List of works - Casey M Bergman

A large palindrome with interchromosomal gene duplications in the pericentromeric region of the D. melanogaster Y chromosome

scientific article published on 5 February 2011

A proposal for the reference-based annotation of de novo transposable element insertions ⬇️

scientific article published on January 1, 2012

An age-of-allele test of neutrality for transposable element insertions

scientific article published on 13 December 2013

Analysis of conserved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences.

scientific article

Annotating genes and genomes with DNA sequences extracted from biomedical articles

scientific article

Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome

scientific article

Benchmarking tools for the alignment of functional noncoding DNA

scientific article

BioContext: an integrated text mining system for large-scale extraction and contextualization of biomolecular events

scientific article

Bringing PLOS Genetics Editors to Preprint Servers

scientific article published on December 2016

Combined evidence annotation of transposable elements in genome sequences

scientific article

Complete Genome Assemblies for Three Variants of the Wolbachia Endosymbiont of Drosophila melanogaster

scientific article published on 07 November 2019

Complete mitochondrial genome of the longhorn date palm stem borer <i>Jebusaea hammerschmidtii</i> (Reiche, 1878)

scientific article published on 15 October 2021

Conserved Noncoding Elements Influence the Transposable Element Landscape in Drosophila.

scientific article published in June 2018

Discovering and detecting transposable elements in genome sequences

scientific article published on 10 October 2007

Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster.

scientific article published on 30 November 2004

Drosophila innate immunity: regional and functional specialization of prophenoloxidases

scientific article published on October 2015

Drosophila melanogaster: a case study of a model genomic sequence and its consequences

scientific article

Drosophila polymorphism database (DPDB): a portal for nucleotide polymorphism in Drosophila

scientific article published on 17 July 2007

Dynamics of Wolbachia pipientis Gene Expression Across the Drosophila melanogaster Life Cycle ⬇️

scientific article

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

scientific article published in October 2003

Evidence for stabilizing selection in a eukaryotic enhancer element.

scientific article

Evolution of Ty1 copy number control in yeast by horizontal transfer and recombination

scientific article published on 21 February 2020

Evolution of genes and genomes on the Drosophila phylogeny

scientific article

Evolutionary genomics of transposable elements in Saccharomyces cerevisiae

scientific article

Evolutionary systems biology of amino acid biosynthetic cost in yeast

scientific article

Functional evolution of a cis-regulatory module

scientific article

Gene expression divergence recapitulates the developmental hourglass model

scientific article

Genomic analysis of P elements in natural populations of Drosophila melanogaster

scientific article published on 15 September 2017

Haplotype-resolved genome assembly enables gene discovery in the red palm weevil Rhynchophorus ferrugineus

scientific article published on 11 May 2021

Horizontal transfer and proliferation of Tsu4 in Saccharomyces paradoxus.

scientific article

Hybrid dysgenesis in Drosophila virilis results in clusters of mitotic recombination and loss-of-heterozygosity but leaves meiotic recombination unaltered

scientific article published on 15 February 2020

Identifying cis-regulatory modules by combining comparative and compositional analysis of DNA.

scientific article published on 10 October 2006

LINNAEUS: a species name identification system for biomedical literature

scientific article

Large-scale discovery of promoter motifs in Drosophila melanogaster

scientific article published on 5 December 2006

Long-read, whole-genome shotgun sequence data for five model organisms

scientific article

McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole-Genome Shotgun Sequencing Data.

scientific article

ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation

scientific article

ORegAnno: an open-access community-driven resource for regulatory annotation

scientific article

Paucity of chimeric gene-transposable element transcripts in the Drosophila melanogaster genome

scientific article

Phased Diploid Genome Assemblies for Three Strains of Candida albicans from Oak Trees

scientific article published on 05 November 2019

Photogenic Flies—A review of Chyb and Gompel's Atlas of Drosophila Morphology: Wild-type and Classical Mutants.

scientific article published on 6 August 2013

Population genomic inferences from sparse high-throughput sequencing of two populations of Drosophila melanogaster

scientific article

Population genomics of domestic and wild yeasts

scientific article

Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster

scientific article (publication date: 2012)

Principles of genome evolution in the Drosophila melanogaster species group

scientific article

Purifying selection maintains highly conserved noncoding sequences in Drosophila

scientific article published on 23 July 2007

REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila

scientific article

REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila

scientific article

Rare recombination events generate sequence diversity among balancer chromosomes in Drosophila melanogaster

scientific article published on 22 February 2016

Recent LTR retrotransposon insertion contrasts with waves of non-LTR insertion since speciation in Drosophila melanogaster

scholarly article

Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila melanogaster genome

scientific article

Strain-specific and pooled genome sequences for populations of Drosophila melanogaster from three continents

scientific article

Testing the palindromic target site model for DNA transposon insertion using the Drosophila melanogaster P-element

scientific article published on October 2008

Text mining for biology - the way forward: opinions from leading scientists

scientific article (publication date: 2008)

Text-mining assisted regulatory annotation

scientific article published on 13 February 2008

The Drosophila melanogaster Genetic Reference Panel

scientific article

The GNAT library for local and remote gene mention normalization

scientific article

The evolution of tRNA genes in Drosophila

scientific article

The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective

scientific article

Tracing the evolutionary history of Drosophila regulatory regions with models that identify transcription factor binding sites

scientific article published on 2 April 2003

Trapping a somatic endogenous retrovirus into a germline piRNA cluster immunizes the germline against further invasion.

scientific article

Unique transposon landscapes are pervasive across Drosophila melanogaster genomes

scientific article

Whole Genome Resequencing Reveals Natural Target Site Preferences of Transposable Elements in Drosophila melanogaster ⬇️

scientific article published on February 9, 2012

Whole genome screen reveals a novel relationship between Wolbachia levels and Drosophila host translation

scientific article published on 13 November 2018

pubmed2ensembl: a resource for mining the biological literature on genes

scientific article

List of works by Casey M Bergman

A large palindrome with interchromosomal gene duplications in the pericentromeric region of the D. melanogaster Y chromosome

A proposal for the reference-based annotation of de novo transposable element insertions ⬇️

An age-of-allele test of neutrality for transposable element insertions

Analysis of conserved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences.

Annotating genes and genomes with DNA sequences extracted from biomedical articles

Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome

Benchmarking tools for the alignment of functional noncoding DNA

BioContext: an integrated text mining system for large-scale extraction and contextualization of biomolecular events

Bringing PLOS Genetics Editors to Preprint Servers

Combined evidence annotation of transposable elements in genome sequences

Complete Genome Assemblies for Three Variants of the Wolbachia Endosymbiont of Drosophila melanogaster

Complete mitochondrial genome of the longhorn date palm stem borer <i>Jebusaea hammerschmidtii</i> (Reiche, 1878)

Conserved Noncoding Elements Influence the Transposable Element Landscape in Drosophila.

Discovering and detecting transposable elements in genome sequences

Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster.

Drosophila innate immunity: regional and functional specialization of prophenoloxidases

Drosophila melanogaster: a case study of a model genomic sequence and its consequences

Drosophila polymorphism database (DPDB): a portal for nucleotide polymorphism in Drosophila

Dynamics of Wolbachia pipientis Gene Expression Across the Drosophila melanogaster Life Cycle ⬇️

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

Evidence for stabilizing selection in a eukaryotic enhancer element.

Evolution of Ty1 copy number control in yeast by horizontal transfer and recombination

Evolution of genes and genomes on the Drosophila phylogeny

Evolutionary genomics of transposable elements in Saccharomyces cerevisiae

Evolutionary systems biology of amino acid biosynthetic cost in yeast

Functional evolution of a cis-regulatory module

Gene expression divergence recapitulates the developmental hourglass model

Genomic analysis of P elements in natural populations of Drosophila melanogaster

Haplotype-resolved genome assembly enables gene discovery in the red palm weevil Rhynchophorus ferrugineus

Horizontal transfer and proliferation of Tsu4 in Saccharomyces paradoxus.

Hybrid dysgenesis in Drosophila virilis results in clusters of mitotic recombination and loss-of-heterozygosity but leaves meiotic recombination unaltered

Identifying cis-regulatory modules by combining comparative and compositional analysis of DNA.

LINNAEUS: a species name identification system for biomedical literature

Large-scale discovery of promoter motifs in Drosophila melanogaster

Long-read, whole-genome shotgun sequence data for five model organisms

McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole-Genome Shotgun Sequencing Data.

ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation

ORegAnno: an open-access community-driven resource for regulatory annotation

Paucity of chimeric gene-transposable element transcripts in the Drosophila melanogaster genome

Phased Diploid Genome Assemblies for Three Strains of Candida albicans from Oak Trees

Photogenic Flies—A review of Chyb and Gompel's Atlas of Drosophila Morphology: Wild-type and Classical Mutants.

Population genomic inferences from sparse high-throughput sequencing of two populations of Drosophila melanogaster

Population genomics of domestic and wild yeasts

Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster

Principles of genome evolution in the Drosophila melanogaster species group

Purifying selection maintains highly conserved noncoding sequences in Drosophila

REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila

REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila

Rare recombination events generate sequence diversity among balancer chromosomes in Drosophila melanogaster

Recent LTR retrotransposon insertion contrasts with waves of non-LTR insertion since speciation in Drosophila melanogaster

Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila melanogaster genome

Strain-specific and pooled genome sequences for populations of Drosophila melanogaster from three continents

Testing the palindromic target site model for DNA transposon insertion using the Drosophila melanogaster P-element

Text mining for biology - the way forward: opinions from leading scientists

Text-mining assisted regulatory annotation

The Drosophila melanogaster Genetic Reference Panel

The GNAT library for local and remote gene mention normalization

The evolution of tRNA genes in Drosophila

The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective

Tracing the evolutionary history of Drosophila regulatory regions with models that identify transcription factor binding sites

Trapping a somatic endogenous retrovirus into a germline piRNA cluster immunizes the germline against further invasion.

Unique transposon landscapes are pervasive across Drosophila melanogaster genomes

Whole Genome Resequencing Reveals Natural Target Site Preferences of Transposable Elements in Drosophila melanogaster ⬇️

Whole genome screen reveals a novel relationship between Wolbachia levels and Drosophila host translation

pubmed2ensembl: a resource for mining the biological literature on genes