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Group: cis-regulatory-evolution - with tag cis-regulatory [217 articles]

Recent papers posted by members of the cis-regulatory-evolution group with tag cis-regulatory
  • Evolution of the mammalian transcription factor binding repertoire via transposable elements.
    Genome research (5 August 2008)
    by Guillaume Bourque, Bernard Leong, Vinsensius B B Vega, Xi Chen, Yen Ling L Lee, Kandhadayar G G Srinivasan, Joon-Lin L Chew, Yijun Ruan, Chia-Lin L Wei, Huck-Hui H Ng, Edison T T Liu
    posted to transposon mammals cis-regulatory by cisevol to the group cis-regulatory-evolution on 2008-09-30 08:23:52 as ** along with 1 person and 1 group carlfulp BergmanLab
  • Waiting for two mutations: with applications to regulatory seqeunce evolution and the limits of Darwinian evolution.
    Genetics (14 September 2008)
    by Rick Durrett, Deena Scmidt
    posted to model cis-regulatory by cisevol to the group cis-regulatory-evolution on 2008-09-17 10:29:08 as **
  • Selective Constraints in Experimentally Defined Primate Regulatory Regions
    PLoS Genet, Vol. 4, No. 8. (2008), e1000157.
    by Daniel J Gaffney, Ran Blekhman, Jacek Majewski
    posted to cis-regulatory mammals by cisevol to the group cis-regulatory-evolution on 2008-08-19 12:05:55 as ** along with 7 people and 1 group alhufton djkt bpcusack aprasad pradiptaray caseybrown maximilianh BergmanLab
  • Genomic analysis of the relationship between gene expression variation and DNA polymorphism in Drosophila simulans
    Genome Biology, Vol. 9, No. 8. (2008)
    by Mara Lawniczak, Alisha Holloway, David Begun, Corbin Jones
    posted to cis-regulatory flies microarray variation by cisevol to the group cis-regulatory-evolution on 2008-08-17 23:46:39 as ** along with 3 people APRegier caseybrown djkt
  • A novel mode of enhancer evolution: The Tal1 stem cell enhancer recruited a MIR element to specifically boost its activity.
    Genome research (7 August 2008)
    by Aileen M M Smith, Maria-Jose J Sanchez, George A A Follows, Sarah Kinston, Ian J J Donaldson, Anthony R R Green, Berthold Göttgens
    posted to cis-regulatory mammals transposon by cisevol to the group cis-regulatory-evolution on 2008-08-11 19:51:00 as ** along with 1 person and 1 group maximilianh BergmanLab
  • Functional Analysis of Gene Duplications in Saccharomyces cerevisiae
    Genetics, Vol. 175, No. 2. (1 February 2007), pp. 933-943.
    by Yuanfang Guan, Maitreya J Dunham, Olga G Troyanskaya
    posted to cis-regulatory duplication fungi by cisevol to the group cis-regulatory-evolution on 2008-07-22 20:17:40 as ** along with 3 people TaqSys csaveanu carlk
  • Integration of Horizontally Transferred Genes into Regulatory Interaction Networks Takes Many Million Years
    Mol Biol Evol (24 December 2007), msm283.
    by Martin J Lercher, Csaba Pal
    posted to bacteria cis-regulatory horizontal_transfer by cisevol to the group cis-regulatory-evolution on 2008-07-12 06:35:02 as ** along with 4 people dquest cjeans marcio cambray
  • Sepsid even-skipped Enhancers Are Functionally Conserved in Drosophila Despite Lack of Sequence Conservation
    PLoS Genet, Vol. 4, No. 6. (27 June 2008), e1000106.
    by Emily E Hare, Brant K Peterson, Venky N Iyer, Rudolf Meier, Michael B Eisen
    posted to cis-regulatory flies by cisevol to the group cis-regulatory-evolution on 2008-06-30 21:50:06 as ** along with 7 people and 1 group maximilianh Stew emptyhb djkt stajich pradiptaray caseybrown Berkeley Mycology
  • 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 cis-regulatory vertebrate by cisevol to the group cis-regulatory-evolution on 2008-06-19 22:33:02 as ** along with 2 people maximilianh brant
  • Evolutionary changes in gene regulation from a comparative analysis of multiple Drosophila species.
    Genome informatics. International Conference on Genome Informatics, Vol. 18 (2007), pp. 12-21.
    by L Hu, D Segrè, TF Smith
    posted to cis-regulatory flies rearrangement by cisevol to the group cis-regulatory-evolution on 2008-06-12 21:57:48 as ** along with 1 person pradiptaray
  • CSMET: Comparative Genomic Motif Detection via Multi-Resolution Phylogenetic Shadowing
    PLoS Comput Biol, Vol. 4, No. 6. (6 June 2008), e1000090.
    by Pradipta Ray, Suyash Shringarpure, Mladen Kolar, Eric P Xing
    posted to cis-regulatory flies model by cisevol to the group cis-regulatory-evolution on 2008-06-07 21:39:11 as ** along with 3 people djkt Stew Ema
  • Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA
    BMC Genomics, Vol. 9 (17 May 2008), 226.
    by Nalini Polavarapu, Leonardo Marino-Ramirez, David Landsman, John F Mcdonald, King I Jordan
    posted to cis-regulatory mammals transposon by cisevol to the group cis-regulatory-evolution on 2008-05-29 22:08:58 as ** along with 2 people and 1 group pradiptaray bryankr BergmanLab
  • Regulatory divergence modifies limb length between mammals
    Genes Dev., Vol. 22, No. 2. (15 January 2008), pp. 141-151.
    by Chris J Cretekos, Ying Wang, Eric D Green, Nisc, James F Martin, John J Rasweiler, Richard R Behringer
    posted to cis-regulatory mammals by cisevol to the group cis-regulatory-evolution on 2008-05-29 10:25:38 as ** along with 2 people carlfulp dchughes
  • Co-evolution of transcription factors and their targets depends on mode of regulation
    Genome Biology, Vol. 7 (19 July 2006), R62.
    by Ruth Hershberg, Hanah Margalit
    posted to bacteria cis-regulatory transcription_factor by cisevol to the group cis-regulatory-evolution on 2008-05-26 11:18:22 as ** along with 4 people and 1 group indigoviolet dpollard cjeans PetrovLab EisenLab
  • Evolutionary origin of regulatory regions of retrogenes in Drosophila
    BMC Genomics, Vol. 9 (22 May 2008), 241.
    by Yongsheng Bai, Claudio Casola, Esther Betran
    posted to cis-regulatory duplication flies transposon by cisevol to the group cis-regulatory-evolution on 2008-05-25 09:18:47 as **
  • Resurrection of DNA function in vivo from an extinct genome.
    PLoS ONE, Vol. 3, No. 5. (2008)
    by AJ Pask, RR Behringer, MB Renfree
    posted to ancient_dna cis-regulatory mammals by cisevol to the group cis-regulatory-evolution on 2008-05-23 19:08:52 as ** along with 1 person pradiptaray
  • Microevolutionary divergence pattern of the segmentation gene hunchback in Drosophila.
    Mol Biol Evol, Vol. 15, No. 11. (November 1998), pp. 1403-1411.
    by D Tautz, L Nigro
    posted to cis-regulatory flies variation by cisevol to the group cis-regulatory-evolution on 2008-05-23 19:03:28 as ** along with 2 people balicea emptyhb
  • A test for adaptive change in DNA sequences controlling transcription.
    Proceedings. Biological sciences / The Royal Society, Vol. 261, No. 1361. (22 August 1995), pp. 203-207.
    by DL Jenkins, CA Ortori, JF Brookfield
    posted to cis-regulatory flies variation by cisevol to the group cis-regulatory-evolution on 2008-05-22 14:18:25 as **
  • Fast Evolution of Core Promoters in Primate Genomes
    Mol Biol Evol, Vol. 25, No. 6. (1 June 2008), pp. 1239-1244.
    by Han Liang, Yeong-Shin Lin, Wen-Hsiung Li
    posted to cis-regulatory mammals by cisevol to the group cis-regulatory-evolution on 2008-05-18 14:41:37 as ** along with 2 people Stew aprasad
  • Retrotransposition as a Source of New Promoters.
    Mol Biol Evol (25 March 2008)
    by Kohji Okamura, Kenta Nakai
    posted to cis-regulatory mammals by cisevol to the group cis-regulatory-evolution on 2008-05-18 14:40:55 as ** along with 3 people rschulz clearbluespring inesdesantiago
  • Transcription of two human genes from a bidirectional endogenous retrovirus promoter.
    Gene (7 November 2005)
    by Catherine A A Dunn, Mark T T Romanish, Leanne E E Gutierrez, Louie N N van de Lagemaat, Dixie L L Mager
    posted to cis-regulatory mammals transposon by cisevol to the group cis-regulatory-evolution on 2008-05-16 15:21:47 as ** along with 1 person and 3 groups dchughes G4ID Genetics-of-Gambling BergmanLab
  • Retrotransposon Tf1 is targeted to Pol II promoters by transcription activators.
    Molecular cell, Vol. 30, No. 1. (11 April 2008), pp. 98-107.
    by YE Leem, TL Ripmaster, FD Kelly, H Ebina, ME Heincelman, K Zhang, SI Grewal, CS Hoffman, HL Levin
    posted to cis-regulatory expression fungi by cisevol to the group cis-regulatory-evolution on 2008-05-10 09:06:08 as ** along with 1 group BergmanLab
  • 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 cis-regulatory flies model by cisevol to the group cis-regulatory-evolution on 2008-04-30 19:02:30 as ** along with 2 people maximilianh xili03
  • Possible involvement of SINEs in mammalian-specific brain formation.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 105, No. 11. (18 March 2008), pp. 4220-4225.
    by T Sasaki, H Nishihara, M Hirakawa, K Fujimura, M Tanaka, N Kokubo, C Kimura-Yoshida, I Matsuo, K Sumiyama, N Saitou, T Shimogori, N Okada
    posted to cis-regulatory mammals transposon by cisevol to the group cis-regulatory-evolution on 2008-04-26 19:38:10 as ** along with 1 person and 1 group FMoncini BergmanLab
  • ReXSpecies - a tool for the analysis of the evolution of gene regulation across species
    BMC Evolutionary Biology, Vol. 8 (14 April 2008), 111.
    by Stephan Struckmann, Marcos J Arauzo-Bravo, Hans R Schoeler, Rolland A Reinbold, Georg Fuellen
    posted to cis-regulatory model by cisevol to the group cis-regulatory-evolution on 2008-04-20 13:27:46 as ** along with 1 person maximilianh
  • [Reconstruction of ancestral regulatory signals along a transcription factor tree]
    Molekuliarnaia biologiia, Vol. 41, No. 5. (t 2007), pp. 918-925.
    by KIu Gorbunov, VA Liubetskiĭĭ
    posted to bacteria cis-regulatory by cisevol to the group cis-regulatory-evolution on 2008-04-06 08:00:36 as ** along with 1 person pradiptaray
  • Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs
    BMC Genomics, Vol. 9 (02 April 2008), 152.
    by Hirokazu Chiba, Riu Yamashita, Kengo Kinoshita, Kenta Nakai
    posted to cis-regulatory mammals by cisevol to the group cis-regulatory-evolution on 2008-04-04 20:12:38 as **
  • Impact of Transcription Units rearrangement on the evolution of the regulatory network of gamma-proteobacteria
    BMC Genomics, Vol. 9 (17 March 2008), 128.
    by Abel, Evelyn G Gonzalez, Vladimir E Angarica, Ana, Julio Collado-Vides
    posted to bacteria cis-regulatory by cisevol to the group cis-regulatory-evolution on 2008-03-20 18:15:11 as **
  • The Evolution of Gene Regulation Underlies a Morphological Difference between Two Drosophila Sister Species.
    Cell, Vol. 132, No. 5. (7 March 2008), pp. 783-793.
    by S Jeong, M Rebeiz, P Andolfatto, T Werner, J True, SB Carroll
    posted to cis-regulatory flies by cisevol to the group cis-regulatory-evolution on 2008-03-11 21:52:21 as ** along with 1 person Stew
  • Links between core promoter and basic gene features influence gene expression
    BMC Genomics, Vol. 9 (25 February 2008), 92.
    by Sandra Moshonov, Rofa Elfakess, Michal Golan-Mashiach, Hadar Sinvani, Rivka Dikstein
    posted to cis-regulatory by cisevol to the group cis-regulatory-evolution on 2008-02-29 09:36:38 as ** along with 1 group BergmanLab
  • Genetic Properties Influencing the Evolvability of Gene Expression.
    Science (24 May 2007)
    by Christian R R Landry, Bernardo Lemos, Scott A A Rifkin, W J J Dickinson, Daniel L L Hartl
    posted to cis-regulatory fungi microarray by cisevol to the group cis-regulatory-evolution on 2008-02-18 19:22:20 as ** along with 10 people and 2 groups jjray brant balicea sebastien_vigneau grahamc emarker heliopais caseybrown emptyhb klo EisenLab ParkinsonLab_at_MaRS
  • Genome-wide B1 retrotransposon binds the transcription factors dioxin receptor and Slug and regulates gene expression in vivo.
    Proc Natl Acad Sci U S A (25 January 2008)
    by Angel Carlos C Roman, Dixan A A Benitez, Jose M M Carvajal-Gonzalez, Pedro M M Fernandez-Salguero
    posted to cis-regulatory mammals transposon by cisevol to the group cis-regulatory-evolution on 2008-02-05 21:18:50 as ** along with 1 person and 1 group maximilianh BergmanLab
  • Do Alu repeats shape the primate transcriptome?
    Genome Biology, Vol. 9, No. 2. (2008)
    by Araxi Urrutia, Leandro B Ocana, Laurence Hurst
    posted to cis-regulatory mammals microarray transposon by cisevol to the group cis-regulatory-evolution on 2008-02-04 22:40:36 as ** along with 4 people and 1 group djkt biomcgary bpcusack dchughes BergmanLab
  • Functional evolution of the p53 regulatory network through its target response elements
    Proceedings of the National Academy of Sciences (10 January 2008), 0704694105.
    by Anil G Jegga, Alberto Inga, Daniel Menendez, Bruce J Aronow, Michael A Resnick
    posted to cis-regulatory mammals by cisevol to the group cis-regulatory-evolution on 2008-01-30 20:38:40 as ** along with 6 people brant cjeans zwang idonaldson renatomilani jyuh
  • On the relation between promoter divergence and gene expression evolution
    Mol Syst Biol, Vol. 4 (15 January 2008)
    by Itay Tirosh, Adina Weinberger, Dana Bezalel, Mark Kaganovich, Naama Barkai
    posted to cis-regulatory fungi microarray by cisevol to the group cis-regulatory-evolution on 2008-01-30 20:35:13 as ** along with 8 people and 1 group balicea kengg zwang biomcgary caseybrown renatomilani mclarenv Jporci BergmanLab
  • Computational discovery of cis-regulatory modules in Drosophila, without prior knowledge of motifs
    Genome Biology, Vol. 9, No. 1. (2008)
    by Andra Ivan, Marc Halfon, Saurabh Sinha
    posted to cis-regulatory flies model by cisevol to the group cis-regulatory-evolution on 2008-01-30 14:21:24 as ** along with 2 people maximilianh csdhwang
  • Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution
    BMC Bioinformatics, Vol. 9 (23 January 2008), 37.
    by Rekin's Janky, Jacques van Helden
    posted to bacteria cis-regulatory model by cisevol to the group cis-regulatory-evolution on 2008-01-28 09:40:50 as ** along with 1 person xili03
  • Human cis natural antisense transcripts initiated by transposable elements.
    Trends Genet (11 January 2008)
    by Andrew B B Conley, Wolfgang J J Miller, I King K Jordan
    posted to cis-regulatory mammals transposon by cisevol to the group cis-regulatory-evolution on 2008-01-20 22:36:40 as ** along with 6 people and 1 group gpappas balicea dchughes sebastien_vigneau timflutre yoanjacquemin BergmanLab
  • Transcriptional Regulation of Pituitary POMC Is Conserved at the Vertebrate Extremes Despite Great Promoter Sequence Divergence
    Mol Endocrinol, Vol. 21, No. 11. (1 November 2007), pp. 2738-2749.
    by Viviana F Bumaschny, Flavio S de Souza, Lopez, Andrea M Santangelo, Manfred Baetscher, Diego H Levi, Malcolm J Low, Marcelo Rubinstein
    posted to cis-regulatory vertebrate by cisevol to the group cis-regulatory-evolution on 2008-01-14 15:41:28 as ** along with 1 person maximilianh
  • Evolution of alternative transcriptional circuits with identical logic
    Nature, Vol. 443, No. 7110. (2006), pp. 415-420.
    by Annie E Tsong, Brian B Tuch, Hao Li, Alexander D Johnson
    posted to cis-regulatory fungi by cisevol to the group cis-regulatory-evolution on 2008-01-12 15:13:22 as ** along with 6 people and 3 groups marcius brant adepace aswin srfairclough emptyhb EisenLab BioinfoCIPF SGU-CIPF
  • Evolution of a combinatorial transcriptional circuit: a case study in yeasts.
    Cell, Vol. 115, No. 4. (14 November 2003), pp. 389-399.
    by AE Tsong, MG Miller, RM Raisner, AD Johnson
    posted to cis-regulatory fungi by cisevol to the group cis-regulatory-evolution on 2008-01-12 15:12:46 as **
  • Coordinated evolution of co-expressed gene clusters in the Drosophila transcriptome
    BMC Evolutionary Biology, Vol. 8 (07 January 2008), 2.
    by Jason G Mezey, Sergey V Nuzhdin, Fangfei Ye, Corbin D Jones
    posted to cis-regulatory flies microarray by cisevol to the group cis-regulatory-evolution on 2008-01-09 21:40:08 as **
  • Evolution of functionally conserved enhancers can be accelerated in large populations: a population-genetic model.
    Proc Biol Sci, Vol. 269, No. 1494. (7 May 2002), pp. 953-960.
    by AJ Carter, GP Wagner
    posted to cis-regulatory model by cisevol to the group cis-regulatory-evolution on 2007-12-15 13:35:20 as ** along with 1 person emptyhb
  • Fine-Tuning Enhancer Models to Predict Transcriptional Targets across Multiple Genomes.
    PLoS ONE, Vol. 2, No. 11. (2007)
    by S Aerts, J van Helden, O Sand, BA Hassan
    posted to cis-regulatory flies model by maximilianh to the group cis-regulatory-evolution on 2007-12-08 15:34:13 as ** along with 4 people brant idonaldson barwil isimpson
  • Prediction of synergistic transcription factors by function conservation
    Genome Biology, Vol. 8, No. 12. (2007)
    by Zihua Hu, Boyu Hu, James Collins
    posted to cis-regulatory mammals model noalignment by maximilianh to the group cis-regulatory-evolution on 2007-12-08 15:12:16 as ** along with 3 people cjeans nklee ale
  • 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 mammals variation by dpollard to the group cis-regulatory-evolution on 2007-12-05 23:03:10 as *** along with 1 group EisenLab
  • 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 cis-regulatory mammals variation by dpollard to the group cis-regulatory-evolution on 2007-12-05 22:53:19 as *** along with 1 group EisenLab
  • Disruption of a GATA motif in the Duffy gene promoter abolishes erythroid gene expression in Duffy-negative individuals.
    Nat Genet, Vol. 10, No. 2. (June 1995), pp. 224-228.
    by C Tournamille, Y Colin, JP Cartron, C Le Van Kim
    posted to cis-regulatory mammals variation by dpollard to the group cis-regulatory-evolution on 2007-12-05 22:51:02 as *** along with 1 group EisenLab
  • Regulation of Body Pigmentation by the Abdominal-B Hox Protein and Its Gain and Loss in Drosophila Evolution
    Cell, Vol. 125, No. 7. (30 June 2006), pp. 1387-1399.
    by Sangyun Jeong, Antonis Rokas, Sean B Carroll
    posted to cis-regulatory flies by dpollard to the group cis-regulatory-evolution on 2007-12-05 22:44:47 as read along with 1 person and 1 group emilyhare EisenLab
  • A transposable element inserted just 5' to a Drosophila glue protein gene alters gene expression and chromatin structure.
    Cell, Vol. 34, No. 1. (August 1983), pp. 75-84.
    by W McGinnis, AW Shermoen, SK Beckendorf
    posted to cis-regulatory flies transposon by cisevol to the group cis-regulatory-evolution on 2007-12-01 16:48:38 as ** along with 1 group BergmanLab
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