M. K. Lawniczak

Twenty-five new microsporidian genomes: Insights into ploidy, reproduction, and the group's pangenome

The paper presents 25 new microsporidian genomes, revealing extreme pangenome diversity and novel tetraploid structures in some species.

High quality chromosomal genome assemblies of three human Plasmodium species directly from natural infections

The paper generates high-quality chromosome-level genomes for three Plasmodium species from natural infections, improving understanding of their biology and evolution.

De novo assembly of complete Plasmodium falciparum isolate genomes using PacBio HiFi sequencing technology

This study uses PacBio HiFi sequencing to assemble complete Plasmodium falciparum genomes from natural infections, revealing full repertoires of immune-related genes.

Efficient and precise discovery of LTR-retrotransposon families using HiRepEat

The paper introduces HiRepEat, a method for efficiently discovering and clustering LTR-retrotransposon families across genomes, showing results on vertebrate and Drosophila genomes.

Convergent evolutionary loss of chemosensory and blood-feeding pathways in non-blood-feeding mosquitoes

The paper identifies convergent gene losses and expression changes associated with blood-feeding loss in non-blood-feeding mosquitoes.

Evaluating the impact of a sample-matched reference genome on single-cell transcriptomic inferences in Plasmodium falciparum

The paper evaluates how using a sample-matched reference genome affects single-cell transcriptomic analysis in Plasmodium falciparum, finding that var genes require a matched genome for accurate expression inference.

Exploring the diversity and spatial distribution of Anopheles mosquitoes and their associated Plasmodium species in Tanzania using the ANOSPP amplicon panel

The paper uses the ANOSPP amplicon panel to analyze Anopheles mosquitoes and Plasmodium species in Tanzania, revealing 15 Anopheles taxa and five Plasmodium species, including new records of P. caprae and An. funestus-like mosquitoes.

340 dipteran genomes reveal the origin of Muller elements and sex chromosomes in Diptera

The paper reconstructs ancestral linkage groups in 340 dipteran genomes to study chromosome evolution, finding conserved groups in Nematoceran lineages and chromosomal fissions in Brachycera.

Assessing the population genetic structure and demographic history of Anopheles gambiae and Anopheles arabiensis at island and mainland sites in Uganda: Implications for testing novel malaria vector control approaches.

This study examines genetic structure and demographic history of Anopheles gambiae and Anopheles arabiensis in Uganda, showing genetic differentiation between species and subtle structure between island and mainland populations, with implications for malaria vector control.

Breaking the cold chain: solutions for room temperature preservation of mosquitoes leading to high quality reference genomes

This study evaluates room temperature preservation methods for mosquitoes to generate high-quality reference genomes, finding that squished samples in ethanol or Allprotect work best for Hi-C data.

CiFi: Accurate long-read chromosome conformation capture with low-input requirements

CiFi improves Hi-C analysis by combining 3C with PacBio HiFi sequencing, enabling better coverage in repetitive regions and low-input samples.

Forty New Genomes Shed Light on Sexual Reproduction and the Origin of Tetraploidy in Microsporidia

The paper presents 40 new microsporidian genomes, revealing evidence of sexual reproduction and autopolyploidy, with tetraploid genomes organized into diploid compartments.

Genomic diversity of the African malaria vector Anopheles funestus

The paper analyzes genomic diversity in Anopheles funestus across Africa, identifying genetic variation, adaptation signals, and conservation of a gene drive target.

An atlas of positive selection in the genomes of major malaria vectors

The paper identifies and characterizes genomic regions under positive selection in malaria vectors using whole-genome sequencing data from 4,306 mosquitoes across twenty-one countries.

Single-cell transcriptional landscapes of Aedes aegypti midgut and fat body after a bloodmeal

This study maps the single-cell transcriptional and metabolic changes in Aedes aegypti midgut and fat body after a bloodmeal, revealing diverse cell populations and a novel fat body-yolk cell type.

Signatures of selection and mechanisms of insecticide resistance in Ugandan Anopheles funestus: Insights from embedding translational genomics into the LLINEUP cluster randomised trial.

This paper uses genomic surveillance in a cluster randomized trial to detect insecticide resistance variants in Ugandan Anopheles funestus and An. gambiae s.l., showing differential population responses to pyrethroid and PBO interventions.

On the path to reference genomes for all biodiversity: lessons learned and laboratory protocols created in the Sanger Tree of Life core laboratory over the first 2000 species

Across 4883 species, standardised high-molecular-weight DNA extraction passed 96% of chordate and 91% of plant species, while fungi failed at 34.2%; ultra-low-input PacBio libraries rescue many low-yield samples.

The 229 chromosomes of the Atlas blue butterfly reveal rules constraining chromosome evolution in Lepidoptera

The study presents a chromosome-level genome assembly of the Atlas blue butterfly, revealing constraints on chromosome evolution in Lepidoptera through extensive fission and fusion events.

A single-cell atlas of the Culex tarsalis midgut during West Nile virus infection

This study creates a single-cell atlas of Culex tarsalis midgut cells during West Nile virus infection, revealing cell-type-specific differences in viral replication and immune responses.

A single cell atlas of sexual development in Plasmodium falciparum

This study presents a single-cell transcriptome atlas of Plasmodium falciparum sexual development, revealing transcriptional heterogeneity in naturally infected individuals.

Discovery of knock-down resistance in the major malaria vector Anopheles funestus.

The paper discovers knock-down resistance (kdr) mutations in Anopheles funestus, a major malaria vector, showing resistance to DDT but not deltamethrin.

A complex Plasmodium falciparum cryptotype circulating at low frequency across the African continent

The paper identifies a cryptotype in Plasmodium falciparum genomes across Africa, characterized by a complex genetic background that is geographically widespread but genetically distinct.

MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio High Fidelity reads

MitoHiFi assembles mitochondrial genomes from PacBio HiFi reads, identifying heteroplasmy variants and excluding nuclear contaminants, and has been used to assemble 374 mitochondrial genomes.

Regulators of male and female sexual development critical for transmission of a malaria parasite

The paper identifies ten genes critical for male and female sexual development in Plasmodium berghei and reveals a regulatory cascade governing gametogenesis.

Single-cell transcriptomics reveals expression profiles of Trypanosoma brucei sexual stages

The paper uses single-cell RNA sequencing to identify and characterize sexual stages in Trypanosoma brucei, revealing gene expression patterns associated with gamete formation.

A single-cell atlas of Plasmodium falciparum transmission through the mosquito

The paper uses single-cell transcriptomics to map gene usage and developmental trajectories of Plasmodium falciparum during mosquito transmission.

Genetic variation at the Cyp6m2 putative insecticide resistance locus in Anopheles gambiae and Anopheles coluzzii

The paper examines genetic variation in the Cyp6m2 gene across Anopheles mosquito populations and finds no evidence of directional selection on missense variants linked to insecticide resistance.

Genome variation and population structure among 1,142 mosquitoes of the African malaria vector species Anopheles gambiae and Anopheles coluzzii

The paper analyzes genome variation in 1,142 Anopheles mosquitoes to study population structure and insecticide resistance.

souporcell: Robust clustering of single cell RNAseq by genotype and ambient RNA inference without reference genotypes

Souporcell clusters single-cell RNAseq data using genetic variants to accurately assign genotypes, detect doublets, and estimate ambient RNA without reference genotypes.

The Malaria Cell Atlas: a comprehensive reference of single parasite transcriptomes across the complete Plasmodium life cycle

The paper creates a comprehensive single-cell transcriptome atlas of the Plasmodium berghei life cycle and applies it to define stages in human malaria parasites.