B. Fang

Fitness consequences of structural variation inferred from a House Finch pangenome

This study constructs a pangenome for House Finches to analyze structural variants (SVs) and their fitness effects, finding that SVs are more deleterious than SNPs and identifying a large inversion linked to disease resistance.

AHR activation accelerates the resolution of TGF-β1 induced fibroblast activation and promotes alveolar type 1 cell regeneration in alveolar organoids

The paper identifies DB-11-BE87 as a compound that promotes AT1 cell regeneration by reducing TGF-β1-induced fibroblast activation through AHR activation in alveolar organoids.

A high-throughput COPD bronchosphere model for disease-relevant phenotypic compound screening

This paper develops a high-throughput bronchosphere model for COPD and screens compounds to identify those that reverse CSE-induced phenotypic changes.

Network models of protein phosphorylation, acetylation, and ubiquitination connect metabolic and cell signaling pathways in lung cancer

The paper uses machine learning to analyze PTM data from lung cancer cell lines, identifying functional modules and networks that reveal crosstalk between signaling pathways and metabolic processes in response to TKIs.

HDAC8-mediated inhibition of EP300 drives a neural crest-like transcriptional state that increases melanoma brain metastasis

WNT5A-RHOA axis is a new vulnerability in small-cell lung cancer

This study identifies the WNT5A-RHOA axis as a critical driver of small-cell lung cancer, offering new therapeutic targets and insights into WNT signaling heterogeneity.

3-Phosphoinositide-dependent kinase 1 drives acquired resistance to osimertinib

This study identifies PDK1 as a driver of osimertinib resistance in NSCLC, showing its inhibition sensitizes resistant cells and correlates with disease progression.

Allopatric origin of sympatric whitefish morphs with insights on the genetic basis of their reproductive isolation

The paper examines the genetic basis of reproductive isolation in sympatric whitefish morphs, finding that ecological adaptations in spawning time evolved in allopatry and maintain partial isolation.

Autophagy Induced by Palmitic Acid: a Brake in NAFLD Neutrophils

This paper shows that palmitic acid induces autophagy in NAFLD neutrophils, leading to granule degradation and reduced adhesion, impairing neutrophil function.

Population structure limits parallel evolution

The paper tests how population structure affects parallel evolution in two stickleback species, finding that genetic drift and subdivision limit local adaptation and parallel evolution.

MEMS directed evolution of two cytochrome P450 enzymes revealing distinct active-sites for convergent function

This study introduces a multi-enzyme directed evolution model to improve screening throughput and efficiency, revealing convergent evolution in two cytochrome P450 enzymes with distinct active sites achieving similar functions.

An enormous Paris polyphylla genome sheds light on genome size evolution and polyphyllin biogenesis

This study reports the largest sequenced plant genome, Paris polyphylla var. yunnanensis, and identifies genes involved in polyphyllin biosynthesis.

Oceans apart: Heterogeneous patterns of parallel evolution in sticklebacks

This study identifies geographic differences in parallel evolution patterns in sticklebacks, showing that most parallel evolution is unique to the Eastern Pacific.

Genome-wide data inferring the evolution and population demography of the novel pneumonia coronavirus (SARS-CoV-2)

This study analyzes SARS-CoV-2 genome data to infer its evolution and population demography using phylogenetic and population genetics methods.

Genetic population structure constrains local adaptation in sticklebacks

The paper identifies genetic factors underlying pelvic reduction in sticklebacks and shows how population structure limits local adaptation.

Systematic Establishment of Robustness and Standards in Patient-Derived Xenograft Experiments and Analysis

The paper tests the reproducibility of PDX drug responses and sequence results across different labs using standardized protocols and workflows.

Collagen Production and Niche Engineering: A Novel Strategy for Cancer Cells to Survive Acidosis and Evolve

The paper identifies collagen production as an adaptation strategy in acidotic cancer cells, showing correlation with patient survival.