The Distant Siblings—A Phylogenomic Roadmap Illuminates the Origins of Extant Diversity in Fungal Aromatic Polyketide Biosynthesis

Genome-scale phylogenetic analysis finds extensive gene transfer among fungi

(2015) Gergely J. Szöllősi et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Insights into the Biosynthesis of 12-Membered Resorcylic Acid Lactones from Heterologous Production in Saccharomyces cerevisiae

(2014) Yuquan Xu et al.   ACS Chemical Biology

TCS: A New Multiple Sequence Alignment Reliability Measure to Estimate Alignment Accuracy and Improve Phylogenetic Tree Reconstruction

(2014) Jia-Ming Chang et al.   MOLECULAR BIOLOGY AND EVOLUTION

CDD: NCBI's conserved domain database

(2014) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

GenBank

(2014) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

Atlas of nonribosomal peptide and polyketide biosynthetic pathways reveals common occurrence of nonmodular enzymes

(2014) H. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Clustering evolving proteins into homologous families

(2013) Cheong Xin Chan et al.   BMC BIOINFORMATICS

State-of the art methodologies dictate new standards for phylogenetic analysis

(2013) Maria Anisimova et al.   BMC EVOLUTIONARY BIOLOGY

The Polyketide Synthase Gene pks4 of Trichoderma reesei Provides Pigmentation and Stress Resistance

(2013) Lea Atanasova et al.   EUKARYOTIC CELL

Phylogenetic analyses of RPB1 and RPB2 support a middle Cretaceous origin for a clade comprising all agriculturally and medically important fusaria

(2013) Kerry O’Donnell et al.   FUNGAL GENETICS AND BIOLOGY

Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss

(2013) Mukul S. Bansal et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Ultrafast Approximation for Phylogenetic Bootstrap

(2013) B. Q. Minh 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

Fragmentation of an aflatoxin-like gene cluster in a forest pathogen

(2013) Rosie E. Bradshaw et al.   NEW PHYTOLOGIST

Activities at the Universal Protein Resource (UniProt)

(2013)   NUCLEIC ACIDS RESEARCH

antiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers

(2013) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2014

(2013) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Lateral Gene Transfer from the Dead

(2013) Gergely J. Szöllősi et al.   SYSTEMATIC BIOLOGY

Efficient Exploration of the Space of Reconciled Gene Trees

(2013) Gergely J. Szöllősi et al.   SYSTEMATIC BIOLOGY

PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment

(2013) Nicolas Lartillot et al.   SYSTEMATIC BIOLOGY

Breaking the Silence: Protein Stabilization Uncovers Silenced Biosynthetic Gene Clusters in the Fungus Aspergillus nidulans

(2012) Jennifer Gerke et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss

(2012) Mukul S. Bansal et al.   BIOINFORMATICS

Bio.Phylo: A unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython

(2012) Eric Talevich et al.   BMC BIOINFORMATICS

Genome-scale coestimation of species and gene trees

(2012) B. Boussau et al.   GENOME RESEARCH

Illuminating the Diversity of Aromatic Polyketide Synthases in Aspergillus nidulans

(2012) Manmeet Ahuja et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Advances in Aspergillus secondary metabolite research in the post-genomic era

(2012) James F. Sanchez et al.   NATURAL PRODUCT REPORTS

The RCSB Protein Data Bank: new resources for research and education

(2012) Peter W. Rose et al.   NUCLEIC ACIDS RESEARCH

Accurate prediction of secondary metabolite gene clusters in filamentous fungi

(2012) M. R. Andersen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi

(2012) Robin A. Ohm et al.   PLoS Pathogens

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

(2011) Diego Darriba et al.   BIOINFORMATICS

Multiple origins of endosymbiosis within the Enterobacteriaceae (γ-Proteobacteria): convergence of complex phylogenetic approaches

(2011) Filip Husník et al.   BMC BIOLOGY

Models, algorithms and programs for phylogeny reconciliation

(2011) J.-P. Doyon et al.   BRIEFINGS IN BIOINFORMATICS

A genome-wide polyketide synthase deletion library uncovers novel genetic links to polyketides and meroterpenoids in Aspergillus nidulans

(2011) Michael L. Nielsen et al.   FEMS MICROBIOLOGY LETTERS

Rock-inhabiting fungi originated during periods of dry climate in the late Devonian and middle Triassic

(2011) Cécile Gueidan et al.   Fungal Biology

Phylogenomic and functional domain analysis of polyketide synthases in Fusarium

(2011) Daren W. Brown et al.   Fungal Biology

Comparative Characterization of Fungal Anthracenone and Naphthacenedione Biosynthetic Pathways Reveals an α-Hydroxylation-Dependent Claisen-like Cyclization Catalyzed by a Dimanganese Thioesterase

(2011) Yanran Li et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A Consistent Phylogenetic Backbone for the Fungi

(2011) I. Ebersberger et al.   MOLECULAR BIOLOGY AND EVOLUTION

A resource for the in silico identification of fungal polyketide synthases from predicted fungal proteomes

(2011) JAVIER A. DELGADO et al.   MOLECULAR PLANT PATHOLOGY

The Genome Portal of the Department of Energy Joint Genome Institute

(2011) I. V. Grigoriev et al.   NUCLEIC ACIDS RESEARCH

ETE: a python Environment for Tree Exploration

(2010) Jaime Huerta-Cepas et al.   BMC BIOINFORMATICS

Phylogenomics reveals subfamilies of fungal nonribosomal peptide synthetases and their evolutionary relationships

(2010) Kathryn E Bushley et al.   BMC EVOLUTIONARY BIOLOGY

Horizontal Transfer of a Large and Highly Toxic Secondary Metabolic Gene Cluster between Fungi

(2010) Jason C. Slot et al.   CURRENT BIOLOGY

SMURF: Genomic mapping of fungal secondary metabolite clusters

(2010) Nora Khaldi et al.   FUNGAL GENETICS AND BIOLOGY

Characterization of a polyketide synthase in Aspergillus niger whose product is a precursor for both dihydroxynaphthalene (DHN) melanin and naphtho-γ-pyrone

(2010) Yi-Ming Chiang et al.   FUNGAL GENETICS AND BIOLOGY

Classification, Prediction, and Verification of the Regioselectivity of Fungal Polyketide Synthase Product Template Domains

(2010) Yanran Li et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Genome Expansion and Gene Loss in Powdery Mildew Fungi Reveal Tradeoffs in Extreme Parasitism

(2010) P. D. Spanu et al.   SCIENCE

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

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

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

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

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

A fungal phylogeny based on 82 complete genomes using the composition vector method

(2009) Hao Wang et al.   BMC EVOLUTIONARY BIOLOGY

Ancient Horizontal Gene Transfer from Bacteria Enhances Biosynthetic Capabilities of Fungi

(2009) Imke Schmitt et al.   PLoS One

Funybase: a Fungal phylogenomic database

(2008) Sylvain Marthey et al.   BMC BIOINFORMATICS

The oldest fossil evidence of animal parasitism by fungi supports a Cretaceous diversification of fungal–arthropod symbioses

(2008) Gi-Ho Sung et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A Computational Screen for Type I Polyketide Synthases in Metagenomics Shotgun Data

(2008) Konrad U. Foerstner et al.   PLoS One

Assessing the Performance of Single-Copy Genes for Recovering Robust Phylogenies

(2008) G. Aguileta et al.   SYSTEMATIC BIOLOGY