Current affairs of microbial genome-wide association studies: approaches, bottlenecks and analytical pitfalls

JE San, S Baichoo, A Kanzi, Y Moosa… - Frontiers in …, 2020 - frontiersin.org
Microbial genome-wide association studies (mGWAS) are a new and exciting research field
that is adapting human GWAS methods to understand how variations in microbial genomes …

[HTML][HTML] How much can k-means be improved by using better initialization and repeats?

P Fränti, S Sieranoja - Pattern Recognition, 2019 - Elsevier
In this paper, we study what are the most important factors that deteriorate the performance
of the k-means algorithm, and how much this deterioration can be overcome either by using …

Understanding UCEs: a comprehensive primer on using ultraconserved elements for arthropod phylogenomics

YM Zhang, JL Williams, A Lucky - Insect Systematics and …, 2019 - academic.oup.com
Targeted enrichment of ultraconserved elements (UCEs) has emerged as a promising tool
for inferring evolutionary history in many taxa, with utility ranging from phylogenetic and …

PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses

R Lanfear, PB Frandsen, AM Wright… - Molecular biology …, 2017 - academic.oup.com
PartitionFinder 2 is a program for automatically selecting best-fit partitioning schemes and
models of evolution for phylogenetic analyses. PartitionFinder 2 is substantially faster and …

Phylogenomic insights into the evolution of stinging wasps and the origins of ants and bees

MG Branstetter, BN Danforth, JP Pitts, BC Faircloth… - Current Biology, 2017 - cell.com
Summary The stinging wasps (Hymenoptera: Aculeata) are an extremely diverse lineage of
hymenopteran insects, encompassing over 70,000 described species and a diversity of life …

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

C Collins, X Didelot - PLoS computational biology, 2018 - journals.plos.org
Genome-Wide Association Studies (GWAS) in microbial organisms have the potential to
vastly improve the way we understand, manage, and treat infectious diseases. Yet, microbial …

Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods

VJ Schuenemann, A Peltzer, B Welte… - Nature …, 2017 - nature.com
Egypt, located on the isthmus of Africa, is an ideal region to study historical population
dynamics due to its geographic location and documented interactions with ancient …

Evolutionary history of Polyneoptera and its implications for our understanding of early winged insects

B Wipfler, H Letsch, PB Frandsen, P Kapli… - Proceedings of the …, 2019 - pnas.org
Polyneoptera represents one of the major lineages of winged insects, comprising around
40,000 extant species in 10 traditional orders, including grasshoppers, roaches, and …

Estimating improved partitioning schemes for ultraconserved elements

VA Tagliacollo, R Lanfear - Molecular biology and evolution, 2018 - academic.oup.com
Ultraconserved (UCEs) are popular markers for phylogenomic studies. They are relatively
simple to collect from distantly-related organisms, and contain sufficient information to infer …

A dimensionality reduction-based multi-step clustering method for robust vessel trajectory analysis

H Li, J Liu, RW Liu, N **ong, K Wu, T Kim - Sensors, 2017 - mdpi.com
The Shipboard Automatic Identification System (AIS) is crucial for navigation safety and
maritime surveillance, data mining and pattern analysis of AIS information have attracted …