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Dr Casey Bergman (BSc, MAT, PhD) - publications

List of publications

2014

  • Blumenstiel, J., Chen, X., He, M. & Bergman, C (2014). An Age-of-Allele Test of Neutrality for Transposable Element Insertions. Genetics, 196(2), 523-38. eScholarID:220403 | PMID:24336751 | DOI:10.1534/genetics.113.158147

2013

  • Prokop, A. & Bergman, C (2013). Photogenic Flies - A review of Chyb and Gompel's Atlas of Drosophila Morphology: Wild-type and Classical Mutants. Frontiers in Evolutionary and Population Genetics, 147. eScholarID:213431 | DOI:10.3389/fgene.2013.00147

2012

  • Bergman, C (2012). A proposal for the reference-based annotation of de novo transposable element insertions. Mob Genet Elements, 2(1), 51-54. eScholarID:168238 | PMID:22754753 | DOI:10.4161/mge.19479
  • Carr, M., Bensasson, D. & Bergman, C (2012). Evolutionary Genomics of Transposable Elements in Saccharomyces cerevisiae. PLoS One, 7(11), e50978. eScholarID:184462 | PMID:23226439 | DOI:10.1371/journal.pone.0050978
  • Gerner, M., Sarafraz, F., Bergman, C. & Nenadic, G (2012). BioContext: an integrated text mining system for large-scale extraction and contextualization of biomolecular events. Bioinformatics, 28(16), 2154-61. eScholarID:168239 | PMID:22711795 | DOI:10.1093/bioinformatics/bts332
  • Linheiro, R. & Bergman, C (2012). Whole Genome Resequencing Reveals Natural Target Site Preferences of Transposable Elements in Drosophila melanogaster. PLoS One, 7(2), e30008. eScholarID:157662 | PMID:22347367 | DOI:10.1371/journal.pone.0030008
  • Mackay, et al (2012). The Drosophila melanogaster Genetic Reference Panel. Nature, 482(7384), 173-8. eScholarID:157661 | PMID:22318601 | DOI:10.1038/nature10811
  • Richardson, M., Weinert, L., Welch, J., Linheiro, R., Magwire, M., Jiggins, F. & Bergman, C (2012). Population Genomics of the Wolbachia Endosymbiont in Drosophila melanogaster. PLoS Genet, 8(12), e1003129. eScholarID:184463 | PMID:23284297 | DOI:10.1371/journal.pgen.1003129

2011

  • Baran, J., Gerner, M., Haeussler, M., Nenadic, G. & Bergman, C (2011). pubmed2ensembl: A Resource for Mining the Biological Literature on Genes. PLoS ONE, 6(9), eScholarID:132782 | PMID:21980353 | DOI:10.1371/journal.pone.0024716
  • Gallo, S., Gerrard, D., Miner, D., Simich, M., Des Soye, B., Bergman, C. & Halfon, M (2011). REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila. Nucleic Acids Res, 39, D118-23. eScholarID:118211 | PMID:20965965 | DOI:10.1093/nar/gkq999
  • Haeussler, M., Gerner, M. & Bergman, C (2011). Annotating genes and genomes with DNA sequences extracted from biomedical articles. Bioinformatics, 27(7), 980. eScholarID:121672 | PMID:21325301 | DOI:10.1093/bioinformatics/btr043
  • Hakenberg, J., Gerner, M., Haeussler, M., Solt, I., Plake, C., Schroeder, M., Gonzalez, G., Nenadic, G. & Bergman, C (2011). The GNAT library for local and remote gene mention normalization. Bioinformatics, 27(19), 2769-2771. eScholarID:132781 | PMID:21813477 | DOI:10.1093/bioinformatics/btr455
  • Méndez-Lago, M., Bergman, C., de Pablos, B., Tracey, A., Whitehead, S. & Villasante, A (2011). A Large Palindrome With Interchromosomal Gene Duplications in the Pericentromeric Region of the D. melanogaster Y Chromosome. Mol Biol Evol, 28(7), 1967-71. eScholarID:125390 | PMID:21297157 | DOI:10.1093/molbev/msr034

2010

  • Barton, M., Delneri, D., Oliver, S., Rattray, M. & Bergman, C (2010). Evolutionary systems biology of amino acid biosynthetic cost in yeast. PLoS One, 5, e11935. eScholarID:89524 | PMID:20808905 | DOI:10.1371/journal.pone.0011935
  • Gerner, M., Nenadic, G. & Bergman, C (2010). LINNAEUS: A species name identification system for biomedical literature. BMC Bioinformatics, 11, 85. eScholarID:76745 | PMID:20149233 | DOI:10.1186/1471-2105-11-85
  • Kalinka, A., Varga, K., Gerrard, D., Preibisch, S., Corcoran, D., Jarrells, J., Ohler, U., Bergman, C. & Tomancak, P (2010). Gene expression divergence recapitulates the developmental hourglass model. Nature, 468(7325), 811. eScholarID:103156 | PMID:21150996 | DOI:10.1038/nature09634
  • Rogers, H., Bergman, C. & Griffiths-Jones, S (2010). The Evolution of tRNA Genes in Drosophila. Genome Biol Evol, 2, 467-77. eScholarID:86407 | PMID:20624748 | DOI:10.1093/gbe/evq034

2009

  • 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. (2009). Population genomics of domestic and wild yeasts. Nature, 458, 337-41. eScholarID:1c8273 | PMID:19212322 | DOI:10.1038/nature07743
  • Sackton, T., Kulathinal, R., Bergman, C., Quinlan, A., Dopman, E., Carneiro, M., Marth, G., Hartl, D. & Clark, A (2009). Population genomic inferences from sparse high-throughput sequencing of two populations of Drosophila melanogaster. Genome Biol Evol, 1, 449-65. eScholarID:86462 | PMID:20333214 | DOI:10.1093/gbe/evp048
  • Yang, H., Keane, J., Bergman, C. & Nenadic, G (2009). Assigning roles to protein mentions: the case of transcription factors. J Biomed Inform, 42, 887-94. eScholarID:75835 | PMID:19364541 | DOI:10.1016/j.jbi.2009.04.001

2008

  • 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; The Open Regulatory Annotation Consortium. (2008). ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Research, 36, D107-13. eScholarID:1c7196 | PMID:18006570 | DOI:10.1093/nar/gkm967
  • Halfon MS, Gallo SM, Bergman CM. (2008). REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila. Nucleic Acids Research, 36, D594-8. eScholarID:1c7195 | PMID:18039705 | DOI:10.1093/nar/gkm876
  • Linheiro RS, Bergman CM. (2008). Testing the palindromic target site model for DNA transposon insertion using the Drosophila melanogaster P-element. Nucleic Acids Research, 36, 6199-208. eScholarID:1c7981 | PMID:18829720 | DOI:10.1093/nar/gkn563
  • 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. (2008). Text mining for biology--the way forward: opinions from leading scientists. Genome Biology, 9 Suppl 2, S7. eScholarID:1c7947 | PMID:18834498 | DOI:10.1186/gb-2008-9-s2-s7
  • Aerts S, Haeussler M, van Vooren S, Griffith OL, Hulpiau P, Jones SJ, Montgomery SB, Bergman CM, The Open Regulatory Annotation Consortium. (2008). Text-mining assisted regulatory annotation. Genome Biology, 9, R31. eScholarID:1c7323 | PMID:18271954 | DOI:10.1186/gb-2008-9-2-r31

2007

  • Bergman CM, Quesneville H. (2007). Discovering and detecting transposable elements in genome sequences. Briefings in Bioinformatics, 8, 382-92. eScholarID:1c7115 | PMID:17932080 | DOI:10.1093/bib/bbm048
  • Casillas S, Egea R, Petit N, Bergman CM, Barbadilla A. (2007). Drosophila Polymorphism Database (DPDB): A Portal for Nucleotide Polymorphism in Drosophila. Fly, 1, 205-11. eScholarID:1c7890 | PMID:18820438
  • Drosophila 12 Genomes Consortium. (2007). Evolution of genes and genomes on the Drosophila phylogeny. Nature, 450, 203-218. eScholarID:1c7048 | PMID:17994087 | DOI:10.1038/nature06341
  • Down TA, Bergman CM, Su J, Hubbard TJ. (2007). Large-scale discovery of promoter motifs in Drosophila melanogaster. PLoS Computational Biology, 3, e7. eScholarID:1c6318 | PMID:17238282 | DOI:10.1371/journal.pcbi.0030007
  • Ranz JM, Maurin D, Chan YS, von Grotthuss M, Hillier LW, Roote J, Ashburner M, Bergman CM. (2007). Principles of genome evolution in the Drosophila melanogaster species group. PLoS Biology, 5, e152. eScholarID:1c6621 | PMID:17550304 | DOI:10.1371/journal.pbio.0050152
  • Casillas S, Barbadilla A, Bergman CM. (2007). Purifying selection maintains highly conserved noncoding sequences in Drosophila. Molecular Biology and Evolution, 24, 2222-34. eScholarID:1c7000 | PMID:17646256 | DOI:10.1093/molbev/msm150
  • Bergman CM, Bensasson D. (2007). Recent LTR retrotransposon insertion contrasts with waves of non-LTR insertion since speciation in Drosophila melanogaster. Proceedings of the National Academy of Sciences (USA), 104, 11340-11345. eScholarID:1c6715 | PMID:17592135 | DOI:10.1073/pnas.0702552104

2006

  • Pierstorff N, Bergman CM, Wiehe T. (2006). Identifying cis-regulatory modules by combining comparative and compositional analysis of DNA. Bioinformatics, 22, 2858-64. eScholarID:1c6195 | PMID:17032682 | DOI:10.1093/bioinformatics/btl499
  • Montgomery SB, Griffith OL, Sleumer MC, Bergman CM, Bilenky M, Pleasance ED, Prychyna Y, Zhang X, Jones SJ. (2006). ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation. Bioinformatics, 22, 637-40. eScholarID:1c5005 | PMID:16397004 | DOI:10.1093/bioinformatics/btk027
  • Bergman CM, Quesneville H, Anxolabehere D, Ashburner M. (2006). Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila melanogaster genome. Genome Biology, 7, R112. eScholarID:1c6233 | PMID:17134480 | DOI:10.1186/gb-2006-7-11-r112

2005

  • Quesneville H, Bergman CM, Andrieu O, Autard D, Nouaud D, Ashburner M, Anxolabehere D. (2005). Combined evidence annotation of transposable elements in genome sequences. PLoS Comput Biology, 1, e22. eScholarID:1c3833 | PMID:16110336 | DOI:10.1371/journal.pcbi.0010022
  • Bergman CM, Carlson JW, Celniker SE. (2005). Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster. Bioinformatics, 21, 1747-9. eScholarID:1c3800 | PMID:15572468 | DOI:10.1093/bioinformatics/bti173
  • Ashburner M, Bergman CM. (2005). Drosophila melanogaster: A case study of a model genomic sequence and its consequences. Genome Research, 15, 1661-7. eScholarID:1c4930 | PMID:16339363 | DOI:10.1101/gr.3726705
  • Ludwig MZ, Palsson A, Alekseeva E, Bergman CM, Nathan J, Kreitman M. (2005). Functional evolution of a cis-regulatory module. PLoS Biology, 3, e93. eScholarID:1c3801 | PMID:15757364 | DOI:10.1371/journal.pbio.0030093
  • Lipatov M, Lenkov K, Petrov DA, Bergman CM. (2005). Paucity of chimeric gene-transposable element transcripts in the Drosophila melanogaster genome. BMC Biology, 3, 24. eScholarID:1c4407 | PMID:16283942 | DOI:10.1186/1741-7007-3-24
  • Russell SR, Bergman CM. (2005). The Drosophila genome(s). Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, 1, 2.4. eScholarID:1c3809 | DOI:10.1002/047001153X.g204311

2004

  • Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB. (2004). Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics, 5, 6. eScholarID:1c3802 | PMID:14736341 | DOI:10.1186/1471-2105-5-6
  • Bergman CM, Patel NH. (2004). Identifying changes in cis-regulatory evolution: approaches and implications. In A. Moya and E. Font, eds (Ed.), Evolution: From Molecules to Ecosystems. (pp. 11). Oxford University Press, Oxford, UK. eScholarID:3c141

2003

  • Johnson AN, Bergman CM, Kreitman M, Newfeld SJ. (2003). Embryonic enhancers in the dpp disk region regulate a second round of Dpp signaling from the dorsal ectoderm to the mesoderm that represses Zfh-1 expression in a subset of pericardial cells. Developmental Biology, 262, 137-51. eScholarID:1c3803 | PMID:14512024 | DOI:10.1016/S0012-1606(03)00350-6
  • Dermitzakis ET, Bergman CM, Clark AG. (2003). Tracing the evolutionary history of Drosophila regulatory regions with models that identify transcription factor binding sites. Molecular Biology and Evolution, 20, 703-14. eScholarID:1c3804 | PMID:12679540 | DOI:10.1093/molbev/msg077

2002

  • Bergman CM, Pfeiffer BD, Rincon-Limas DE, Hoskins RA, Gnirke A, Mungall CJ, Wang AM, Kronmiller B, Pacleb J, Park S, Stapleton M, Wan K, George RA, de Jong PJ, Botas J, Rubin GM, Celniker SE. (2002). Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome. Genome Biology, 3, RESEARCH0086. eScholarID:1c3805 | PMID:12537575 | DOI:10.1186/gb-2002-3-12-research0086
  • Kaminker JS, Bergman CM, Kronmiller B, Carlson J, Svirskas R, Patel S, Frise E, Wheeler DA, Lewis SE, Rubin GM, Ashburner M, Celniker SE. (2002). The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Genome Biology, 3, RESEARCH0084. eScholarID:1c3806 | PMID:12537573 | DOI:10.1186/gb-2002-3-12-research0084

2001

  • Bergman CM, Kreitman M. (2001). Analysis of conserved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences. Genome Research, 11, 1335-45. eScholarID:1c3807 | PMID:11483574 | DOI:10.1101/gr.178701

2000

  • Ludwig MZ, Bergman C, Patel NH, Kreitman M. (2000). Evidence for stabilizing selection in a eukaryotic enhancer element. Nature, 403, 564-7. eScholarID:1c3808 | PMID:10676967 | DOI:10.1038/35000615