SunUp and Sunset genomes revealed impact of particle bombardment mediated transformation and domestication history in papaya

Towards complete and error-free genome assemblies of all vertebrate species

(2021) Arang Rhie et al.   NATURE

Genomes of the Banyan Tree and Pollinator Wasp Provide Insights into Fig-Wasp Coevolution

(2020) Xingtan Zhang et al.   CELL

The bracteatus pineapple genome and domestication of clonally propagated crops

(2019) Li-Yu Chen et al.   NATURE GENETICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

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

Genomics of the origin and evolution of Citrus

(2018) Guohong Albert Wu et al.   NATURE

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

(2017) Sergey Koren et al.   GENOME RESEARCH

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

(2017) Olga Dudchenko et al.   SCIENCE

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Chromosomer: a reference-based genome arrangement tool for producing draft chromosome sequences

(2016) Gaik Tamazian et al.   GigaScience

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Origin and domestication of papaya Yhchromosome

(2015) Robert VanBuren et al.   GENOME RESEARCH

De Novo Plant Genome Assembly Based on Chromatin Interactions: A Case Study of Arabidopsis thaliana

(2015) Ting Xie et al.   Molecular Plant

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data

(2014) Tae-Ho Lee et al.   BMC GENOMICS

Genomic analyses provide insights into the history of tomato breeding

(2014) Tao Lin et al.   NATURE GENETICS

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

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

A Whole-Genome Analysis of a Transgenic Rice Seed-Based Edible Vaccine Against Cedar Pollen Allergy

(2013) T. Kawakatsu et al.   DNA RESEARCH

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

Construction of physical maps for the sex-specific regions of papaya sex chromosomes

(2012) Jong-Kuk Na et al.   BMC GENOMICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

How important are transposons for plant evolution?

(2012) Damon Lisch   NATURE REVIEWS GENETICS

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

Sequencing papaya X and Yh chromosomes reveals molecular basis of incipient sex chromosome evolution

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

miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants

(2011) Xiaozeng Yang et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

The Structure of Morphological and Genetic Diversity in Natural Populations of Carica papaya (Caricaceae) in Costa Rica

(2011) Jennifer E. Brown et al.   BIOTROPICA

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

An epigenetic view of plant cells cultured in vitro: somaclonal variation and beyond

(2011) C. Miguel et al.   JOURNAL OF EXPERIMENTAL BOTANY

TEclass--a tool for automated classification of unknown eukaryotic transposable elements

(2009) G. Abrusan et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)

(2008) Ray Ming et al.   NATURE

Characterization of Insertion Sites in Rainbow Papaya, the First Commercialized Transgenic Fruit Crop

(2008) Jon Y. Suzuki et al.   Tropical Plant Biology