Robust detection of point mutations involved in multidrug-resistant Mycobacterium tuberculosis in the presence of co-occurrent resistance markers

Bayesian reconstruction of Mycobacterium tuberculosis transmission networks in a high incidence area over two decades in Malawi reveals associated risk factors and genomic variants

(2020) Benjamin Sobkowiak et al.   Microbial Genomics

Genome-wide analysis of Mycobacterium tuberculosis polymorphisms reveals lineage-specific associations with drug resistance

(2019) Yaa E. A. Oppong et al.   BMC GENOMICS

Beyond multidrug resistance: Leveraging rare variants with machine and statistical learning models in Mycobacterium tuberculosis resistance prediction

(2019) Michael L. Chen et al.   EBioMedicine

Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs

(2019) Jody E. Phelan et al.   Genome Medicine

A pan-genome-based machine learning approach for predicting antimicrobial resistance activities of the Escherichia coli strains

(2018) Hsuan-Lin Her et al.   BIOINFORMATICS

pyseer: a comprehensive tool for microbial pangenome-wide association studies

(2018) John A Lees et al.   BIOINFORMATICS

Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis

(2018) Francesc Coll et al.   NATURE GENETICS

A phylogenetic method to perform genome-wide association studies in microbes that accounts for population structure and recombination

(2018) Caitlin Collins et al.   PLoS Computational Biology

Predicting bacterial resistance from whole-genome sequences using k-mers and stability selection

(2018) Pierre Mahé et al.   BMC BIOINFORMATICS

Two Methods for Mapping and Visualizing Associated Data on Phylogeny Using Ggtree

(2018) Guangchuang Yu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Prediction of antibiotic resistance in Escherichia coli from large-scale pan-genome data

(2018) Danesh Moradigaravand et al.   PLoS Computational Biology

A fast and agnostic method for bacterial genome-wide association studies: Bridging the gap between k-mers and genetic events

(2018) Magali Jaillard et al.   PLoS Genetics

Removing the bottleneck in whole genome sequencing of Mycobacterium tuberculosis for rapid drug resistance analysis: a call to action

(2017) Ruth McNerney et al.   INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES

Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance

(2016) Jody Phelan et al.   BMC Medicine

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

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

The advent of genome-wide association studies for bacteria

(2015) Peter E Chen et al.   CURRENT OPINION IN MICROBIOLOGY

Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage

(2015) Matthias Merker et al.   NATURE GENETICS

The effect of splitting on random forests

(2014) Hemant Ishwaran   MACHINE LEARNING

Genomic insights into tuberculosis

(2014) James E. Galagan   NATURE REVIEWS GENETICS

A robust SNP barcode for typing Mycobacterium tuberculosis complex strains

(2014) Francesc Coll et al.   Nature Communications

Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis

(2013) Maha R Farhat et al.   NATURE GENETICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

FaST linear mixed models for genome-wide association studies

(2011) Christoph Lippert et al.   NATURE METHODS

Permutation importance: a corrected feature importance measure

(2010) André Altmann et al.   BIOINFORMATICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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