Predictive computational phenotyping and biomarker discovery using reference-free genome comparisons

Identifying lineage effects when controlling for population structure improves power in bacterial association studies

(2016) Sarah G. Earle et al.   Nature Microbiology

Mechanisms of BK virus infection of renal cells and therapeutic implications

(2015) Christiane Mbianda et al.   JOURNAL OF CLINICAL VIROLOGY

Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage

(2015) Matthias Merker et al.   NATURE GENETICS

Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis

(2015) Phelim Bradley et al.   Nature Communications

The Resistome of Pseudomonas aeruginosa in Relationship to Phenotypic Susceptibility

(2014) Veronica N. Kos et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Fast alignment-free sequence comparison using spaced-word frequencies

(2014) Chris-Andre Leimeister et al.   BIOINFORMATICS

Development and Applications of CRISPR-Cas9 for Genome Engineering

(2014) Patrick D. Hsu et al.   CELL

Ten years of next-generation sequencing technology

(2014) Erwin L. van Dijk et al.   TRENDS IN GENETICS

Genomic Analyses of DNA Transformation and Penicillin Resistance in Streptococcus pneumoniae Clinical Isolates

(2013) Fereshteh Fani et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis

(2013) O. Bonham-Carter et al.   BRIEFINGS IN BIOINFORMATICS

New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing

(2013) K. Song et al.   BRIEFINGS IN BIOINFORMATICS

The Next-Generation Sequencing Revolution and Its Impact on Genomics

(2013) Daniel C. Koboldt et al.   CELL

Clostridium difficile erm(B)-containing elements and the burden on the in vitro fitness

(2013) F. Wasels et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Population genomics of post-vaccine changes in pneumococcal epidemiology

(2013) Nicholas J Croucher et al.   NATURE GENETICS

The Effects of Methionine Acquisition and Synthesis on Streptococcus Pneumoniae Growth and Virulence

(2013) Shilpa Basavanna et al.   PLoS One

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

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

Ray Meta: scalable de novo metagenome assembly and profiling

(2012) Sébastien Boisvert et al.   GENOME BIOLOGY

Genomic biomarkers in predictive medicine. An interim analysis

(2011) Richard Simon   EMBO Molecular Medicine

Molecular basis and mechanisms of drug resistance in Mycobacterium tuberculosis: classical and new drugs

(2011) P. E. Almeida Da Silva et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

Genetic Organisation, Mobility and Predicted Functions of Genes on Integrated, Mobile Genetic Elements in Sequenced Strains of Clostridium difficile

(2011) Michael S. M. Brouwer et al.   PLoS One

Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies

(2010) Sébastien Boisvert et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Origins and Evolution of Antibiotic Resistance

(2010) J. Davies et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Insights into the structure, function and evolution of the radical-SAM 23S rRNA methyltransferase Cfr that confers antibiotic resistance in bacteria

(2009) Katarzyna H. Kaminska et al.   NUCLEIC ACIDS RESEARCH

Epigenetic inheritance based evolution of antibiotic resistance in bacteria

(2008) Mike Adam et al.   BMC EVOLUTIONARY BIOLOGY

What are decision trees?

(2008) Carl Kingsford et al.   NATURE BIOTECHNOLOGY