Comparative Microbiome Study of Mummified Peach Fruits by Metagenomics and Metatranscriptomics

Identification of the Fungal Pathogens of Postharvest Disease on Peach Fruits and the Control Mechanisms of Bacillus subtilis JK-14

(2019) Shuwu Zhang et al.   Toxins

New high-quality draft genome of the brown rot fungal pathogen Monilinia fructicola

(2019) Rita Milvia De Miccolis Angelini et al.   Genome Biology and Evolution

Whole Genome Shotgun Sequencing Detects Greater Lichen Fungal Diversity Than Amplicon-Based Methods in Environmental Samples

(2019) Kyle Garrett Keepers et al.   Frontiers in Ecology and Evolution

Draft genome resources for the phytopathogenic fungi Monilinia fructicola, M. fructigena, M. polystroma and M. laxa, the causal agents of brown rot

(2018) Yazmin Rivera et al.   PHYTOPATHOLOGY

Identification of fungi in shotgun metagenomics datasets

(2018) Paul D. Donovan et al.   PLoS One

Peach RNA viromes in six different peach cultivars

(2018) Yeonhwa Jo et al.   Scientific Reports

Virome Characterization of a Collection of S. sclerotiorum from Australia

(2018) Fan Mu et al.   Frontiers in Microbiology

Advantages of meta-total RNA sequencing (MeTRS) over shotgun metagenomics and amplicon-based sequencing in the profiling of complex microbial communities

(2018) Fabien Cottier et al.   npj Biofilms and Microbiomes

Postharvest biocontrol ability of killer yeasts against Monilinia fructigena and Monilinia fructicola on stone fruit

(2017) Monika Grzegorczyk et al.   FOOD MICROBIOLOGY

Influence of temperature on decay, mycelium development and sporodochia production caused by Monilinia fructicola and M. laxa on stone fruits

(2017) M. Bernat et al.   FOOD MICROBIOLOGY

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing

(2016) Ravi Ranjan et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies

(2016) Daryl M Gohl et al.   NATURE BIOTECHNOLOGY

Widespread 3′-end uridylation in eukaryotic RNA viruses

(2016) Yayun Huo et al.   Scientific Reports

Low abundance of Archaeorhizomycetes among fungi in soil metatranscriptomes

(2016) Michal Choma et al.   Scientific Reports

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data

(2016) Daniel H. Huson et al.   PLoS Computational Biology

Prospects and challenges for fungal metatranscriptomics of complex communities

(2015) Cheryl R. Kuske et al.   Fungal Ecology

Conducting a Microbiome Study

(2014) Julia K. Goodrich et al.   CELL

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

QTL mapping for brown rot (Monilinia fructigena) resistance in an intraspecific peach (Prunus persica L. Batsch) F1 progeny

(2014) Igor Pacheco et al.   Tree Genetics & Genomes

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh 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

Fungal Endophytic Communities in Grapevines (Vitis vinifera L.) Respond to Crop Management

(2012) Michael Pancher et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Combination of salicylic acid and ultrasound to control postharvest blue mold caused by Penicillium expansum in peach fruit

(2011) Zhenfeng Yang et al.   Innovative Food Science & Emerging Technologies

Estimating Biodiversity of Fungi in Activated Sludge Communities Using Culture-Independent Methods

(2011) Tegan N. Evans et al.   MICROBIAL ECOLOGY

Soil fungal communities as indicators for replanting new peach orchards in intensively cultivated areas

(2010) Luisa M. Manici et al.   EUROPEAN JOURNAL OF AGRONOMY

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Contribution of Pathogens to Peach Fruit Rot in Northern Greece and their Sensitivity to Iprodione, Carbendazim, Thiophanate-methyl and Tebuconazole Fungicides

(2009) Thomas Thomidis et al.   JOURNAL OF PHYTOPATHOLOGY