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Group: BergmanLab - library [112 articles]

Недавние статьи, отправленные по почте членами BergmanLab группы
  • Report of a chimeric origin of transposable elements in a bovine-coding gene.
    Genetics and molecular research : GMR, Vol. 7, No. 1. (2008), pp. 107-116.
    by LM Almeida, ME Amaral, IT Silva, WA Silva, PK Riggs, CM Carareto
    posted to transposon mammals by cisevol to the group BergmanLab on 2008-05-16 15:24:54 as **
  • 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 transposon mammals cis-regulatory by cisevol to the group BergmanLab on 2008-05-16 15:21:47 as ** along with 1 person and 3 groups dchughes cis-regulatory-evolution G4ID Genetics-of-Gambling
  • 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 fungi expression cis-regulatory by cisevol to the group BergmanLab on 2008-05-10 09:06:08 as ** along with 1 group cis-regulatory-evolution
  • Molecular dissection of Penelope transposable element regulatory machinery
    Nucl. Acids Res. (4 March 2008), gkm1166.
    by Nataliya Schostak, Konstantin Pyatkov, Elena Zelentsova, Irina Arkhipova, Dmitrii Shagin, Irina Shagina, Elena Mudrik, Anatolii Blintsov, Ivan Clark, David J Finnegan, Michael Evgen'ev
    posted to te by idonaldson to the group BergmanLab on 2008-05-07 09:55:17 as ** along with 1 person mblwhoi
  • 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 transposon mammals cis-regulatory by cisevol to the group BergmanLab on 2008-04-26 19:38:10 as ** along with 1 person and 1 group FMoncini cis-regulatory-evolution
  • Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets.
    Genome research (14 April 2008)
    by Chaim Linhart, Yonit Halperin, Ron Shamir
    posted to tool tfbs motif-discovery by idonaldson to the group BergmanLab on 2008-04-25 14:12:52 as *** along with 3 people maximilianh ealloza maralena
  • Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs.
    J Mol Biol, Vol. 158, No. 4. (15 July 1982), pp. 573-597.
    by T Ikemura
    posted to fungi codon_bias by cisevol to the group BergmanLab on 2008-04-25 12:49:50 as ** along with 1 person bjorns
  • The Cost of Expression of Escherichia coli lac Operon Proteins Is in the Process, Not in the Products.
    Genetics, Vol. 178, No. 3. (March 2008), pp. 1653-1660.
    by DM Stoebel, AM Dean, DE Dykhuizen
    posted to expression cost bacteria by cisevol to the group BergmanLab on 2008-04-23 19:50:24 as **
  • Systems biology of SNPs
    Mol Syst Biol, Vol. 2 (4 July 2006), pp. E1-E4.
    by Neema Jamshidi, Bernhard O Palsson
    posted to snp evolutionary-rate 2008-3-mdb by michaelbarton to the group BergmanLab on 2008-04-22 18:13:07 as ***** along with 6 people and 4 groups dchughes raiyar massivemayhem cat_worth dbgrant jo_davies structural_bioinformatics G4ID steinmetzlab Genetics-of-Gambling
  • Transposable elements and the evolution of regulatory networks.
    Nat Rev Genet (27 March 2008)
    by Cédric Feschotte
    posted to networks regulation review te by idonaldson to the group BergmanLab on 2008-04-21 10:24:26 as *** along with 5 people roys cmzmasek jonsta247 djkt bootsy
  • Overlapping genes in the human and mouse genomes
    BMC Genomics, Vol. 9 (14 April 2008), 169.
    by Chaitanya R Sanna, Wen-Hsiung Li, Liqing Zhang
    posted to mammals overlapping_gene by cisevol to the group BergmanLab on 2008-04-20 13:34:08 as **
  • Non-random retention of protein-coding overlapping genes in Metazoa
    BMC Genomics, Vol. 9 (16 April 2008), 174.
    by Giulia Solda', Mikita Suyama, Paride Pelucchi, Silvia Boi, Alessandro Guffanti, Ermanno Rizzi, Peer Bork, Maria L Tenchini, Francesca D Ciccarelli
    posted to mammals overlapping_gene by cisevol to the group BergmanLab on 2008-04-20 13:33:08 as **
  • Birth and death of gene overlaps in vertebrates
    BMC Evolutionary Biology, Vol. 7 (16 October 2007), 193.
    by Izabela Makalowska, Chiao-Feng Lin, Kristina Hernandez
    posted to mammals overlapping_gene transposon by cisevol to the group BergmanLab on 2008-04-16 13:01:04 as **
  • Local conservation scores without a priori assumptions on neutral substitution rates
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Janis Dingel, Pavol Hanus, Niccolo Leonardi, Joachim Hagenauer, Juergen Zech, Jakob Mueller
    posted to model noncoding by cisevol to the group BergmanLab on 2008-04-13 16:34:32 as ** along with 3 people and 1 group aprasad maximilianh RamuAnandakrishnan cis-regulatory-evolution
  • Multiple effects govern endogenous retrovirus survival patterns in human gene introns
    Genome Biology, Vol. 7 (27 September 2006), R86.
    by Louie N van de Lagemaat, Patrik Medstrand, Dixie L Mager
    posted to erv human introns by paulcartwright to the group BergmanLab on 2008-04-02 14:31:05 as *** along with 1 person yoanjacquemin
  • Turning junk into gold: domestication of transposable elements and the creation of new genes in eukaryotes
    BioEssays, Vol. 28, No. 9. (2006), pp. 913-922.
    by Jean-Nicolas Volff
    posted to domestication genes new te by paulcartwright to the group BergmanLab on 2008-04-02 14:23:05 as *** along with 2 people and 2 groups dchughes braingrind G4ID Genetics-of-Gambling
  • Influence of the transposable element neighborhood on human gene expression in normal and tumor tissues
    Gene, Vol. 396, No. 2. (15 July 2007), pp. 303-311.
    by Emmanuelle Lerat, Marie Semon
    posted to expression gene te tissue by paulcartwright to the group BergmanLab on 2008-04-02 14:15:03 as ***
  • Phylogenetic and genomewide analyses suggest a functional relationship between kayak, the Drosophila fos homolog, and fig, a predicted protein phosphatase 2c nested within a kayak intron.
    Genetics, Vol. 177, No. 3. (November 2007), pp. 1349-1361.
    by SG Hudson, MJ Garrett, JW Carlson, G Micklem, SE Celniker, ES Goldstein, SJ Newfeld
    posted to drosophila overlapping_gene by cisevol to the group BergmanLab on 2008-03-28 07:23:37 as **
  • Modern origin of numerous alternatively spliced human introns from tandem arrays
    PNAS, Vol. 104, No. 3. (16 January 2007), pp. 882-886.
    by Degen Zhuo, Richard Madden, Sherif A Elela, Benoit Chabot
    posted to alternative human introns splicing by paulcartwright to the group BergmanLab on 2008-03-26 12:43:41 as read along with 3 people and 3 groups dchughes grahamc usagi-kirin G4ID ParkinsonLab_at_MaRS Genetics-of-Gambling
  • Comparison of multiple vertebrate genomes reveals the birth and evolution of human exons
    PNAS, Vol. 103, No. 36. (5 September 2006), pp. 13427-13432.
    by Xiang H Zhang, Lawrence A Chasin
    posted to evolution exon vertebrate by paulcartwright to the group BergmanLab on 2008-03-26 12:42:51 as read along with 4 people and 2 groups eoghanharr aprasad dayjm dchughes G4ID Genetics-of-Gambling
  • Alternative splicing and RNA selection pressure — evolutionary consequences for eukaryotic genomes
    Nature Reviews Genetics, Vol. 7, No. 7. (13 June 2006), pp. 499-509.
    by Yi Xing, Christopher Lee
    posted to alternative evolution rna splicing by paulcartwright to the group BergmanLab on 2008-03-26 12:41:52 as read along with 2 people and 1 group eoghanharr jwestbrook King_Lab
  • Gene function and expression level influence the insertion/fixation dynamics of distinct transposon families in mammalian introns
    Genome Biology, Vol. 7 (20 December 2006), R120.
    by Manuela Sironi, Giorgia Menozzi, Giacomo P Comi, Matteo Cereda, Rachele Cagliani, Nereo Bresolin, Uberto Pozzoli
    posted to families fixation insertion intron mammal transposon by paulcartwright to the group BergmanLab on 2008-03-26 12:39:42 as read along with 2 people and 2 groups dchughes FMoncini G4ID Genetics-of-Gambling
  • Fixation of conserved sequences shapes human intron size and influences transposon-insertion dynamics.
    Trends Genet, Vol. 21, No. 9. (September 2005), pp. 484-488.
    by M Sironi, G Menozzi, GP Comi, N Bresolin, R Cagliani, U Pozzoli
    posted to human insertion intron transposon by paulcartwright to the group BergmanLab on 2008-03-26 12:30:56 as read along with 2 people dchughes FMoncini
  • The origin of recent introns: transposons?
    Genome Biol, Vol. 5, No. 12. (2004)
    by SW Roy
    posted to intron transposon by paulcartwright to the group BergmanLab on 2008-03-26 12:24:37 as read
  • RNA-editing-mediated exon evolution
    Genome Biology, Vol. 8 (27 February 2007), R29.
    by Galit Lev-Maor, Rotem Sorek, Erez Y Levanon, Nurit Paz, Eli Eizenberg, Gil Ast
    posted to editing evolution exon rna by paulcartwright to the group BergmanLab on 2008-03-26 12:18:48 as read along with 1 person N0131826
  • Identification of splicing silencers and enhancers in sense Alus: a role for pseudoacceptors in splice site repression.
    Mol Cell Biol, Vol. 25, No. 16. (August 2005), pp. 6912-6920.
    by H Lei, I Vorechovsky
    posted to alu splicing by paulcartwright to the group BergmanLab on 2008-03-26 12:12:52 as read
  • Regulation of gene expression by alternative untranslated regions
    Trends in Genetics, Vol. 22, No. 3. (March 2006), pp. 119-122.
    by Thomas A Hughes
    posted to expression gene utr by paulcartwright to the group BergmanLab on 2008-03-26 12:10:13 as read along with 2 people and 2 groups bertelsen dchughes G4ID Genetics-of-Gambling
  • LINE-1 retrotransposons: Modulators of quantity and quality of mammalian gene expression?
    Bioessays, Vol. 27, No. 8. (August 2005), pp. 775-784.
    by JS Han, JD Boeke
    posted to expression gene l1 by paulcartwright to the group BergmanLab on 2008-03-26 12:08:53 as read along with 1 person ushishir
  • Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes
    Nature, Vol. 429, No. 6989. (20 May 2004), pp. 268-274.
    by Jeffrey S Han, Suzanne T Szak, Jef D Boeke
    posted to l1 transcription by paulcartwright to the group BergmanLab on 2008-03-26 12:07:35 as read along with 2 people and 2 groups dchughes saru G4ID Genetics-of-Gambling
  • Chimeric retrogenes suggest a role for the nucleolus in LINE amplification.
    FEBS Lett, Vol. 581, No. 16. (26 June 2007), pp. 2877-2882.
    by A Buzdin, E Gogvadze, MH Lebrun
    posted to chimera transposon by cisevol to the group BergmanLab on 2008-03-26 11:43:00 as **
  • At least 50% of human-specific HERV-K (HML-2) long terminal repeats serve in vivo as active promoters for host nonrepetitive DNA transcription.
    J Virol, Vol. 80, No. 21. (November 2006), pp. 10752-10762.
    by A Buzdin, E Kovalskaya-Alexandrova, E Gogvadze, E Sverdlov
    posted to mammals transposon by cisevol to the group BergmanLab on 2008-03-26 11:40:35 as ** along with 1 person yoanjacquemin
  • Exonization of the LTR transposable elements in human genome
    BMC Genomics, Vol. 8 (28 August 2007), 291.
    by Jittima Piriyapongsa, Nalini Polavarapu, Mark Borodovsky, John Mcdonald
    posted to mammals transposon by cisevol to the group BergmanLab on 2008-03-25 22:07:43 as ** along with 2 people yoanjacquemin FMoncini
  • Characterization of new hAT transposable elements in 12 Drosophila genomes.
    Genetica (14 March 2008)
    by Mauro de Freitas Ortiz, Elgion L Loreto
    posted to flies transposon by cisevol to the group BergmanLab on 2008-03-15 19:59:35 as ** along with 1 person operon
  • Computation-Based Discovery of Cis-Regulatory Modules by Hidden Markov Model.
    J Comput Biol (11 March 2008)
    by Jing Wu, Jun Xie
    posted to cis-regulatory model by cisevol to the group BergmanLab on 2008-03-13 19:45:10 as ** along with 2 people maximilianh csdhwang
  • Selective inhibition of Alu retrotransposition by APOBEC3G
    Gene, Vol. 390, No. 1-2. (1 April 2007), pp. 199-205.
    by Amy E Hulme, Hal P Bogerd, Bryan R Cullen, John V Moran
    posted to alu apobec inhibition by paulcartwright to the group BergmanLab on 2008-03-10 15:51:25 as read
  • Cellular inhibitors of long interspersed element 1 and Alu retrotransposition
    PNAS, Vol. 103, No. 23. (6 June 2006), pp. 8780-8785.
    by Hal P Bogerd, Heather L Wiegand, Amy E Hulme, Jose L Garcia-Perez, Sue K O'Shea, John V Moran, Bryan R Cullen
    posted to alu apobec inhibition l1 by paulcartwright to the group BergmanLab on 2008-03-10 14:51:16 as read along with 1 person and 2 groups dchughes G4ID Genetics-of-Gambling
  • The impact of multiple splice sites in human L1 elements
    Gene, Vol. 411, No. 1-2. (31 March 2008), pp. 38-45.
    by VP Belancio, AM Roy-Engel, P Deininger
    posted to human l1 sites splice by paulcartwright to the group BergmanLab on 2008-03-03 17:29:39 as read along with 1 person dchughes
  • A scenario on the stepwise evolution of the genetic code.
    Genomics Proteomics Bioinformatics, Vol. 5, No. 3-4. (v 2007), pp. 143-151.
    by JF Xiao, J Yu
    posted to dna evolution rna by paulcartwright to the group BergmanLab on 2008-03-03 17:01:16 as read
  • U7 snRNAs: A Computational Survey.
    Genomics Proteomics Bioinformatics, Vol. 5, No. 3-4. (v 2007), pp. 187-195.
    by M Marz, A Mosig, BM Stadler, PF Stadler
    posted to retroelement snrna u7 by paulcartwright to the group BergmanLab on 2008-03-03 16:58:04 as read
  • DA and Xiao-two giant and composite LTR-retrotransposon-like elements identified in the human genome.
    Genomics, Vol. 91, No. 3. (March 2008), pp. 249-258.
    by X Ji, S Zhao
    posted to da ltr te xiao by paulcartwright to the group BergmanLab on 2008-03-03 14:28:30 as read
  • Non-coding RNAs, epigenetics and complexity
    Gene, Vol. 410, No. 1. (29 February 2008), pp. 9-17.
    by Fabricio F Costa
    posted to epigenetics noncoding rna by paulcartwright to the group BergmanLab on 2008-03-03 12:53:32 as read along with 1 person dchughes
  • Alternative splicing of Alu exons--two arms are better than one.
    Nucleic Acids Res (14 February 2008)
    by Nurit Gal-Mark, Schraga Schwartz, Gil Ast
    posted to alu exonisation te by paulcartwright to the group BergmanLab on 2008-03-03 12:48:59 as read along with 1 person dchughes
  • 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 BergmanLab on 2008-02-29 09:36:38 as ** along with 1 group cis-regulatory-evolution
  • Great exaptations
    Journal of Biology, Vol. 7 (15 February 2008), 5.
    by Kathleen H Burns, Jef D Boeke
    posted to mammals transposon by cisevol to the group BergmanLab on 2008-02-26 11:48:41 as **
  • Transposable elements as drivers of genomic and biological diversity in vertebrates.
    Chromosome Res, Vol. 16, No. 1. (2008), pp. 203-215.
    by A Böhne, F Brunet, D Galiana-Arnoux, C Schultheis, JN Volff
    posted to te by idonaldson to the group BergmanLab on 2008-02-25 10:08:34 as ** along with 1 person dchughes
  • Transposable elements as tools for genomics and genetics in Drosophila
    Brief Funct Genomic Proteomic, Vol. 2, No. 1. (1 January 2003), pp. 57-71.
    by Edward Ryder, Steven Russell
    posted to drosophila p-element transposon by cisevol to the group BergmanLab on 2008-02-23 13:48:18 as ** along with 2 people RMGraze yulian2108
  • Combining models of protein translation and population genetics to predict protein production rates from codon usage patterns.
    Mol Biol Evol, Vol. 24, No. 11. (November 2007), pp. 2362-2372.
    by MA Gilchrist
    posted to codon_usage rate_of_evolution by cisevol to the group BergmanLab on 2008-02-21 14:11:12 as ** along with 1 person operon
  • Comparative expression analysis uncovers novel features of endogenous antisense transcription.
    Hum Mol Genet (18 February 2008)
    by Yuki Okada, Chiaki Tashiro, Koji Numata, Kazufumi Watanabe, Hajime Nakaoka, Naoyuki Yamamoto, Kazue Okubo, Rieko Ikeda, Rintaro Saito, Akio Kanai, Kuniya Abe, Masaru Tomita, Hidenori Kiyosawa
    posted to mammals overlapping_gene by cisevol to the group BergmanLab on 2008-02-20 21:33:15 as **
  • Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets
    Genome Res. (7 February 2008), gr.7080508.
    by David S Johnson, Wei Li, Benjamin D Gordon, Arindam Bhattacharjee, Bo Curry, Jayati Ghosh, Leonardo Brizuela, Jason S Carroll, Myles Brown, Paul Flicek, Christopher M Koch, Ian Dunham, Mark Bieda, Xiaoqin Xu, Peggy J Farnham, Philipp Kapranov, David A Nix, Thomas R Gingeras, Xinmin Zhang, Heather Holster, Nan Jiang, Roland Green, Jun S Song, Scott A Mccuine, Elizabeth Anton, Loan Nguyen, Nathan D Trinklein, Zhen Ye, Keith Ching, David Hawkins, Bing Ren, Peter C Scacheri, Joel Rozowsky, Alexander Karpikov, Ghia Euskirchen, Sherman Weissman, Mark Gerstein, Michael Snyder, Annie Yang, Zarmik Moqtaderi, Heather Hirsch, Hennady P Shulha, Yutao Fu, Zhiping Weng, Kevin Struhl, Richard M Myers, Jason D Lieb, Shirley X Liu
    posted to chip-on-chip comparison by idonaldson to the group BergmanLab on 2008-02-20 14:35:30 as *** along with 10 people and 1 group gracio stajich lp2 magusina jfr kengg djkt xiaobeizhao cabbagezs caseybrown Berkeley Mycology
  • Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies
    Genome Res., Vol. 17, No. 6. (1 June 2007), pp. 898-909.
    by Ghia M Euskirchen, Joel S Rozowsky, Chia-Lin Wei, Wah H Lee, Zhengdong D Zhang, Stephen Hartman, Olof Emanuelsson, Viktor Stolc, Sherman Weissman, Mark B Gerstein, Yijun Ruan, Michael Snyder
    posted to chip-on-chip chip-seq comparison by idonaldson to the group BergmanLab on 2008-02-20 14:32:16 as ** along with 5 people and 3 groups kengg jtaylor ghattem epigenetics blobbybirdman Bioinformatics Plantandetc UH - Computational Biology
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