Population genetic inference from resequencing data.

The next generation of molecular markers from massively parallel sequencing of pooled DNA samples. Genetics (2010) 3.23

Estimation of allele frequencies from high-coverage genome-sequencing projects. Genetics (2009) 2.81

Population genetic inference from genomic sequence variation. Genome Res (2010) 2.29

Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance. Genome Res (2011) 2.21

De novo transcriptome sequencing in Anopheles funestus using Illumina RNA-seq technology. PLoS One (2010) 1.95

The genomics of selection in dogs and the parallel evolution between dogs and humans. Nat Commun (2013) 1.86

ECHO: a reference-free short-read error correction algorithm. Genome Res (2011) 1.68

Genome-wide footprints of pig domestication and selection revealed through massive parallel sequencing of pooled DNA. PLoS One (2011) 1.60

Population genomic inferences from sparse high-throughput sequencing of two populations of Drosophila melanogaster. Genome Biol Evol (2009) 1.36

mlRho - a program for estimating the population mutation and recombination rates from shotgun-sequenced diploid genomes. Mol Ecol (2010) 1.13

Detecting selective sweeps from pooled next-generation sequencing samples. Mol Biol Evol (2012) 1.13

Assessing the accuracy and power of population genetic inference from low-pass next-generation sequencing data. Front Genet (2012) 0.94

Estimating population genetic parameters and comparing model goodness-of-fit using DNA sequences with error. Genome Res (2009) 0.93

Parameter-free methods distinguish Wnt pathway models and guide design of experiments. Proc Natl Acad Sci U S A (2015) 0.93

Inferring population mutation rate and sequencing error rate using the SNP frequency spectrum in a sample of DNA sequences. Mol Biol Evol (2009) 0.92

Inference of population mutation rate and detection of segregating sites from next-generation sequence data. Genetics (2011) 0.91

Partial short-read sequencing of a highly inbred Iberian pig and genomics inference thereof. Heredity (Edinb) (2011) 0.90

Neutrality tests for sequences with missing data. Genetics (2012) 0.86

Estimating DNA polymorphism from next generation sequencing data with high error rate by dual sequencing applications. BMC Genomics (2013) 0.84

Genotype-Frequency Estimation from High-Throughput Sequencing Data. Genetics (2015) 0.82

Genome-wide estimation of linkage disequilibrium from population-level high-throughput sequencing data. Genetics (2014) 0.81

Inferring Heterozygosity from Ancient and Low Coverage Genomes. Genetics (2016) 0.80

A novel approach to estimating heterozygosity from low-coverage genome sequence. Genetics (2013) 0.80

Population genetic studies in the genomic sequencing era. Dongwuxue Yanjiu (2015) 0.77

Allelic variation in PtoPsbW associated with photosynthesis, growth, and wood properties in Populus tomentosa. Mol Genet Genomics (2016) 0.75

Genome sequencing in microfabricated high-density picolitre reactors. Nature (2005) 150.21

Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res (1998) 106.16

The sequence of the human genome. Science (2001) 101.55

On the number of segregating sites in genetical models without recombination. Theor Popul Biol (1975) 60.96

Whole-genome re-sequencing. Curr Opin Genet Dev (2006) 35.24

Whole-genome sequencing and variant discovery in C. elegans. Nat Methods (2008) 31.92

Paired-end mapping reveals extensive structural variation in the human genome. Science (2007) 30.46

Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics (1985) 20.92

Accurate multiplex polony sequencing of an evolved bacterial genome. Science (2005) 20.91

Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis. Nat Genet (1999) 17.09

The fine-scale structure of recombination rate variation in the human genome. Science (2004) 17.05

Quality scores and SNP detection in sequencing-by-synthesis systems. Genome Res (2008) 10.49

Fragment assembly with short reads. Bioinformatics (2004) 9.47

Advanced sequencing technologies: methods and goals. Nat Rev Genet (2004) 9.31

Two-locus sampling distributions and their application. Genetics (2001) 7.42

An utter refutation of the "fundamental theorem of the HapMap". Eur J Hum Genet (2006) 3.41

Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals. Genome Res (2008) 2.46

An isochore map of human chromosomes. Genome Res (2006) 2.36

Inference of population genetic parameters in metagenomics: a clean look at messy data. Genome Res (2006) 2.17

Inferring population parameters from single-feature polymorphism data. Genetics (2006) 0.92

Next generation sequencing technologies. Drug Discov Today Technol (2005) 0.82

Population genomics of human gene expression. Nat Genet (2007) 24.49

Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science (2007) 23.38

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol (2008) 21.72

The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature (2012) 20.47

Genome-wide associations of gene expression variation in humans. PLoS Genet (2005) 17.27

Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature (2010) 10.66

An Arabidopsis example of association mapping in structured samples. PLoS Genet (2006) 7.03

Autophagy mediates the mitotic senescence transition. Genes Dev (2009) 6.80

MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype. Genome Biol (2007) 6.41

beadarray: R classes and methods for Illumina bead-based data. Bioinformatics (2007) 6.08

Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics. Proc Natl Acad Sci U S A (2013) 5.68

An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Res (2008) 4.84

High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer. Genome Biol (2007) 4.70

Fast and flexible simulation of DNA sequence data. Genome Res (2008) 4.45

Linkage disequilibrium: what history has to tell us. Trends Genet (2002) 4.33

Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes. PLoS Genet (2005) 4.25

Species-specific transcription in mice carrying human chromosome 21. Science (2008) 4.03

Statistical issues in the analysis of Illumina data. BMC Bioinformatics (2008) 3.66

Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization. Genome Biol (2007) 3.54

A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data. Nucleic Acids Res (2009) 3.50

Piwi and piRNAs act upstream of an endogenous siRNA pathway to suppress Tc3 transposon mobility in the Caenorhabditis elegans germline. Mol Cell (2008) 3.37

Defining stem cell dynamics in models of intestinal tumor initiation. Science (2013) 3.26

Similar gene expression patterns characterize aging and oxidative stress in Drosophila melanogaster. Proc Natl Acad Sci U S A (2004) 2.94

Spatial coupling of mTOR and autophagy augments secretory phenotypes. Science (2011) 2.58

Fine-scale mapping of disease genes with multiple mutations via spatial clustering techniques. Am J Hum Genet (2003) 2.57

BayesPeak: Bayesian analysis of ChIP-seq data. BMC Bioinformatics (2009) 2.47

Modern computational approaches for analysing molecular genetic variation data. Nat Rev Genet (2006) 2.24

Transcriptional profiling of MnSOD-mediated lifespan extension in Drosophila reveals a species-general network of aging and metabolic genes. Genome Biol (2007) 2.12

Independence of repressive histone marks and chromatin compaction during senescent heterochromatic layer formation. Mol Cell (2012) 2.02

Inferring clonal expansion and cancer stem cell dynamics from DNA methylation patterns in colorectal cancers. Proc Natl Acad Sci U S A (2009) 1.98

Population-based genetic and evolutionary analysis of Chlamydia trachomatis urogenital strain variation in the United States. J Bacteriol (2004) 1.94

Dating primate divergences through an integrated analysis of palaeontological and molecular data. Syst Biol (2010) 1.85

Genome-wide mapping of ORC and Mcm2p binding sites on tiling arrays and identification of essential ARS consensus sequences in S. cerevisiae. BMC Genomics (2006) 1.83

R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips. Bioinformatics (2009) 1.83

Genome-wide replication profiles indicate an expansive role for Rpd3L in regulating replication initiation timing or efficiency, and reveal genomic loci of Rpd3 function in Saccharomyces cerevisiae. Genes Dev (2009) 1.78

CNAseg--a novel framework for identification of copy number changes in cancer from second-generation sequencing data. Bioinformatics (2010) 1.74

Application of Bayesian spatial statistical methods to analysis of haplotypes effects and gene mapping. Genet Epidemiol (2003) 1.73

Exploring population genetic models with recombination using efficient forward-time simulations. Genetics (2008) 1.72

Forkhead transcription factors establish origin timing and long-range clustering in S. cerevisiae. Cell (2012) 1.70

Counting divisions in a human somatic cell tree: how, what and why? Cell Cycle (2006) 1.62

Bayesian spatial modeling of haplotype associations. Hum Hered (2003) 1.59

Pretumor progression: clonal evolution of human stem cell populations. Am J Pathol (2004) 1.57

Continuous clonal labeling reveals small numbers of functional stem cells in intestinal crypts and adenomas. Cell Stem Cell (2013) 1.56

The pitfalls of platform comparison: DNA copy number array technologies assessed. BMC Genomics (2009) 1.55

Haplotype structure and phenotypic associations in the chromosomal regions surrounding two Arabidopsis thaliana flowering time loci. Genetics (2004) 1.55

Enhanced stem cell survival in familial adenomatous polyposis. Am J Pathol (2004) 1.51

A unique recent origin of the allotetraploid species Arabidopsis suecica: Evidence from nuclear DNA markers. Mol Biol Evol (2006) 1.51

O fly, where art thou? J R Soc Interface (2008) 1.50

Sequential DNA methylation changes are associated with DNMT3B overexpression in colorectal neoplastic progression. Gut (2010) 1.44

Modifier effects between regulatory and protein-coding variation. PLoS Genet (2008) 1.42

Statistical tests of the coalescent model based on the haplotype frequency distribution and the number of segregating sites. Genetics (2005) 1.41

The stem cell population of the human colon crypt: analysis via methylation patterns. PLoS Comput Biol (2007) 1.38

Approximately sufficient statistics and bayesian computation. Stat Appl Genet Mol Biol (2008) 1.36

Spike-in validation of an Illumina-specific variance-stabilizing transformation. BMC Res Notes (2008) 1.28

Single-molecule genomic data delineate patient-specific tumor profiles and cancer stem cell organization. Cancer Res (2012) 1.28

Association mapping with single-feature polymorphisms. Genetics (2006) 1.25

Estimating the rate of gene conversion on human chromosome 21. Am J Hum Genet (2004) 1.24

Counting human somatic cell replications: methylation mirrors endometrial stem cell divisions. Proc Natl Acad Sci U S A (2005) 1.24

BayesPeak--an R package for analysing ChIP-seq data. Bioinformatics (2011) 1.23

The microRNA miR-124 controls gene expression in the sensory nervous system of Caenorhabditis elegans. Nucleic Acids Res (2010) 1.22

Inferring relative numbers of human leucocyte genome replications. Br J Haematol (2008) 1.22

Non-linear analysis of GeneChip arrays. Nucleic Acids Res (2006) 1.21

Characterisation of microRNA expression in post-natal mouse mammary gland development. BMC Genomics (2009) 1.21

Drosophila melanogaster p53 has developmental stage-specific and sex-specific effects on adult life span indicative of sexual antagonistic pleiotropy. Aging (Albany NY) (2009) 1.19

Rad53 regulates replication fork restart after DNA damage in Saccharomyces cerevisiae. Genes Dev (2008) 1.19

Modeling evolutionary dynamics of epigenetic mutations in hierarchically organized tumors. PLoS Comput Biol (2011) 1.18

High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta. BMC Genet (2010) 1.18

Explaining differences in saturation levels for Affymetrix GeneChip arrays. Nucleic Acids Res (2007) 1.16

Genome-wide analysis of a G-quadruplex-specific single-chain antibody that regulates gene expression. Nucleic Acids Res (2009) 1.15

Population-based genetic epidemiologic analysis of Chlamydia trachomatis serotypes and lack of association between ompA polymorphisms and clinical phenotypes. Microbes Infect (2006) 1.15

Hydrogen peroxide stimulates activity and alters behavior in Drosophila melanogaster. PLoS One (2009) 1.15

Estimating a nucleotide substitution rate for maize from polymorphism at a major domestication locus. Mol Biol Evol (2005) 1.14

A screen of apoptosis and senescence regulatory genes for life span effects when over-expressed in Drosophila. Aging (Albany NY) (2009) 1.14

Many colorectal cancers are "flat" clonal expansions. Cell Cycle (2009) 1.10

Estimating recombination rates from single-nucleotide polymorphisms using summary statistics. Genetics (2006) 1.09

Genetic variation in Native Americans, inferred from Latino SNP and resequencing data. Mol Biol Evol (2011) 1.08

Cell cycle genes are the evolutionarily conserved targets of the E2F4 transcription factor. PLoS One (2007) 1.07

Age-related human small intestine methylation: evidence for stem cell niches. BMC Med (2005) 1.06

Lack of increases in methylation at three CpG-rich genomic loci in non-mitotic adult tissues during aging. BMC Med Genet (2007) 1.04

Transcriptional dynamics elicited by a short pulse of notch activation involves feed-forward regulation by E(spl)/Hes genes. PLoS Genet (2013) 1.03

Pediatric malignant germ cell tumors show characteristic transcriptome profiles. Cancer Res (2008) 1.03

Three-dimensional tracking and behaviour monitoring of multiple fruit flies. J R Soc Interface (2012) 1.02

Simultaneous tracking of fly movement and gene expression using GFP. BMC Biotechnol (2008) 1.02

Relative influences of crossing over and gene conversion on the pattern of linkage disequilibrium in Arabidopsis thaliana. Genetics (2005) 1.02

Endometrial-peritoneal interactions during endometriotic lesion establishment. Am J Pathol (2008) 1.01

Variation in genetic admixture and population structure among Latinos: the Los Angeles Latino eye study (LALES). BMC Genet (2009) 1.01

Flexible analysis of RNA-seq data using mixed effects models. Bioinformatics (2013) 1.01

The molecular signature of normal squamous esophageal epithelium identifies the presence of a field effect and can discriminate between patients with Barrett's esophagus and patients with Barrett's-associated adenocarcinoma. Cancer Epidemiol Biomarkers Prev (2005) 1.00

MMASS: an optimized array-based method for assessing CpG island methylation. Nucleic Acids Res (2006) 1.00

The level of origin firing inversely affects the rate of replication fork progression. J Cell Biol (2013) 1.00

High DNA methylation pattern intratumoral diversity implies weak selection in many human colorectal cancers. PLoS One (2011) 0.98

Critical role of nuclear calcium/calmodulin-dependent protein kinase IIdeltaB in cardiomyocyte survival in cardiomyopathy. J Biol Chem (2009) 0.98

Boosting Wnt activity during colorectal cancer progression through selective hypermethylation of Wnt signaling antagonists. BMC Cancer (2014) 0.98

Colorectal pretumor progression before and after loss of DNA mismatch repair. Am J Pathol (2004) 0.97

A multigene expression panel for the molecular diagnosis of Barrett's esophagus and Barrett's adenocarcinoma of the esophagus. Oncogene (2004) 0.97

Light causes phosphorylation of nonactivated visual pigments in intact mouse rod photoreceptor cells. J Biol Chem (2005) 0.95