Pedigree-based and phylogenetic methods support surprising patterns of mutation rate and spectrum in the gray mouse lemur

CR Campbell, GP Tiley, JW Poelstra, KE Hunnicutt… - Heredity, 2021 - nature.com
Mutations are the raw material on which evolution acts, and knowledge of their frequency
and genomic distribution is crucial for understanding how evolution operates at both long …

RecGraph: recombination-aware alignment of sequences to variation graphs

J Avila Cartes, P Bonizzoni, S Ciccolella… - …, 2024 - academic.oup.com
Motivation Bacterial genomes present more variability than human genomes, which requires
important adjustments in computational tools that are developed for human data. In …

The challenge and promise of estimating the de novo mutation rate from whole‐genome comparisons among closely related individuals

AD Yoder, GP Tiley - Molecular Ecology, 2021 - Wiley Online Library
Germline mutations are the raw material for natural selection, driving species evolution and
the generation of earth's biodiversity. Without this driver of genetic diversity, life on earth …

A proteomic glimpse into the effect of antimalarial drugs on Plasmodium falciparum proteome towards highlighting possible therapeutic targets

M Dousti, R Manzano-Román, S Rashidi… - Pathogens and …, 2021 - academic.oup.com
There is no effective vaccine against malaria; therefore, chemotherapy is to date the only
choice to fight against this infectious disease. However, there is growing evidences of drug …

[HTML][HTML] Role for gene conversion in the evolution of cell-surface antigens of the malaria parasite Plasmodium falciparum

B Letcher, S Maciuca, Z Iqbal - Plos Biology, 2024 - journals.plos.org
While the malaria parasite Plasmodium falciparum has low average genome-wide diversity
levels, likely due to its recent introduction from a gorilla-infecting ancestor (approximately …

Sequential motifs in observed walks

T LaRock, I Scholtes… - Journal of Complex …, 2022 - academic.oup.com
The structure of complex networks can be characterized by counting and analysing network
motifs. Motifs are small graph structures that occur repeatedly in a network, such as triangles …

[HTML][HTML] Evidence for linkage of pfmdr1, pfcrt, and pfk13 polymorphisms to lumefantrine and mefloquine susceptibilities in a Plasmodium falciparum cross

ST Windle, KD Lane, NB Gadalla, A Liu, J Mu… - International Journal for …, 2020 - Elsevier
Background Lumefantrine and mefloquine are used worldwide in artemisinin-based
combination therapy (ACT) of malaria. Better understanding of drug susceptibility and …

Gene conversion drives allelic dimorphism in two paralogous surface antigens of the malaria parasite P. falciparum

B Letcher, S Maciuca, Z Iqbal - bioRxiv, 2023 - biorxiv.org
While the malaria parasite P. falciparum has low average genome-wide diversity levels,
likely due to its recent introduction from a gorilla-infecting ancestor (∼ 10,000-50,000 years …

[SÁCH][B] Large-Scale Analysis of Population Structural Variants Using Terabytes of SRA Sequencing Data

M Shokrof - 2024 - search.proquest.com
Studying structural variants (SV) in populations is crucial since they cause more diversity
and have more effects on gene function than small variants. However, population scale …

Whole-Exome Sequencing Implicates the USP34 rs777591A > G Intron Variant in Chronic Obstructive Pulmonary Disease in a Kashi Cohort

J Xu, L Li, J Ren, X Zhong, C **e, A Zheng… - Frontiers in Cell and …, 2022 - frontiersin.org
Genetic factors are important factors in chronic obstructive pulmonary disease (COPD)
onset. Plenty of risk and new causative genes for COPD have been identified in patients of …