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Group: BergmanLab - library [126 articles]

Recent papers posted by members of the BergmanLab group
  • DNAlive: A tool for the physical analysis of DNA at the genomic scale.
    Bioinformatics (Oxford, England) (9 June 2008)
    by J Ramon R Goñi, Carlos Fenollosa, Alberto Pérez, David Torrents, Modesto Orozco
    posted to dna_structure by cisevol to the group BergmanLab on 2008-07-20 17:04:34 as ** along with 1 person sebastien_vigneau
  • Early vertebrate whole genome duplications were predated by a period of intense genome rearrangement
    Genome Res. (14 July 2008), gr.080119.108.
    by Andrew L Hufton, Detlef Groth, Martin Vingron, Hans Lehrach, Albert J Poustka, Georgia Panopoulou
    posted to vertebrate rearrangement by cisevol to the group BergmanLab on 2008-07-17 20:29:47 as ** along with 2 people alhufton neils
  • Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster
    Genome Res. (26 June 2008), gr.077131.108.
    by Alisha Holloway, David Begun, Adam Siepel, Katherine Pollard
    posted to coding cns-ranking by maximilianh to the group BergmanLab on 2008-07-07 22:22:57 as ** along with 1 person and 1 group cisevol cis-regulatory-evolution
  • Retroviral promoters in the human genome
    Bioinformatics, Vol. 24, No. 14. (15 July 2008), pp. 1563-1567.
    by Andrew B Conley, Jittima Piriyapongsa, King I Jordan
    posted to te promoter by idonaldson to the group BergmanLab on 2008-07-07 10:54:07 as ** along with 2 people and 1 group cisevol maximilianh cis-regulatory-evolution
  • A-to-I RNA editing alters less-conserved residues of highly conserved coding regions: Implications for dual functions in evolution.
    RNA (New York, N.Y.) (20 June 2008)
    by Yun Yang, Jianning Lv, Bin Gui, Heng Yin, Xiaojie Wu, Yaozhou Zhang, Yongfeng Jin
    posted to rna_editing by cisevol to the group BergmanLab on 2008-07-03 15:30:10 as **
  • Transgenesis upgrades for Drosophila melanogaster
    Development, Vol. 134, No. 20. (15 October 2007), pp. 3571-3584.
    by Koen J Venken, Hugo J Bellen
    posted to transposon drosophila by cisevol to the group BergmanLab on 2008-07-03 13:58:43 as ** along with 1 person emmahe
  • 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 gene-duplication ecoli by michaelbarton to the group BergmanLab on 2008-06-30 13:49:56 as *** along with 17 people and 3 groups aheilbut chad_davis austin AbnerCYH hryk margaritis cactus dbikard Garamonfok caseybrown biehl aalibes tmmurali dullhunk neils cmzmasek josedavid SynBioSys Centre de Recherches Interdisciplinaires GEB
  • Precise detection of rearrangement breakpoints in mammalian chromosomes
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Claire Lemaitre, Eric Tannier, Christian Gautier, Marie F Sagot
    posted to rearrangement breakpoints by cisevol to the group BergmanLab on 2008-06-19 10:56:24 as ** along with 2 people timflutre Neeperando
  • The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli
    Nature Biotechnology, Vol. 26, No. 6. (06 June 2008), pp. 659-667.
    by Adam M Feist, Bernhard
    posted to genome-scale-models ecoli by michaelbarton to the group BergmanLab on 2008-06-14 10:35:25 as ***** along with 2 people and 1 group AlexanderPico ptrobajo TNT
  • 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 transposon mammals cis-regulatory by cisevol to the group BergmanLab on 2008-05-29 22:08:58 as ** along with 1 person and 1 group pradiptaray cis-regulatory-evolution
  • Promoter elements associated with RNA Pol II stalling in the Drosophila embryo
    Proceedings of the National Academy of Sciences (27 May 2008), 0802406105.
    by David A Hendrix, Joung-Woo Hong, Julia Zeitlinger, Daniel S Rokhsar, Michael S Levine
    posted to promoter drosophila by cisevol to the group BergmanLab on 2008-05-29 21:08:32 as ** along with 1 person oelemento
  • DataGraph
    posted to no-tag by michaelbarton to the group BergmanLab on 2008-05-23 16:37:08 as read
  • Evidence against the energetic cost hypothesis for the short introns in highly expressed genes
    BMC Evolutionary Biology, Vol. 8 (20 May 2008), 154.
    by Yi-Fei Huang, Deng-Ke Niu
    posted to transcription introns cost by cisevol to the group BergmanLab on 2008-05-20 19:19:42 as ** along with 1 person and 1 group stajich Berkeley Mycology
  • Expected Gene Order Distances and Model Selection in Bacteria.
    Bioinformatics (Oxford, England) (1 April 2008)
    by Daniel Dalevi, Niklas Eriksen
    posted to gene_order bacteria by cisevol to the group BergmanLab on 2008-05-19 19:23:21 as ** along with 3 people sharpton Ema maximilianh
  • 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 6 people tmmurali isimpson fpattyn 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 8 people pradiptaray smbe2008 eskay 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 ** along with 1 person maximilianh
  • 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 ** along with 1 person pradiptaray
  • 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 *** along with 1 person klo
  • 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 3 people and 1 group pradiptaray 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 3 people and 2 groups klo 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 3 people wenhan 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 3 people pradiptaray 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
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