl method network system by dpollard to the group EisenLab on 2008-02-12 23:12:26 as *** along with 5 people jyuh raiyar xingxu caseybrown smgomez
  • Independent effects of cis- and trans-regulatory variation on gene expression in Drosophila melanogaster
    Genetics (3 February 2008), genetics.107.082032.
    by Patricia J Wittkopp, Belinda K Haerum, Andrew G Clark
    posted to cis-regulatory transcription by stajich to the group EisenLab on 2008-02-04 08:13:01 as ** along with 3 people mimulus_99 brant djkt
  • Multi-scale correlations in continuous genomic data.
    Pac Symp Biocomput (2008), pp. 201-215.
    by RE Thurman, WS Noble, JA Stamatoyannopoulos
    posted to correlation histone hypersensitive nucleosome by dpollard to the group EisenLab on 2008-02-01 07:05:30 as ** along with 2 people jyuh operon
  • Using DNA duplex stability information for transcription factor binding site discovery.
    Pac Symp Biocomput (2008), pp. 453-464.
    by R Gordân, AJ Hartemink
    posted to binding_site biophysical_model method motif_detection prediction transcription_factor by dpollard to the group EisenLab on 2008-02-01 06:21:42 as ** along with 1 person bootsy
  • Use of an evolutionary model to provide evidence for a wide heterogeneity of required affinities between transcription factors and their binding sites in yeast.
    Pac Symp Biocomput (2008), pp. 489-500.
    by RW Lusk, MB Eisen
    posted to affinity binding_site transcription_factor variation yeast by dpollard to the group EisenLab on 2008-02-01 06:19:09 as read along with 1 person and 1 group maximilianh cis-regulatory-evolution
  • Alignment Uncertainty and Genomic Analysis
    Science, Vol. 319, No. 5862. (25 January 2008), pp. 473-476.
    by Karen M Wong, Marc A Suchard, John P Huelsenbeck
    posted to alignment alignment_accuracy by dpollard to the group EisenLab on 2008-02-01 06:16:51 as *** along with 19 people and 1 group adacier jyuh bpb aprasad dayjm tny djkt cjeans zwang lisa1 cactus biomcgary lilou kinestetika dandaman gjuggler renatomilani mclarenv youdon microbiology_nijmegen
  • The effect of the guide tree on multiple sequence alignments and subsequent phylogenetic analyses.
    Pac Symp Biocomput (2008), pp. 25-36.
    by S Nelesen, K Liu, D Zhao, CR Linder, T Warnow
    posted to accuracy alignment alignment_accuracy method multiple_alignment phylogeny reconstruction by dpollard to the group EisenLab on 2008-02-01 06:14:52 as **
  • Multiple RTK pathways downregulate Groucho-mediated repression in Drosophila embryogenesis.
    Development (23 January 2008)
    by Einat Cinnamon, Aharon Helman, Rachel Ben-Haroush Schyr, Amir Orian, Gerardo Jiménez, Ze'ev Paroush
    posted to post_transcriptional_modification repression by dpollard to the group EisenLab on 2008-02-01 06:09:59 as **
  • Delimiting the conserved features of hunchback function for the trunk organization of insects.
    Development (23 January 2008)
    by Henrique Marques-Souza, Manuel Aranda, Diethard Tautz
    posted to drosophila expression_pattern gene_function_evolution insects pattern targets transcription_factor tribolium by dpollard to the group EisenLab on 2008-02-01 06:06:54 as **
  • Evigan: A Hidden Variable Model for Integrating Gene Evidence for Eukaryotic Gene Prediction.
    Bioinformatics (10 January 2008)
    by Qian Liu, Aaron J J Mackey, David S S Roos, Fernando C N C Pereira
    posted to combiners comparative gene_prediction genome_annotation by stajich to the group EisenLab on 2008-01-13 21:12:18 as ** along with 2 people and 1 group gongScience mingzhi Berkeley Mycology
  • Fungal CSL transcription factors
    BMC Genomics, Vol. 8 (13 July 2007), 233.
    by Martin Prevorovsky, Frantisek Puta, Petr Folk
    posted to fungal notch transcription_factor by stajich to the group EisenLab on 2008-01-11 19:44:32 as ** along with 1 group Berkeley Mycology
  • Contrasting the Efficacy of Selection on the X and Autosomes in Drosophila.
    Mol Biol Evol (13 December 2007)
    by Nadia D D Singh, Amanda M M Larracuente, Andrew G G Clark
    posted to drosophila selection x_vs_autosomes by dpollard to the group EisenLab on 2008-01-11 18:03:53 as ****
  • CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction
    Genome Biology, Vol. 8 (20 December 2007), R269.
    by Samuel S Gross, Chuong B Do, Marina Sirota, Serafim Batzoglou
    posted to comparative_genomics gene_prediction by stajich to the group EisenLab on 2007-12-23 21:48:05 as *** along with 2 people and 1 group GustavoLacerda renatomilani Berkeley Mycology
  • The Making of a Fly: The Genetics of Animal Design
    (15 April 1992)
    by Peter A Lawrence
    posted to no-tag by indigoviolet to the group EisenLab on 2007-12-15 03:00:50 as **
  • WebLogo: A Sequence Logo Generator
    Genome Res., Vol. 14, No. 6. (1 June 2004), pp. 1188-1190.
    by Gavin E Crooks, Gary Hon, John-Marc Chandonia, Steven E Brenner
    posted to no-tag by indigoviolet to the group EisenLab on 2007-12-12 15:10:46 as ** along with 4 people and 1 group analogAI xiaobeizhao sobolevnrm yevishere baker-group
  • Sequence logos: a new way to display consensus sequences.
    Nucleic Acids Res, Vol. 18, No. 20. (25 October 1990), pp. 6097-6100.
    by TD Schneider, RM Stephens
    posted to no-tag by indigoviolet to the group EisenLab on 2007-12-12 15:08:00 as ** along with 2 people analogAI yevishere
  • Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters.
    J Mol Biol, Vol. 193, No. 4. (20 February 1987), pp. 723-750.
    by OG Berg, PH von Hippel
    posted to no-tag by indigoviolet to the group EisenLab on 2007-12-12 15:05:58 as ** along with 7 people and 1 group zambujo brant jjray lusk discreteonyxorb cisevol Ema cis-regulatory-evolution
  • An overview of the structures of protein-DNA complexes.
    Genome Biol, Vol. 1, No. 1. (2000)
    by NM Luscombe, SE Austin, HM Berman, JM Thornton
    posted to no-tag by indigoviolet to the group EisenLab on 2007-12-12 14:49:58 as ** along with 4 people kaarsinogen medic0747 emptyhb jonsta247
  • Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster.
    Bioinformatics, Vol. 21, No. 8. (15 April 2005), pp. 1747-1749.
    by CM Bergman, JW Carlson, SE Celniker
    posted to no-tag by indigoviolet to the group EisenLab on 2007-12-12 14:40:40 as ** along with 1 person and 1 group yas T_lab
  • GOstat: find statistically overrepresented Gene Ontologies within a group of genes.
    Bioinformatics, Vol. 20, No. 9. (12 June 2004), pp. 1464-1465.
    by T Beissbarth, TP Speed
    posted to no-tag by indigoviolet to the group EisenLab on 2007-12-12 14:40:11 as ** along with 5 people Yanno miguel RMGraze jdiggans yevishere
  • Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
    Nat Genet, Vol. 25, No. 1. (May 2000), pp. 25-29.
    by M Ashburner, CA Ball, JA Blake, D Botstein, H Butler, JM Cherry, AP Davis, K Dolinski, SS Dwight, JT Eppig, MA Harris, DP Hill, L Issel-Tarver, A Kasarskis, S Lewis, JC Matese, JE Richardson, M Ringwald, GM Rubin, G Sherlock
    posted to no-tag by indigoviolet to the group EisenLab on 2007-12-12 14:35:50 as ** along with 27 people and 4 groups CitoJam aalibes miguel dragonrez lfriedl chad_davis yas balajis benny dullhunk nirfriedman fisherp caporaso helliontroy zlu gurkanbebek djkt massivemayhem incovoma leechuck aconesa sgoetz javamint bootsy PunkRock natstreet naegele kdl Bioinformatics T_lab biomedical-nlp
  • 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 indigoviolet to the group EisenLab on 2007-12-12 14:32:29 as **
  • Gene Recognition Via Spliced Sequence Alignment
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 93, No. 17. (1996), pp. 9061-9066.
    by Mikhail S Gelfand, Andrey A Mironov, Pavel A Pevzner
    posted to no-tag by indigoviolet to the group EisenLab on 2007-12-12 14:20:24 as **
  • TRANSFAC: a database on transcription factors and their DNA binding sites.
    Nucleic Acids Res, Vol. 24, No. 1. (1 January 1996), pp. 238-241.
    by E Wingender, P Dietze, H Karas, R Knüppel
    posted to database by indigoviolet to the group EisenLab on 2007-12-12 14:09:36 as ** along with 2 people ea dquest
  • Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase.
    Science, Vol. 249, No. 4968. (3 August 1990), pp. 505-510.
    by C Tuerk, L Gold
    posted to no-tag by indigoviolet to the group EisenLab on 2007-12-12 14:09:06 as ** along with 1 person leelarcombe
  • Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
    Bioinformatics, Vol. 15, No. 7. (1 July 1999), pp. 563-577.
    by Gz Hertz, Gd Stormo
    posted to algorithm motif by indigoviolet to the group EisenLab on 2007-12-12 14:01:38 as ** along with 3 people tuck dquest lusk
  • A computational genomics approach to the identification of gene networks
    Nucl. Acids Res., Vol. 25, No. 18. (15 September 1997), pp. 3594-3604.
    by A Wagner
    posted to motif by indigoviolet to the group EisenLab on 2007-12-12 11:05:07 as **
  • A graph-based motif detection algorithm models complex nucleotide dependencies in transcription factor binding sites.
    Nucleic Acids Res, Vol. 34, No. 20. (2006), pp. 5730-5739.
    by BT Naughton, E Fratkin, S Batzoglou, DL Brutlag
    posted to motif by indigoviolet to the group EisenLab on 2007-12-12 11:00:03 as ** along with 3 people xili03 nklee yevishere
  • Combining evidence using p-values: application to sequence homology searches.
    Bioinformatics, Vol. 14, No. 1. (1998), pp. 48-54.
    by TL Bailey, M Gribskov
    posted to algorithm by indigoviolet to the group EisenLab on 2007-12-12 10:57:32 as **
  • Methods and statistics for combining motif match scores.
    J Comput Biol, Vol. 5, No. 2. (1998), pp. 211-221.
    by TL Bailey, M Gribskov
    posted to motif by indigoviolet to the group EisenLab on 2007-12-12 10:56:53 as **
  • Statistical extraction of Drosophila cis-regulatory modules using exhaustive assessment of local word frequency.
    BMC Bioinformatics, Vol. 4 (22 December 2003)
    by AG Nazina, DA Papatsenko
    posted to algorithm enhancer-prediction by indigoviolet to the group EisenLab on 2007-12-12 09:21:45 as **
  • Detection of cis -element clusters in higher eukaryotic DNA
    Bioinformatics, Vol. 17, No. 10. (1 October 2001), pp. 878-889.
    by Martin C Frith, Ulla Hansen, Zhiping Weng
    posted to algorithm enhancer-prediction by indigoviolet to the group EisenLab on 2007-12-12 09:15:36 as **
  • Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences
    Nucl. Acids Res., Vol. 30, No. 14. (15 July 2002), pp. 3214-3224.
    by Martin C Frith, John L Spouge, Ulla Hansen, Zhiping Weng
    posted to algorithm enhancer-prediction by indigoviolet to the group EisenLab on 2007-12-12 09:15:32 as ** along with 1 person xili03
  • JASPAR: an open-access database for eukaryotic transcription factor binding profiles.
    Nucleic Acids Res, Vol. 32, No. Database issue. (1 January 2004)
    by A Sandelin, W Alkema, P Engström, WW Wasserman, B Lenhard
    posted to database motif by indigoviolet to the group EisenLab on 2007-12-12 09:14:43 as ** along with 4 people and 1 group aalibes jguinney nklee heliopais Motif Discovery
  • ClusterDraw web server: a tool to identify and visualize clusters of binding motifs for transcription factors
    Bioinformatics, Vol. 23, No. 8. (15 April 2007), pp. 1032-1034.
    by Papatsenko, Dmitri
    posted to algorithm enhancer-prediction by indigoviolet to the group EisenLab on 2007-12-12 09:12:26 as ** along with 1 person jyuh
  • Cluster-Buster: finding dense clusters of motifs in DNA sequences
    Nucl. Acids Res., Vol. 31, No. 13. (1 July 2003), pp. 3666-3668.
    by Martin C Frith, Michael C Li, Zhiping Weng
    posted to algorithm enhancer-prediction by indigoviolet to the group EisenLab on 2007-12-12 09:10:10 as **
  • Decoding human regulatory circuits.
    Genome Res, Vol. 14, No. 10A. (October 2004), pp. 1967-1974.
    by W Thompson, MJ Palumbo, WW Wasserman, JS Liu, CE Lawrence
    posted to algorithm enhancer-prediction by indigoviolet to the group EisenLab on 2007-12-12 09:09:40 as ** along with 1 person chad_davis
  • De novo cis-regulatory module elicitation for eukaryotic genomes
    PNAS, Vol. 102, No. 20. (17 May 2005), pp. 7079-7084.
    by Mayetri Gupta, Jun S Liu
    posted to algorithm enhancer-prediction by indigoviolet to the group EisenLab on 2007-12-12 08:37:53 as ** along with 2 people tuck lusk
  • Modulefinder: a tool for computational discovery of cis regulatory modules.
    Pac Symp Biocomput (2005), pp. 519-530.
    by AA Philippakis, FS He, ML Bulyk
    posted to algorithm enhancer-prediction by indigoviolet to the group EisenLab on 2007-12-12 07:50:58 as ** along with 1 person ccr
  • Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm.
    Bioinformatics, Vol. 19 Suppl 1 (2003)
    by O Johansson, W Alkema, WW Wasserman, J Lagergren
    posted to algorithm enhancer-prediction by indigoviolet to the group EisenLab on 2007-12-12 07:47:27 as ** along with 1 person xili03
  • MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes.
    BMC Bioinformatics, Vol. 6 (2005)
    by VD Marinescu, IS Kohane, A Riva
    posted to algorithm motif by indigoviolet to the group EisenLab on 2007-12-12 05:44:21 as **
  • CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments.
    Bioinformatics, Vol. 19 Suppl 1 (2003)
    by R Sharan, I Ovcharenko, A Ben-Hur, RM Karp
    posted to algorithm enhancer-prediction by indigoviolet to the group EisenLab on 2007-12-12 05:41:45 as ** along with 1 person dquest
  • Identification of regulatory regions which confer muscle-specific gene expression
    Journal of Molecular Biology, Vol. 278, No. 1. (24 April 1998), pp. 167-181.
    by Wyeth W Wasserman, James W Fickett
    posted to algorithm enhancer-prediction by indigoviolet to the group EisenLab on 2007-12-12 05:40:08 as ** along with 1 person gpalidwor
  • Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura.
    Bioinformatics, Vol. 20, No. 16. (1 November 2004), pp. 2738-2750.
    by YH Grad, FP Roth, MS Halfon, GM Church
    posted to algorithm enhancer-prediction by indigoviolet to the group EisenLab on 2007-12-11 10:22:44 as ** along with 1 person maximilianh
  • Finding cis-regulatory modules in Drosophila using phylogenetic hidden Markov models
    Bioinformatics, Vol. 23, No. 16. (15 August 2007), pp. 2031-2037.
    by Wendy S Wong, Rasmus Nielsen
    posted to algorithm enhancer-prediction by indigoviolet to the group EisenLab on 2007-12-11 05:05:47 as ** along with 2 people cabbagezs csdhwang
  • Distinguishing protein-coding and noncoding genes in the human genome
    Proceedings of the National Academy of Sciences (26 November 2007), 0709013104.
    by Michele Clamp, Ben Fry, Mike Kamal, Xiaohui Xie, James Cuff, Michael F Lin, Manolis Kellis, Kerstin Lindblad-Toh, Eric S Lander
    posted to annotation comparative_genomics gene_finding genome_annotation human noncoding orf by stajich to the group EisenLab on 2007-12-09 07:19:20 as ** along with 14 people and 2 groups tmmurali rvosa balicea sebastien_vigneau giovanni neils cjeans cabbagezs maximilianh oelemento gjuggler slroberd renatomilani gracio FAB-lab Berkeley Mycology
  • Characterization of the Duffy gene promoter: evidence for tissue-specific abolishment of expression in Fy(a-b-) of black individuals.
    Biochem Biophys Res Commun, Vol. 222, No. 3. (24 May 1996), pp. 852-859.
    by S Iwamoto, J Li, N Sugimoto, H Okuda, E Kajii
    posted to cis_regulatory_elements expression_divergence expression_pattern expression_polymorphism human modularity regulatory_evolution regulatory_sequence_evolution by dpollard to the group EisenLab on 2007-12-05 23:03:10 as *** along with 1 group cis-regulatory-evolution
  • Detection of the signature of natural selection in humans: evidence from the Duffy blood group locus.
    Am J Hum Genet, Vol. 66, No. 5. (May 2000), pp. 1669-1679.
    by MT Hamblin, A Di Rienzo
    posted to binding_site cis_regulatory_elements regulatory_evolution regulatory_polymorphism regulatory_sequence_evolution turnover by dpollard to the group EisenLab on 2007-12-05 22:53:19 as *** along with 1 group cis-regulatory-evolution
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