Global analysis of biosynthetic gene clusters reveals vast potential of secondary metabolite production in Penicillium species

Biosynthetic gene clusters for relevant secondary metabolites produced by Penicillium roqueforti in blue cheeses

(2016) Carlos García-Estrada et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Genome sequencing and secondary metabolism of the postharvest pathogen Penicillium griseofulvum

(2016) Houda Banani et al.   BMC GENOMICS

Comprehensive curation and analysis of fungal biosynthetic gene clusters of published natural products

(2016) Yong Fuga Li et al.   FUNGAL GENETICS AND BIOLOGY

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

The evolution of genome mining in microbes – a review

(2016) Nadine Ziemert et al.   NATURAL PRODUCT REPORTS

New sections in Penicillium containing novel species producing patulin, pyripyropens or other bioactive compounds

(2016) J. Houbraken et al.   PERSOONIA

Penicillium arizonense, a new, genome sequenced fungal species, reveals a high chemical diversity in secreted metabolites

(2016) Sietske Grijseels et al.   Scientific Reports

Combining Stable Isotope Labeling and Molecular Networking for Biosynthetic Pathway Characterization

(2015) Andreas Klitgaard et al.   ANALYTICAL CHEMISTRY

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Investigation of a 6-MSA Synthase Gene Cluster inAspergillus aculeatusReveals 6-MSA-derived Aculinic Acid, Aculins A-B and Epi-Aculin A

(2015) Lene M. Petersen et al.   CHEMBIOCHEM

Genome, Transcriptome, and Functional Analyses ofPenicillium expansumProvide New Insights Into Secondary Metabolism and Pathogenicity

(2015) Ana-Rosa Ballester et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Minimum Information about a Biosynthetic Gene cluster

(2015) Marnix H Medema et al.   Nature Chemical Biology

Computational approaches to natural product discovery

(2015) Marnix H Medema et al.   Nature Chemical Biology

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

(2015) Tilmann Weber et al.   NUCLEIC ACIDS RESEARCH

Molecular and Chemical Characterization of the Biosynthesis of the 6-MSA-Derived Meroterpenoid Yanuthone D in Aspergillus niger

(2014) Dorte K. Holm et al.   CHEMISTRY & BIOLOGY

Sequencing, physical organization and kinetic expression of the patulin biosynthetic gene cluster from Penicillium expansum

(2014) Joanna Tannous et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Characterization of four new antifungal yanuthones from Aspergillus niger

(2014) Lene M Petersen et al.   JOURNAL OF ANTIBIOTICS

Accurate Dereplication of Bioactive Secondary Metabolites from Marine-Derived Fungi by UHPLC-DAD-QTOFMS and a MS/HRMS Library

(2014) Sara Kildgaard et al.   Marine Drugs

Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm

(2014) Alexandre Lomsadze et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Molecular Genetic Characterization of Terreic Acid Pathway in Aspergillus terreus

(2014) Chun-Jun Guo et al.   ORGANIC LETTERS

Diversity and evolution of secondary metabolism in the marine actinomycete genus Salinispora

(2014) N. Ziemert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic Signatures of Specialized Metabolism in Plants

(2014) L. Chae et al.   SCIENCE

Identification and nomenclature of the genus Penicillium

(2014) C.M. Visagie et al.   STUDIES IN MYCOLOGY

A Systematic Computational Analysis of Biosynthetic Gene Cluster Evolution: Lessons for Engineering Biosynthesis

(2014) Marnix H. Medema et al.   PLoS Computational Biology

A New Record of Penicillium antarcticum from Marine Environments in Korea

(2014) Myung Soo Park et al.   MYCOBIOLOGY

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Detecting Sequence Homology at the Gene Cluster Level with MultiGeneBlast

(2013) Marnix H. Medema et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum

(2013) Rasmus Agren et al.   PLoS Computational Biology

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Patulin and secondary metabolite production by marine-derived Penicillium strains

(2012) Marieke Vansteelandt et al.   Fungal Biology

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

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

Regulation of fungal secondary metabolism

(2012) Axel A. Brakhage   NATURE REVIEWS MICROBIOLOGY

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

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

The Natural Product Domain Seeker NaPDoS: A Phylogeny Based Bioinformatic Tool to Classify Secondary Metabolite Gene Diversity

(2012) Nadine Ziemert et al.   PLoS One

Reevaluating Assembly Evaluations with Feature Response Curves: GAGE and Assemblathons

(2012) Francesco Vezzi et al.   PLoS One

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Isolation and phosphate-solubilizing ability of a fungus, Penicillium sp. from soil of an alum mine

(2011) Bo Chai et al.   JOURNAL OF BASIC MICROBIOLOGY

Dereplication of Microbial Natural Products by LC-DAD-TOFMS

(2011) Kristian F. Nielsen et al.   JOURNAL OF NATURAL PRODUCTS

Fungal Indole Alkaloid Biosynthesis: Genetic and Biochemical Investigation of the Tryptoquialanine Pathway inPenicillium aethiopicum

(2011) Xue Gao et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Soil Microorganisms Mediating Phosphorus Availability Update on Microbial Phosphorus

(2011) A. E. Richardson et al.   PLANT PHYSIOLOGY

Identification of the Viridicatumtoxin and Griseofulvin Gene Clusters from Penicillium aethiopicum

(2010) Yit-Heng Chooi et al.   CHEMISTRY & BIOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Reconstitution of a fungal meroterpenoid biosynthesis reveals the involvement of a novel family of terpene cyclases

(2010) Takayuki Itoh et al.   Nature Chemistry

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Biosynthesis and Toxicological Effects of Patulin

(2010) Olivier Puel et al.   Toxins

A Brief History of the Antibiotic Era: Lessons Learned and Challenges for the Future

(2010) Rustam I. Aminov   Frontiers in Microbiology

Biotechnological production and applications of statins

(2009) Javier Barrios-González et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

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

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

Status and prospect of lignocellulosic bioethanol production in China

(2009) Xu Fang et al.   BIORESOURCE TECHNOLOGY

Cloning and characterization of novel methylsalicylic acid synthase gene involved in the biosynthesis of isoasperlactone and asperlactone in Aspergillus westerdijkiae

(2009) Nafees Bacha et al.   FUNGAL GENETICS AND BIOLOGY

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Molecular cloning and functional characterization of two CYP619 cytochrome P450s involved in biosynthesis of patulin in Aspergillus clavatus

(2009) M. P. Artigot et al.   MICROBIOLOGY-SGM