Casey Bergman - Publications

University of Georgia, Athens, Athens, GA, United States 
evolution, genomics, noncoding DNA

61 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Dias GB, Altammami MA, El-Shafie HAF, Alhoshani FM, Al-Fageeh MB, Bergman CM, Manee MM. Haplotype-resolved genome assembly enables gene discovery in the red palm weevil Rhynchophorus ferrugineus. Scientific Reports. 11: 9987. PMID 33976235 DOI: 10.1038/s41598-021-89091-w  1
2020 Czaja W, Bensasson D, Ahn HW, Garfinkel DJ, Bergman CM. Evolution of Ty1 copy number control in yeast by horizontal transfer and recombination. Plos Genetics. 16: e1008632. PMID 32084126 DOI: 10.1371/Journal.Pgen.1008632  1
2020 Hemmer LW, Dias GB, Smith B, Van Vaerenberghe K, Howard A, Bergman CM, Blumenstiel JP. Hybrid dysgenesis in results in clusters of mitotic recombination and loss-of-heterozygosity but leaves meiotic recombination unaltered. Mobile Dna. 11: 10. PMID 32082426 DOI: 10.1186/S13100-020-0205-0  1
2019 Hamlin JAP, Dias GB, Bergman CM, Bensasson D. Phased Diploid Genome Assemblies for Three Strains of from Oak Trees. G3 (Bethesda, Md.). PMID 31540974 DOI: 10.1534/G3.119.400486  1
2018 Manee MM, Jackson J, Bergman CM. Conserved noncoding elements influence the transposable element landscape in Drosophila. Genome Biology and Evolution. PMID 29850787 DOI: 10.1093/gbe/evy104  0.88
2017 Bergman CM, Han S, Nelson MG, Bondarenko V, Kozeretska I. Genomic analysis of P elements in natural populations of Drosophila melanogaster. Peerj. 5: e3824. PMID 28929030 DOI: 10.7717/Peerj.3824  1
2017 Nelson MG, Linheiro RS, Bergman CM. McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole Genome Shotgun Sequencing Data. G3 (Bethesda, Md.). PMID 28637810 DOI: 10.1534/g3.117.043893  1
2016 Barsh GS, Bergman CM, Brown CD, Singh ND, Copenhaver GP. Bringing PLOS Genetics Editors to Preprint Servers. Plos Genetics. 12: e1006448. PMID 27906975 DOI: 10.1371/Journal.Pgen.1006448  0.2
2016 Miller DE, Cook KR, Yeganeh Kazemi N, Smith CB, Cockrell AJ, Hawley RS, Bergman CM. Rare recombination events generate sequence diversity among balancer chromosomes in Drosophila melanogaster. Proceedings of the National Academy of Sciences of the United States of America. PMID 26903656 DOI: 10.1073/pnas.1601232113  1
2015 Rahman R, Chirn GW, Kanodia A, Sytnikova YA, Brembs B, Bergman CM, Lau NC. Unique transposon landscapes are pervasive across Drosophila melanogaster genomes. Nucleic Acids Research. PMID 26578579 DOI: 10.1093/nar/gkv1193  1
2015 Gutzwiller F, Carmo CR, Miller DE, Rice DW, Newton IL, Hawley RS, Teixeira L, Bergman CM. Dynamics of Wolbachia pipientis Gene Expression Across the Drosophila melanogaster Life Cycle. G3 (Bethesda, Md.). PMID 26497146 DOI: 10.1534/G3.115.021931  1
2015 Dudzic JP, Kondo S, Ueda R, Bergman CM, Lemaitre B. Drosophila innate immunity: regional and functional specialization of prophenoloxidases. Bmc Biology. 13: 81. PMID 26437768 DOI: 10.1186/s12915-015-0193-6  1
2015 Bergman CM, Haddrill PR. Strain-specific and pooled genome sequences for populations of Drosophila melanogaster from three continents. F1000research. 4: 31. PMID 25717372 DOI: 10.12688/f1000research.6090.1  1
2014 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. Long-read, whole-genome shotgun sequence data for five model organisms. Scientific Data. 1: 140045. PMID 25977796 DOI: 10.1038/Sdata.2014.45  1
2014 Blumenstiel JP, Chen X, He M, Bergman CM. An age-of-allele test of neutrality for transposable element insertions. Genetics. 196: 523-38. PMID 24336751 DOI: 10.1534/Genetics.113.158147  1
2013 Prokop A, Bergman CM. Photogenic flies-A review of chyb and gompel's atlas of drosophila morphology: Wild-type and classical mutants Frontiers in Genetics. 4. DOI: 10.3389/Fgene.2013.00147  1
2012 Richardson MF, Weinert LA, Welch JJ, Linheiro RS, Magwire MM, Jiggins FM, Bergman CM. Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster. Plos Genetics. 8: e1003129. PMID 23284297 DOI: 10.1371/Journal.Pgen.1003129  1
2012 Carr M, Bensasson D, Bergman CM. Evolutionary genomics of transposable elements in Saccharomyces cerevisiae. Plos One. 7: e50978. PMID 23226439 DOI: 10.1371/Journal.Pone.0050978  1
2012 Gerner M, Sarafraz F, Bergman CM, Nenadic G. BioContext: an integrated text mining system for large-scale extraction and contextualization of biomolecular events. Bioinformatics (Oxford, England). 28: 2154-61. PMID 22711795 DOI: 10.1093/Bioinformatics/Bts332  1
2012 Linheiro RS, Bergman CM. Whole genome resequencing reveals natural target site preferences of transposable elements in Drosophila melanogaster. Plos One. 7: e30008. PMID 22347367 DOI: 10.1371/journal.pone.0030008  1
2012 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, ... ... Bergman CM, et al. The Drosophila melanogaster Genetic Reference Panel. Nature. 482: 173-8. PMID 22318601 DOI: 10.1038/Nature10811  1
2011 Baran J, Gerner M, Haeussler M, Nenadic G, Bergman CM. pubmed2ensembl: a resource for mining the biological literature on genes. Plos One. 6: e24716. PMID 21980353 DOI: 10.1371/Journal.Pone.0024716  1
2011 Hakenberg J, Gerner M, Haeussler M, Solt I, Plake C, Schroeder M, Gonzalez G, Nenadic G, Bergman CM. The GNAT library for local and remote gene mention normalization. Bioinformatics (Oxford, England). 27: 2769-71. PMID 21813477 DOI: 10.1093/Bioinformatics/Btr455  1
2011 Haeussler M, Gerner M, Bergman CM. Annotating genes and genomes with DNA sequences extracted from biomedical articles. Bioinformatics (Oxford, England). 27: 980-6. PMID 21325301 DOI: 10.1093/Bioinformatics/Btr043  1
2011 Méndez-Lago M, Bergman CM, de Pablos B, Tracey A, Whitehead SL, Villasante A. A large palindrome with interchromosomal gene duplications in the pericentromeric region of the D. melanogaster Y chromosome. Molecular Biology and Evolution. 28: 1967-71. PMID 21297157 DOI: 10.1093/molbev/msr034  1
2011 Gallo SM, Gerrard DT, Miner D, Simich M, Des Soye B, Bergman CM, Halfon MS. REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila. Nucleic Acids Research. 39: D118-23. PMID 20965965 DOI: 10.1093/Nar/Gkq999  1
2010 Kalinka AT, Varga KM, Gerrard DT, Preibisch S, Corcoran DL, Jarrells J, Ohler U, Bergman CM, Tomancak P. Gene expression divergence recapitulates the developmental hourglass model. Nature. 468: 811-4. PMID 21150996 DOI: 10.1038/Nature09634  1
2010 Barton MD, Delneri D, Oliver SG, Rattray M, Bergman CM. Evolutionary systems biology of amino acid biosynthetic cost in yeast. Plos One. 5: e11935. PMID 20808905 DOI: 10.1371/Journal.Pone.0011935  1
2010 Rogers HH, Bergman CM, Griffiths-Jones S. The evolution of tRNA genes in Drosophila. Genome Biology and Evolution. 2: 467-77. PMID 20624748 DOI: 10.1093/Gbe/Evq034  1
2010 Gerner M, Nenadic G, Bergman CM. LINNAEUS: a species name identification system for biomedical literature. Bmc Bioinformatics. 11: 85. PMID 20149233 DOI: 10.1186/1471-2105-11-85  1
2009 Sackton TB, Kulathinal RJ, Bergman CM, Quinlan AR, Dopman EB, Carneiro M, Marth GT, Hartl DL, Clark AG. Population genomic inferences from sparse high-throughput sequencing of two populations of Drosophila melanogaster. Genome Biology and Evolution. 1: 449-65. PMID 20333214 DOI: 10.1093/Gbe/Evp048  1
2009 Yang H, Keane J, Bergman CM, Nenadic G. Assigning roles to protein mentions: the case of transcription factors. Journal of Biomedical Informatics. 42: 887-94. PMID 19364541 DOI: 10.1016/J.Jbi.2009.04.001  1
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, et al. Population genomics of domestic and wild yeasts. Nature. 458: 337-41. PMID 19212322 DOI: 10.1038/Nature07743  1
2008 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, et al. Text mining for biology--the way forward: opinions from leading scientists. Genome Biology. 9: S7. PMID 18834498 DOI: 10.1186/Gb-2008-9-S2-S7  1
2008 Linheiro RS, Bergman CM. Testing the palindromic target site model for DNA transposon insertion using the Drosophila melanogaster P-element. Nucleic Acids Research. 36: 6199-208. PMID 18829720 DOI: 10.1093/nar/gkn563  1
2008 Aerts S, Haeussler M, van Vooren S, Griffith OL, Hulpiau P, Jones SJ, Montgomery SB, Bergman CM. Text-mining assisted regulatory annotation. Genome Biology. 9: R31. PMID 18271954 DOI: 10.1186/Gb-2008-9-2-R31  1
2008 Halfon MS, Gallo SM, Bergman CM. REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila. Nucleic Acids Research. 36: D594-8. PMID 18039705 DOI: 10.1093/nar/gkm876  1
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, ... ... Bergman CM, et al. ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Research. 36: D107-13. PMID 18006570 DOI: 10.1093/Nar/Gkm967  1
2007 Casillas S, Egea R, Petit N, Bergman CM, Barbadilla A. Drosophila polymorphism database (DPDB): a portal for nucleotide polymorphism in Drosophila. Fly. 1: 205-11. PMID 18820438 DOI: 10.4161/Fly.5043  1
2007 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, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450: 203-18. PMID 17994087 DOI: 10.1038/Nature06341  1
2007 Bergman CM, Quesneville H. Discovering and detecting transposable elements in genome sequences. Briefings in Bioinformatics. 8: 382-92. PMID 17932080 DOI: 10.1093/Bib/Bbm048  1
2007 Casillas S, Barbadilla A, Bergman CM. Purifying selection maintains highly conserved noncoding sequences in Drosophila. Molecular Biology and Evolution. 24: 2222-34. PMID 17646256 DOI: 10.1093/Molbev/Msm150  1
2007 Bergman CM, Bensasson D. Recent LTR retrotransposon insertion contrasts with waves of non-LTR insertion since speciation in Drosophila melanogaster. Proceedings of the National Academy of Sciences of the United States of America. 104: 11340-5. PMID 17592135 DOI: 10.1073/Pnas.0702552104  1
2007 Ranz JM, Maurin D, Chan YS, von Grotthuss M, Hillier LW, Roote J, Ashburner M, Bergman CM. Principles of genome evolution in the Drosophila melanogaster species group. Plos Biology. 5: e152. PMID 17550304 DOI: 10.1371/journal.pbio.0050152  1
2007 Down TA, Bergman CM, Su J, Hubbard TJ. Large-scale discovery of promoter motifs in Drosophila melanogaster. Plos Computational Biology. 3: e7. PMID 17238282 DOI: 10.1371/journal.pcbi.0030007  1
2006 Bergman CM, Quesneville H, Anxolabéhère D, Ashburner M. Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila melanogaster genome. Genome Biology. 7: R112. PMID 17134480 DOI: 10.1186/Gb-2006-7-11-R112  1
2006 Pierstorff N, Bergman CM, Wiehe T. Identifying cis-regulatory modules by combining comparative and compositional analysis of DNA. Bioinformatics (Oxford, England). 22: 2858-64. PMID 17032682 DOI: 10.1093/Bioinformatics/Btl499  1
2006 Montgomery SB, Griffith OL, Sleumer MC, Bergman CM, Bilenky M, Pleasance ED, Prychyna Y, Zhang X, Jones SJ. ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation. Bioinformatics (Oxford, England). 22: 637-40. PMID 16397004 DOI: 10.1093/bioinformatics/btk027  1
2005 Ashburner M, Bergman CM. Drosophila melanogaster: a case study of a model genomic sequence and its consequences. Genome Research. 15: 1661-7. PMID 16339363 DOI: 10.1101/gr.3726705  1
2005 Lipatov M, Lenkov K, Petrov DA, Bergman CM. Paucity of chimeric gene-transposable element transcripts in the Drosophila melanogaster genome. Bmc Biology. 3: 24. PMID 16283942 DOI: 10.1186/1741-7007-3-24  1
2005 Quesneville H, Bergman CM, Andrieu O, Autard D, Nouaud D, Ashburner M, Anxolabehere D. Combined evidence annotation of transposable elements in genome sequences. Plos Computational Biology. 1: 166-75. PMID 16110336 DOI: 10.1371/Journal.Pcbi.0010022  1
2005 Ludwig MZ, Palsson A, Alekseeva E, Bergman CM, Nathan J, Kreitman M. Functional evolution of a cis-regulatory module. Plos Biology. 3: e93. PMID 15757364 DOI: 10.1371/journal.pbio.0030093  1
2005 Bergman CM, Carlson JW, Celniker SE. Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster. Bioinformatics (Oxford, England). 21: 1747-9. PMID 15572468 DOI: 10.1093/Bioinformatics/Bti173  1
2004 Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB. Correction: Benchmarking tools for the alignment of functional noncoding DNA. Bmc Bioinformatics. 5: 73. PMID 15186509 DOI: 10.1186/1471-2105-5-73  1
2004 Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB. Benchmarking tools for the alignment of functional noncoding DNA. Bmc Bioinformatics. 5: 6. PMID 14736341 DOI: 10.1186/1471-2105-5-6  1
2003 Johnson AN, Bergman CM, Kreitman M, Newfeld SJ. 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. PMID 14512024 DOI: 10.1016/S0012-1606(03)00350-6  1
2003 Dermitzakis ET, Bergman CM, Clark AG. Tracing the evolutionary history of Drosophila regulatory regions with models that identify transcription factor binding sites. Molecular Biology and Evolution. 20: 703-14. PMID 12679540 DOI: 10.1093/Molbev/Msg077  1
2002 Bergman CM, Pfeiffer BD, Rincón-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, et al. Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome. Genome Biology. 3: RESEARCH0086. PMID 12537575 DOI: 10.1186/Gb-2002-3-12-Research0086  1
2002 Kaminker JS, Bergman CM, Kronmiller B, Carlson J, Svirskas R, Patel S, Frise E, Wheeler DA, Lewis SE, Rubin GM, Ashburner M, Celniker SE. The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Genome Biology. 3: RESEARCH0084. PMID 12537573 DOI: 10.1186/Gb-2002-3-12-Research0084  1
2001 Bergman CM, Kreitman M. Analysis of conserved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences. Genome Research. 11: 1335-45. PMID 11483574 DOI: 10.1101/gr.178701  1
2000 Ludwig MZ, Bergman C, Patel NH, Kreitman M. Evidence for stabilizing selection in a eukaryotic enhancer element. Nature. 403: 564-7. PMID 10676967 DOI: 10.1038/35000615  1
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