Haplotype-resolved genomes of geminivirus-resistant and geminivirus-susceptible African cassava cultivars

Origin and evolution of the octoploid strawberry genome

(2019) Patrick P. Edger et al.   NATURE GENETICS

Piercing the dark matter: bioinformatics of long-range sequencing and mapping

(2018) Fritz J. Sedlazeck et al.   NATURE REVIEWS GENETICS

An NB-LRR gene, TYNBS1, is responsible for resistance mediated by the Ty-2 Begomovirus resistance locus of tomato

(2018) Hirotaka Yamaguchi et al.   THEORETICAL AND APPLIED GENETICS

Genome-wide association mapping and genomic prediction for CBSD resistance in Manihot esculenta

(2018) Siraj Ismail Kayondo et al.   Scientific Reports

Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies

(2018) Michael J. Roach et al.   BMC BIOINFORMATICS

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

(2017) Sergey Koren et al.   GENOME RESEARCH

Molecular insights into Cassava brown streak virus susceptibility and resistance by profiling of the early host response

(2017) Ravi B. Anjanappa et al.   MOLECULAR PLANT PATHOLOGY

The genome of Chenopodium quinoa

(2017) David E. Jarvis et al.   NATURE

A chromosome conformation capture ordered sequence of the barley genome

(2017) Martin Mascher et al.   NATURE

Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation

(2017) Punna Ramu et al.   NATURE GENETICS

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome

(2017) Derek M Bickhart et al.   NATURE GENETICS

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

(2017) Nicolas Daccord et al.   NATURE GENETICS

Gene expression atlas for the food security crop cassava

(2017) Mark C. Wilson et al.   NEW PHYTOLOGIST

Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants

(2017) Pascal Schläpfer et al.   PLANT PHYSIOLOGY

QTL associated with resistance to cassava brown streak and cassava mosaic diseases in a bi-parental cross of two Tanzanian farmer varieties, Namikonga and Albert

(2017) E. A. Masumba et al.   THEORETICAL AND APPLIED GENETICS

Crops that feed the world: Production and improvement of cassava for food, feed, and industrial uses

(2017) Aditya Parmar et al.   Food Security

Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce

(2017) Sebastian Reyes-Chin-Wo et al.   Nature Communications

The Search for Resistance to Cassava Mosaic Geminiviruses: How Much We Have Accomplished, and What Lies Ahead

(2017) Vincent N. Fondong   Frontiers in Plant Science

Cassava Mosaic and Brown Streak Diseases: Current Perspectives and Beyond

(2017) Chrissie Rey et al.   Annual Review of Virology

A time series transcriptome analysis of cassava (Manihot esculenta Crantz) varieties challenged with Ugandan cassava brown streak virus

(2017) T. Amuge et al.   Scientific Reports

Loss of CMD2-mediated resistance to cassava mosaic disease in plants regenerated through somatic embryogenesis

(2016) Getu Beyene et al.   MOLECULAR PLANT PATHOLOGY

Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity

(2016) Jessen V Bredeson et al.   NATURE BIOTECHNOLOGY

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

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

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

BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes

(2016) Helena Staňková et al.   PLANT BIOTECHNOLOGY JOURNAL

Marker-Based Estimates Reveal Significant Non-additive Effects in Clonally Propagated Cassava (Manihot esculenta): Implications for the Prediction of Total Genetic Value and the Selection of Varieties

(2016) M. D. Wolfe et al.   G3-Genes Genomes Genetics

Genome-Wide Association and Prediction Reveals Genetic Architecture of Cassava Mosaic Disease Resistance and Prospects for Rapid Genetic Improvement

(2016) Marnin D. Wolfe et al.   Plant Genome

Cassava Breeding I: The Value of Breeding Value

(2016) Hernán Ceballos et al.   Frontiers in Plant Science

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum

(2015) Robert VanBuren et al.   NATURE

Assembling large genomes with single-molecule sequencing and locality-sensitive hashing

(2015) Konstantin Berlin et al.   NATURE BIOTECHNOLOGY

Assembly and diploid architecture of an individual human genome via single-molecule technologies

(2015) Matthew Pendleton et al.   NATURE METHODS

CG gene body DNA methylation changes and evolution of duplicated genes in cassava

(2015) Haifeng Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Novel Route Controlling Begomovirus Resistance by the Messenger RNA Surveillance Factor Pelota

(2015) Moshe Lapidot et al.   PLoS Genetics

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

PROTEIN DISULFIDE ISOMERASE LIKE 5-1is a susceptibility factor to plant viruses

(2014) Ping Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-resolution mapping of resistance to cassava mosaic geminiviruses in cassava using genotyping-by-sequencing and its implications for breeding

(2014) Ismail Y. Rabbi et al.   VIRUS RESEARCH

Cassava genome from a wild ancestor to cultivated varieties

(2014) Wenquan Wang et al.   Nature Communications

InCHlib – interactive cluster heatmap for web applications

(2014) Ctibor Škuta et al.   Journal of Cheminformatics

High-Resolution Linkage Map and Chromosome-Scale Genome Assembly for Cassava ( Manihot esculenta Crantz) from 10 Populations

(2014)   G3-Genes Genomes Genetics

Dominant resistance against plant viruses

(2014) Dryas de Ronde et al.   Frontiers in Plant Science

Oleanolic acid and ursolic acid: Novel hepatitis C virus antivirals that inhibit NS5B activity

(2013) Lingbao Kong et al.   ANTIVIRAL RESEARCH

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Rational design and synthesis of topoisomerase I and II inhibitors based on oleanolic acid moiety for new anti-cancer drugs

(2013) Ahmed Ashour et al.   BIOORGANIC & MEDICINAL CHEMISTRY

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

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

Geminiviruses: masters at redirecting and reprogramming plant processes

(2013) Linda Hanley-Bowdoin et al.   NATURE REVIEWS MICROBIOLOGY

Virus infection of a weed increases vector attraction to and vector fitness on the weed

(2013) Gong Chen et al.   Scientific Reports

The Tomato Yellow Leaf Curl Virus Resistance Genes Ty-1 and Ty-3 Are Allelic and Code for DFDGD-Class RNA–Dependent RNA Polymerases

(2013) Maarten G. Verlaan et al.   PLoS Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Molecular Marker Analysis and Validation of Resistance to Cassava Mosaic Disease in Elite Cassava Genotypes in Nigeria

(2012) E. Okogbenin et al.   CROP SCIENCE

Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly

(2012) Ernest T Lam et al.   NATURE BIOTECHNOLOGY

The Cassava Genome: Current Progress, Future Directions

(2012) Simon Prochnik et al.   Tropical Plant Biology

Peroxidase Activity after Viral Infection and Whitefly Infestation in Juvenile and Mature Leaves of Solanum lycopersicum

(2011) Hamady Dieng et al.   JOURNAL OF PHYTOPATHOLOGY

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Recent trends in global production and utilization of bio-ethanol fuel

(2009) Mustafa Balat et al.   APPLIED ENERGY

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

Cassava mosaic geminiviruses: actual knowledge and perspectives

(2009) BASAVAPRABHU L. PATIL et al.   MOLECULAR PLANT PATHOLOGY

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

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

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

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

Class III peroxidases in plant defence reactions

(2008) L. Almagro et al.   JOURNAL OF EXPERIMENTAL BOTANY