inGAP-family: Accurate Detection of Meiotic Recombination Loci and Causal Mutations by Filtering Out Artificial Variants due to Genome Complexities

GSA: Genome Sequence Archive *

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1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana

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Genomic architecture of heterosis for yield traits in rice

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Rapid identification of causal mutations in tomato EMS populations via mapping-by-sequencing

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A high-quality human reference panel reveals the complexity and distribution of genomic structural variants

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mirTrios: an integrated pipeline for detection of de novo and rare inherited mutations from trios-based next-generation sequencing

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High-Throughput Sequencing Technologies

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WASP: allele-specific software for robust molecular quantitative trait locus discovery

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Widely distributed hot and cold spots in meiotic recombination as shown by the sequencing of rice F2plants

(2015) Weina Si et al.   NEW PHYTOLOGIST

Somatic mutation in cancer and normal cells

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Causes and consequences of crossing-over evidenced via a high-resolution recombinational landscape of the honey bee

(2015) Haoxuan Liu et al.   GENOME BIOLOGY

PacBio Sequencing and Its Applications

(2015) Anthony Rhoads et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

A Bayesian framework for de novo mutation calling in parents-offspring trios

(2014) Qiang Wei et al.   BIOINFORMATICS

A gradient-boosting approach for filtering de novo mutations in parent–offspring trios

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Detection of genomic variations and DNA polymorphisms and impact on analysis of meiotic recombination and genetic mapping

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De novo mutations in epileptic encephalopathies

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DeNovoGear: de novo indel and point mutation discovery and phasing

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The genomic landscape of meiotic crossovers and gene conversions in Arabidopsis thaliana

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Characterizing and measuring bias in sequence data

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Genome-wide Single-Cell Analysis of Recombination Activity and De Novo Mutation Rates in Human Sperm

(2012) Jianbin Wang et al.   CELL

Genome sequencing reveals agronomically important loci in rice using MutMap

(2012) Akira Abe et al.   NATURE BIOTECHNOLOGY

De novo mutations in human genetic disease

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Fast Isogenic Mapping-by-Sequencing of Ethyl Methanesulfonate-Induced Mutant Bulks

(2012) B. Hartwig et al.   PLANT PHYSIOLOGY

Great majority of recombination events in Arabidopsis are gene conversion events

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A Likelihood-Based Framework for Variant Calling and De Novo Mutation Detection in Families

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Analysis of Arabidopsis genome-wide variations before and after meiosis and meiotic recombination by resequencing Landsberg erecta and all four products of a single meiosis

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

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Whole-genome sequencing of multiple Arabidopsis thaliana populations

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Exome sequencing as a tool for Mendelian disease gene discovery

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

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

inGAP-sv: a novel scheme to identify and visualize structural variation from paired end mapping data

(2011) Ji Qi et al.   NUCLEIC ACIDS RESEARCH

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

ReCombine: A Suite of Programs for Detection and Analysis of Meiotic Recombination in Whole-Genome Datasets

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Reference-guided assembly of four diverse Arabidopsis thaliana genomes

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

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The flowering gene SINGLE FLOWER TRUSS drives heterosis for yield in tomato

(2010) Uri Krieger et al.   NATURE GENETICS

inGAP: an integrated next-generation genome analysis pipeline

(2009) Ji Qi 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

Characterization of meiotic crossovers and gene conversion by whole-genome sequencing in Saccharomyces cerevisiae

(2009) Ji Qi et al.   BMC GENOMICS

Genome-wide association study identifies variants at CLU and PICALM associated with Alzheimer's disease

(2009) Denise Harold et al.   NATURE GENETICS

SHOREmap: simultaneous mapping and mutation identification by deep sequencing

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Continuous base identification for single-molecule nanopore DNA sequencing

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High-Resolution Mapping of Crossovers Reveals Extensive Variation in Fine-Scale Recombination Patterns Among Humans

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