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Author Details

Casey M Bergman
University of Georgia
2000
75
39
PMIDPaper TitleJournal TitlePublished Year
36824955Reproducible evaluation of transposable element detectors with McClintock 2 guides accurate inference of Ty insertion patterns in yeast.bioRxiv2023
37452430Reproducible evaluation of transposable element detectors with McClintock 2 guides accurate inference of Ty insertion patterns in yeast.Mob DNA2023
35049349Genome Assembly of the Ty1-Less Saccharomyces paradoxus Strain DG1768.Microbiol Resour Announc2022
35536183Ongoing transposition in cell culture reveals the phylogeny of diverse Drosophila S2 sublines.Genetics2022
36156149Local assembly of long reads enables phylogenomics of transposable elements in a polyploid cell line.Nucleic Acids Res2022
34849844A novel transposable element-based authentication protocol for Drosophila cell lines.G3 (Bethesda)2022
34989601Long-Read Genome Assembly of Saccharomyces uvarum Strain CBS 7001.Microbiol Resour Announc2022
33976235Haplotype-resolved genome assembly enables gene discovery in the red palm weevil Rhynchophorus ferrugineus.Sci Rep2021
34849875Transposable element profiles reveal cell line identity and loss of heterozygosity in Drosophila cell culture.Genetics2021
34676292Complete mitochondrial genome of the longhorn date palm stem borer <i>Jebusaea hammerschmidtii</i> (Reiche, 1878).Mitochondrial DNA B Resour2021
32718933A Meta-Analysis of <i>Wolbachia</i> Transcriptomics Reveals a Stage-Specific <i>Wolbachia</i> Transcriptional Response Shared Across Different Hosts.G3 (Bethesda)2020
32084126Evolution of Ty1 copy number control in yeast by horizontal transfer and recombination.PLoS Genet2020
32082426Hybrid dysgenesis in <i>Drosophila virilis</i> results in clusters of mitotic recombination and loss-of-heterozygosity but leaves meiotic recombination unaltered.Mob DNA2020
31540974Phased Diploid Genome Assemblies for Three Strains of <i>Candida albicans</i> from Oak Trees.G3 (Bethesda)2019
31699757Complete Genome Assemblies for Three Variants of the <i>Wolbachia</i> Endosymbiont of Drosophila melanogaster.Microbiol Resour Announc2019
31227013Trapping a somatic endogenous retrovirus into a germline piRNA cluster immunizes the germline against further invasion.Genome Biol2019
30422992Whole genome screen reveals a novel relationship between Wolbachia levels and Drosophila host translation.PLoS Pathog2018
29942366Horizontal transfer and proliferation of Tsu4 in Saccharomyces paradoxus.Mob DNA2018
29850787Conserved Noncoding Elements Influence the Transposable Element Landscape in Drosophila.Genome Biol Evol2018
28929030Genomic analysis of <i>P</i> elements in natural populations of <i>Drosophila melanogaster</i>.PeerJ2017
28637810McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole-Genome Shotgun Sequencing Data.G3 (Bethesda)2017
26903656Rare recombination events generate sequence diversity among balancer chromosomes in Drosophila melanogaster.Proc Natl Acad Sci U S A2016
27906975Bringing PLOS Genetics Editors to Preprint Servers.PLoS Genet2016
25717372Strain-specific and pooled genome sequences for populations of Drosophila melanogaster from three continents.F1000Res2015
26437768Drosophila innate immunity: regional and functional specialization of prophenoloxidases.BMC Biol2015
26497146Dynamics of Wolbachia pipientis Gene Expression Across the Drosophila melanogaster Life Cycle.G3 (Bethesda)2015
26578579Unique transposon landscapes are pervasive across Drosophila melanogaster genomes.Nucleic Acids Res2015
24336751An age-of-allele test of neutrality for transposable element insertions.Genetics2014
25977796Long-read, whole-genome shotgun sequence data for five model organisms.Sci Data2014
22347367Whole genome resequencing reveals natural target site preferences of transposable elements in Drosophila melanogaster.PLoS One2012
23226439Evolutionary genomics of transposable elements in Saccharomyces cerevisiae.PLoS One2012
23284297Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster.PLoS Genet2012
22754753A proposal for the reference-based annotation of de novo transposable element insertions.Mob Genet Elements2012
22711795BioContext: an integrated text mining system for large-scale extraction and contextualization of biomolecular events.Bioinformatics2012
22318601The Drosophila melanogaster Genetic Reference Panel.Nature2012
20965965REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila.Nucleic Acids Res2011
21813477The GNAT library for local and remote gene mention normalization.Bioinformatics2011
21980353pubmed2ensembl: a resource for mining the biological literature on genes.PLoS One2011
21325301Annotating genes and genomes with DNA sequences extracted from biomedical articles.Bioinformatics2011
21297157A large palindrome with interchromosomal gene duplications in the pericentromeric region of the D. melanogaster Y chromosome.Mol Biol Evol2011
20149233LINNAEUS: a species name identification system for biomedical literature.BMC Bioinformatics2010
21150996Gene expression divergence recapitulates the developmental hourglass model.Nature2010
20808905Evolutionary systems biology of amino acid biosynthetic cost in yeast.PLoS One2010
20624748The evolution of tRNA genes in Drosophila.Genome Biol Evol2010
19212322Population genomics of domestic and wild yeasts.Nature2009
20333214Population genomic inferences from sparse high-throughput sequencing of two populations of Drosophila melanogaster.Genome Biol Evol2009
19364541Assigning roles to protein mentions: the case of transcription factors.J Biomed Inform2009
18039705REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila.Nucleic Acids Res2008
18834498Text mining for biology--the way forward: opinions from leading scientists.Genome Biol2008
18829720Testing the palindromic target site model for DNA transposon insertion using the Drosophila melanogaster P-element.Nucleic Acids Res2008
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Collaborators

Susan E Celniker
Lawrence Berkeley National Laboratory
Co-authored papers 7
Michael Ashburner
University of Cambridge
Co-authored papers 5
Maximilian Haeussler
Genomics Institute, University of California Santa Cruz
Co-authored papers 5
Goran Nenadic
Co-authored papers 5
Michael B Eisen
Howard Hughes Medical Institute, University of California Berkeley
Co-authored papers 3
Stephen B Montgomery
Stanford University
Co-authored papers 3
Andrew G Clark
Co-authored papers 3
Steven J M Jones
University of British Columbia
Co-authored papers 3
Obi L Griffith
Washington University
Co-authored papers 3
Joseph W Carlson
US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory
Co-authored papers 2
LaDeana W Hillier
University of Washington
Co-authored papers 2
Roger A Hoskins
University of California berkeley
Co-authored papers 2
Gerald M Rubin
The University of Florida
Co-authored papers 2
Brent Kronmiller
Center for Quantitative Life Sciences, Oregon State University
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Rob J Kulathinal
Co-authored papers 2
Adam M Phillippy
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Harvard University
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Kim D Pruitt
National Center for Biotechnology Information, National Institutes of Health
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Udo Hahn
Friedrich Schiller University Jena
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Elizabeth Bailes
Co-authored papers 1
Jane M Landolin
Co-authored papers 1
Emmanouil T Dermitzakis
University of Geneva
Co-authored papers 1
Dmitri A Petrov
Stanford University
Co-authored papers 1
Eli Venter
Vanderbilt University, Columbia University Medical Center
Co-authored papers 1
Jean L Chang
Co-authored papers 1
Aaron R Quinlan
University of Utah
Co-authored papers 1
Derek Wilson
Co-authored papers 1
Malachi Griffith
Washington University
Co-authored papers 1
Manolis Kellis
Massachusetts Institute of Technology
Co-authored papers 1
Karin A Remington
The J. Craig Venter Institute.
Co-authored papers 1
Release 1.2