Published in Mol Biol Evol on July 28, 2003
Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution. Proc Natl Acad Sci U S A (2004) 7.42
The impact of recombination on nucleotide substitutions in the human genome. PLoS Genet (2008) 3.16
Whole-genome analysis of Alu repeat elements reveals complex evolutionary history. Genome Res (2004) 2.37
Analysis of sequence conservation at nucleotide resolution. PLoS Comput Biol (2007) 2.01
Integrated genetic and epigenetic analysis identifies haplotype-specific methylation in the FTO type 2 diabetes and obesity susceptibility locus. PLoS One (2010) 1.93
Genome-wide patterns and properties of de novo mutations in humans. Nat Genet (2015) 1.65
Genomic heterogeneity of background substitutional patterns in Drosophila melanogaster. Genetics (2004) 1.61
Contrasting GC-content dynamics across 33 mammalian genomes: relationship with life-history traits and chromosome sizes. Genome Res (2010) 1.52
Indel-based evolutionary distance and mouse-human divergence. Genome Res (2004) 1.47
The neoselectionist theory of genome evolution. Proc Natl Acad Sci U S A (2007) 1.46
Substantial regional variation in substitution rates in the human genome: importance of GC content, gene density, and telomere-specific effects. J Mol Evol (2005) 1.45
Transcription induces strand-specific mutations at the 5' end of human genes. Genome Res (2008) 1.41
Evolutionary history of mammalian transposons determined by genome-wide defragmentation. PLoS Comput Biol (2007) 1.38
Transition-transversion bias is not universal: a counter example from grasshopper pseudogenes. PLoS Genet (2007) 1.38
Mutations of different molecular origins exhibit contrasting patterns of regional substitution rate variation. PLoS Comput Biol (2008) 1.35
The decline of isochores in mammals: an assessment of the GC content variation along the mammalian phylogeny. J Mol Evol (2004) 1.28
Noncoding DNA, isochores and gene expression: nucleosome formation potential. Nucleic Acids Res (2005) 1.27
A comparison of models to infer the distribution of fitness effects of new mutations. Genetics (2013) 1.22
Genomic regionality in rates of evolution is not explained by clustering of genes of comparable expression profile. Genome Res (2004) 1.14
Homology-dependent methylation in primate repetitive DNA. Proc Natl Acad Sci U S A (2005) 1.13
Human-specific CpG "beacons" identify loci associated with human-specific traits and disease. Epigenetics (2012) 1.07
A novel method distinguishes between mutation rates and fixation biases in patterns of single-nucleotide substitution. J Mol Evol (2005) 0.93
GC content evolution of the human and mouse genomes: insights from the study of processed pseudogenes in regions of different recombination rates. J Mol Evol (2006) 0.93
The GC content of primates and rodents genomes is not at equilibrium: a reply to Antezana. J Mol Evol (2006) 0.93
Pitfalls of the most commonly used models of context dependent substitution. Biol Direct (2008) 0.92
Phyloepigenomic comparison of great apes reveals a correlation between somatic and germline methylation states. Genome Res (2011) 0.91
Effect of the assignment of ancestral CpG state on the estimation of nucleotide substitution rates in mammals. BMC Evol Biol (2008) 0.89
Molecular reconstruction of extinct LINE-1 elements and their interaction with nonautonomous elements. Mol Biol Evol (2012) 0.88
Faster-X adaptive protein evolution in house mice. Genetics (2013) 0.87
Minor shift in background substitutional patterns in the Drosophila saltans and willistoni lineages is insufficient to explain GC content of coding sequences. BMC Biol (2006) 0.87
Comparative promoter region analysis powered by CORG. BMC Genomics (2005) 0.86
Ancestral inference and the study of codon bias evolution: implications for molecular evolutionary analyses of the Drosophila melanogaster subgroup. PLoS One (2007) 0.84
Why are young and old repetitive elements distributed differently in the human genome? J Mol Evol (2005) 0.83
Strong regional heterogeneity in base composition evolution on the Drosophila X chromosome. Genetics (2006) 0.83
The sex-specific impact of meiotic recombination on nucleotide composition. Genome Biol Evol (2012) 0.82
Reverse polarization in amino acid and nucleotide substitution patterns between human-mouse orthologs of two compositional extrema. DNA Res (2007) 0.82
Is there an acceleration of the CpG transition rate during the mammalian radiation? Bioinformatics (2008) 0.81
The rate, not the spectrum, of base pair substitutions changes at a GC-content transition in the human NF1 gene region: implications for the evolution of the mammalian genome structure. Genetics (2006) 0.81
Analysis of site frequency spectra from Arabidopsis with context-dependent corrections for ancestral misinference. Plant Physiol (2008) 0.81
Recombination-associated sequence homogenization of neighboring Alu elements: signature of nonallelic gene conversion. Mol Biol Evol (2010) 0.79
Evaluation of Ancestral Sequence Reconstruction Methods to Infer Nonstationary Patterns of Nucleotide Substitution. Genetics (2015) 0.78
Expansion of CORE-SINEs in the genome of the Tasmanian devil. BMC Genomics (2012) 0.76
Epigenetic inheritance: a contributor to species differentiation? DNA Cell Biol (2012) 0.76
Are Synonymous Sites in Primates and Rodents Functionally Constrained? J Mol Evol (2015) 0.75
Inference of transposable element ancestry. PLoS Genet (2014) 0.75
Single genome retrieval of context-dependent variability in mutation rates for human germline. BMC Genomics (2017) 0.75
On schemes of combinatorial transcription logic. Proc Natl Acad Sci U S A (2003) 6.02
Transcriptional regulation by the numbers: models. Curr Opin Genet Dev (2005) 5.20
Interdependence of cell growth and gene expression: origins and consequences. Science (2010) 5.00
High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography. PLoS Biol (2008) 4.74
Identification of direct residue contacts in protein-protein interaction by message passing. Proc Natl Acad Sci U S A (2008) 4.37
Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proc Natl Acad Sci U S A (2011) 4.08
Pervasive hitchhiking at coding and regulatory sites in humans. PLoS Genet (2009) 4.02
Selection on codon bias. Annu Rev Genet (2008) 3.83
Growth rate-dependent global effects on gene expression in bacteria. Cell (2009) 3.57
Transcriptional regulation by the numbers: applications. Curr Opin Genet Dev (2005) 3.40
Quantitative characteristics of gene regulation by small RNA. PLoS Biol (2007) 3.35
Pervasive natural selection in the Drosophila genome? PLoS Genet (2009) 3.27
Physical constraints and functional characteristics of transcription factor-DNA interaction. Proc Natl Acad Sci U S A (2002) 3.07
Evidence that mutation is universally biased towards AT in bacteria. PLoS Genet (2010) 2.95
Pesticide resistance via transposition-mediated adaptive gene truncation in Drosophila. Science (2005) 2.56
Combinatorial transcriptional control of the lactose operon of Escherichia coli. Proc Natl Acad Sci U S A (2007) 2.51
Evidence that adaptation in Drosophila is not limited by mutation at single sites. PLoS Genet (2010) 2.41
The large genome constraint hypothesis: evolution, ecology and phenotype. Ann Bot (2005) 2.33
Preferential duplication of conserved proteins in eukaryotic genomes. PLoS Biol (2004) 1.96
Genomewide spatial correspondence between nonsynonymous divergence and neutral polymorphism reveals extensive adaptation in Drosophila. Genetics (2007) 1.89
Growth-rate-dependent partitioning of RNA polymerases in bacteria. Proc Natl Acad Sci U S A (2008) 1.87
Drosophila melanogaster recombination rate calculator. Gene (2010) 1.78
DNA sequence evolution with neighbor-dependent mutation. J Comput Biol (2003) 1.76
General rules for optimal codon choice. PLoS Genet (2009) 1.71
Coordination of bacterial proteome with metabolism by cyclic AMP signalling. Nature (2013) 1.70
Pervasive and persistent redundancy among duplicated genes in yeast. PLoS Genet (2008) 1.66
Nonlinear protein degradation and the function of genetic circuits. Proc Natl Acad Sci U S A (2005) 1.65
Genomics-aided structure prediction. Proc Natl Acad Sci U S A (2012) 1.63
Genomic heterogeneity of background substitutional patterns in Drosophila melanogaster. Genetics (2004) 1.61
Population genomics of rapid adaptation by soft selective sweeps. Trends Ecol Evol (2013) 1.60
High-resolution protein complexes from integrating genomic information with molecular simulation. Proc Natl Acad Sci U S A (2009) 1.57
On the selection and evolution of regulatory DNA motifs. J Mol Evol (2002) 1.55
Genome patterns of selection and introgression of haplotypes in natural populations of the house mouse (Mus musculus). PLoS Genet (2012) 1.54
Features of protein-protein interactions in two-component signaling deduced from genomic libraries. Methods Enzymol (2007) 1.54
Identification and measurement of neighbor-dependent nucleotide substitution processes. Bioinformatics (2005) 1.54
High rate of recent transposable element-induced adaptation in Drosophila melanogaster. PLoS Biol (2008) 1.52
Bacterial growth laws and their applications. Curr Opin Biotechnol (2011) 1.52
Substantial regional variation in substitution rates in the human genome: importance of GC content, gene density, and telomere-specific effects. J Mol Evol (2005) 1.45
Small RNAs establish gene expression thresholds. Curr Opin Microbiol (2008) 1.44
Sequential establishment of stripe patterns in an expanding cell population. Science (2011) 1.44
Reduced selection leads to accelerated gene loss in Shigella. Genome Biol (2007) 1.41
Stochasticity and traffic jams in the transcription of ribosomal RNA: Intriguing role of termination and antitermination. Proc Natl Acad Sci U S A (2008) 1.41
Relaxed purifying selection and possibly high rate of adaptation in primate lineage-specific genes. Genome Biol Evol (2010) 1.40
Stochastic fluctuations in metabolic pathways. Proc Natl Acad Sci U S A (2007) 1.39
Do disparate mechanisms of duplication add similar genes to the genome? Trends Genet (2005) 1.39
Frequent adaptation and the McDonald-Kreitman test. Proc Natl Acad Sci U S A (2013) 1.37
Strong purifying selection at synonymous sites in D. melanogaster. PLoS Genet (2013) 1.34
Rates of DNA duplication and mitochondrial DNA insertion in the human genome. J Mol Evol (2003) 1.34
The innate growth bistability and fitness landscapes of antibiotic-resistant bacteria. Science (2013) 1.34
Heterozygote advantage as a natural consequence of adaptation in diploids. Proc Natl Acad Sci U S A (2011) 1.33
Host species and environmental effects on bacterial communities associated with Drosophila in the laboratory and in the natural environment. PLoS One (2013) 1.30
Protein evolution in the context of Drosophila development. J Mol Evol (2005) 1.29
On the rapidity of antibiotic resistance evolution facilitated by a concentration gradient. Proc Natl Acad Sci U S A (2012) 1.28
X-linked genes evolve higher codon bias in Drosophila and Caenorhabditis. Genetics (2005) 1.26
Sources and sinks: a stochastic model of evolution in heterogeneous environments. Phys Rev Lett (2010) 1.24
Genome-wide patterns of adaptation to temperate environments associated with transposable elements in Drosophila. PLoS Genet (2010) 1.24
Mechanically probing the folding pathway of single RNA molecules. Biophys J (2003) 1.23
Dissecting the specificity of protein-protein interaction in bacterial two-component signaling: orphans and crosstalks. PLoS One (2011) 1.20
Molecular crowding limits translation and cell growth. Proc Natl Acad Sci U S A (2013) 1.19
Empirical validation of pooled whole genome population re-sequencing in Drosophila melanogaster. PLoS One (2012) 1.16
Deterministic characterization of stochastic genetic circuits. Proc Natl Acad Sci U S A (2007) 1.15
Similar levels of X-linked and autosomal nucleotide variation in African and non-African populations of Drosophila melanogaster. BMC Evol Biol (2007) 1.15
The adaptive role of transposable elements in the Drosophila genome. Gene (2009) 1.14
Coevolutionary signals across protein lineages help capture multiple protein conformations. Proc Natl Acad Sci U S A (2013) 1.14
Broker genes in human disease. Genome Biol Evol (2010) 1.13
Quantifying the sequence-function relation in gene silencing by bacterial small RNAs. Proc Natl Acad Sci U S A (2011) 1.11
Need-based activation of ammonium uptake in Escherichia coli. Mol Syst Biol (2012) 1.10
Origins and rates of aneuploidy in human blastomeres. Fertil Steril (2011) 1.10
Codon bias and noncoding GC content correlate negatively with recombination rate on the Drosophila X chromosome. J Mol Evol (2005) 1.09
T-lex: a program for fast and accurate assessment of transposable element presence using next-generation sequencing data. Nucleic Acids Res (2010) 1.09
Regional and time-resolved mutation patterns of the human genome. Bioinformatics (2004) 1.08
Hybrid alignment: high-performance with universal statistics. Bioinformatics (2002) 1.07
Similarly strong purifying selection acts on human disease genes of all evolutionary ages. Genome Biol Evol (2009) 1.07
Designing sequential transcription logic: a simple genetic circuit for conditional memory. Syst Synth Biol (2007) 1.07
Co-evolving motions at protein-protein interfaces of two-component signaling systems identified by covariance analysis. Biochemistry (2008) 1.06
Dynamics of competitive evolution on a smooth landscape. Phys Rev Lett (2003) 1.05
Nonadaptive explanations for signatures of partial selective sweeps in Drosophila. Mol Biol Evol (2008) 1.04
Enhancer choice in cis and in trans in Drosophila melanogaster: role of the promoter. Genetics (2004) 1.03
How intron splicing affects the deletion and insertion profile in Drosophila melanogaster. Genetics (2002) 1.03
SEGE: A database on 'intron less/single exonic' genes from eukaryotes. Bioinformatics (2002) 1.02
Evolutionary biology for the 21st century. PLoS Biol (2013) 1.01
Paucity of chimeric gene-transposable element transcripts in the Drosophila melanogaster genome. BMC Biol (2005) 1.00
Rapid sequence turnover at an intergenic locus in Drosophila. Mol Biol Evol (2004) 1.00
Inference of direct residue contacts in two-component signaling. Methods Enzymol (2010) 1.00
Population genomics of transposable elements in Drosophila. Annu Rev Genet (2014) 0.97
Computational modeling of phosphotransfer complexes in two-component signaling. Methods Enzymol (2010) 0.97
LDx: estimation of linkage disequilibrium from high-throughput pooled resequencing data. PLoS One (2012) 0.95
Evolutionary selection between alternative modes of gene regulation. Proc Natl Acad Sci U S A (2009) 0.94
A novel method distinguishes between mutation rates and fixation biases in patterns of single-nucleotide substitution. J Mol Evol (2005) 0.93
Faster than neutral evolution of constrained sequences: the complex interplay of mutational biases and weak selection. Genome Biol Evol (2011) 0.93
Evolution of genome content: population dynamics of transposable elements in flies and humans. Methods Mol Biol (2012) 0.93
A recent adaptive transposable element insertion near highly conserved developmental loci in Drosophila melanogaster. Mol Biol Evol (2009) 0.92
Speed, sensitivity, and bistability in auto-activating signaling circuits. PLoS Comput Biol (2011) 0.91
Gene length may contribute to graded transcriptional responses in the Drosophila embryo. Dev Biol (2011) 0.90
Translocation of structured polynucleotides through nanopores. Phys Biol (2004) 0.90
On ribosome load, codon bias and protein abundance. PLoS One (2012) 0.89
Stripe formation in bacterial systems with density-suppressed motility. Phys Rev Lett (2012) 0.88
Minor shift in background substitutional patterns in the Drosophila saltans and willistoni lineages is insufficient to explain GC content of coding sequences. BMC Biol (2006) 0.87