Published in Mol Biol Evol on July 23, 2007
The Drosophila melanogaster Genetic Reference Panel. Nature (2012) 7.94
Morphological evolution caused by many subtle-effect substitutions in regulatory DNA. Nature (2011) 1.83
An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nat Genet (2013) 1.68
Positive and negative selection on noncoding DNA in Drosophila simulans. Mol Biol Evol (2008) 1.47
Standard and generalized McDonald-Kreitman test: a website to detect selection by comparing different classes of DNA sites. Nucleic Acids Res (2008) 1.34
On the utility of short intron sequences as a reference for the detection of positive and negative selection in Drosophila. Mol Biol Evol (2010) 1.26
Evidence that strong positive selection drives neofunctionalization in the tandemly duplicated polyhomeotic genes in Drosophila. Proc Natl Acad Sci U S A (2008) 1.17
Effective population size and the efficacy of selection on the X chromosomes of two closely related Drosophila species. Genome Biol Evol (2010) 1.14
The role of background selection in shaping patterns of molecular evolution and variation: evidence from variability on the Drosophila X chromosome. Genetics (2012) 1.13
Causes of natural variation in fitness: evidence from studies of Drosophila populations. Proc Natl Acad Sci U S A (2015) 1.10
Controlling type-I error of the McDonald-Kreitman test in genomewide scans for selection on noncoding DNA. Genetics (2008) 1.08
Studying patterns of recent evolution at synonymous sites and intronic sites in Drosophila melanogaster. J Mol Evol (2009) 1.03
Background selection as baseline for nucleotide variation across the Drosophila genome. PLoS Genet (2014) 1.02
Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster. Genome Res (2008) 0.99
Genomic complexity of the variable region-containing chitin-binding proteins in amphioxus. BMC Genet (2008) 0.94
The mystery of extreme non-coding conservation. Philos Trans R Soc Lond B Biol Sci (2013) 0.94
Strong mutational bias toward deletions in the Drosophila melanogaster genome is compensated by selection. Genome Biol Evol (2013) 0.93
Nucleosomes shape DNA polymorphism and divergence. PLoS Genet (2014) 0.90
More radical amino acid replacements in primates than in rodents: support for the evolutionary role of effective population size. Gene (2009) 0.90
Mutations within lncRNAs are effectively selected against in fruitfly but not in human. Genome Biol (2013) 0.89
Elevated levels of expression associated with regions of the Drosophila genome that lack crossing over. Biol Lett (2008) 0.86
Patterns of DNA-sequence divergence between Drosophila miranda and D. pseudoobscura. J Mol Evol (2009) 0.84
A Genomic Map of the Effects of Linked Selection in Drosophila. PLoS Genet (2016) 0.82
Methods to detect selection on noncoding DNA. Methods Mol Biol (2012) 0.81
Heterogeneity in genetic diversity among non-coding loci fails to fit neutral coalescent models of population history. PLoS One (2012) 0.80
The conserved chimeric transcript UPGRADE2 is associated with unreduced pollen formation and is exclusively found in apomictic Boechera species. Plant Physiol (2013) 0.80
Evidence that purifying selection acts on promoter sequences. Genetics (2011) 0.79
Lineage-specific conserved noncoding sequences of plant genomes: their possible role in nucleosome positioning. Genome Biol Evol (2014) 0.79
A new genome-wide method to track horizontally transferred sequences: application to Drosophila. Genome Biol Evol (2014) 0.78
The effects of purifying selection on patterns of genetic differentiation between Drosophila melanogaster populations. Heredity (Edinb) (2014) 0.78
De novo prediction of cis-regulatory elements and modules through integrative analysis of a large number of ChIP datasets. BMC Genomics (2014) 0.77
Evolutionary genomics of Colias Phosphoglucose Isomerase (PGI) introns. J Mol Evol (2012) 0.77
Highly constrained intergenic Drosophila ultraconserved elements are candidate ncRNAs. Genome Biol Evol (2015) 0.76
Changes in selective pressures associated with human population expansion may explain metabolic and immune related pathways enriched for signatures of positive selection. BMC Genomics (2016) 0.76
Molecular Population Genetics. Genetics (2017) 0.75
GC Content Heterogeneity Transition of Conserved Noncoding Sequences Occurred at the Emergence of Vertebrates. Genome Biol Evol (2016) 0.75
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
Population genomics of domestic and wild yeasts. Nature (2009) 11.79
The Drosophila melanogaster Genetic Reference Panel. Nature (2012) 7.94
The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Genome Biol (2002) 5.80
Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics (2004) 4.00
ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Res (2007) 3.80
LINNAEUS: a species name identification system for biomedical literature. BMC Bioinformatics (2010) 3.51
Functional evolution of a cis-regulatory module. PLoS Biol (2005) 3.21
Gene expression divergence recapitulates the developmental hourglass model. Nature (2010) 3.20
REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila. Nucleic Acids Res (2010) 2.84
Combined evidence annotation of transposable elements in genome sequences. PLoS Comput Biol (2005) 2.47
REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila. Nucleic Acids Res (2007) 1.99
Text mining for biology--the way forward: opinions from leading scientists. Genome Biol (2008) 1.91
Annotating genes and genomes with DNA sequences extracted from biomedical articles. Bioinformatics (2011) 1.91
Principles of genome evolution in the Drosophila melanogaster species group. PLoS Biol (2007) 1.89
The GNAT library for local and remote gene mention normalization. Bioinformatics (2011) 1.75
Tracing the evolutionary history of Drosophila regulatory regions with models that identify transcription factor binding sites. Mol Biol Evol (2003) 1.75
Large-scale discovery of promoter motifs in Drosophila melanogaster. PLoS Comput Biol (2006) 1.46
Whole genome resequencing reveals natural target site preferences of transposable elements in Drosophila melanogaster. PLoS One (2012) 1.40
Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster. PLoS Genet (2012) 1.37
Population genomic inferences from sparse high-throughput sequencing of two populations of Drosophila melanogaster. Genome Biol Evol (2009) 1.36
Standard and generalized McDonald-Kreitman test: a website to detect selection by comparing different classes of DNA sites. Nucleic Acids Res (2008) 1.34
BioContext: an integrated text mining system for large-scale extraction and contextualization of biomolecular events. Bioinformatics (2012) 1.29
Text-mining assisted regulatory annotation. Genome Biol (2008) 1.26
Drosophila melanogaster: a case study of a model genomic sequence and its consequences. Genome Res (2005) 1.15
Identifying cis-regulatory modules by combining comparative and compositional analysis of DNA. Bioinformatics (2006) 1.14
Testing the palindromic target site model for DNA transposon insertion using the Drosophila melanogaster P-element. Nucleic Acids Res (2008) 1.08
The evolution of tRNA genes in Drosophila. Genome Biol Evol (2010) 1.06
InvFEST, a database integrating information of polymorphic inversions in the human genome. Nucleic Acids Res (2013) 1.03
DPDB: a database for the storage, representation and analysis of polymorphism in the Drosophila genus. Bioinformatics (2005) 1.03
Evolutionary systems biology of amino acid biosynthetic cost in yeast. PLoS One (2010) 1.03
Paucity of chimeric gene-transposable element transcripts in the Drosophila melanogaster genome. BMC Biol (2005) 1.00
Conservation of regulatory sequences and gene expression patterns in the disintegrating Drosophila Hox gene complex. Genome Res (2005) 0.98
PDA: a pipeline to explore and estimate polymorphism in large DNA databases. Nucleic Acids Res (2004) 0.95
Evolutionary genomics of transposable elements in Saccharomyces cerevisiae. PLoS One (2012) 0.91
PDA v.2: improving the exploration and estimation of nucleotide polymorphism in large datasets of heterogeneous DNA. Nucleic Acids Res (2006) 0.90
pubmed2ensembl: a resource for mining the biological literature on genes. PLoS One (2011) 0.89
Assigning roles to protein mentions: the case of transcription factors. J Biomed Inform (2009) 0.89
A large palindrome with interchromosomal gene duplications in the pericentromeric region of the D. melanogaster Y chromosome. Mol Biol Evol (2011) 0.83
PopDrowser: the Population Drosophila Browser. Bioinformatics (2011) 0.83
MamPol: a database of nucleotide polymorphism in the Mammalia class. Nucleic Acids Res (2006) 0.83
Drosophila polymorphism database (DPDB): a portal for nucleotide polymorphism in Drosophila. Fly (Austin) (2007) 0.80
An age-of-allele test of neutrality for transposable element insertions. Genetics (2013) 0.80
Protein polymorphism is negatively correlated with conservation of intronic sequences and complexity of expression patterns in Drosophila melanogaster. J Mol Evol (2007) 0.78
Fast sequence evolution of Hox and Hox-derived genes in the genus Drosophila. BMC Evol Biol (2006) 0.78