Genome Sequence, Assembly and Characterization of Two Metschnikowia fructicola Strains Used as Biocontrol Agents of Postharvest Diseases

Genome Mutational and Transcriptional Hotspots Are Traps for Duplicated Genes and Sources of Adaptations

(2017) Mario A. Fares et al.   Genome Biology and Evolution

Combining independent de novo assemblies optimizes the coding transcriptome for nonconventional model eukaryotic organisms

(2016) Nicolas Cerveau et al.   BMC BIOINFORMATICS

The MarR-like protein PchR (YvmB) regulates expression of genes involved in pulcherriminic acid biosynthesis and in the initiation of sporulation in Bacillus subtilis

(2016) Paola Randazzo et al.   BMC MICROBIOLOGY

InterPro in 2017—beyond protein family and domain annotations

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

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

Genome Sequencing and Comparative Analysis of Saccharomyces cerevisiae Strains of the Peterhof Genetic Collection

(2016) Polina B. Drozdova et al.   PLoS One

Alternative management technologies for postharvest disease control: The journey from simplicity to complexity

(2016) Michael Wisniewski et al.   POSTHARVEST BIOLOGY AND TECHNOLOGY

The science, development, and commercialization of postharvest biocontrol products

(2016) Samir Droby et al.   POSTHARVEST BIOLOGY AND TECHNOLOGY

Comparative genomics of biotechnologically important yeasts

(2016) Robert Riley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Development of biocontrol products for postharvest diseases of fruit: The importance of elucidating the mechanisms of action of yeast antagonists

(2016) Davide Spadaro et al.   TRENDS IN FOOD SCIENCE & TECHNOLOGY

A stable phylogeny of the large-sporedMetschnikowiaclade

(2016) Marc-André Lachance et al.   YEAST

Impact of the omic technologies for understanding the modes of action of biological control agents against plant pathogens

(2015) Sebastien Massart et al.   BIOCONTROL

Draft genome of a commonly misdiagnosed multidrug resistant pathogen Candida auris

(2015) Sharanya Chatterjee et al.   BMC GENOMICS

An assembly and alignment-free method of phylogeny reconstruction from next-generation sequencing data

(2015) Huan Fan et al.   BMC GENOMICS

Postharvest application of a novel chitinase cloned from Metschnikowia fructicola and overexpressed in Pichia pastoris to control brown rot of peaches

(2015) Houda Banani et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters

(2015) Tilmann Weber et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Methylation Patterns in Salmonella enterica Subsp. enterica Serovars

(2015) Cary Pirone-Davies et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Insights into Secondary Metabolism from a Global Analysis of Prokaryotic Biosynthetic Gene Clusters

(2014) Peter Cimermancic et al.   CELL

Genetic and phenotypic intra-species variation inCandida albicans

(2014) Matthew P. Hirakawa et al.   GENOME RESEARCH

De-novo assembly and characterization of the transcriptome of Metschnikowia fructicola reveals differences in gene expression following interaction with Penicillium digitatum and grapefruit peel

(2013) Vera Hershkovitz et al.   BMC GENOMICS

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

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

Comparative Genomic Analysis Indicates that Niche Adaptation of Terrestrial Flavobacteria Is Strongly Linked to Plant Glycan Metabolism

(2013) Max Kolton et al.   PLoS One

Whole Genome Duplication and Enrichment of Metal Cation Transporters Revealed by De Novo Genome Sequencing of Extremely Halotolerant Black Yeast Hortaea werneckii

(2013) Metka Lenassi et al.   PLoS One

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

(2012) Pablo Cingolani et al.   FLY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Terpenoid synthase structures: a so far incomplete view of complex catalysis

(2012) Yang Gao et al.   NATURAL PRODUCT REPORTS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

A new strain of Metschnikowia fructicola for postharvest control of Penicillium expansum and patulin accumulation on four cultivars of apple

(2012) Davide Spadaro et al.   POSTHARVEST BIOLOGY AND TECHNOLOGY

Essential Oils in Food Preservation: Mode of Action, Synergies, and Interactions with Food Matrix Components

(2012) Morten Hyldgaard et al.   Frontiers in Microbiology

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Proteinortho: Detection of (Co-)orthologs in large-scale analysis

(2011) Marcus Lechner et al.   BMC BIOINFORMATICS

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Global changes in gene expression of grapefruit peel tissue in response to the yeast biocontrol agent Metschnikowia fructicola

(2011) VERA HERSHKOVITZ et al.   MOLECULAR PLANT PATHOLOGY

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea

(2011) Joelle Amselem et al.   PLoS Genetics

CAZymes Analysis Toolkit (CAT): Web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database

(2010) Byung H Park et al.   GLYCOBIOLOGY

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

Superoxide anion and hydrogen peroxide in the yeast antagonist–fruit interaction: A new role for reactive oxygen species in postharvest biocontrol?

(2010) Dumitru Macarisin et al.   POSTHARVEST BIOLOGY AND TECHNOLOGY

The Yap family and its role in stress response

(2010) Claudina Rodrigues-Pousada et al.   YEAST

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

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Evolution of pathogenicity and sexual reproduction in eight Candida genomes

(2009) Geraldine Butler et al.   NATURE

Twenty years of postharvest biocontrol research: Is it time for a new paradigm?

(2009) Samir Droby et al.   POSTHARVEST BIOLOGY AND TECHNOLOGY

Selection and evaluation of new antagonists for their efficacy against postharvest brown rot of peaches

(2009) Dianpeng Zhang et al.   POSTHARVEST BIOLOGY AND TECHNOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

(2008) B. L. Cantarel et al.   NUCLEIC ACIDS RESEARCH

Metschnikowia pulcherrima strain MACH1 outcompetes Botrytis cinerea, Alternaria alternata and Penicillium expansum in apples through iron depletion

(2008) Duraisamy Saravanakumar et al.   POSTHARVEST BIOLOGY AND TECHNOLOGY

Use of AFLP for differentiation of Metschnikowia pulcherrima strains for postharvest disease biological control

(2007) D. Spadaro et al.   MICROBIOLOGICAL RESEARCH