Comprehensive variation discovery and recovery of missing sequence in the pig genome using multiple de novo assemblies

A genome-wide scan for signatures of directional selection in domesticated pigs

(2015) Sunjin Moon et al.   BMC GENOMICS

Whole-genome resequencing analyses of five pig breeds, including Korean wild and native, and three European origin breeds

(2015) Jung-Woo Choi et al.   DNA RESEARCH

Considerations on pig models for appetite, metabolic syndrome and obese type 2 diabetes: From food intake to metabolic disease

(2015) Sietse Jan Koopmans et al.   EUROPEAN JOURNAL OF PHARMACOLOGY

Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing

(2015) Huashui Ai et al.   NATURE GENETICS

Genetic variation and the de novo assembly of human genomes

(2015) Mark J. P. Chaisson et al.   NATURE REVIEWS GENETICS

Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios

(2015) Søren Besenbacher et al.   Nature Communications

Advancing Benchmarks for Genome Sequencing

(2015) Justin M. Zook et al.   Cell Systems

Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears

(2014) Shiping Liu et al.   CELL

Resolving the complexity of the human genome using single-molecule sequencing

(2014) Mark J. P. Chaisson et al.   NATURE

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits

(2014) Ying-hui Li et al.   NATURE BIOTECHNOLOGY

Comprehensive variation discovery in single human genomes

(2014) Neil I Weisenfeld et al.   NATURE GENETICS

Rapid diversification of fiveOryzaAA genomes associated with rice adaptation

(2014) Qun-Jie Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes

(2014) D. E. Neafsey et al.   SCIENCE

Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication

(2014) M. Carneiro et al.   SCIENCE

Genome Sequencing Reveals Loci under Artificial Selection that Underlie Disease Phenotypes in the Laboratory Rat

(2013) Santosh S. Atanur et al.   CELL

Pan genome of the phytoplankton Emiliania underpins its global distribution

(2013) Betsy A. Read et al.   NATURE

Using population admixture to help complete maps of the human genome

(2013) Giulio Genovese et al.   NATURE GENETICS

Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars

(2013) Mingzhou Li et al.   NATURE GENETICS

The missense of smell: functional variability in the human odorant receptor repertoire

(2013) Joel D Mainland et al.   NATURE NEUROSCIENCE

Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus

(2013) Laurent AF Frantz et al.   GENOME BIOLOGY

Analyses of pig genomes provide insight into porcine demography and evolution

(2012) Martien A. M. Groenen et al.   NATURE

Hybrid error correction and de novo assembly of single-molecule sequencing reads

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

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

Regions of Homozygosity in the Porcine Genome: Consequence of Demography and the Recombination Landscape

(2012) Mirte Bosse et al.   PLoS Genetics

Multiple reference genomes and transcriptomes for Arabidopsis thaliana

(2011) Xiangchao Gan et al.   NATURE

Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques

(2011) Guangmei Yan et al.   NATURE BIOTECHNOLOGY

Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly

(2011) Yingrui Li et al.   NATURE BIOTECHNOLOGY

Cardiomyopathy in α-Kinase 3 (ALPK3)–Deficient Mice

(2011) I. Van Sligtenhorst et al.   VETERINARY PATHOLOGY

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

(2010) A. McKenna et al.   GENOME RESEARCH

Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows

(2010) LAURENT EXCOFFIER et al.   Molecular Ecology Resources

Whole-genome resequencing reveals loci under selection during chicken domestication

(2010) Carl-Johan Rubin et al.   NATURE

Characterization of missing human genome sequences and copy-number polymorphic insertions

(2010) Jeffrey M Kidd et al.   NATURE METHODS

Limitations of next-generation genome sequence assembly

(2010) Can Alkan et al.   NATURE METHODS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Upregulation of PKD1L2 provokes a complex neuromuscular disease in the mouse

(2009) Francesca E. Mackenzie et al.   HUMAN MOLECULAR GENETICS

Building the sequence map of the human pan-genome

(2009) Ruiqiang Li et al.   NATURE BIOTECHNOLOGY

A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective

(2008) M. Foll et al.   GENETICS