Building a sequence map of the pig pan-genome from multiple de novo assemblies and Hi-C data

Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice

(2018) Qiang Zhao et al.   NATURE GENETICS

De novo human genome assemblies reveal spectrum of alternative haplotypes in diverse populations

(2018) Karen H. Y. Wong et al.   Nature Communications

Assembly of a pan-genome from deep sequencing of 910 humans of African descent

(2018) Rachel M. Sherman et al.   NATURE GENETICS

Porcine Y-chromosome variation is consistent with the occurrence of paternal gene flow from non-Asian to Asian populations

(2017) Sara Guirao-Rico et al.   HEREDITY

3D Chromatin Architecture of Large Plant Genomes Determined by Local A/B Compartments

(2017) Pengfei Dong et al.   Molecular Plant

Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure

(2017) Sean P. Gordon et al.   Nature Communications

Promoter-enhancer interactions identified from Hi-C data using probabilistic models and hierarchical topological domains

(2017) Gil Ron et al.   Nature Communications

CNVcaller: highly efficient and widely applicable software for detecting copy number variations in large populations

(2017) Xihong Wang et al.   GigaScience

de novo assemblies of three Oryza glaberrima accessions provide first insights about pan-genome of African rices

(2016) Cécile Monat et al.   Genome Biology and Evolution

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

(2016) Mingzhou Li et al.   GENOME RESEARCH

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

RPAN: rice pan-genome browser for ∼3000 rice genomes

(2016) Chen Sun et al.   NUCLEIC ACIDS RESEARCH

The pangenome of an agronomically important crop plant Brassica oleracea

(2016) Agnieszka A. Golicz et al.   Nature Communications

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation

(2016) Wei Shen et al.   PLoS One

Exploring evidence of positive selection reveals genetic basis of meat quality traits in Berkshire pigs through whole genome sequencing

(2015) Hyeonsoo Jeong et al.   BMC GENETICS

Integrative analysis of haplotype-resolved epigenomes across human tissues

(2015) Danny Leung et al.   NATURE

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Ballgown bridges the gap between transcriptome assembly and expression analysis

(2015) Alyssa C Frazee et al.   NATURE BIOTECHNOLOGY

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

(2015) Huashui Ai et al.   NATURE GENETICS

Evidence of long-term gene flow and selection during domestication from analyses of Eurasian wild and domestic pig genomes

(2015) Laurent A F Frantz et al.   NATURE GENETICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

De novo deletion of chromosome 11q12.3 in monozygotic twins affected by Poland Syndrome

(2014) Carlotta Maria Vaccari et al.   BMC Medical Genetics

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

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

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

Insights into the Maize Pan-Genome and Pan-Transcriptome

(2014) C. N. Hirsch et al.   PLANT CELL

Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes

(2014) D. E. Neafsey et al.   SCIENCE

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

(2013) Mingzhou Li et al.   NATURE GENETICS

Comparative Epigenomic Annotation of Regulatory DNA

(2012) Shu Xiao et al.   CELL

A fast algorithm for matrix balancing

(2012) P. A. Knight et al.   IMA JOURNAL OF NUMERICAL ANALYSIS

Analyses of pig genomes provide insight into porcine demography and evolution

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

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

The sequence and analysis of a Chinese pig genome

(2012) Xiaodong Fang et al.   GigaScience

Regulation of Peroxisomal Lipid Metabolism by Catalytic Activity of Tumor Suppressor H-rev107

(2011) Toru Uyama et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

(2011) Guangmei Yan et al.   NATURE BIOTECHNOLOGY

KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases

(2011) Chen Xie et al.   NUCLEIC ACIDS RESEARCH

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

(2010) A. McKenna et al.   GENOME RESEARCH

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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Building the sequence map of the human pan-genome

(2009) Ruiqiang Li et al.   NATURE BIOTECHNOLOGY

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY