Casey Bergman - Publications

Affiliations: 
University of Georgia, Athens, Athens, GA, United States 
Area:
evolution, genomics, noncoding DNA
Website:
http://bergmanlab.genetics.uga.edu/

67 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
2024 Hannon-Hatfield JA, Chen J, Bergman CM, Garfinkel DJ. Evolution of a restriction factor by domestication of a yeast retrotransposon. Molecular Biology and Evolution. PMID 38442736 DOI: 10.1093/molbev/msae050  0.7
2023 Chen J, Garfinkel DJ, Bergman CM. Horizontal transfer and recombination fuel Ty4 retrotransposon evolution in . Biorxiv : the Preprint Server For Biology. PMID 38187645 DOI: 10.1101/2023.12.20.572574  0.751
2023 Chen J, Basting PJ, Han S, Garfinkel DJ, Bergman CM. Reproducible evaluation of transposable element detectors with McClintock 2 guides accurate inference of Ty insertion patterns in yeast. Mobile Dna. 14: 8. PMID 37452430 DOI: 10.1186/s13100-023-00296-4  0.813
2023 Chen J, Basting PJ, Han S, Garfinkel DJ, Bergman CM. Reproducible evaluation of transposable element detectors with McClintock 2 guides accurate inference of Ty insertion patterns in yeast. Biorxiv : the Preprint Server For Biology. PMID 36824955 DOI: 10.1101/2023.02.13.528343  0.813
2022 Han S, Dias GB, Basting PJ, Viswanatha R, Perrimon N, Bergman CM. Local assembly of long reads enables phylogenomics of transposable elements in a polyploid cell line. Nucleic Acids Research. PMID 36156149 DOI: 10.1093/nar/gkac794  0.833
2022 Han S, Dias GB, Basting PJ, Nelson MG, Patel S, Marzo M, Bergman CM. Ongoing transposition in cell culture reveals the phylogeny of diverse Drosophila S2 sub-lines. Genetics. PMID 35536183 DOI: 10.1093/genetics/iyac077  0.78
2022 Chen J, McQueary H, Hall DW, Philippsen P, Garfinkel DJ, Bergman CM. Genome Assembly of the Ty1-Less Saccharomyces paradoxus Strain DG1768. Microbiology Resource Announcements. 11: e0086821. PMID 35049349 DOI: 10.1128/mra.00868-21  0.684
2022 Chen J, Garfinkel DJ, Bergman CM. Long-Read Genome Assembly of Saccharomyces uvarum Strain CBS 7001. Microbiology Resource Announcements. e0097221. PMID 34989601 DOI: 10.1128/mra.00972-21  0.738
2021 Han S, Basting PJ, Dias GB, Luhur A, Zelhof AC, Bergman CM. Transposable element profiles reveal cell line identity and loss of heterozygosity in Drosophila cell culture. Genetics. 219. PMID 34849875 DOI: 10.1093/genetics/iyab113  0.798
2021 Mariyappa D, Rusch DB, Han S, Luhur A, Overton D, Miller DFB, Bergman CM, Zelhof AC. A novel transposable element based authentication protocol for Drosophila cell lines. G3 (Bethesda, Md.). PMID 34849844 DOI: 10.1093/g3journal/jkab403  0.631
2021 Dias GB, Aldossary AM, El-Shafie HAF, Alhoshani FM, Al-Fageeh MB, Bergman CM, Manee MM. Complete mitochondrial genome of the longhorn date palm stem borer (Reiche, 1878). Mitochondrial Dna. Part B, Resources. 6: 3214-3216. PMID 34676292 DOI: 10.1080/23802359.2021.1989334  0.825
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  0.831
2020 Chung M, Basting PJ, Patkus RS, Grote A, Luck AN, Ghedin E, Slatko BE, Michalski M, Foster J, Bergman CM, Dunning Hotopp JC. A Meta-Analysis of Transcriptomics Reveals a Stage-Specific Transcriptional Response Shared Across Different Hosts. G3 (Bethesda, Md.). PMID 32718933 DOI: 10.1534/g3.120.401534  0.775
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  0.737
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  0.691
2019 Basting PJ, Bergman CM. Complete Genome Assemblies for Three Variants of the Endosymbiont of Drosophila melanogaster. Microbiology Resource Announcements. 8. PMID 31699757 DOI: 10.1128/MRA.00956-19  0.824
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  0.822
2019 Duc C, Yoth M, Jensen S, Mouniée N, Bergman CM, Vaury C, Brasset E. Trapping a somatic endogenous retrovirus into a germline piRNA cluster immunizes the germline against further invasion. Genome Biology. 20: 127. PMID 31227013 DOI: 10.1186/s13059-019-1736-x  0.316
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  0.813
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  0.7
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  0.832
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  0.405
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  0.795
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  0.469
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  0.685
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  0.322
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  0.836
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  0.774
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  0.706
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  0.825
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  0.792
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  0.838
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  0.783
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  0.823
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  0.774
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  0.774
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  0.475
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  0.656
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  0.723
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  0.615
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  0.587
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  0.759
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  0.802
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  0.791
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  0.776
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  0.339
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  0.791
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  0.72
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  0.417
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  0.74
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  0.827
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  0.731
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  0.781
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  0.302
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  0.67
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  0.686
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  0.8
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  0.794
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  0.665
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  0.724
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  0.784
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  0.528
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  0.44
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  0.708
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  0.767
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  0.635
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  0.733
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