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List of works by Casey M Bergman

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Evolution of genes and genomes on the Drosophila phylogeny

scientific article
The Drosophila melanogaster Genetic Reference Panel

scientific article
Population genomics of domestic and wild yeasts

scientific article
Evidence for stabilizing selection in a eukaryotic enhancer element.

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

scientific article
Gene expression divergence recapitulates the developmental hourglass model

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

scientific article
Combined evidence annotation of transposable elements in genome sequences

scientific article
Functional evolution of a cis-regulatory module

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

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

scientific article
Principles of genome evolution in the Drosophila melanogaster species group

scientific article
LINNAEUS: a species name identification system for biomedical literature

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

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

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

scientific article
Discovering and detecting transposable elements in genome sequences

scientific article published on 10 October 2007
Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster

scientific article (publication date: 2012)
Benchmarking tools for the alignment of functional noncoding DNA

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

scientific article published on February 9, 2012
Long-read, whole-genome shotgun sequence data for five model organisms

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

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

scholarly article
Purifying selection maintains highly conserved noncoding sequences in Drosophila

scientific article published on 23 July 2007
Large-scale discovery of promoter motifs in Drosophila melanogaster

scientific article published on 5 December 2006
Population genomic inferences from sparse high-throughput sequencing of two populations of Drosophila melanogaster

scientific article
Drosophila innate immunity: regional and functional specialization of prophenoloxidases

scientific article published on October 2015
Text mining for biology - the way forward: opinions from leading scientists

scientific article (publication date: 2008)
The GNAT library for local and remote gene mention normalization

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

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

scientific article
Evolutionary systems biology of amino acid biosynthetic cost in yeast

scientific article
Unique transposon landscapes are pervasive across Drosophila melanogaster genomes

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

scientific article
Evolutionary genomics of transposable elements in Saccharomyces cerevisiae

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

scientific article published on 13 December 2013
The evolution of tRNA genes in Drosophila

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

scientific article published on 10 October 2006
Testing the palindromic target site model for DNA transposon insertion using the Drosophila melanogaster P-element

scientific article published on October 2008
Dynamics of Wolbachia pipientis Gene Expression Across the Drosophila melanogaster Life Cycle

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

scientific article
Text-mining assisted regulatory annotation

scientific article published on 13 February 2008
Annotating genes and genomes with DNA sequences extracted from biomedical articles

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

scientific article published on 22 February 2016
A large palindrome with interchromosomal gene duplications in the pericentromeric region of the D. melanogaster Y chromosome

scientific article published on 5 February 2011
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
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

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