Long-read bitter gourd (Momordica charantia) genome and the genomic architecture of nonclassic domestication

Multi-allelic APRR2 Gene is Associated with Fruit Pigment Accumulation in Melon and Watermelon

(2019) Elad Oren et al.   JOURNAL OF EXPERIMENTAL BOTANY

A chromosome-scale genome assembly of cucumber (Cucumis sativus L.)

(2019) Qing Li et al.   GigaScience

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

Global genetic differentiation of complex traits shaped by natural selection in humans

(2018) Jing Guo et al.   Nature Communications

A RAD-Based Genetic Map for Anchoring Scaffold Sequences and Identifying QTLs in Bitter Gourd (Momordica charantia)

(2018) Junjie Cui et al.   Frontiers in Plant Science

PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files

(2018) Chi Zhang et al.   BIOINFORMATICS

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2017) Honghe Sun et al.   Molecular Plant

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

Young inversion with multiple linked QTLs under selection in a hybrid zone

(2017) Cheng-Ruei Lee et al.   Nature Ecology & Evolution

Diversity Among a Wide Asian Collection of Bitter Gourd Landraces and their Genetic Relationships with Commercial Hybrid Cultivars

(2016) N. P. S. Dhillon et al.   JOURNAL OF THE AMERICAN SOCIETY FOR HORTICULTURAL SCIENCE

pophelper: an R package and web app to analyse and visualize population structure

(2016) R. M. Francis   Molecular Ecology Resources

Robust and scalable inference of population history from hundreds of unphased whole genomes

(2016) Jonathan Terhorst et al.   NATURE GENETICS

Use of targeted SNP selection for an improved anchoring of the melon (Cucumis melo L.) scaffold genome assembly

(2015) Jason M Argyris et al.   BMC GENOMICS

Bitter melon (Momordica charantiaL.) bioactive composition and health benefits: A review

(2015) Sing P. Tan et al.   FOOD REVIEWS INTERNATIONAL

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

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

ALLMAPS: robust scaffold ordering based on multiple maps

(2015) Haibao Tang et al.   GENOME BIOLOGY

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Screening Genetic Resources of Capsicum Peppers in Their Primary Center of Diversity in Bolivia and Peru

(2015) Maarten van Zonneveld et al.   PLoS One

Development of Novel Simple Sequence Repeat Markers in Bitter Gourd (Momordica charantia L.) Through Enriched Genomic Libraries and Their Utilization in Analysis of Genetic Diversity and Cross-Species Transferability

(2014) Swati Saxena et al.   APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY

The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication

(2014) Muhua Wang et al.   NATURE GENETICS

Genomic analyses provide insights into the history of tomato breeding

(2014) Tao Lin et al.   NATURE GENETICS

Mapping of the Gynoecy in Bitter Gourd (Momordica charantia) Using RAD-Seq Analysis

(2014) Hideo Matsumura et al.   PLoS One

SweeD: Likelihood-Based Detection of Selective Sweeps in Thousands of Genomes

(2013) Pavlos Pavlidis et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Evolution of crop species: genetics of domestication and diversification

(2013) Rachel S. Meyer et al.   NATURE REVIEWS GENETICS

Network Inference Analysis Identifies an APRR2-Like Gene Linked to Pigment Accumulation in Tomato and Pepper Fruits

(2013) Y. Pan et al.   PLANT PHYSIOLOGY

Comparative population genomics of maize domestication and improvement

(2012) Matthew B Hufford et al.   NATURE GENETICS

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

(2012) Shaogui Guo et al.   NATURE GENETICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

SyMAP v3.4: a turnkey synteny system with application to plant genomes

(2011) Carol Soderlund et al.   NUCLEIC ACIDS RESEARCH

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

(2010) Murray P Cox et al.   BMC BIOINFORMATICS

Karyotype Diversity in Three Cultivars of Momordica charantia L.

(2010) Md. Yahia Zaman et al.   CYTOLOGIA

Population differentiation as a test for selective sweeps

(2010) H. Chen et al.   GENOME RESEARCH

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

(2010) A. McKenna et al.   GENOME RESEARCH

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

High-throughput functional annotation and data mining with the Blast2GO suite

(2008) S. Gotz et al.   NUCLEIC ACIDS RESEARCH

Efficient and Accurate Construction of Genetic Linkage Maps from the Minimum Spanning Tree of a Graph

(2008) Yonghui Wu et al.   PLoS Genetics

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY