The ancestral levels of transcription and the evolution of sexual phenotypes in filamentous fungi

Addressing inaccuracies in BLOSUM computation improves homology search performance

(2016) Martin Hess et al.   BMC BIOINFORMATICS

Comparative Analysis of Gene Regulatory Networks: From Network Reconstruction to Evolution

(2015) Dawn Thompson et al.   Annual Review of Cell and Developmental Biology

The significance and scope of evolutionary developmental biology: a vision for the 21st century

(2015) Armin P. Moczek et al.   EVOLUTION & DEVELOPMENT

Evolutionary Divergence of Gene and Protein Expression in the Brains of Humans and Chimpanzees

(2015) Amy L. Bauernfeind et al.   Genome Biology and Evolution

Discovering Regulatory Network Topologies Using Ensemble Methods on GPGPUs With Special Reference to the Biological Clock of Neurospora crassa

(2015) Ahmad Al-Omari et al.   IEEE Access

Quantifying the impact of development on phenotypic variation and evolution

(2014) Karen E. Sears   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

(2014)   NATURE BIOTECHNOLOGY

Using next-generation sequencing to isolate mutant genes from forward genetic screens

(2014) Korbinian Schneeberger   NATURE REVIEWS GENETICS

Competition between target sites of regulators shapes post-transcriptional gene regulation

(2014) Marvin Jens et al.   NATURE REVIEWS GENETICS

Gene Expression Differences among Three Neurospora Species Reveal Genes Required for Sexual Reproduction in Neurospora crassa

(2014) Nina A. Lehr et al.   PLoS One

Neurospora crassa Female Development Requires the PACC and Other Signal Transduction Pathways, Transcription Factors, Chromatin Remodeling, Cell-To-Cell Fusion, and Autophagy

(2014) Jennifer L. Chinnici et al.   PLoS One

Comparison of the transcriptional landscapes between human and mouse tissues

(2014) Shin Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Secret lifestyles of Neurospora crassa

(2014) Hsiao-Che Kuo et al.   Scientific Reports

The mechanism of ascus firing – Merging biophysical and mycological viewpoints

(2014) Frances Trail et al.   Fungal Biology Reviews

Bayesian Network Webserver: a comprehensive tool for biological network modeling

(2013) Jesse D. Ziebarth et al.   BIOINFORMATICS

Global Gene Expression and Focused Knockout Analysis Reveals Genes Associated with Fungal Fruiting Body Development in Neurospora crassa

(2013) Zheng Wang et al.   EUKARYOTIC CELL

THE EVOLUTION OF PHENOTYPIC CORRELATIONS AND “DEVELOPMENTAL MEMORY”

(2013) Richard A. Watson et al.   EVOLUTION

Arboretum: Reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules

(2013) S. Roy et al.   GENOME RESEARCH

Evolution at two levels of gene expression in yeast

(2013) C. G. Artieri et al.   GENOME RESEARCH

A comparative systems analysis of polysaccharide-elicited responses inNeurospora crassareveals carbon source-specific cellular adaptations

(2013) J. Philipp Benz et al.   MOLECULAR MICROBIOLOGY

BLAST: a more efficient report with usability improvements

(2013) Grzegorz M. Boratyn et al.   NUCLEIC ACIDS RESEARCH

Genome Wide Association Identifies Novel Loci Involved in Fungal Communication

(2013) Javier Palma-Guerrero et al.   PLoS Genetics

Role of Fig1, a Component of the Low-Affinity Calcium Uptake System, in Growth and Sexual Development of Filamentous Fungi

(2012) Brad Cavinder et al.   EUKARYOTIC CELL

Transcriptome analyses during fruiting body formation in Fusarium graminearum and Fusarium verticillioides reflect species life history and ecology

(2012) Usha Rani Sikhakolli et al.   FUNGAL GENETICS AND BIOLOGY

Differential impact of nutrition on developmental and metabolic gene expression during fruiting body development in Neurospora crassa

(2012) Zheng Wang et al.   FUNGAL GENETICS AND BIOLOGY

Abundant Gene-by-Environment Interactions in Gene Expression Reaction Norms to Copper within Saccharomyces cerevisiae

(2012) Andrea Hodgins-Davis et al.   Genome Biology and Evolution

Comparative studies of gene expression and the evolution of gene regulation

(2012) Irene Gallego Romero et al.   NATURE REVIEWS GENETICS

Beetle horns and horned beetles: emerging models in developmental evolution and ecology

(2012) Teiya Kijimoto et al.   Wiley Interdisciplinary Reviews-Developmental Biology

Genome-wide approaches to the study of adaptive gene expression evolution

(2011) Hunter B. Fraser   BIOESSAYS

ReMark: an automatic program for clustering orthologs flexibly combining a Recursive and a Markovclustering algorithms

(2011) K. Kim et al.   BIOINFORMATICS

Molecular phylogeny of the higher and lower taxonomy of the Fusarium genus and differences in the evolutionary histories of multiple genes

(2011) Maiko Watanabe et al.   BMC EVOLUTIONARY BIOLOGY

Global Analysis of Serine-Threonine Protein Kinase Genes in Neurospora crassa

(2011) Gyungsoon Park et al.   EUKARYOTIC CELL

Identification and Characterization of Genes Required for Cell-to-Cell Fusion in Neurospora crassa

(2011) Ci Fu et al.   EUKARYOTIC CELL

Mid1, a Mechanosensitive Calcium Ion Channel, Affects Growth, Development, and Ascospore Discharge in the Filamentous Fungus Gibberella zeae

(2011) Brad Cavinder et al.   EUKARYOTIC CELL

A comprehensive phylogeny of Neurospora reveals a link between reproductive mode and molecular evolution in fungi

(2011) Kristiina Nygren et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

FungiDB: an integrated functional genomics database for fungi

(2011) J. E. Stajich et al.   NUCLEIC ACIDS RESEARCH

Population genomics and local adaptation in wild isolates of a model microbial eukaryote

(2011) C. E. Ellison et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rediscovery by Whole Genome Sequencing: Classical Mutations and Genome Polymorphisms in Neurospora crassa

(2011) Kevin McCluskey et al.   G3-Genes Genomes Genetics

A Phenome-Based Functional Analysis of Transcription Factors in the Cereal Head Blight Fungus, Fusarium graminearum

(2011) Hokyoung Son et al.   PLoS Pathogens

Functional Analysis of the Kinome of the Wheat Scab Fungus Fusarium graminearum

(2011) Chenfang Wang et al.   PLoS Pathogens

Identification and functional characterization of genes involved in the sexual reproduction of the ascomycete fungus Gibberella zeae

(2010) Jungkwan Lee et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

LOX: inferring Level Of eXpression from diverse methods of census sequencing

(2010) Z. Zhang et al.   BIOINFORMATICS

Multi-targeted priming for genome-wide gene expression assays

(2010) Aleksandra B Adomas et al.   BMC GENOMICS

Evolution of Transcription Networks — Lessons from Yeasts

(2010) Hao Li et al.   CURRENT BIOLOGY

Conflict between reproductive gene trees and species phylogeny among heterothallic and pseudohomothallic members of the filamentous ascomycete genus Neurospora

(2010) Rebecka Strandberg et al.   FUNGAL GENETICS AND BIOLOGY

The Fungal Genetics Stock Center: a repository for 50 years of fungal genetics research

(2010) K. McCluskey et al.   JOURNAL OF BIOSCIENCES

FGDB: revisiting the genome annotation of the plant pathogen Fusarium graminearum

(2010) P. Wong et al.   NUCLEIC ACIDS RESEARCH

Evidence for widespread adaptive evolution of gene expression in budding yeast

(2010) H. B. Fraser et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dispersal of fungal spores on a cooperatively generated wind

(2010) Marcus Roper et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bias and Evolution of the Mutationally Accessible Phenotypic Space in a Developmental System

(2010) Christian Braendle et al.   PLoS Genetics

Genetic Diversity and Fitness of Fusarium graminearum Populations from Rice in Korea

(2009) J. Lee et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Expression pattern divergence of duplicated genes in rice

(2009) Zhe Li et al.   BMC BIOINFORMATICS

From elements to modules: regulatory evolution in Ascomycota fungi

(2009) Dana J Wohlbach et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Neurospora as a model fungus for studies in cytogenetics and sexual biology at Stanford

(2009) Namboori B. Raju   JOURNAL OF BIOSCIENCES

Evolving gene expression: from G to E to G×E

(2009) Andrea Hodgins-Davis et al.   TRENDS IN ECOLOGY & EVOLUTION

Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution

(2008) Sean B. Carroll   CELL

Transposon-tagging identifies novel pathogenicity genes in Fusarium graminearum

(2008) Marie Dufresne et al.   FUNGAL GENETICS AND BIOLOGY

From Genotype to Phenotype: Systems Biology Meets Natural Variation

(2008) P. N. Benfey et al.   SCIENCE

Evolution of Eukaryotic Transcription Circuits

(2008) B. B. Tuch et al.   SCIENCE

The Evolution of Combinatorial Gene Regulation in Fungi

(2008) Brian B Tuch et al.   PLOS BIOLOGY