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Items: 1 to 50 of 70

1.

Trapping a somatic endogenous retrovirus into a germline piRNA cluster immunizes the germline against further invasion.

Duc C, Yoth M, Jensen S, Mouniée N, Bergman CM, Vaury C, Brasset E.

Genome Biol. 2019 Jun 21;20(1):127. doi: 10.1186/s13059-019-1736-x.

2.

Whole genome screen reveals a novel relationship between Wolbachia levels and Drosophila host translation.

Grobler Y, Yun CY, Kahler DJ, Bergman CM, Lee H, Oliver B, Lehmann R.

PLoS Pathog. 2018 Nov 13;14(11):e1007445. doi: 10.1371/journal.ppat.1007445. eCollection 2018 Nov.

3.

Are ocean conditions and plastic debris resulting in a 'double whammy' for marine birds?

Drever MC, Provencher JF, O'Hara PD, Wilson L, Bowes V, Bergman CM.

Mar Pollut Bull. 2018 Aug;133:684-692. doi: 10.1016/j.marpolbul.2018.06.028. Epub 2018 Jun 19.

4.

Horizontal transfer and proliferation of Tsu4 in Saccharomyces paradoxus.

Bergman CM.

Mob DNA. 2018 Jun 12;9:18. doi: 10.1186/s13100-018-0122-7. eCollection 2018.

5.

Conserved Noncoding Elements Influence the Transposable Element Landscape in Drosophila.

Manee MM, Jackson J, Bergman CM.

Genome Biol Evol. 2018 Jun 1;10(6):1533-1545. doi: 10.1093/gbe/evy104.

6.

Genomic analysis of P elements in natural populations of Drosophila melanogaster.

Bergman CM, Han S, Nelson MG, Bondarenko V, Kozeretska I.

PeerJ. 2017 Sep 15;5:e3824. doi: 10.7717/peerj.3824. eCollection 2017.

7.

McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole-Genome Shotgun Sequencing Data.

Nelson MG, Linheiro RS, Bergman CM.

G3 (Bethesda). 2017 Aug 7;7(8):2763-2778. doi: 10.1534/g3.117.043893.

8.

Bringing PLOS Genetics Editors to Preprint Servers.

Barsh GS, Bergman CM, Brown CD, Singh ND, Copenhaver GP.

PLoS Genet. 2016 Dec 1;12(12):e1006448. doi: 10.1371/journal.pgen.1006448. eCollection 2016 Dec. No abstract available.

9.

Rare recombination events generate sequence diversity among balancer chromosomes in Drosophila melanogaster.

Miller DE, Cook KR, Yeganeh Kazemi N, Smith CB, Cockrell AJ, Hawley RS, Bergman CM.

Proc Natl Acad Sci U S A. 2016 Mar 8;113(10):E1352-61. doi: 10.1073/pnas.1601232113. Epub 2016 Feb 22.

10.

Unique transposon landscapes are pervasive across Drosophila melanogaster genomes.

Rahman R, Chirn GW, Kanodia A, Sytnikova YA, Brembs B, Bergman CM, Lau NC.

Nucleic Acids Res. 2015 Dec 15;43(22):10655-72. doi: 10.1093/nar/gkv1193. Epub 2015 Nov 17.

11.

Dynamics of Wolbachia pipientis Gene Expression Across the Drosophila melanogaster Life Cycle.

Gutzwiller F, Carmo CR, Miller DE, Rice DW, Newton IL, Hawley RS, Teixeira L, Bergman CM.

G3 (Bethesda). 2015 Oct 23;5(12):2843-56. doi: 10.1534/g3.115.021931.

12.

Drosophila innate immunity: regional and functional specialization of prophenoloxidases.

Dudzic JP, Kondo S, Ueda R, Bergman CM, Lemaitre B.

BMC Biol. 2015 Oct 1;13:81. doi: 10.1186/s12915-015-0193-6.

13.

Strain-specific and pooled genome sequences for populations of Drosophila melanogaster from three continents.

Bergman CM, Haddrill PR.

F1000Res. 2015 Jan 29;4:31. doi: 10.12688/f1000research.6090.1. eCollection 2015.

14.

Long-read, whole-genome shotgun sequence data for five model organisms.

Kim KE, Peluso P, Babayan P, Yeadon PJ, Yu C, Fisher WW, Chin CS, Rapicavoli NA, Rank DR, Li J, Catcheside DE, Celniker SE, Phillippy AM, Bergman CM, Landolin JM.

Sci Data. 2014 Nov 25;1:140045. doi: 10.1038/sdata.2014.45. eCollection 2014.

15.

An age-of-allele test of neutrality for transposable element insertions.

Blumenstiel JP, Chen X, He M, Bergman CM.

Genetics. 2014 Feb;196(2):523-38. doi: 10.1534/genetics.113.158147. Epub 2013 Dec 13.

16.

Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster.

Richardson MF, Weinert LA, Welch JJ, Linheiro RS, Magwire MM, Jiggins FM, Bergman CM.

PLoS Genet. 2012;8(12):e1003129. doi: 10.1371/journal.pgen.1003129. Epub 2012 Dec 20.

17.

Evolutionary genomics of transposable elements in Saccharomyces cerevisiae.

Carr M, Bensasson D, Bergman CM.

PLoS One. 2012;7(11):e50978. doi: 10.1371/journal.pone.0050978. Epub 2012 Nov 30.

18.
19.

BioContext: an integrated text mining system for large-scale extraction and contextualization of biomolecular events.

Gerner M, Sarafraz F, Bergman CM, Nenadic G.

Bioinformatics. 2012 Aug 15;28(16):2154-61. doi: 10.1093/bioinformatics/bts332. Epub 2012 Jun 17.

20.

A switch in pathogenic mechanism in myelin oligodendrocyte glycoprotein-induced experimental autoimmune encephalomyelitis in IFN-γ-inducible lysosomal thiol reductase-free mice.

Bergman CM, Marta CB, Maric M, Pfeiffer SE, Cresswell P, Ruddle NH.

J Immunol. 2012 Jun 15;188(12):6001-9. doi: 10.4049/jimmunol.1101898. Epub 2012 May 14.

21.

Whole genome resequencing reveals natural target site preferences of transposable elements in Drosophila melanogaster.

Linheiro RS, Bergman CM.

PLoS One. 2012;7(2):e30008. doi: 10.1371/journal.pone.0030008. Epub 2012 Feb 9.

22.

The Drosophila melanogaster Genetic Reference Panel.

Mackay TF, Richards S, Stone EA, Barbadilla A, Ayroles JF, Zhu D, Casillas S, Han Y, Magwire MM, Cridland JM, Richardson MF, Anholt RR, Barrón M, Bess C, Blankenburg KP, Carbone MA, Castellano D, Chaboub L, Duncan L, Harris Z, Javaid M, Jayaseelan JC, Jhangiani SN, Jordan KW, Lara F, Lawrence F, Lee SL, Librado P, Linheiro RS, Lyman RF, Mackey AJ, Munidasa M, Muzny DM, Nazareth L, Newsham I, Perales L, Pu LL, Qu C, Ràmia M, Reid JG, Rollmann SM, Rozas J, Saada N, Turlapati L, Worley KC, Wu YQ, Yamamoto A, Zhu Y, Bergman CM, Thornton KR, Mittelman D, Gibbs RA.

Nature. 2012 Feb 8;482(7384):173-8. doi: 10.1038/nature10811.

23.

pubmed2ensembl: a resource for mining the biological literature on genes.

Baran J, Gerner M, Haeussler M, Nenadic G, Bergman CM.

PLoS One. 2011;6(9):e24716. doi: 10.1371/journal.pone.0024716. Epub 2011 Sep 29.

24.

The GNAT library for local and remote gene mention normalization.

Hakenberg J, Gerner M, Haeussler M, Solt I, Plake C, Schroeder M, Gonzalez G, Nenadic G, Bergman CM.

Bioinformatics. 2011 Oct 1;27(19):2769-71. doi: 10.1093/bioinformatics/btr455. Epub 2011 Aug 3.

25.

Annotating genes and genomes with DNA sequences extracted from biomedical articles.

Haeussler M, Gerner M, Bergman CM.

Bioinformatics. 2011 Apr 1;27(7):980-6. doi: 10.1093/bioinformatics/btr043. Epub 2011 Feb 16.

26.

A large palindrome with interchromosomal gene duplications in the pericentromeric region of the D. melanogaster Y chromosome.

Méndez-Lago M, Bergman CM, de Pablos B, Tracey A, Whitehead SL, Villasante A.

Mol Biol Evol. 2011 Jul;28(7):1967-71. doi: 10.1093/molbev/msr034. Epub 2011 Feb 5.

27.

Gene expression divergence recapitulates the developmental hourglass model.

Kalinka AT, Varga KM, Gerrard DT, Preibisch S, Corcoran DL, Jarrells J, Ohler U, Bergman CM, Tomancak P.

Nature. 2010 Dec 9;468(7325):811-4. doi: 10.1038/nature09634.

PMID:
21150996
28.

REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila.

Gallo SM, Gerrard DT, Miner D, Simich M, Des Soye B, Bergman CM, Halfon MS.

Nucleic Acids Res. 2011 Jan;39(Database issue):D118-23. doi: 10.1093/nar/gkq999. Epub 2010 Oct 21.

29.

Evolutionary systems biology of amino acid biosynthetic cost in yeast.

Barton MD, Delneri D, Oliver SG, Rattray M, Bergman CM.

PLoS One. 2010 Aug 17;5(8):e11935. doi: 10.1371/journal.pone.0011935. Erratum in: PLoS One. 2010;5(10) doi: 10.1371/annotation/b60feca4-9a4f-4311-8a07-4bf16a2f9316.

30.

The evolution of tRNA genes in Drosophila.

Rogers HH, Bergman CM, Griffiths-Jones S.

Genome Biol Evol. 2010 Jul 12;2:467-77. doi: 10.1093/gbe/evq034.

31.

Lymphotoxin-alpha contributes to lymphangiogenesis.

Mounzer RH, Svendsen OS, Baluk P, Bergman CM, Padera TP, Wiig H, Jain RK, McDonald DM, Ruddle NH.

Blood. 2010 Sep 23;116(12):2173-82. doi: 10.1182/blood-2009-12-256065. Epub 2010 Jun 21.

32.

LINNAEUS: a species name identification system for biomedical literature.

Gerner M, Nenadic G, Bergman CM.

BMC Bioinformatics. 2010 Feb 11;11:85. doi: 10.1186/1471-2105-11-85.

33.

Assigning roles to protein mentions: the case of transcription factors.

Yang H, Keane J, Bergman CM, Nenadic G.

J Biomed Inform. 2009 Oct;42(5):887-94. doi: 10.1016/j.jbi.2009.04.001. Epub 2009 Apr 11.

34.

Population genomics of domestic and wild yeasts.

Liti G, Carter DM, Moses AM, Warringer J, Parts L, James SA, Davey RP, Roberts IN, Burt A, Koufopanou V, Tsai IJ, Bergman CM, Bensasson D, O'Kelly MJ, van Oudenaarden A, Barton DB, Bailes E, Nguyen AN, Jones M, Quail MA, Goodhead I, Sims S, Smith F, Blomberg A, Durbin R, Louis EJ.

Nature. 2009 Mar 19;458(7236):337-41. doi: 10.1038/nature07743. Epub 2009 Feb 11.

35.

Depletion of CD4(+)CD25(+) T cells exacerbates experimental autoimmune encephalomyelitis induced by mouse, but not rat, antigens.

Akirav EM, Bergman CM, Hill M, Ruddle NH.

J Neurosci Res. 2009 Nov 15;87(15):3511-9. doi: 10.1002/jnr.21981.

36.

Population genomic inferences from sparse high-throughput sequencing of two populations of Drosophila melanogaster.

Sackton TB, Kulathinal RJ, Bergman CM, Quinlan AR, Dopman EB, Carneiro M, Marth GT, Hartl DL, Clark AG.

Genome Biol Evol. 2009 Nov 18;1:449-65. doi: 10.1093/gbe/evp048.

37.

Text mining for biology--the way forward: opinions from leading scientists.

Altman RB, Bergman CM, Blake J, Blaschke C, Cohen A, Gannon F, Grivell L, Hahn U, Hersh W, Hirschman L, Jensen LJ, Krallinger M, Mons B, O'Donoghue SI, Peitsch MC, Rebholz-Schuhmann D, Shatkay H, Valencia A.

Genome Biol. 2008;9 Suppl 2:S7. doi: 10.1186/gb-2008-9-s2-s7. Epub 2008 Sep 1.

38.

Testing the palindromic target site model for DNA transposon insertion using the Drosophila melanogaster P-element.

Linheiro RS, Bergman CM.

Nucleic Acids Res. 2008 Nov;36(19):6199-208. doi: 10.1093/nar/gkn563. Epub 2008 Oct 1.

39.

Drosophila polymorphism database (DPDB): a portal for nucleotide polymorphism in Drosophila.

Casillas S, Egea R, Petit N, Bergman CM, Barbadilla A.

Fly (Austin). 2007 Jul-Aug;1(4):205-11. Epub 2007 Jul 17.

PMID:
18820438
40.

Text-mining assisted regulatory annotation.

Aerts S, Haeussler M, van Vooren S, Griffith OL, Hulpiau P, Jones SJ, Montgomery SB, Bergman CM; Open Regulatory Annotation Consortium.

Genome Biol. 2008;9(2):R31. doi: 10.1186/gb-2008-9-2-r31. Epub 2008 Feb 13.

41.

REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila.

Halfon MS, Gallo SM, Bergman CM.

Nucleic Acids Res. 2008 Jan;36(Database issue):D594-8. Epub 2007 Nov 26.

42.

ORegAnno: an open-access community-driven resource for regulatory annotation.

Griffith OL, Montgomery SB, Bernier B, Chu B, Kasaian K, Aerts S, Mahony S, Sleumer MC, Bilenky M, Haeussler M, Griffith M, Gallo SM, Giardine B, Hooghe B, Van Loo P, Blanco E, Ticoll A, Lithwick S, Portales-Casamar E, Donaldson IJ, Robertson G, Wadelius C, De Bleser P, Vlieghe D, Halfon MS, Wasserman W, Hardison R, Bergman CM, Jones SJ; Open Regulatory Annotation Consortium.

Nucleic Acids Res. 2008 Jan;36(Database issue):D107-13. Epub 2007 Nov 15.

43.

Evolution of genes and genomes on the Drosophila phylogeny.

Drosophila 12 Genomes Consortium, Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW, Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D, Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak SA, Bradley RK, Brand AD, Brent MR, Brooks AN, Brown RH, Butlin RK, Caggese C, Calvi BR, Bernardo de Carvalho A, Caspi A, Castrezana S, Celniker SE, Chang JL, Chapple C, Chatterji S, Chinwalla A, Civetta A, Clifton SW, Comeron JM, Costello JC, Coyne JA, Daub J, David RG, Delcher AL, Delehaunty K, Do CB, Ebling H, Edwards K, Eickbush T, Evans JD, Filipski A, Findeiss S, Freyhult E, Fulton L, Fulton R, Garcia AC, Gardiner A, Garfield DA, Garvin BE, Gibson G, Gilbert D, Gnerre S, Godfrey J, Good R, Gotea V, Gravely B, Greenberg AJ, Griffiths-Jones S, Gross S, Guigo R, Gustafson EA, Haerty W, Hahn MW, Halligan DL, Halpern AL, Halter GM, Han MV, Heger A, Hillier L, Hinrichs AS, Holmes I, Hoskins RA, Hubisz MJ, Hultmark D, Huntley MA, Jaffe DB, Jagadeeshan S, Jeck WR, Johnson J, Jones CD, Jordan WC, Karpen GH, Kataoka E, Keightley PD, Kheradpour P, Kirkness EF, Koerich LB, Kristiansen K, Kudrna D, Kulathinal RJ, Kumar S, Kwok R, Lander E, Langley CH, Lapoint R, Lazzaro BP, Lee SJ, Levesque L, Li R, Lin CF, Lin MF, Lindblad-Toh K, Llopart A, Long M, Low L, Lozovsky E, Lu J, Luo M, Machado CA, Makalowski W, Marzo M, Matsuda M, Matzkin L, McAllister B, McBride CS, McKernan B, McKernan K, Mendez-Lago M, Minx P, Mollenhauer MU, Montooth K, Mount SM, Mu X, Myers E, Negre B, Newfeld S, Nielsen R, Noor MA, O'Grady P, Pachter L, Papaceit M, Parisi MJ, Parisi M, Parts L, Pedersen JS, Pesole G, Phillippy AM, Ponting CP, Pop M, Porcelli D, Powell JR, Prohaska S, Pruitt K, Puig M, Quesneville H, Ram KR, Rand D, Rasmussen MD, Reed LK, Reenan R, Reily A, Remington KA, Rieger TT, Ritchie MG, Robin C, Rogers YH, Rohde C, Rozas J, Rubenfield MJ, Ruiz A, Russo S, Salzberg SL, Sanchez-Gracia A, Saranga DJ, Sato H, Schaeffer SW, Schatz MC, Schlenke T, Schwartz R, Segarra C, Singh RS, Sirot L, Sirota M, Sisneros NB, Smith CD, Smith TF, Spieth J, Stage DE, Stark A, Stephan W, Strausberg RL, Strempel S, Sturgill D, Sutton G, Sutton GG, Tao W, Teichmann S, Tobari YN, Tomimura Y, Tsolas JM, Valente VL, Venter E, Venter JC, Vicario S, Vieira FG, Vilella AJ, Villasante A, Walenz B, Wang J, Wasserman M, Watts T, Wilson D, Wilson RK, Wing RA, Wolfner MF, Wong A, Wong GK, Wu CI, Wu G, Yamamoto D, Yang HP, Yang SP, Yorke JA, Yoshida K, Zdobnov E, Zhang P, Zhang Y, Zimin AV, Baldwin J, Abdouelleil A, Abdulkadir J, Abebe A, Abera B, Abreu J, Acer SC, Aftuck L, Alexander A, An P, Anderson E, Anderson S, Arachi H, Azer M, Bachantsang P, Barry A, Bayul T, Berlin A, Bessette D, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Bourzgui I, Brown A, Cahill P, Channer S, Cheshatsang Y, Chuda L, Citroen M, Collymore A, Cooke P, Costello M, D'Aco K, Daza R, De Haan G, DeGray S, DeMaso C, Dhargay N, Dooley K, Dooley E, Doricent M, Dorje P, Dorjee K, Dupes A, Elong R, Falk J, Farina A, Faro S, Ferguson D, Fisher S, Foley CD, Franke A, Friedrich D, Gadbois L, Gearin G, Gearin CR, Giannoukos G, Goode T, Graham J, Grandbois E, Grewal S, Gyaltsen K, Hafez N, Hagos B, Hall J, Henson C, Hollinger A, Honan T, Huard MD, Hughes L, Hurhula B, Husby ME, Kamat A, Kanga B, Kashin S, Khazanovich D, Kisner P, Lance K, Lara M, Lee W, Lennon N, Letendre F, LeVine R, Lipovsky A, Liu X, Liu J, Liu S, Lokyitsang T, Lokyitsang Y, Lubonja R, Lui A, MacDonald P, Magnisalis V, Maru K, Matthews C, McCusker W, McDonough S, Mehta T, Meldrim J, Meneus L, Mihai O, Mihalev A, Mihova T, Mittelman R, Mlenga V, Montmayeur A, Mulrain L, Navidi A, Naylor J, Negash T, Nguyen T, Nguyen N, Nicol R, Norbu C, Norbu N, Novod N, O'Neill B, Osman S, Markiewicz E, Oyono OL, Patti C, Phunkhang P, Pierre F, Priest M, Raghuraman S, Rege F, Reyes R, Rise C, Rogov P, Ross K, Ryan E, Settipalli S, Shea T, Sherpa N, Shi L, Shih D, Sparrow T, Spaulding J, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Strader C, Tesfaye S, Thomson T, Thoulutsang Y, Thoulutsang D, Topham K, Topping I, Tsamla T, Vassiliev H, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Young G, Yu Q, Zembek L, Zhong D, Zimmer A, Zwirko Z, Jaffe DB, Alvarez P, Brockman W, Butler J, Chin C, Gnerre S, Grabherr M, Kleber M, Mauceli E, MacCallum I.

Nature. 2007 Nov 8;450(7167):203-18.

PMID:
17994087
44.

Discovering and detecting transposable elements in genome sequences.

Bergman CM, Quesneville H.

Brief Bioinform. 2007 Nov;8(6):382-92. Epub 2007 Oct 10. Review.

PMID:
17932080
45.

Purifying selection maintains highly conserved noncoding sequences in Drosophila.

Casillas S, Barbadilla A, Bergman CM.

Mol Biol Evol. 2007 Oct;24(10):2222-34. Epub 2007 Jul 23.

PMID:
17646256
46.

Recent LTR retrotransposon insertion contrasts with waves of non-LTR insertion since speciation in Drosophila melanogaster.

Bergman CM, Bensasson D.

Proc Natl Acad Sci U S A. 2007 Jul 3;104(27):11340-5. Epub 2007 Jun 25.

47.

Principles of genome evolution in the Drosophila melanogaster species group.

Ranz JM, Maurin D, Chan YS, von Grotthuss M, Hillier LW, Roote J, Ashburner M, Bergman CM.

PLoS Biol. 2007 Jun;5(6):e152.

48.

Large-scale discovery of promoter motifs in Drosophila melanogaster.

Down TA, Bergman CM, Su J, Hubbard TJ.

PLoS Comput Biol. 2007 Jan 19;3(1):e7. Epub 2006 Dec 5.

49.
50.

Identifying cis-regulatory modules by combining comparative and compositional analysis of DNA.

Pierstorff N, Bergman CM, Wiehe T.

Bioinformatics. 2006 Dec 1;22(23):2858-64. Epub 2006 Oct 10.

PMID:
17032682

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