Graph pangenome captures missing heritability and empowers tomato breeding

Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

(2021) Haoyu Cheng et al.   NATURE METHODS

Haplotype-resolved diverse human genomes and integrated analysis of structural variation

(2021) Peter Ebert et al.   SCIENCE

Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations

(2021) Peng Qin et al.   CELL

Towards population-scale long-read sequencing

(2021) Wouter De Coster et al.   NATURE REVIEWS GENETICS

De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes

(2021) Matthew B. Hufford et al.   SCIENCE

Identification of the Carbohydrate and Organic Acid Metabolism Genes Responsible for Brix in Tomato Fruit by Transcriptome and Metabolome Analysis

(2021) Ning Li et al.   Frontiers in Genetics

Pangenomics enables genotyping of known structural variants in 5202 diverse genomes

(2021) Jouni Sirén et al.   SCIENCE

A structural variation reference for medical and population genetics

(2020) Ryan L. Collins et al.   NATURE

Evaluating and improving heritability models using summary statistics

(2020) Doug Speed et al.   NATURE GENETICS

Pan-Genome of Wild and Cultivated Soybeans

(2020) Yucheng Liu et al.   CELL

Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato

(2020) Michael Alonge et al.   CELL

HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads

(2020) Sergey Nurk et al.   GENOME RESEARCH

PRAM: a novel pooling approach for discovering intergenic transcripts from large-scale RNA sequencing experiments

(2020) Peng Liu et al.   GENOME RESEARCH

The GTEx Consortium atlas of genetic regulatory effects across human tissues

(2020)   SCIENCE

Construction of a chromosome-scale long-read reference genome assembly for potato

(2020) Gina M Pham et al.   GigaScience

The barley pan-genome reveals the hidden legacy of mutation breeding

(2020) Murukarthick Jayakodi et al.   NATURE

Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding

(2020) Xin Wang et al.   Nature Communications

SVIM: Structural Variant Identification using Mapped Long Reads

(2019) David Heller et al.   BIOINFORMATICS

Fast and accurate genomic analyses using genome graphs

(2019) Goran Rakocevic et al.   NATURE GENETICS

Probabilistic fine-mapping of transcriptome-wide association studies

(2019) Nicholas Mancuso et al.   NATURE GENETICS

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor

(2019) Lei Gao et al.   NATURE GENETICS

Solving the missing heritability problem

(2019) Alexander I. Young   PLoS Genetics

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Rewiring of the Fruit Metabolome in Tomato Breeding

(2018) Guangtao Zhu et al.   CELL

Accurate detection of complex structural variations using single-molecule sequencing

(2018) Fritz J. Sedlazeck et al.   NATURE METHODS

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

Variation graph toolkit improves read mapping by representing genetic variation in the reference

(2018) Erik Garrison et al.   NATURE BIOTECHNOLOGY

A universal SNP and small-indel variant caller using deep neural networks

(2018) Ryan Poplin et al.   NATURE BIOTECHNOLOGY

A chemical genetic roadmap to improved tomato flavor

(2017) Denise Tieman et al.   SCIENCE

Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast

(2017) Daniel C. Jeffares et al.   Nature Communications

Assemblytics: a web analytics tool for the detection of variants from an assembly

(2016) Maria Nattestad et al.   BIOINFORMATICS

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

TACO produces robust multisample transcriptome assemblies from RNA-seq

(2016) Yashar S Niknafs et al.   NATURE METHODS

An integrated map of structural variation in 2,504 human genomes

(2015) Peter H. Sudmant et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

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

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

The genome of the stress-tolerant wild tomato species Solanum pennellii

(2014) Anthony Bolger et al.   NATURE GENETICS

Genomic analyses provide insights into the history of tomato breeding

(2014) Tao Lin et al.   NATURE GENETICS

Exploring genetic variation in the tomato (SolanumsectionLycopersicon) clade by whole-genome sequencing

(2014) et al.   PLANT JOURNAL

Whole genome resequencing in tomato reveals variation associated with introgression and breeding events

(2013) Mathilde Causse et al.   BMC GENOMICS

An Evolutionary Perspective on Epistasis and the Missing Heritability

(2013) Gibran Hemani et al.   PLoS Genetics

Improved Heritability Estimation from Genome-wide SNPs

(2012) Doug Speed et al.   AMERICAN JOURNAL OF HUMAN GENETICS

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses

(2012) Oliver Stegle et al.   Nature Protocols

Development of a Large SNP Genotyping Array and Generation of High-Density Genetic Maps in Tomato

(2012) Sung-Chur Sim et al.   PLoS One

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Ridge Regression and Other Kernels for Genomic Selection with R Package rrBLUP

(2011) Jeffrey B. Endelman   Plant Genome

Genome-wide association studies in plants: the missing heritability is in the field

(2011) Benjamin Brachi et al.   GENOME BIOLOGY

GCTA: A Tool for Genome-wide Complex Trait Analysis

(2010) Jian Yang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Common SNPs explain a large proportion of the heritability for human height

(2010) Jian Yang et al.   NATURE GENETICS

Missing heritability and strategies for finding the underlying causes of complex disease

(2010) Evan E. Eichler et al.   NATURE REVIEWS GENETICS

Finding the missing heritability of complex diseases

(2009) Teri A. Manolio et al.   NATURE

Unstable Tandem Repeats in Promoters Confer Transcriptional Evolvability

(2009) M. D. Vinces et al.   SCIENCE

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Personal genomes: The case of the missing heritability

(2008) Brendan Maher   NATURE

Sizing up human height variation

(2008) Peter M Visscher   NATURE GENETICS