High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome

Association and linkage mapping to unravel genetic architecture of phenological traits and lateral bearing in Persian walnut (Juglans regia L.)

(2020) Anthony Bernard et al.   BMC GENOMICS

High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome

(2020) Annarita Marrano et al.   GigaScience

Sequencing a Juglans regia × J. microcarpa hybrid yields high-quality genome assemblies of parental species

(2019) Tingting Zhu et al.   Horticulture Research

First simple sequence repeat-based genetic linkage map reveals a major QTL for leafing time in walnut (Juglans regia L.)

(2019) Sina Kefayati et al.   Tree Genetics & Genomes

Durum wheat genome highlights past domestication signatures and future improvement targets

(2019) Marco Maccaferri et al.   NATURE GENETICS

Genome-wide patterns of population structure and association mapping of nut-related traits in Persian walnut populations from Iran using the Axiom J. regia 700K SNP array

(2019) Mohammad Mehdi Arab et al.   Scientific Reports

Expanding Alternative Splicing Identification by Integrating Multiple Sources of Transcription Data in Tomato

(2019) Sarah Clark et al.   Frontiers in Plant Science

Chromosome-scale genome assembly of kiwifruit Actinidia eriantha with single-molecule sequencing and chromatin interaction mapping

(2019) Wei Tang et al.   GigaScience

The genomes of pecan and Chinese hickory provide insights into Carya evolution and nut nutrition

(2019) Youjun Huang et al.   GigaScience

Phylogenomics Reveals an Ancient Hybrid Origin of the Persian Walnut

(2019) Bo-Wen Zhang et al.   MOLECULAR BIOLOGY AND EVOLUTION

High-quality, genome-wide SNP genotypic data for pedigreed germplasm of the diploid outbreeding species apple, peach, and sweet cherry through a common workflow

(2019) Stijn Vanderzande et al.   PLoS One

Mutation of a bHLH transcription factor allowed almond domestication

(2019) R. Sánchez-Pérez et al.   SCIENCE

Deciphering of the Genetic Control of Phenology, Yield, and Pellicle Color in Persian Walnut (Juglans regia L.)

(2019) Annarita Marrano et al.   Frontiers in Plant Science

Hybrid de novo genome assembly of Chinese chestnut (Castanea mollissima)

(2019) Yu Xing et al.   GigaScience

EnTAP: Bringing Faster and Smarter Functional Annotation to Non‐Model Eukaryotic Transcriptomes

(2019) Alexander J. Hart et al.   Molecular Ecology Resources

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Draft genome of a high value tropical timber tree, Teak (Tectona grandis L. f): insights into SSR diversity, phylogeny and conservation

(2018) Ramasamy Yasodha et al.   DNA RESEARCH

The Rosa genome provides new insights into the domestication of modern roses

(2018) Olivier Raymond et al.   NATURE GENETICS

Genomic Variation Among and Within Six Juglans Species

(2018) Kristian A. Stevens et al.   G3-Genes Genomes Genetics

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

A reference genome of the European beech (Fagus sylvatica L.)

(2018) Bagdevi Mishra et al.   GigaScience

A new genomic tool for walnut (Juglans regia L.): development and validation of the high-density Axiom™ J. regia 700K SNP genotyping array

(2018) Annarita Marrano et al.   PLANT BIOTECHNOLOGY JOURNAL

Analysis of genetic diversity and structure in a worldwide walnut (Juglans regia L.) germplasm using SSR markers

(2018) Anthony Bernard et al.   PLoS One

Association genetics of carbon isotope discrimination and leaf morphology in a breeding population of Juglans regia L.

(2018) Randi A. Famula et al.   Tree Genetics & Genomes

A chromosome-scale assembly of the sorghum genome using nanopore sequencing and optical mapping

(2018) Stéphane Deschamps et al.   Nature Communications

Hybrid assembly of the large and highly repetitive genome ofAegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm

(2017) Aleksey V. Zimin et al.   GENOME RESEARCH

A world of opportunities with nanopore sequencing

(2017) Richard M Leggett et al.   JOURNAL OF EXPERIMENTAL BOTANY

The genome of Chenopodium quinoa

(2017) David E. Jarvis et al.   NATURE

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

(2017) Nicolas Daccord et al.   NATURE GENETICS

GeSeq – versatile and accurate annotation of organelle genomes

(2017) Michael Tillich et al.   NUCLEIC ACIDS RESEARCH

De Novo Assembly of a NewSolanum pennelliiAccession Using Nanopore Sequencing

(2017) Maximilian H.-W. Schmidt et al.   PLANT CELL

Genome-wide characterization of differential transcript usage in Arabidopsis thaliana

(2017) Dries Vaneechoutte et al.   PLANT JOURNAL

Walnut: past and future of genetic improvement

(2017) Anthony Bernard et al.   Tree Genetics & Genomes

Rethinking the history of common walnut (Juglans regia L.) in Europe: Its origins and human interactions

(2017) Paola Pollegioni et al.   PLoS One

BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data

(2016) Vagheesh Narasimhan et al.   BIOINFORMATICS

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

(2016) Nicholas H. Putnam et al.   GENOME RESEARCH

PediHaplotyper: software for consistent assignment of marker haplotypes in pedigrees

(2016) Roeland E. Voorrips et al.   MOLECULAR BREEDING

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

Are We There Yet? Reliably Estimating the Completeness of Plant Genome Sequences

(2016) Elisabeth Veeckman et al.   PLANT CELL

The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of non-structural polyphenols

(2016) Pedro J. Martínez-García et al.   PLANT JOURNAL

Genetic diversity and genetic structure of Persian walnut (Juglans regia) accessions from 14 European, African, and Asian countries using SSR markers

(2016) Aziz Ebrahimi et al.   Tree Genetics & Genomes

First Draft Assembly and Annotation of the Genome of a California Endemic Oak Quercus lobata Nee (Fagaceae)

(2016) V. L. Sork et al.   G3-Genes Genomes Genetics

Oxford Nanopore MinION Sequencing and Genome Assembly

(2016) Hengyun Lu et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Synteny analysis in Rosids with a walnut physical map reveals slow genome evolution in long-lived woody perennials

(2015) Ming-Cheng Luo et al.   BMC GENOMICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

PacBio Sequencing and Its Applications

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

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Walnut allergens: molecular characterization, detection and clinical relevance

(2014) J. Costa et al.   CLINICAL AND EXPERIMENTAL ALLERGY

Structural variation and genome complexity: is dispensable really dispensable?

(2014) Fabio Marroni et al.   CURRENT OPINION IN PLANT BIOLOGY

Bayesian QTL analyses using pedigreed families of an outcrossing species, with application to fruit firmness in apple

(2014) M. C. A. M. Bink et al.   THEORETICAL AND APPLIED GENETICS

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

A high-performance computing toolset for relatedness and principal component analysis of SNP data

(2012) X. Zheng et al.   BIOINFORMATICS

Hi–C: A comprehensive technique to capture the conformation of genomes

(2012) Jon-Matthew Belton et al.   METHODS

Preparation of megabase-sized DNA from a variety of organisms using the nuclei method for advanced genomics research

(2012) Meiping Zhang 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

Walnut (Juglans spp.) ecophysiology in response to environmental stresses and potential acclimation to climate change

(2011) Martin-Michel Gauthier et al.   ANNALS OF FOREST SCIENCE

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Identification of a walnut (Juglans regia L.) germplasm collection and evaluation of their genetic variability by microsatellite markers

(2011) L. Ruiz-Garcia et al.   SPANISH JOURNAL OF AGRICULTURAL 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

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

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

Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content

(2009) Nathan M. Springer et al.   PLoS Genetics

Aggressive assembly of pyrosequencing reads with mates

(2008) Jason R. Miller et al.   BIOINFORMATICS