High-quality genome assembly of the soybean fungal pathogen Cercospora kikuchii

Chromosomal assembly of the nuclear genome of the endosymbiont-bearing trypanosomatid Angomonas deanei

(2021) John W Davey et al.   G3-Genes Genomes Genetics

Comparative genomics and association analysis identifies virulence genes of Cercospora sojina in soybean

(2020) Xin Gu et al.   BMC GENOMICS

101 Dothideomycetes genomes: a test case for predicting lifestyles and emergence of pathogens

(2020) S. Haridas et al.   STUDIES IN MYCOLOGY

“CATAStrophy,” a Genome-Informed Trophic Classification of Filamentous Plant Pathogens – How Many Different Types of Filamentous Plant Pathogens Are There?

(2020) James K. Hane et al.   Frontiers in Microbiology

Cercospora cf. nicotianae is a causal agent of Cercospora leaf blight of soybean

(2020) Francisco J. Sautua et al.   EUROPEAN JOURNAL OF PLANT PATHOLOGY

RepeatModeler2 for automated genomic discovery of transposable element families

(2020) Jullien M. Flynn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Conserved Glycoside Hydrolase Family 7 Cellobiohydrolase PsGH7a of Phytophthora sojae Is Required for Full Virulence on Soybean

(2020) Xinwei Tan et al.   Frontiers in Microbiology

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

(2019) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

Improved prediction of fungal effector proteins from secretomes with EffectorP 2.0

(2018) Jana Sperschneider et al.   MOLECULAR PLANT PATHOLOGY

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

(2018) Han Zhang et al.   NUCLEIC ACIDS RESEARCH

De novo genome assembly of Cercospora beticola for microsatellite marker development and validation

(2017) Niloofar Vaghefi et al.   Fungal Ecology

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

(2017) Sergey Koren et al.   GENOME RESEARCH

LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons

(2017) Shujun Ou et al.   PLANT PHYSIOLOGY

Cercospora cf. flagellaris and Cercospora cf. sigesbeckiae Are Associated with Cercospora Leaf Blight and Purple Seed Stain on Soybean in North America

(2016) S. Albu et al.   PHYTOPATHOLOGY

Chromatin Biology Impacts Adaptive Evolution of Filamentous Plant Pathogens

(2016) Michael F. Seidl et al.   PLoS Pathogens

SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation

(2016) Wei Shen et al.   PLoS One

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS: Table 1.

(2015) Katharina J. Hoff et al.   BIOINFORMATICS

More Cercospora Species Infect Soybeans across the Americas than Meets the Eye

(2015) Ana Paula Gomes Soares et al.   PLoS One

Assessment and refinement of eukaryotic gene structure prediction with gene-structure-aware multiple protein sequence alignment

(2014) Osamu Gotoh et al.   BMC BIOINFORMATICS

Correction: Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi

(2014) Zhongtao Zhao et al.   BMC GENOMICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

GenomeTools: A Comprehensive Software Library for Efficient Processing of Structured Genome Annotations

(2013) Gordon Gremme et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

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

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Species concepts in Cercospora: spotting the weeds among the roses

(2013) J.Z. Groenewald et al.   STUDIES IN MYCOLOGY

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Benchmarking spliced alignment programs including Spaln2, an extended version of Spaln that incorporates additional species-specific features

(2012) Hiroaki Iwata et al.   NUCLEIC ACIDS RESEARCH

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

The Accessory Genome as a Cradle for Adaptive Evolution in Pathogens

(2012) Daniel Croll et al.   PLoS Pathogens

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

(2010) Li-Jun Ma et al.   NATURE

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

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

(2008) Mario Stanke et al.   BIOINFORMATICS