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Results: 1 to 20 of 55

1.

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.

PMID:
24336751
[PubMed - in process]
Free PMC Article
2.

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.

PMID:
23284297
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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.

PMID:
23226439
[PubMed - indexed for MEDLINE]
Free PMC Article
4.
5.

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.

PMID:
22711795
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

PMID:
22586035
[PubMed - indexed for MEDLINE]
Free Article
7.

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.

PMID:
22347367
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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.

PMID:
22318601
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
21980353
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
21813477
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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.

PMID:
21325301
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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.

PMID:
21297157
[PubMed - indexed for MEDLINE]
Free Article
13.

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
[PubMed - indexed for MEDLINE]
14.

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.

PMID:
20965965
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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.

PMID:
20808905
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

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.

PMID:
20624748
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

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.

PMID:
20566898
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

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.

PMID:
20149233
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

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.

PMID:
19364541
[PubMed - indexed for MEDLINE]
Free Article
20.

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.

PMID:
19212322
[PubMed - indexed for MEDLINE]
Free PMC Article

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