The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine

Building Phylogenetic Trees from Molecular Data with MEGA

(2013) B. G. Hall   MOLECULAR BIOLOGY AND EVOLUTION

pIRS: Profile-based Illumina pair-end reads simulator

(2012) Xuesong Hu et al.   BIOINFORMATICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Emerging fungal threats to animal, plant and ecosystem health

(2012) Matthew C. Fisher et al.   NATURE

Yersinia pestis: New Evidence for an Old Infection

(2012) Kirsten I. Bos et al.   PLoS One

A High-Coverage Genome Sequence from an Archaic Denisovan Individual

(2012) M. Meyer et al.   SCIENCE

Genome Analyses of an Aggressive and Invasive Lineage of the Irish Potato Famine Pathogen

(2012) David E. L. Cooke et al.   PLoS Pathogens

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

(2012) Ruibang Luo et al.   GigaScience

Understanding and Exploiting Late Blight Resistance in the Age of Effectors

(2011) Vivianne G.A.A. Vleeshouwers et al.   Annual Review of Phytopathology

Cloning and Characterization of R3b; Members of the R3 Superfamily of Late Blight Resistance Genes Show Sequence and Functional Divergence

(2011) Guangcun Li et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

A draft genome of Yersinia pestis from victims of the Black Death

(2011) Kirsten I. Bos et al.   NATURE

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

(2011) Xun Xu et al.   NATURE BIOTECHNOLOGY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Presence/absence, differential expression and sequence polymorphisms between PiAVR2 and PiAVR2-like in Phytophthora infestans determine virulence on R2 plants

(2011) Eleanor M. Gilroy et al.   NEW PHYTOLOGIST

Analyses of genome architecture and gene expression reveal novel candidate virulence factors in the secretome of Phytophthora infestans

(2010) Sylvain Raffaele et al.   BMC GENOMICS

Heterokaryotic nuclear conditions and a heterogeneous nuclear population are observed by flow cytometry in Phytophthora infestans

(2010) Mursel Catal et al.   CYTOMETRY PART A

Sampling-through-time in birth–death trees

(2010) Tanja Stadler   JOURNAL OF THEORETICAL BIOLOGY

Ancient human genome sequence of an extinct Palaeo-Eskimo

(2010) Morten Rasmussen et al.   NATURE

Genome Evolution Following Host Jumps in the Irish Potato Famine Pathogen Lineage

(2010) S. Raffaele et al.   SCIENCE

Targeted Investigation of the Neandertal Genome by Array-Based Sequence Capture

(2010) H. A. Burbano et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans

(2009) Brian J. Haas et al.   NATURE

Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA

(2009) Adrian W. Briggs et al.   NUCLEIC ACIDS RESEARCH

A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing

(2008) Richard E. Green et al.   CELL

Phytophthora infestans: the plant (and R gene) destroyer

(2008) WILLIAM FRY   MOLECULAR PLANT PATHOLOGY

The Phytophthora infestans Avirulence Gene Avr4 Encodes an RXLR-dEER Effector

(2008) Pieter M. J. A. van Poppel et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Sequencing the nuclear genome of the extinct woolly mammoth

(2008) Webb Miller et al.   NATURE