| 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 |
0.707 |
|
| 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 |
0.756 |
|
| 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 |
0.692 |
|
| 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 |
0.743 |
|
| 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 |
0.63 |
|
| 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 |
0.686 |
|
| 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 |
0.708 |
|
| 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 |
0.476 |
|
| 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 |
0.724 |
|
| 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 |
0.591 |
|
| 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 |
0.796 |
|
| 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 |
0.666 |
|
| 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 |
0.725 |
|
| 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 |
0.785 |
|
| 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 |
0.709 |
|
| 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 |
0.768 |
|
| 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 |
|
| Show low-probability matches. |