Weekly Reading List: June 9, 2025

HHS secretary Kennedy says the US might launch alternatives to leading medical journals

Resting T cells are difficult to manipulate, and are a reservoir for latent HIV. Here, the authors develop a lipid nanoparticle formulation with the ability to transfect resting primary human T cells, enabling delivery of mRNAs that result in reactivation of latent HIV. This could help development of HIV cure strategies.

The stress and isolation of the pandemic have left social and emotional scars that are already being seen in children, but scientists also predict there could be huge economic costs.

Boom in infections in the West African nation is driven by the same viral strain that caused a global outbreak in 2022.

Data from the All of Us program confirm what many geneticists have long promoted

Bankrupt genetic analysis company 23andMe will hold a second auction for its cache of DNA data with an opening bid of $305 million from a group led by the company’s former chief executive officer, Anne Wojcicki.

Innovation is Aerobic

Postscript

Comprehensive pan-cancer analysis of loss of the Y chromosome (LOY) in benign and malignant cells establishes a new model linking LOY in circulating and tumour-infiltrating immune cells to LOY in malignant cells.

This is the web edition of STAT’s AI Prognosis, our subscriber-exclusive newsletter.

Nature Human Behaviour - NIH indirect cost cuts will affect the economy and employment

Cutting federal support for NIH and NSF is a national lobotomy that will negatively affect our nation’s economy, education, and productivity.

Opinion: Prediction: General-purpose AI could start getting worse

The northern white rhinoceros (NWR; Ceratotherium simum cottoni) is functionally extinct, with only two nonreproductive females remaining alive. Extraordinary measures are underway to rescue this species, including using a collection of NWR induced pluripotent stem cells (iPSCs) to generate gametes for assisted reproduction technologies. Because of the critical importance of genomic integrity in germ cells used for reproduction, these approaches require extensive genomic analyses to exclude aberrations that are acquired during culture of iPSCs.

Massive study finds limited connection between ageing and taurine levels in people, monkeys and mice.

Some have already lost grants, while others fear for students and future funding

Alan Alda's father wanted him to become a doctor, but it wasn't meant to be. "I failed chemistry really disastrously ... " Alda says. "I really didn't want to be a doctor; I wanted to be a writer and an actor."

At midnight on Friday, May 30, 2025, the government’s deadline to notice an appeal from the U.S. District Court for the Eastern District of Texas’s decision vacating the LDT Rule lapsed without the…

OmiCLIP is a visual–omics foundation model that integrates histology and spatial transcriptomics. The associated Loki platform offers accurate and robust tools for alignment, annotation, cell-type decomposition and spatial gene expression prediction.

In this Review, Ferretti et al. discuss advances in our understanding of interactions between the human genome and the microbiome, including the effects of the microbiome on host gene regulation.

The complete telomere-to-telomere human genome assembly (T2T-CHM13) and the draft human pangenome reference provide unique opportunities to refine DNA methylation (DNAm) studies. Here, we find that T2T-CHM13 calls 7.4% more CpGs genome wide compared to GRCh38 across four widely used short-read DNAm profiling methods and improves the evaluation of probe cross-reactivity and mismatch for Illumina DNAm arrays, yielding new and more reproducible sets of unambiguous probes. The pangenome reference further expands CpG calling by 4.5% in short-read sequencing data and identifies cross-population and population-specific unambiguous probes in DNAm arrays, owing to its improved representation of genetic diversity.

The NIH archives of the Human Genome Project could fall victim to Trump administration cuts, writes a former archivist.

Multi-Modal LLM for Gene Function Prediction. Contribute to Shashi-Sekar/GeneChat development by creating an account on GitHub.

Polygenic scores aim to capture genetic risk but may miss nonlinear genetic and environmental interactions. Here, the authors show that neural networks detect limited nonlinearity and do not outperform linear models, highlighting constraints in current deep-learning approaches.

Standard QTL mapping approaches consider variant effects on a single gene at a time, despite abundant evidence for allelic pleiotropy, where a single variant can affect multiple genes simultaneously. While allelic pleiotropy describes variant effects on both local and distal genes or a mixture of molecular effects on a single gene, here we specifically investigate allelic expression “proxitropy”: where a single variant influences the expression of multiple, neighboring genes. We introduce a multi-gene eQTL mapping framework - cis-principal component expression QTL (cis-pc eQTL or pcQTL) - to identify variants associated with shared axes of expression variation across a cluster of neighboring genes. We perform pcQTL mapping in 13 GTEx human tissues and discover novel loci undetected by single-gene approaches. In total, we identify an average of 1396 pcQTLs/tissue, 27% of which were not discovered by single-gene methods. These novel pcQTL colocalized with an additional 142 GWAS trait-associated variants and increased the number of colocalizations by 34% over single-gene QTL mapping. These findings highlight that moving beyond single-gene-at-a-time approaches toward multi-gene methods can offer a more comprehensive view of gene regulation and complex trait-associated variation. ### Competing Interest Statement S.B.M is on the scientific advisory board of MyOme, PhiTech and Valinor Therapeutics. NIH, R01MH12524, U01AG072573, U01HG012069, T32HG000044

SpotSweeper is a spatially aware method for quality control of spatially resolved transcriptomics data that corrects for spatial confounding missed by existing methods, including both local and regional artifacts, across diverse technologies.