Sequencing pools of individuals — mining genome-wide polymorphism data without big funding

Effective Variant Detection by Targeted Deep Sequencing of DNA Pools: An Example from Parkinson's Disease

(2014) Lasse Pihlstrøm et al.   ANNALS OF HUMAN GENETICS

A Genome-Wide Scan for Evidence of Selection in a Maize Population Under Long-Term Artificial Selection for Ear Number

(2014) T. M. Beissinger et al.   GENETICS

Systems Genomics of Metabolic Phenotypes in Wild-Type Drosophila melanogaster

(2014) Laura K. Reed et al.   GENETICS

Resequencing studies of nonmodel organisms using closely related reference genomes: optimal experimental designs and bioinformatics approaches for population genomics

(2014) B. Nevado et al.   MOLECULAR ECOLOGY

Experimental evolution reveals habitat-specific fitness dynamics amongWolbachiaclades inDrosophila melanogaster

(2014) Elisabetta Versace et al.   MOLECULAR ECOLOGY

Illumina claims $1,000 genome win

(2014) Cormac Sheridan   NATURE BIOTECHNOLOGY

Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle

(2014) Hans D Daetwyler et al.   NATURE GENETICS

PyClone: statistical inference of clonal population structure in cancer

(2014) Andrew Roth et al.   NATURE METHODS

Using next-generation sequencing to isolate mutant genes from forward genetic screens

(2014) Korbinian Schneeberger   NATURE REVIEWS GENETICS

TEMP: a computational method for analyzing transposable element polymorphism in populations

(2014) Jiali Zhuang et al.   NUCLEIC ACIDS RESEARCH

Host adaptation to viruses relies on few genes with different cross-resistance properties

(2014) N. E. Martins et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic changes under rapid evolution: selection for parasitoid resistance

(2014) K. M. Jalvingh et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Viral Quasispecies Assembly via Maximal Clique Enumeration

(2014) Armin Töpfer et al.   PLoS Computational Biology

Classic Selective Sweeps Revealed by Massive Sequencing in Cattle

(2014) Saber Qanbari et al.   PLoS Genetics

Influenza Virus Drug Resistance: A Time-Sampled Population Genetics Perspective

(2014) Matthieu Foll et al.   PLoS Genetics

A unified approach for allele frequency estimation, SNP detection and association studies based on pooled sequencing data using EM algorithms

(2013) Quan Chen et al.   BMC GENOMICS

V-Phaser 2: variant inference for viral populations

(2013) Xiao Yang et al.   BMC GENOMICS

FUNCTIONAL AND POPULATION GENOMIC DIVERGENCE WITHIN AND BETWEEN TWO SPECIES OF KILLIFISH ADAPTED TO DIFFERENT OSMOTIC NICHES

(2013) Genevieve M. Kozak et al.   EVOLUTION

Detecting and Measuring Selection from Gene Frequency Data

(2013) R. Vitalis et al.   GENETICS

Robust Identification of Local Adaptation from Allele Frequencies

(2013) T. Gunther et al.   GENETICS

Genome-Wide Association Study of Extreme Longevity in Drosophila melanogaster

(2013) Molly K. Burke et al.   Genome Biology and Evolution

The Genomic Signal of Partial Sweeps in Mimulus guttatus

(2013) John K. Kelly et al.   Genome Biology and Evolution

RNA-seq-based mapping and candidate identification of mutations from forward genetic screens

(2013) A. C. Miller et al.   GENOME RESEARCH

Genome evolution during progression to breast cancer

(2013) D. E. Newburger et al.   GENOME RESEARCH

MMAPPR: Mutation Mapping Analysis Pipeline for Pooled RNA-seq

(2013) J. T. Hill et al.   GENOME RESEARCH

eALPS: Estimating Abundance Levels in Pooled Sequencing Using Available Genotyping Data

(2013) Itamar Eskin et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Probabilistic Inference of Viral Quasispecies Subject to Recombination

(2013) Armin Töpfer et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Maximum Likelihood Estimation of Frequencies of Known Haplotypes from Pooled Sequence Data

(2013) D. Kessner et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Guide for the Design of Evolve and Resequencing Studies

(2013) Robert Kofler et al.   MOLECULAR BIOLOGY AND EVOLUTION

Massive Habitat-Specific Genomic Response in D. melanogaster Populations during Experimental Evolution in Hot and Cold Environments

(2013) Ray Tobler et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inference of chromosomal inversion dynamics from Pool-Seq data in natural and laboratory populations ofDrosophila melanogaster

(2013) Martin Kapun et al.   MOLECULAR ECOLOGY

Estimation of population allele frequencies from next-generation sequencing data: pool-versus individual-based genotyping

(2013) Mathieu Gautier et al.   MOLECULAR ECOLOGY

Population genomics from pool sequencing

(2013) Luca Ferretti et al.   MOLECULAR ECOLOGY

RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling

(2013) B. Arnold et al.   MOLECULAR ECOLOGY

Population genomic footprints of selection and associations with climate in natural populations ofArabidopsis hallerifrom the Alps

(2013) Martin C. Fischer et al.   MOLECULAR ECOLOGY

The impact of transposable elements in environmental adaptation

(2013) Elena Casacuberta et al.   MOLECULAR ECOLOGY

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Accuracy of allele frequency estimation using pooled RNA-Seq

(2013) M. Konczal et al.   Molecular Ecology Resources

Pool-hmm: a Python program for estimating the allele frequency spectrum and detecting selective sweeps from next generation sequencing of pooled samples

(2013) Simon Boitard et al.   Molecular Ecology Resources

The genomic signature of dog domestication reveals adaptation to a starch-rich diet

(2013) Erik Axelsson et al.   NATURE

Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations

(2013) Gregory I. Lang et al.   NATURE

The role of replicates for error mitigation in next-generation sequencing

(2013) Kimberly Robasky et al.   NATURE REVIEWS GENETICS

The Implications of Clonal Genome Evolution for Cancer Medicine

(2013) Samuel Aparicio et al.   NEW ENGLAND JOURNAL OF MEDICINE

An Integrated Transcriptome-Wide Analysis of Cave and Surface Dwelling Astyanax mexicanus

(2013) Joshua B. Gross et al.   PLoS One

An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis

(2013) Cristian Del Fabbro et al.   PLoS One

Intra-Specific Regulatory Variation in Drosophila pseudoobscura

(2013) Anton Suvorov et al.   PLoS One

Systematic functional regulatory assessment of disease-associated variants

(2013) Konrad J. Karczewski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-throughput DNA sequencing errors are reduced by orders of magnitude using circle sequencing

(2013) D. I. Lou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics

(2013) Ekta Khurana et al.   SCIENCE

Genome sequencing and population genomics in non-model organisms

(2013) Hans Ellegren   TRENDS IN ECOLOGY & EVOLUTION

Detection of Mixed Infection from Bacterial Whole Genome Sequence Data Allows Assessment of Its Role in Clostridium difficile Transmission

(2013) David W. Eyre et al.   PLoS Computational Biology

A Genome-Wide, Fine-Scale Map of Natural Pigmentation Variation in Drosophila melanogaster

(2013) Héloïse Bastide et al.   PLoS Genetics

Whole Genome, Whole Population Sequencing Reveals That Loss of Signaling Networks Is the Major Adaptive Strategy in a Constant Environment

(2013) Daniel J. Kvitek et al.   PLoS Genetics

Private Selective Sweeps Identified from Next-Generation Pool-Sequencing Reveal Convergent Pathways under Selection in Two Inbred Schistosoma mansoni Strains

(2013) Julie A. J. Clément et al.   PLoS Neglected Tropical Diseases

An empirical Bayes mixture model for SNP detection in pooled sequencing data

(2012) B. Zhou   BIOINFORMATICS

Network-enabled gene expression analysis

(2012) David Edwards et al.   BMC BIOINFORMATICS

SNP calling by sequencing pooled samples

(2012) Emanuele Raineri et al.   BMC BIOINFORMATICS

The Life History of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

Disease gene identification strategies for exome sequencing

(2012) Christian Gilissen et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

GENOMIC BASIS OF AGING AND LIFE-HISTORY EVOLUTION INDROSOPHILA MELANOGASTER

(2012) Silvia C. Remolina et al.   EVOLUTION

Biases and Errors on Allele Frequency Estimation and Disease Association Tests of Next-Generation Sequencing of Pooled Samples

(2012) Xiaowei Chen et al.   GENETIC EPIDEMIOLOGY

Investigating Natural Variation in Drosophila Courtship Song by the Evolve and Resequence Approach

(2012) T. L. Turner et al.   GENETICS

CloudMap: A Cloud-Based Pipeline for Analysis of Mutant Genome Sequences

(2012) Gregory Minevich et al.   GENETICS

Mutation mapping and identification by whole-genome sequencing

(2012) I. Leshchiner et al.   GENOME RESEARCH

Genome-wide patterns of natural variation reveal strong selective sweeps and ongoing genomic conflict in Drosophila mauritiana

(2012) V. Nolte et al.   GENOME RESEARCH

Identification of novel causative genes determining the complex trait of high ethanol tolerance in yeast using pooled-segregant whole-genome sequence analysis

(2012) S. Swinnen et al.   GENOME RESEARCH

Linking disease associations with regulatory information in the human genome

(2012) M. A. Schaub et al.   GENOME RESEARCH

Inferring Population Histories Using Genome-Wide Allele Frequency Data

(2012) Mathieu Gautier et al.   MOLECULAR BIOLOGY AND EVOLUTION

Detecting Selective Sweeps from Pooled Next-Generation Sequencing Samples

(2012) S. Boitard et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-wide patterns of latitudinal differentiation among populations ofDrosophila melanogasterfrom North America

(2012) Daniel K. Fabian et al.   MOLECULAR ECOLOGY

The effect of RAD allele dropout on the estimation of genetic variation within and between populations

(2012) Mathieu Gautier et al.   MOLECULAR ECOLOGY

Adaptation ofDrosophilato a novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles

(2012) PABLO OROZCO-terWENGEL et al.   MOLECULAR ECOLOGY

Clonal evolution in cancer

(2012) Mel Greaves et al.   NATURE

Genomic approaches to studying the human microbiota

(2012) George M. Weinstock   NATURE

Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing

(2012) Li Ding et al.   NATURE

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Extremely low-coverage sequencing and imputation increases power for genome-wide association studies

(2012) Bogdan Pasaniuc et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Empirical Validation of Pooled Whole Genome Population Re-Sequencing in Drosophila melanogaster

(2012) Yuan Zhu et al.   PLoS One

LDx: Estimation of Linkage Disequilibrium from High-Throughput Pooled Resequencing Data

(2012) Alison F. Feder et al.   PLoS One

Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring

(2012) S. Lamichhaney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Strong signatures of selection in the domestic pig genome

(2012) C.-J. Rubin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tangled bank of experimentally evolved Burkholderia biofilms reflects selection during chronic infections

(2012) C. C. Traverse et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Association Studies Reveal a Simple Genetic Basis of Resistance to Naturally Coevolving Viruses in Drosophila melanogaster

(2012) Michael M. Magwire et al.   PLoS Genetics

The Rose-comb Mutation in Chickens Constitutes a Structural Rearrangement Causing Both Altered Comb Morphology and Defective Sperm Motility

(2012) Freyja Imsland et al.   PLoS Genetics

Sequencing of Pooled DNA Samples (Pool-Seq) Uncovers Complex Dynamics of Transposable Element Insertions in Drosophila melanogaster

(2012) Robert Kofler et al.   PLoS Genetics

vipR: variant identification in pooled DNA using R

(2011) A. Altmann et al.   BIOINFORMATICS

QuRe: software for viral quasispecies reconstruction from next-generation sequencing data

(2011) Mattia C. F. Prosperi et al.   BIOINFORMATICS

PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)

(2011) R. Kofler et al.   BIOINFORMATICS

Inferring viral quasispecies spectra from 454 pyrosequencing reads

(2011) Irina Astrovskaya et al.   BMC BIOINFORMATICS

ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data

(2011) Osvaldo Zagordi et al.   BMC BIOINFORMATICS

PoPoolation DB: a user-friendly web-based database for the retrieval of natural polymorphisms in Drosophila

(2011) Ram Pandey et al.   BMC GENETICS

Next-Generation Mapping of Complex Traits with Phenotype-Based Selection and Introgression

(2011) Eric J. Earley et al.   GENETICS

Efficient Mapping and Cloning of Mutations in Zebrafish by Low-Coverage Whole-Genome Sequencing

(2011) M. E. Bowen et al.   GENETICS

Ecological Genomics of Anopheles gambiae Along a Latitudinal Cline: A Population-Resequencing Approach

(2011) C. Cheng et al.   GENETICS

Revealing the genetic structure of a trait by sequencing a population under selection

(2011) L. Parts et al.   GENOME RESEARCH

Quantifying Selection Acting on a Complex Trait Using Allele Frequency Time Series Data

(2011) C. J. R. Illingworth et al.   MOLECULAR BIOLOGY AND EVOLUTION

De novo transcriptome assembly and polymorphism detection in the flowering plant Silene vulgaris (Caryophyllaceae)

(2011) DANIEL B. SLOAN et al.   Molecular Ecology Resources

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Exome sequencing as a tool for Mendelian disease gene discovery

(2011) Michael J. Bamshad et al.   NATURE REVIEWS GENETICS

Genome-wide genetic marker discovery and genotyping using next-generation sequencing

(2011) John W. Davey et al.   NATURE REVIEWS GENETICS

SNVer: a statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data

(2011) Zhi Wei et al.   NUCLEIC ACIDS RESEARCH

Next-generation mapping of Arabidopsis genes

(2011) Ryan S. Austin et al.   PLANT JOURNAL

PoolHap: Inferring Haplotype Frequencies from Pooled Samples by Next Generation Sequencing

(2011) Quan Long et al.   PLoS One

PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals

(2011) Robert Kofler et al.   PLoS One

Experimental selection of hypoxia-tolerant Drosophila melanogaster

(2011) D. Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detection and quantification of rare mutations with massively parallel sequencing

(2011) I. Kinde et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adaptation to Climate Across the Arabidopsis thaliana Genome

(2011) A. M. Hancock et al.   SCIENCE

Two Evolutionary Histories in the Genome of Rice: the Roles of Domestication Genes

(2011) Ziwen He et al.   PLoS Genetics

Population-Based Resequencing of Experimentally Evolved Populations Reveals the Genetic Basis of Body Size Variation in Drosophila melanogaster

(2011) Thomas L. Turner et al.   PLoS Genetics

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

(2011) André E Minoche et al.   GENOME BIOLOGY

A statistical method for the detection of variants from next-generation resequencing of DNA pools

(2010) V. Bansal   BIOINFORMATICS

Genomic Differentiation Between Temperate and Tropical Australian Populations of Drosophila melanogaster

(2010) B. Kolaczkowski et al.   GENETICS

The Next Generation of Molecular Markers From Massively Parallel Sequencing of Pooled DNA Samples

(2010) Andreas Futschik et al.   GENETICS

High-throughput discovery of rare insertions and deletions in large cohorts

(2010) F. L. M. Vallania et al.   GENOME RESEARCH

Dindel: Accurate indel calls from short-read data

(2010) C. A. Albers et al.   GENOME RESEARCH

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Dissection of genetically complex traits with extremely large pools of yeast segregants

(2010) Ian M. Ehrenreich et al.   NATURE

Whole-genome resequencing reveals loci under selection during chicken domestication

(2010) Carl-Johan Rubin et al.   NATURE

Genome-wide analysis of a long-term evolution experiment with Drosophila

(2010) Molly K. Burke et al.   NATURE

Integrating common and rare genetic variation in diverse human populations

(2010)   NATURE

Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils

(2010) Thomas L Turner et al.   NATURE GENETICS

High-throughput, pooled sequencing identifies mutations in NUBPL and FOXRED1 in human complex I deficiency

(2010) Sarah E Calvo et al.   NATURE GENETICS

Genotype imputation for genome-wide association studies

(2010) Jonathan Marchini et al.   NATURE REVIEWS GENETICS

Genome-Wide Effects of Long-Term Divergent Selection

(2010) Anna M. Johansson et al.   PLoS Genetics

Bulk Segregant Analysis by High-Throughput Sequencing Reveals a Novel Xylose Utilization Gene from Saccharomyces cerevisiae

(2010) Jared W. Wenger et al.   PLoS Genetics

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

(2009) Jacob F. Degner et al.   BIOINFORMATICS

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

(2009) Daniel C. Koboldt et al.   BIOINFORMATICS

Finding the missing heritability of complex diseases

(2009) Teri A. Manolio et al.   NATURE

SHOREmap: simultaneous mapping and mutation identification by deep sequencing

(2009) Korbinian Schneeberger et al.   NATURE METHODS

Quantification of rare allelic variants from pooled genomic DNA

(2009) Todd E Druley et al.   NATURE METHODS

The 1001 Genomes Project for Arabidopsis thaliana

(2009) Detlef Weigel et al.   GENOME BIOLOGY

The Evolution of Gene Regulation Underlies a Morphological Difference between Two Drosophila Sister Species

(2008) Sangyun Jeong et al.   CELL

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

Regulatory changes underlying expression differences within and between Drosophila species

(2008) Patricia J Wittkopp et al.   NATURE GENETICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Adaptations to Climate in Candidate Genes for Common Metabolic Disorders

(2008) Angela M. Hancock et al.   PLoS Genetics