Qingyun Liu

Polyketide synthase 12 is an in vivo essential source of novel mycolyl lipids in Mycobacterium tuberculosis

The paper identifies pks12 as an in vivo essential gene in Mtb by combining genomic, metabolomic, and phenotypic analyses, revealing its role in mycolyl lipid synthesis and host-pathogen interface structure.

Desiccation-induced DNA damage facilitates drug resistance in Mycobacterium tuberculosis

This study shows desiccation-induced DNA damage in Mtb leads to mutations and drug resistance by affecting DNA repair and gene expression.

Encoded metabolic remodeling amplifies drug resistance in Mycobacterium tuberculosis

This study identifies idsA2 mutations as a mechanism of ethambutol resistance in Mtb by showing they enhance drug resistance through metabolic remodeling.

Parallel Emergence and Adaptive Evolution of Multicountry Circulating Mycobacterium abscessus Clones

The paper analyzes global M. abscessus genomes to show that recently emerged clones spread across countries and show shifts in selective pressures during expansion.

Population-level genome sequencing reveals distinct Mycobacterium tuberculosis intrahost mutational trajectories in simian immunodeficiency virus co-infected and antiretroviral treated non-human primates

This study uses whole genome sequencing of Mycobacterium tuberculosis in non-human primates to identify distinct mutational trajectories in SIV-co-infected and ART-treated animals, revealing differential immune pressures and mutation patterns.

Granuloma Dual RNA-Seq Reveals Composite Transcriptional Programs Driven by Neutrophils and Necrosis within Tuberculous Granulomas

The paper uses dual RNA-seq in zebrafish to study transcriptional programs in tuberculous granulomas, finding neutrophils and necrosis drive bacterial survival and adaptation.

Immunopeptidomics informs discovery and delivery of Mycobacterium tuberculosis MHC-II antigens for vaccine design

This study identifies MHC-II antigens from Mycobacterium tuberculosis using mass spectrometry and evaluates mRNA vaccine immunogens to enhance T cell recognition.

A host-directed adjuvant resuscitates and sensitizes intracellular bacterial persisters to antibiotics

This study identifies a host-directed adjuvant, KL1, that increases intracellular bacterial energy and sensitizes persisters to antibiotics by modulating host immune responses and reducing reactive species production.

Evolution of Mycobacterium tuberculosis transcription regulation is associated with increased transmission and drug resistance

The paper identifies variants in Mycobacterium tuberculosis associated with decreased virulence gene expression and increased transmissibility, particularly in drug-resistant strains.

Conserved mycobacterial sRNA B11 regulates lipooligosaccharide synthesis at post-transcriptional level

This study identifies B11, a conserved mycobacterial sRNA, as a post-transcriptional regulator of lipooligosaccharide synthesis, revealing its mechanism of action through RNA-seq and mass spectrometry.

Golden pompano genome resource enables discovery of valuable gene determining growth traits

The paper identifies a gene associated with growth in golden pompano using genomic and genetic analyses of a natural population.

Local adaptation in populations of Mycobacterium tuberculosis endemic to the Indian Ocean Rim

The paper analyzes whole genome sequences of Mycobacterium tuberculosis lineages L1 and L3 to show South Asia's role in their dispersion and identify local adaptation at the esxH locus.

Unsupervised clustering analysis of SARS-Cov-2population structure reveals six major subtypes atearly stage across the world

This study uses clustering algorithms to analyze SARS-CoV-2 genomic data and identifies six major subtypes with distinct geographical distributions.

Whole Genome and Embryo Transcriptome Analysis of Vertebrate Identifies nxhl Controlling Angiogenesis by Targeting VE-PTP

This study identifies nxhl as a novel upstream regulator of VE-PTP in angiogenesis by interacting with NCL, revealing a new signaling pathway with therapeutic potential for angiogenesis-dependent diseases.

Genomic variant identification methods alter Mycobacterium tuberculosis transmission inference

This study shows that different genomic variant calling methods lead to inconsistent transmission inferences and phylogenies in Mycobacterium tuberculosis outbreaks.