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Group: EisenLab - library [1111 articles]

Recent papers posted by members of the EisenLab group
  • Genomic Analysis of Adaptive Differentiation in Drosophila melanogaster
    Genetics, Vol. 179, No. 1. (1 May 2008), pp. 455-473.
    by Thomas L Turner, Mia T Levine, Melissa L Eckert, David J Begun
    posted to drosophila clinal adaptation by stajich to the group EisenLab on 2008-05-21 04:40:09 as ***** along with 1 person and 1 group pradiptaray Berkeley Mycology
  • Highly conserved non-coding sequences are associated with vertebrate development.
    PLoS Biol, Vol. 3, No. 1. (January 2005)
    by A Woolfe, M Goodson, DK Goode, P Snell, GK McEwen, T Vavouri, SF Smith, P North, H Callaway, K Kelly, K Walter, I Abnizova, W Gilks, YJ Edwards, JE Cooke, G Elgar
    posted to no-tag by Stew to the group EisenLab on 2007-09-13 18:02:33 as ***** along with 7 people and 1 group awoolfe djkt sujaikumar maximilianh cisevol rrhudson gelgar cis-regulatory-evolution
  • CONDOR: a database resource of developmentally associated conserved non-coding elements
    BMC Developmental Biology, Vol. 7 (30 August 2007), 100.
    by Adam Woolfe, Debbie K Goode, Julie Cooke, Heather Callaway, Sarah Smith, Phil Snell, Gayle K Mcewen, Greg Elgar
    posted to non-coding evolution elgar conserved cis-regulatory by Stew to the group EisenLab on 2007-09-04 16:17:41 as ***** along with 1 person maximilianh
  • Tinkering with transcription factor proteins: the role of transcription factor adaptation in developmental evolution.
    Novartis Found Symp, Vol. 284 (2007)
    by GP Wagner, AM Pyle
    posted to no-tag by Stew to the group EisenLab on 2007-08-24 05:26:51 as *****
  • Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.
    Genome Res, Vol. 15, No. 8. (August 2005), pp. 1034-1050.
    by A Siepel, G Bejerano, JS Pedersen, AS Hinrichs, M Hou, K Rosenbloom, H Clawson, J Spieth, LW Hillier, S Richards, GM Weinstock, RK Wilson, RA Gibbs, WJ Kent, W Miller, D Haussler
    posted to phastcons by brant to the group EisenLab on 2007-07-26 21:03:04 as ***** along with 14 people and 1 group pradiptaray bpb aprasad balajis eckart_bindewald indigoviolet adepace djkt olympos sujaikumar Stew cisevol dmc elfar cis-regulatory-evolution
  • Identification and characterization of multi-species conserved sequences.
    Genome Res, Vol. 13, No. 12. (December 2003), pp. 2507-2518.
    by EH Margulies, M Blanchette, D Haussler, ED Green,
    posted to mcs by brant to the group EisenLab on 2007-07-26 21:02:19 as ***** along with 5 people nklee operon ujh sujaikumar bezdan
  • Prospects for whole-genome linkage disequilibrium mapping of common disease genes.
    Nat Genet, Vol. 22, No. 2. (June 1999), pp. 139-144.
    by L Kruglyak
    posted to no-tag by indigoviolet to the group EisenLab on 2007-07-10 03:34:50 as *****
  • Advances in Genetics http://www.sciencedirect.com/science/bookseries/00652660
    posted to no-tag by indigoviolet to the group EisenLab on 2007-07-09 10:12:03 as *****
  • A gene-centric approach to genome-wide association studies
    Nature Reviews Genetics, Vol. 7, No. 11., pp. 885-891.
    by Eric Jorgenson, John S Witte
    posted to no-tag by indigoviolet to the group EisenLab on 2007-06-10 10:26:14 as ***** along with 5 people and 1 group jyuh giovanni massivemayhem dbgrant jonsta247 GeschwindLab
  • Genome-wide association studies: theoretical and practical concerns
    Nature Reviews Genetics, Vol. 6, No. 2. (01 February 2005), pp. 109-118.
    by William YS Wang, Bryan J Barratt, David G Clayton, John A Todd
    posted to no-tag by indigoviolet to the group EisenLab on 2007-06-10 10:25:58 as ***** along with 5 people oilcan pcahan1 tabu joepickrell massivemayhem
  • A stochastic model for the evolution of transcription factor binding site abundance.
    J Theor Biol (7 March 2007)
    by Günter P P Wagner, Wolfgang Otto, Vincent Lynch, Peter F F Stadler
    posted to turnover model binding_site by dpollard to the group EisenLab on 2007-05-23 01:02:56 as ***** along with 1 person and 1 group cisevol cis-regulatory-evolution
  • Topology and robustness in the Drosophila segment polarity network.
    PLoS Biol, Vol. 2, No. 6. (June 2004), pp. 805-815.
    by NT Ingolia
    posted to tech--network_modeling system--dmel_embryo key--systems_biology key--segmentation key--robustness key--regulatory_network by adepace to the group EisenLab on 2007-04-20 16:50:43 as ***** along with 1 person rklancer
  • Comparative analysis indicates regulatory neofunctionalization of yeast duplicates
    Genome Biology, Vol. 8 (05 April 2007), R50.
    by Itay Tirosh, Naama Barkai
    posted to tech--phylogenetic_comparison system--yeast key--gene_expression key--evolution by adepace to the group EisenLab on 2007-04-06 18:31:51 as ***** along with 3 people and 1 group stajich cisevol ajpowell cis-regulatory-evolution
  • Short, long, and beyond: molecular and embryological approaches to insect segmentation.
    Annu Rev Entomol, Vol. 47 (2002), pp. 669-699.
    by GK Davis, NH Patel
    posted to type--review key--segmentation key--expression_pattern key--evolution by adepace to the group EisenLab on 2007-04-05 18:05:07 as *****
  • Activation of posterior pair-rule stripe expression in response to maternal caudal and zygotic knirps activities.
    Mech Dev, Vol. 71, No. 1-2. (February 1998), pp. 177-186.
    by T Häder, A La Rosée, U Ziebold, M Busch, H Taubert, H Jäckle, R Rivera-Pomar
    posted to gene--caudal gene--h gene--kni key--crm by adepace to the group EisenLab on 2007-02-18 20:09:59 as *****
  • Redundant functions of the genes knirps and knirps-related for the establishment of anterior Drosophila head structures.
    Proc Natl Acad Sci U S A, Vol. 91, No. 18. (30 August 1994), pp. 8567-8571.
    by M González-Gaitán, M Rothe, EA Wimmer, H Taubert, H Jäckle
    posted to system--dmel_embryo key--expression_pattern key--evolution gene--kni by adepace to the group EisenLab on 2007-02-06 01:53:50 as *****
  • A self-organizing system of repressor gradients establishes segmental complexity in Drosophila.
    Nature, Vol. 426, No. 6968. (18 December 2003), pp. 849-853.
    by DE Clyde, MS Corado, X Wu, A Paré, D Papatsenko, S Small
    posted to tech--network_modeling key--expression_pattern key--binding_sites gene--kni gene--hb gene--eve by adepace to the group EisenLab on 2007-02-05 06:31:36 as *****
  • Evolutionary changes in cis and trans gene regulation
    Nature, Vol. 430, No. 6995. (1 July 2004), pp. 85-88.
    by Patricia J Wittkopp, Belinda K Haerum, Andrew G Clark
    posted to tech--phylogenetic_comparison system--drosophilidae key--molecular_evolution key--gene_expression by adepace to the group EisenLab on 2007-01-27 16:40:00 as ***** along with 8 people and 1 group lyongu dpollard balicea tabu emmahe emarker mimulus_99 cisevol cis-regulatory-evolution
  • Ecological adaptation during incipient speciation revealed by precise gene replacement.
    Science, Vol. 302, No. 5651. (5 December 2003), pp. 1754-1757.
    by AJ Greenberg, JR Moran, JA Coyne, CI Wu
    posted to tech--population_genetics system--dmel key--phenotypic_evolution by adepace to the group EisenLab on 2007-01-27 16:13:22 as ***** along with 2 people and 1 group stevanspringer RMGraze FAB-lab
  • Inference of positive and negative selection on the 5' regulatory regions of Drosophila genes.
    Mol Biol Evol, Vol. 21, No. 2. (February 2004), pp. 374-383.
    by MH Kohn, S Fang, CI Wu
    posted to tech--population_genetics system--dmel key--promoters key--molecular_evolution by adepace to the group EisenLab on 2007-01-27 16:06:00 as ***** along with 1 person and 1 group cisevol cis-regulatory-evolution
  • Genomic sources of regulatory variation in cis and in trans.
    Cell Mol Life Sci, Vol. 62, No. 16. (August 2005), pp. 1779-1783.
    by PJ Wittkopp
    posted to type--review key--regulatory_network key--molecular_evolution by adepace to the group EisenLab on 2007-01-27 16:01:43 as ***** along with 2 people brant mimulus_99
  • Genetic analysis of genome-wide variation in human gene expression.
    Nature, Vol. 430, No. 7001. (12 August 2004), pp. 743-747.
    by M Morley, CM Molony, TM Weber, JL Devlin, KG Ewens, RS Spielman, VG Cheung
    posted to tech--population_genetics system--primates key--gene_expression by adepace to the group EisenLab on 2007-01-26 21:14:36 as ***** along with 8 people snuppepuppan kentsis RMGraze qfwills vplagnol nagendraproj jo_davies mimulus_99
  • From DNA to RNA to disease and back: the 'central dogma' of regulatory disease variation.
    Hum Genomics, Vol. 2, No. 6. (June 2006), pp. 383-390.
    by BE Stranger, ET Dermitzakis
    posted to type--review tech--population_genetics system--primates key--gene_expression key--disease by adepace to the group EisenLab on 2007-01-26 00:24:29 as *****
  • Genetics of gene expression surveyed in maize, mouse and man.
    Nature, Vol. 422, No. 6929. (20 March 2003), pp. 297-302.
    by EE Schadt, SA Monks, TA Drake, AJ Lusis, N Che, V Colinayo, TG Ruff, SB Milligan, JR Lamb, G Cavet, PS Linsley, M Mao, RB Stoughton, SH Friend
    posted to tech--population_genetics tech--microarray system--primates system--mouse key--gene_expression by adepace to the group EisenLab on 2007-01-26 00:02:10 as ***** along with 6 people koller lp2 hms jo_davies parkcc mcgannd
  • Digitizing life at the level of the cell: high-performance laser-scanning microscopy and image analysis for in toto imaging of development.
    Mech Dev, Vol. 120, No. 11. (November 2003), pp. 1407-1420.
    by SG Megason, SE Fraser
    posted to type--review tech--quantitative_imaging by adepace to the group EisenLab on 2007-01-25 19:31:13 as *****
  • Automated cell lineage tracing in Caenorhabditis elegans.
    Proc Natl Acad Sci U S A, Vol. 103, No. 8. (21 February 2006), pp. 2707-2712.
    by Z Bao, JI Murray, T Boyle, SL Ooi, MJ Sandel, RH Waterston
    posted to tech--quantitative_imaging system--celegans key--expression_pattern by adepace to the group EisenLab on 2007-01-25 19:16:22 as ***** along with 1 person dlmace
  • Known maternal gradients are not sufficient for the establishment of gap domains in Drosophila melanogaster.
    Mech Dev (14 November 2006)
    by Johannes Jaeger, David H H Sharp, John Reinitz
    posted to tech--quantitative_imaging tech--network_modeling key--regulatory_network key--morphogen key--expression_pattern by adepace to the group EisenLab on 2007-01-25 19:13:38 as *****
  • Evolution of yellow gene regulation and pigmentation in Drosophila.
    Curr Biol, Vol. 12, No. 18. (17 September 2002), pp. 1547-1556.
    by PJ Wittkopp, K Vaccaro, SB Carroll
    posted to system--drosophilidae key--phenotypic_evolution key--expression_pattern gene--yellow by adepace to the group EisenLab on 2007-01-18 02:37:13 as *****
  • scute expression in Calliphora vicina reveals an ancestral pattern of longitudinal stripes on the thorax of higher Diptera.
    Development, Vol. 129, No. 3. (February 2002), pp. 563-572.
    by D Pistillo, N Skaer, P Simpson
    posted to system--diptera key--phenotypic_evolution key--gene_expression gene--proneural by adepace to the group EisenLab on 2007-01-18 02:35:00 as *****
  • Expression of achaete-scute homologues in discrete proneural clusters on the developing notum of the medfly Ceratitis capitata, suggests a common origin for the stereotyped bristle patterns of higher Diptera.
    Development, Vol. 127, No. 7. (April 2000), pp. 1411-1420.
    by C Wülbeck, P Simpson
    posted to system--diptera key--phenotypic_evolution key--expression_pattern gene--proneural by adepace to the group EisenLab on 2007-01-18 02:32:00 as *****
  • Regulatory evolution of shavenbaby/ovo underlies multiple cases of morphological parallelism.
    Nature, Vol. 424, No. 6951. (21 August 2003), pp. 935-938.
    by E Sucena, I Delon, I Jones, F Payre, DL Stern
    posted to system--drosophilidae key--phenotypic_evolution key--gene_expression gene--shavenbaby by adepace to the group EisenLab on 2007-01-18 02:27:04 as *****
  • Dynamics of Drosophila embryonic patterning network perturbed in space and time using microfluidics
    Nature, Vol. 434, No. 7037., pp. 1134-1138.
    by Elena M Lucchetta, Ji H Lee, Lydia A Fu, Nipam H Patel, Rustem F Ismagilov
    posted to system--dmel_embryo key--robustness key--regulatory_network by adepace to the group EisenLab on 2007-01-17 17:20:39 as ***** along with 1 person rklancer
  • Shavenbaby couples patterning to epidermal cell shape control.
    PLoS Biol, Vol. 4, No. 9. (September 2006)
    by H Chanut-Delalande, I Fernandes, F Roch, F Payre, S Plaza
    posted to system--drosophilidae key--phenotypic_evolution key--modularity gene--shavenbaby by adepace to the group EisenLab on 2007-01-17 17:00:53 as *****
  • Conservation of Endo16 expression in sea urchins despite evolutionary divergence in both cis and trans-acting components of transcriptional regulation.
    Development, Vol. 130, No. 17. (September 2003), pp. 4187-4199.
    by LA Romano, GA Wray
    posted to system--sea_urchin key--regulatory_network key--expression_pattern key--crm by adepace to the group EisenLab on 2007-01-17 02:28:28 as *****
  • Evolution of spatial expression pattern.
    Evol Dev, Vol. 5, No. 6. (c 2003), pp. 593-599.
    by LJ Johnson, JF Brookfield
    posted to tech--simulation key--expression_pattern key--evolution by adepace to the group EisenLab on 2007-01-17 02:24:13 as *****
  • Structure and evolution of a pair-rule interaction element: runt regulatory sequences in D. melanogaster and D. virilis
    Mechanisms of Development, Vol. 80, No. 1. (January 1999), pp. 87-99.
    by Christian Wolff, Melissa Pepling, Peter Gergen, Martin Klingler
    posted to tech--phylogenetic_comparison system--drosophilidae key--evolution key--crm gene--runt by adepace to the group EisenLab on 2007-01-17 01:09:26 as *****
  • Rapid evolution of cis-regulatory sequences via local point mutations.
    Mol Biol Evol, Vol. 18, No. 9. (September 2001), pp. 1764-1770.
    by JR Stone, GA Wray
    posted to key--molecular_evolution key--crm key--binding_sites by adepace to the group EisenLab on 2007-01-17 01:01:47 as ***** along with 1 person and 1 group cisevol cis-regulatory-evolution
  • Common genetic variants account for differences in gene expression among ethnic groups.
    Nat Genet (7 January 2007)
    by Richard S S Spielman, Laurel A A Bastone, Joshua T T Burdick, Michael Morley, Warren J J Ewens, Vivian G G Cheung
    posted to tech--population_genetics tech--microarray system--primates key--phenotypic_evolution key--gene_expression by adepace to the group EisenLab on 2007-01-16 22:06:47 as ***** along with 6 people and 3 groups aprasad balicea dchughes vplagnol mgaldzic xingxu G4ID CHIP Genetics-of-Gambling
  • Genome-wide associations of gene expression variation in humans.
    PLoS Genet, Vol. 1, No. 6. (December 2005)
    by BE Stranger, MS Forrest, AG Clark, MJ Minichiello, S Deutsch, R Lyle, S Hunt, B Kahl, SE Antonarakis, S Tavaré, P Deloukas, ET Dermitzakis
    posted to tech--population_genetics tech--microarray system--primates key--gene_expression by adepace to the group EisenLab on 2007-01-16 21:57:08 as ***** along with 7 people and 2 groups shikin rdiaz qfwills noano ashandanj jo_davies cisevol Bioinformatics cis-regulatory-evolution
  • Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments.
    Trends Genet, Vol. 21, No. 2. (February 2005), pp. 93-102.
    by JM Johnson, S Edwards, D Shoemaker, EE Schadt
    posted to type--review tech--microarray key--transcription key--gene_expression by adepace to the group EisenLab on 2007-01-16 20:17:35 as ***** along with 6 people and 2 groups greg briann cassj eoghanharr imouthesmp xico spliceml WetBiology
  • Role of duplicate genes in genetic robustness against null mutations
    Nature, Vol. 421, No. 6918. (2 January 2003), pp. 63-66.
    by Zhenglong Gu, Lars M Steinmetz, Xun Gu, Curt Scharfe, Ronald W Davis, Wen-Hsiung Li
    posted to system--yeast key--robustness by adepace to the group EisenLab on 2007-01-16 20:07:52 as ***** along with 3 people cite0000 lingchong koller
  • Evolvability is a selectable trait.
    Proc Natl Acad Sci U S A, Vol. 101, No. 32. (10 August 2004), pp. 11531-11536.
    by DJ Earl, MW Deem
    posted to key--molecular_evolution key--evolution by adepace to the group EisenLab on 2007-01-16 19:47:10 as ***** along with 4 people tomhebbron eldan Retchless jjray
  • Elucidating mechanisms underlying robustness of morphogen gradients.
    Curr Opin Genet Dev, Vol. 14, No. 4. (August 2004), pp. 435-439.
    by A Eldar, BZ Shilo, N Barkai
    posted to key--gene_expression key--morphogen by adepace to the group EisenLab on 2007-01-07 04:54:36 as *****
  • A logical analysis of the Drosophila gap-gene system.
    J Theor Biol, Vol. 211, No. 2. (21 July 2001), pp. 115-141.
    by L Sánchez, D Thieffry
    posted to key--gene_expression key--regulatory_network system--dmel_embryo tech--network_modeling by adepace to the group EisenLab on 2007-01-07 04:32:03 as ***** along with 2 people and 1 group bayesian dpollard UH - Computational Biology
  • Dynamical modelling of pattern formation during embryonic development.
    Curr Opin Genet Dev, Vol. 13, No. 4. (August 2003), pp. 326-330.
    by D Thieffry, L Sanchez
    posted to key--gene_expression system--dmel_embryo tech--network_modeling type--review by adepace to the group EisenLab on 2007-01-07 04:29:54 as *****
  • Segmenting the fly embryo: a logical analysis of the pair-rule cross-regulatory module.
    J Theor Biol, Vol. 224, No. 4. (21 October 2003), pp. 517-537.
    by L Sánchez, D Thieffry
    posted to key--gene_expression key--regulatory_network system--dmel_embryo tech--network_modeling by adepace to the group EisenLab on 2007-01-07 04:29:08 as *****
  • A genomic regulatory network for development.
    Science, Vol. 295, No. 5560. (1 March 2002), pp. 1669-1678.
    by EH Davidson, JP Rast, P Oliveri, A Ransick, C Calestani, CH Yuh, T Minokawa, G Amore, V Hinman, C Arenas-Mena, O Otim, CT Brown, CB Livi, PY Lee, R Revilla, AG Rust, Z Pan, MJ Schilstra, PJ Clarke, MI Arnone, L Rowen, RA Cameron, DR McClay, L Hood, H Bolouri
    posted to key--expression_pattern key--gene_expression key--regulatory_network key--systems_biology system--sea_urchin tech--network_modeling tech--motif_analysis by adepace to the group EisenLab on 2007-01-07 04:23:39 as ***** along with 6 people dquest edvin balajis margaritis ccr lusk
  • The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster.
    J Theor Biol, Vol. 223, No. 1. (7 July 2003), pp. 1-18.
    by R Albert, HG Othmer
    posted to key--expression_pattern key--regulatory_network system--dmel_embryo tech--network_modeling by adepace to the group EisenLab on 2007-01-02 01:31:15 as *****
  • Predicting gene expression from sequence.
    Cell, Vol. 117, No. 2. (16 April 2004), pp. 185-198.
    by MA Beer, S Tavazoie
    posted to key--crm key--expression_pattern key--transcription tech--motif_analysis tech--network_modeling by adepace to the group EisenLab on 2007-01-02 01:27:37 as ***** along with 8 people and 3 groups klo ana xwbcn nickluscombe noano koller jrest phoenixzxl structural_bioinformatics Bioinformatics EBI-regulation
  • 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 system--mouse system--primates tech--motif_analysis tech--phylogenetic_comparison by adepace to the group EisenLab on 2007-01-01 19:56:23 as ***** along with 22 people and 3 groups mariakmejia snuppepuppan BioGeek briann jtextori tmmurali okarsligil jfr balajis lyongu eckart_bindewald mtagaya fisherp nickluscombe panetebrother smiddha franklin oscarluoinau heliopais ale emptyhb maralena Bioinformatics microRNA EBI-regulation
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