Cantaloupe melon genome reveals 3D chromatin features and structural relationship with the ancestral cucurbitaceae karyotype

QTLs and candidate genes analyses for fruit size under domestication and differentiation in melon (Cucumis melo L.) based on high resolution maps

(2021) Qun Lian et al.   BMC PLANT BIOLOGY

An Improved Melon Reference Genome With Single-Molecule Sequencing Uncovers a Recent Burst of Transposable Elements With Potential Impact on Genes

(2020) Raúl Castanera et al.   Frontiers in Plant Science

Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization

(2020) Joachim Wolff et al.   NUCLEIC ACIDS RESEARCH

Comparative Metabolomics and Molecular Phylogenetics of Melon (Cucumis melo, Cucurbitaceae) Biodiversity

(2020) Annick Moing et al.   Metabolites

The Chromosome-Scale Genome of Melon Dissects Genetic Architecture of Important Agronomic Traits

(2020) Jinghua Yang et al.   iScience

Comparative genomics of muskmelon reveals a potential role for retrotransposons in the modification of gene expression

(2020) Ryoichi Yano et al.   Communications Biology

Tissue‐specific Hi‐C analyses of rice, foxtail millet and maize suggest non‐canonical function of plant chromatin domains

(2019) Pengfei Dong et al.   Journal of Integrative Plant Biology

Genome of ‘Charleston Gray’, the principal American watermelon cultivar, and genetic characterization of 1,365 accessions in the U.S. National Plant Germplasm System watermelon collection

(2019) Shan Wu et al.   PLANT BIOTECHNOLOGY JOURNAL

Origin and domestication of Cucurbitaceae crops: insights from phylogenies, genomics and archaeology

(2019) Guillaume Chomicki et al.   NEW PHYTOLOGIST

Resequencing of 414 cultivated and wild watermelon accessions identifies selection for fruit quality traits

(2019) Shaogui Guo et al.   NATURE GENETICS

A comprehensive genome variation map of melon identifies multiple domestication events and loci influencing agronomic traits

(2019) Guangwei Zhao et al.   NATURE GENETICS

The wax gourd genomes offer insights into the genetic diversity and ancestral cucurbit karyotype

(2019) Dasen Xie et al.   Nature Communications

Snakemake—a scalable bioinformatics workflow engine

(2018) Johannes Köster et al.   BIOINFORMATICS

Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization

(2018) Joachim Wolff et al.   NUCLEIC ACIDS RESEARCH

High-resolution TADs reveal DNA sequences underlying genome organization in flies

(2018) Fidel Ramírez et al.   Nature Communications

An improved assembly and annotation of the melon (Cucumis melo L.) reference genome

(2018) Valentino Ruggieri et al.   Scientific Reports

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

Repeated domestication of melon (Cucumis melo ) in Africa and Asia and a new close relative from India

(2018) Josef Endl et al.   AMERICAN JOURNAL OF BOTANY

QTL mapping of melon fruit quality traits using a high-density GBS-based genetic map

(2018) L. Pereira et al.   BMC PLANT BIOLOGY

Direct determination of diploid genome sequences

(2017) Neil I. Weisenfeld et al.   GENOME RESEARCH

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Karyotype Stability and Unbiased Fractionation in the Paleo-Allotetraploid Cucurbita Genomes

(2017) Honghe Sun et al.   Molecular Plant

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

(2017) Pengfei Dong et al.   Molecular Plant

Two independent modes of chromatin organization revealed by cohesin removal

(2017) Wibke Schwarzer et al.   NATURE

A chromosome conformation capture ordered sequence of the barley genome

(2017) Martin Mascher et al.   NATURE

Reconstructing the genome of the most recent common ancestor of flowering plants

(2017) Florent Murat et al.   NATURE GENETICS

Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction

(2017) Xia Wang et al.   NATURE GENETICS

PCSD: a plant chromatin state database

(2017) Yue Liu et al.   NUCLEIC ACIDS RESEARCH

The bottle gourd genome provides insights into Cucurbitaceae evolution and facilitates mapping of a Papaya ring-spot virus resistance locus

(2017) Shan Wu et al.   PLANT JOURNAL

The quest for epigenetic regulation underlying unisexual flower development in Cucumis melo

(2017) David Latrasse et al.   Epigenetics & Chromatin

The repetitive landscape of the 5100 Mbp barley genome

(2017) Thomas Wicker et al.   Mobile DNA

Extraction of high-molecular-weight genomic DNA for long-read sequencing of single molecules

(2016) Baptiste Mayjonade et al.   BIOTECHNIQUES

Ancestors of modern plant crops

(2016) Jérôme Salse   CURRENT OPINION IN PLANT BIOLOGY

Put your 3D glasses on: plant chromatin is on show

(2016) Natalia Y. Rodriguez-Granados et al.   JOURNAL OF EXPERIMENTAL BOTANY

iTAK: A Program for Genome-wide Prediction and Classification of Plant Transcription Factors, Transcriptional Regulators, and Protein Kinases

(2016) Yi Zheng et al.   Molecular Plant

InterPro in 2017—beyond protein family and domain annotations

(2016) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes

(2016) Todd M. Lowe et al.   NUCLEIC ACIDS RESEARCH

On TADs and LADs: Spatial Control Over Gene Expression

(2016) Adriana Gonzalez-Sandoval et al.   TRENDS IN GENETICS

Overview of the origins and history of the five major cucurbit crops: issues for ancient DNA analysis of archaeological specimens

(2016) Harry S. Paris   VEGETATION HISTORY AND ARCHAEOBOTANY

The number of known plants species in the world and its annual increase

(2016) MAARTEN J.M. CHRISTENHUSZ et al.   Phytotaxa

Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale

(2015) Hani Z. Girgis   BMC BIOINFORMATICS

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

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

MAGIC populations in crops: current status and future prospects

(2015) B. Emma Huang et al.   THEORETICAL AND APPLIED GENETICS

The power of single molecule real-time sequencing technology in the de novo assembly of a eukaryotic genome

(2015) Hiroaki Sakai et al.   Scientific Reports

EuGene-PP: a next-generation automated annotation pipeline for prokaryotic genomes

(2014) E. Sallet et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Hi-C Analysis in Arabidopsis Identifies the KNOT, a Structure with Similarities to the flamenco Locus of Drosophila

(2014) Stefan Grob et al.   MOLECULAR CELL

Genome-wide Hi-C Analyses in Wild-Type and Mutants Reveal High-Resolution Chromatin Interactions in Arabidopsis

(2014) Suhua Feng et al.   MOLECULAR CELL

PASTEC: An Automatic Transposable Element Classification Tool

(2014) Claire Hoede et al.   PLoS One

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

PlantTFcat: an online plant transcription factor and transcriptional regulator categorization and analysis tool

(2013) Xinbin Dai et al.   BMC BIOINFORMATICS

Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment

(2013) Jennifer E. Phillips-Cremins et al.   CELL

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

Functional implications of genome topology

(2013) Giacomo Cavalli et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Phenotypic diversity in wild and cultivated melons (Cucumis melo)

(2013) Michel Pitrat   Plant Biotechnology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

Gene Density, Transcription, and Insulators Contribute to the Partition of the Drosophila Genome into Physical Domains

(2012) Chunhui Hou et al.   MOLECULAR CELL

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions

(2012) Shaogui Guo et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The genome of melon (Cucumis melo L.)

(2012) J. Garcia-Mas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

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

(2011) Chen Xie et al.   NUCLEIC ACIDS RESEARCH

Considering Transposable Element Diversification in De Novo Annotation Approaches

(2011) Timothée Flutre et al.   PLoS One

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Chromatin Higher-order Structure and Dynamics

(2010) C. L. Woodcock et al.   Cold Spring Harbor Perspectives in Biology

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

(2009) Chongzhi Zang et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The genome of the cucumber, Cucumis sativus L.

(2009) Sanwen Huang et al.   NATURE GENETICS

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS