A cautionary note on the use of unsupervised machine learning algorithms to characterise malaria parasite population structure from genetic distance matrices

Malaria in Venezuela: changes in the complexity of infection reflects the increment in transmission intensity

(2020) M. Andreína Pacheco et al.   MALARIA JOURNAL

Median-joining network analysis of SARS-CoV-2 genomes is neither phylogenetic nor evolutionary

(2020) Santiago J. Sánchez-Pacheco et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Testing for dependence on tree structures

(2020) Merle Behr et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The impact of antimalarial resistance on the genetic structure of Plasmodium falciparum in the DRC

(2020) Robert Verity et al.   Nature Communications

Determinants of dihydroartemisinin-piperaquine treatment failure in Plasmodium falciparum malaria in Cambodia, Thailand, and Vietnam: a prospective clinical, pharmacological, and genetic study

(2019) Rob W van der Pluijm et al.   LANCET INFECTIOUS DISEASES

Ten quick tips for effective dimensionality reduction

(2019) Lan Huong Nguyen et al.   PLoS Computational Biology

The origins and relatedness structure of mixed infections vary with local prevalence of P. falciparum malaria

(2019) Sha Joe Zhu et al.   eLife

A method for genome-wide genealogy estimation for thousands of samples

(2019) Leo Speidel et al.   NATURE GENETICS

Major subpopulations of Plasmodium falciparum in sub-Saharan Africa

(2019) Alfred Amambua-Ngwa et al.   SCIENCE

A short comment on statistical versus mathematical modelling

(2019) Andrea Saltelli   Nature Communications

Origins of the current outbreak of multidrug-resistant malaria in southeast Asia: a retrospective genetic study

(2018) Roberto Amato et al.   LANCET INFECTIOUS DISEASES

hmmIBD: software to infer pairwise identity by descent between haploid genotypes

(2018) Stephen F. Schaffner et al.   MALARIA JOURNAL

De Novo Mutations Resolve Disease Transmission Pathways in Clonal Malaria

(2018) Seth N Redmond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Supervised Machine Learning for Population Genetics: A New Paradigm

(2018) Daniel R. Schrider et al.   TRENDS IN GENETICS

Genomic analysis of a pre-elimination Malaysian Plasmodium vivax population reveals selective pressures and changing transmission dynamics

(2018) Sarah Auburn et al.   Nature Communications

Identity-by-descent analyses for measuring population dynamics and selection in recombining pathogens

(2018) Lyndal Henden et al.   PLoS Genetics

A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots

(2018) Daniel J. Lawson et al.   Nature Communications

Mapping malaria by combining parasite genomic and epidemiologic data

(2018) Amy Wesolowski et al.   BMC Medicine

Tanglegrams Are Misleading for Visual Evaluation of Tree Congruence

(2018) Damien M de Vienne   MOLECULAR BIOLOGY AND EVOLUTION

The spread of artemisinin-resistant Plasmodium falciparum in the Greater Mekong subregion: a molecular epidemiology observational study

(2017) Mallika Imwong et al.   LANCET INFECTIOUS DISEASES

Spread of a single multidrug resistant malaria parasite lineage ( PfPailin ) to Vietnam

(2017) Mallika Imwong et al.   LANCET INFECTIOUS DISEASES

Quantifying connectivity between local Plasmodium falciparum malaria parasite populations using identity by descent

(2017) Aimee R. Taylor et al.   PLoS Genetics

XIBD: software for inferring pairwise identity by descent on the X chromosome

(2016) Lyndal Henden et al.   BIOINFORMATICS

Genomic epidemiology of artemisinin resistant malaria

(2016)   eLife

On the use of median-joining networks in evolutionary biology

(2015) Sungsik Kong et al.   CLADISTICS

The fine-scale genetic structure of the British population

(2015) Stephen Leslie et al.   NATURE

Genetic architecture of artemisinin-resistant Plasmodium falciparum

(2015) Olivo Miotto et al.   NATURE GENETICS

Modeling malaria genomics reveals transmission decline and rebound in Senegal

(2015) Rachel F. Daniels et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Getting Things in Order: An Introduction to theRPackageseriation

(2015) Michael Hahsler et al.   Journal of Statistical Software

fastcluster: Fast Hierarchical, Agglomerative Clustering Routines forRandPython

(2015) Daniel Müllner   Journal of Statistical Software

Spread of Artemisinin Resistance in Plasmodium falciparum Malaria

(2014) Elizabeth A. Ashley et al.   NEW ENGLAND JOURNAL OF MEDICINE

Multiple populations of artemisinin-resistant Plasmodium falciparum in Cambodia

(2013) Olivo Miotto et al.   NATURE GENETICS

Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing

(2012) Magnus Manske et al.   NATURE

Inference of Population Structure using Dense Haplotype Data

(2012) Daniel John Lawson et al.   PLoS Genetics

Tanglegrams for rooted phylogenetic trees and networks

(2011) C. Scornavacca et al.   BIOINFORMATICS

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

The influence of family groups on inferences made with the program Structure

(2009) E. C. ANDERSON et al.   Molecular Ecology Resources

A Genealogical Interpretation of Principal Components Analysis

(2009) Gil McVean   PLoS Genetics