Batch effects in a multiyear sequencing study: False biological trends due to changes in read lengths

Population genomics analyses of European ibex species show lower diversity and higher inbreeding in reintroduced populations

(2017) Christine Grossen et al.   Evolutionary Applications

RADseq provides unprecedented insights into molecular ecology and evolutionary genetics: comment on Breaking RAD by Lowry et al . (2016)

(2017) Garrett J. McKinney et al.   Molecular Ecology Resources

Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions

(2016) Sean Hoban et al.   AMERICAN NATURALIST

BatchQC: interactive software for evaluating sample and batch effects in genomic data

(2016) Solaiappan Manimaran et al.   BIOINFORMATICS

Exome sequencing reveals genetic differentiation due to high-altitude adaptation in the Tibetan cashmere goat (Capra hircus)

(2016) Shen Song et al.   BMC GENOMICS

Breaking RAD: an evaluation of the utility of restriction site-associated DNA sequencing for genome scans of adaptation

(2016) David B. Lowry et al.   Molecular Ecology Resources

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

Metagenomic Investigation of Plasma in Individuals with ME/CFS Highlights the Importance of Technical Controls to Elucidate Contamination and Batch Effects

(2016) Ruth R. Miller et al.   PLoS One

Bioinformatic processing of RAD-seq data dramatically impacts downstream population genetic inference

(2016) Aaron B. A. Shafer et al.   Methods in Ecology and Evolution

The challenge of separating signatures of local adaptation from those of isolation by distance and colonization history: The case of two white pines

(2016) Simon Nadeau et al.   Ecology and Evolution

Removing Batch Effects from Longitudinal Gene Expression - Quantile Normalization Plus ComBat as Best Approach for Microarray Transcriptome Data

(2016) Christian Müller et al.   PLoS One

Reliable Detection of Loci Responsible for Local Adaptation: Inference of a Null Model through Trimming the Distribution of FST

(2015) Michael C. Whitlock et al.   AMERICAN NATURALIST

Different gene expressions between cattle and yak provide insights into high-altitude adaptation

(2015) K. Wang et al.   ANIMAL GENETICS

Genome-Wide Scan for Adaptive Divergence and Association with Population-Specific Covariates

(2015) M. Gautier   GENETICS

The UK10K project identifies rare variants in health and disease

(2015)   NATURE

Improved genome inference in the MHC using a population reference graph

(2015) Alexander Dilthey et al.   NATURE GENETICS

Large-scale whole-genome sequencing of the Icelandic population

(2015) Daniel F Gudbjartsson et al.   NATURE GENETICS

Identification of Laying-Related SNP Markers in Geese Using RAD Sequencing

(2015) ShiGang Yu et al.   PLoS One

Toward better understanding of artifacts in variant calling from high-coverage samples

(2014) Heng Li   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Genomic Signatures Reveal New Evidences for Selection of Important Traits in Domestic Cattle

(2014) Lingyang Xu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evaluation of demographic history and neutral parameterization on the performance ofFSToutlier tests

(2014) Katie E. Lotterhos et al.   MOLECULAR ECOLOGY

Sequencing depth and coverage: key considerations in genomic analyses

(2014) David Sims et al.   NATURE REVIEWS GENETICS

Genome-Wide Analysis of Cold Adaptation in Indigenous Siberian Populations

(2014) Alexia Cardona et al.   PLoS One

Non-random DNA fragmentation in next-generation sequencing

(2014) Maria S. Poptsova et al.   Scientific Reports

Introgression from Domestic Goat Generated Variation at the Major Histocompatibility Complex of Alpine Ibex

(2014) Christine Grossen et al.   PLoS Genetics

Hypoxia Adaptations in the Grey Wolf (Canis lupus chanco) from Qinghai-Tibet Plateau

(2014) Wenping Zhang et al.   PLoS Genetics

dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms

(2014) Jonathan B. Puritz et al.   PeerJ

Stratified randomization controls better for batch effects in 450K methylation analysis: a cautionary tale

(2014) Olive D. Buhule et al.   Frontiers in Genetics

Robust Identification of Local Adaptation from Allele Frequencies

(2013) T. Gunther et al.   GENETICS

Assessing the Effect of Sequencing Depth and Sample Size in Population Genetics Inferences

(2013) Matteo Fumagalli   PLoS One

Characterizing and measuring bias in sequence data

(2013) Michael G Ross et al.   GENOME BIOLOGY

GWASTools: an R/Bioconductor package for quality control and analysis of genome-wide association studies

(2012) S. M. Gogarten et al.   BIOINFORMATICS

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

(2012) Jeffrey T. Leek et al.   BIOINFORMATICS

Improving ancient DNA read mapping against modern reference genomes

(2012) Mikkel Schubert et al.   BMC GENOMICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

A Critical Assessment of Storytelling: Gene Ontology Categories and the Importance of Validating Genomic Scans

(2012) Pavlos Pavlidis et al.   MOLECULAR BIOLOGY AND EVOLUTION

Special features of RAD Sequencing data: implications for genotyping

(2012) John W. Davey et al.   MOLECULAR ECOLOGY

Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)

(2012) Yang Dong et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Retraction

(2011) P. Sebastiani et al.   SCIENCE

Overcoming bias and systematic errors in next generation sequencing data

(2011) Margaret A Taub et al.   Genome Medicine

Calling SNPs without a reference sequence

(2010) Aakrosh Ratan et al.   BMC BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

Into the unknown: expression profiling without genome sequence information in CHO by next generation sequencing

(2010) Fabian Birzele et al.   NUCLEIC ACIDS RESEARCH

A strong genetic footprint of the re-introduction history of Alpine ibex (Capra ibex ibex)

(2009) IRIS BIEBACH et al.   MOLECULAR ECOLOGY