Analysis of the Genome and Transcriptome of Cryptococcus neoformans var. grubii Reveals Complex RNA Expression and Microevolution Leading to Virulence Attenuation

Non-coding RNAs in the development and pathogenesis of eukaryotic microbes

(2013) Nadia Chacko et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Stalled Spliceosomes Are a Signal for RNAi-Mediated Genome Defense

(2013) Phillip A. Dumesic et al.   CELL

Sex-Induced Silencing Operates During Opposite-Sex and Unisexual Reproduction in Cryptococcus neoformans

(2013) X. Wang et al.   GENETICS

Efficient neocentromere formation is suppressed by gene conversion to maintain centromere function at native physical chromosomal loci in Candida albicans

(2013) J. Thakur et al.   GENOME RESEARCH

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

Alternative cleavage and polyadenylation: extent, regulation and function

(2013) Ran Elkon et al.   NATURE REVIEWS GENETICS

An efficient method for genome-wide polyadenylation site mapping and RNA quantification

(2013) Stefan Wilkening et al.   NUCLEIC ACIDS RESEARCH

Species-specific factors mediate extensive heterogeneity of mRNA 3' ends in yeasts

(2013) Z. Moqtaderi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conserved Regulation of Cardiac Calcium Uptake by Peptides Encoded in Small Open Reading Frames

(2013) E. G. Magny et al.   SCIENCE

Ordered Kinetochore Assembly in the Human-Pathogenic Basidiomycetous Yeast Cryptococcus neoformans

(2013) L. Kozubowski et al.   mBio

Comparative Genomics of Serial Isolates of Cryptococcus neoformans Reveals Gene Associated With Carbon Utilization and Virulence

(2013) Kate L. Ormerod et al.   G3-Genes Genomes Genetics

Unisexual and Heterosexual Meiotic Reproduction Generate Aneuploidy and Phenotypic Diversity De Novo in the Yeast Cryptococcus neoformans

(2013) Min Ni et al.   PLOS BIOLOGY

Introns Regulate Gene Expression in Cryptococcus neoformans in a Pab2p Dependent Pathway

(2013) Carolin Goebels et al.   PLoS Genetics

A normalization strategy for comparing tag count data

(2012) Koji Kadota et al.   Algorithms for Molecular Biology

Microsporidian genome analysis reveals evolutionary strategies for obligate intracellular growth

(2012) C. A. Cuomo et al.   GENOME RESEARCH

RNA Polymerase II Collision Interrupts Convergent Transcription

(2012) David J. Hobson et al.   MOLECULAR CELL

Natural antisense transcripts in fungi

(2012) Michael E. Donaldson et al.   MOLECULAR MICROBIOLOGY

Quantification of stochastic noise of splicing and polyadenylation in Entamoeba histolytica

(2012) Chung-Chau Hon et al.   NUCLEIC ACIDS RESEARCH

Tackling Human Fungal Infections

(2012) G. D. Brown et al.   SCIENCE

Uncovering the Genome-Wide Transcriptional Responses of the Filamentous Fungus Aspergillus niger to Lignocellulose Using RNA Sequencing

(2012) Stéphane Delmas et al.   PLoS Genetics

DREME: motif discovery in transcription factor ChIP-seq data

(2011) Timothy L. Bailey   BIOINFORMATICS

Building a double hexamer of DNA helicase at eukaryotic replication origins

(2011) Karim Labib   EMBO JOURNAL

Diversity in Requirement of Genetic and Epigenetic Factors for Centromere Function in Fungi

(2011) Babhrubahan Roy et al.   EUKARYOTIC CELL

Mechanisms and Consequences of Alternative Polyadenylation

(2011) Dafne Campigli Di Giammartino et al.   MOLECULAR CELL

XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast

(2011) E. L. van Dijk et al.   NATURE

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

FungiDB: an integrated functional genomics database for fungi

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

Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation

(2011) X. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative Functional Genomics of the Fission Yeasts

(2011) N. Rhind et al.   SCIENCE

Genome Variation in Cryptococcus gattii, an Emerging Pathogen of Immunocompetent Hosts

(2011) C. A. D'Souza et al.   mBio

A Detailed History of Intron-rich Eukaryotic Ancestors Inferred from a Global Survey of 100 Complete Genomes

(2011) Miklos Csuros et al.   PLoS Computational Biology

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Endophytic Life Strategies Decoded by Genome and Transcriptome Analyses of the Mutualistic Root Symbiont Piriformospora indica

(2011) Alga Zuccaro et al.   PLoS Pathogens

Genomewide characterization of non-polyadenylated RNAs

(2011) Li Yang et al.   GENOME BIOLOGY

Characterizing the role of RNA silencing components in Cryptococcus neoformans

(2010) Guilhem Janbon et al.   FUNGAL GENETICS AND BIOLOGY

Sex-induced silencing defends the genome of Cryptococcus neoformans via RNAi

(2010) X. Wang et al.   GENES & DEVELOPMENT

A Tetrad Analysis of the Basidiomycete Fungus Cryptococcus neoformans

(2010) A. Idnurm   GENETICS

Dindel: Accurate indel calls from short-read data

(2010) C. A. Albers et al.   GENOME RESEARCH

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Comprehensive comparative analysis of strand-specific RNA sequencing methods

(2010) Joshua Z Levin et al.   NATURE METHODS

Dynamics of a novel centromeric histone variant CenH3 reveals the evolutionary ancestral timing of centromere biogenesis

(2010) Manu Dubin et al.   NUCLEIC ACIDS RESEARCH

Widespread Gene Conversion in Centromere Cores

(2010) Jinghua Shi et al.   PLOS BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Estimation of the current global burden of cryptococcal meningitis among persons living with HIV/AIDS

(2009) Benjamin J Park et al.   AIDS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

(2009) Ken Chen et al.   NATURE METHODS

Transcriptome analysis by strand-specific sequencing of complementary DNA

(2009) Dmitri Parkhomchuk et al.   NUCLEIC ACIDS RESEARCH

Chromosomal Rearrangements between Serotype A and D Strains in Cryptococcus neoformans

(2009) Sheng Sun et al.   PLoS One

Progressive lengthening of 3' untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development

(2009) Z. Ji et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Systematic Genetic Analysis of Virulence in the Human Fungal Pathogen Cryptococcus neoformans

(2008) Oliver W. Liu et al.   CELL

Genome Annotation in Plants and Fungi: EuGene as a Model Platform

(2008) Sylvain Foissac et al.   Current Bioinformatics

UGE1andUGE2Regulate the UDP-Glucose/UDP-Galactose Equilibrium inCryptococcus neoformans

(2008) Frédérique Moyrand et al.   EUKARYOTIC CELL

Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training

(2008) V. Ter-Hovhannisyan et al.   GENOME RESEARCH

A ncRNA Modulates Histone Modification and mRNA Induction in the Yeast GAL Gene Cluster

(2008) Jonathan Houseley et al.   MOLECULAR CELL

Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution

(2008) Brian T. Wilhelm et al.   NATURE

Rapid evolution of Cse4p-rich centromeric DNA sequences in closely related pathogenic yeasts, Candida albicans and Candida dubliniensis

(2008) S. Padmanabhan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Heterochromatin and RNAi Are Required to Establish CENP-A Chromatin at Centromeres

(2008) H. D. Folco et al.   SCIENCE