Weekly Reading List: July 7, 2025

After a quarter of a century, the website remains an essential tool for navigating the genome and understanding its structure, function and clinical impact.

The best AI Agents are currently failing about 70 percent of the tasks assigned to them, as investments are expected to drop off a cliff.

Genetic studies on Native American populations have transformed our understanding of the demographic history of the Americas. However, a region that has not been investigated through ancient genomics so far is Colombia, the entry point into South America. Here, we report genome-wide data of 21 individuals from the Bogotá Altiplano in Colombia between 6000 and 500 years ago. We reveal that preceramic hunter-gatherers represent a previously unknown basal lineage that derives from the initial South American radiation.

Why did two private equity firms with more than $460 billion under management want a little old gene therapy biotech called bluebird bio? We wanted to know.

A computational model called Centaur, developed by fine-tuning a language model on a huge dataset called Psych-101, can predict and simulate human nature in experiments expressible in natural language, even in previously unseen situations.

RFK Jr.’s plan to circumvent established medical journals smacks more of retaliation than reform, write three former NEJM editors.

Amyotrophic lateral sclerosis (ALS) remains one of medicine's most formidable challenges, with its genetic forms offering unique opportunities for targeted intervention. Among these, mutations in the FUS gene cause a particularly severe form of ALS, often affecting young patients, with rapid progression and poor outcomes.1 The development of gene-silencing therapies has gained momentum, with notable progress in the treatment of SOD1-ALS, for which tofersen (an antisense oligonucleotide targeting SOD1) showed promising results in the VALOR trial,2 particularly when administered early in the disease course.

PhD programmes need to better prepare students for careers outside universities, researchers warn.

Despite profound impact on bio-medical research, progress in understanding has been slow.

Analyzing readouts of inflammaging across four cohorts, Franck and colleagues identify strong variation and observe that inflammaging, in its known form, primarily emerges in industrialized—but not nonindustrialized—populations.

Three life science firms have received awards of grant and equity funding from the European Innovation Council (EIC) Accelerator. Swedish proteomics firm Pixelgen and Swedish sequencing company Single Technologies each received €12.5 million ($14.7 million) in grant and equity funding, while UK-based molecular diagnostics firm Mitra Bio received €2.5 million. The awards were announced by the EIC on Monday

Scientific discovery relies on scientists generating novel hypotheses that undergo rigorous experimental validation. To augment this process, we introduce an AI co-scientist, a multi-agent system built on Gemini 2.0. The AI co-scientist is intended to help uncover new, original knowledge and to formulate demonstrably novel research hypotheses and proposals, building upon prior evidence and aligned to scientist-provided research objectives and guidance. The system’s design incorporates a generate, debate, and evolve approach to hypothesis generation, inspired by the scientific method and accelerated by scaling test-time compute. Key contributions include: (1) a multi-agent architecture with an asynchronous task execution framework for flexible compute scaling; (2) a tournament evolution process for self-improving hypotheses generation. Automated evaluations show continued benefits of test-time compute, improving hypothesis quality. While general purpose, we focus development and validation in three biomedical areas: drug repurposing, novel target discovery, and explaining mechanisms of bacterial evolution and anti-microbial resistance. For drug repurposing, the system proposes candidates with promising validation findings, including candidates for acute myeloid leukemia that show tumor inhibition in vitro at clinically applicable concentrations. For novel target discovery, the AI co-scientist proposed new epigenetic targets for liver fibrosis, validated by anti-fibrotic activity and liver cell regeneration in human hepatic organoids. Finally, the AI co-scientist recapitulated unpublished experimental results via a parallel in silico discovery of a novel gene transfer mechanism in bacterial evolution. These results, detailed in separate, co-timed reports, demonstrate the potential to augment biomedical and scientific discovery and usher an era of AI empowered scientists.

Whole-genome sequencing of an ancient male Egyptian revealed a mixture of North African Neolithic and eastern Fertile Crescent ancestry, suggesting human migration between Egypt and Mesopotamia by the Old Kingdom period.

Discover the latest developments in the neuroplastogens field, including Elkedonia’s funding to address neuropsychiatric disorders.

Cambridge’s Institute of Astronomy is trying to find a photo of Annie Walker, who died in 1940, to give her star billing

This study utilized multiomics combined with a comprehensive machine learning-based predictive modeling approach to identify, validate, and prioritize circulating immunometabolic biomarkers in distinguishing tuberculosis (TB) from nontuberculous mycobacteria (NTM) infections, latent tuberculosis infection (LTBI), and other lung diseases (ODx). Functional omics data were collected from two discovery cohorts (76 patients in the TB-NTM cohort and 72 patients in the TB-LTBI-ODx cohort) and one validation cohort (68 TB patients and 30 LTBI patients). Mutiomics integrative analysis identified three plasma multiome biosignatures that could distinguish active TB from non-TB with promising performance, achieving area under the receiver operating characteristic curve (AUC) values of 0.70–0.90 across groups in both the discovery and validation cohorts.

Biocompatible chemistry merges chemo-catalytic reactions with cellular metabolism for sustainable small-molecule synthesis. Now a biocompatible Lossen rearrangement has been demonstrated to control bacterial cell growth and chemistry and applied to the remediation and upcycling of polyethylene terephthalate plastic waste in whole-cell reactions and fermentations to produce valuable industrial chemicals, including the drug paracetamol.

Commercial beekeepers in the US reported severe colony losses early in 2025, as colonies were being staged for their critical role in the almond pollination season in California. Average reported losses since the preceding spring exceeded 60%, with substantial variation among operations. Many colonies were still actively collapsing in January, 2025, when pooled and individual samples were collected then screened for levels of known honey bee pathogens and parasites. Deformed wing virus strains A and B, along with Acute bee paralysis virus, were found at unusually high levels, either in pooled colony samples or in individual bees exhibiting shaking behaviors and morbidity. Differences between these two analyses suggest that direct collections of morbid bees provide a superior diagnostic for causal viruses, a suggestion borne out by confirmation of symptoms and morbidity following isolation and new inoculations. Since these viruses are known to be vectored by parasitic Varroa mites, mites from collapsed colonies were in turn screened for resistance to amitraz, a critical miticide used widely by beekeepers. Miticide resistance was found in all collected Varroa , underscoring the urgent need for new control strategies for this parasite. While viruses are a likely end-stage cause of colony death, other stressors such as nutritional stress and agrochemicals may have also played significant roles. ### Competing Interest Statement The authors have declared no competing interest.

The manufacture and use of tools, while widespread in terrestrial animals1, has been less frequently reported in marine taxa2. In cetaceans, clear examples of tool use are largely restricted to foraging contexts, with no reports of cetaceans fashioning tools by modifying objects. Here, we report evidence of the widespread manufacture and use of allogrooming tools in a population of resident killer whales (Orcinus orca ater).

Mutational signature analysis of blood cells isolated from 23 chemotherapy-exposed samples and 9 nonexposed controls characterizes the effects of various drugs on mutational burden, signature exposure and cell types.

Visualization is an indispensable facet of genomic data analysis. Despite the abundance of specialized visualization tools, there remains a distinct need for tailored solutions. However, their implementation typically requires extensive programming expertise from bioinformaticians and software developers, especially when building interactive applications. Toolkits based on visualization grammars offer a more accessible, declarative way to author new visualizations. Yet, current grammar-based solutions fall short in adequately supporting the interactive analysis of large datasets with extensive sample collections, a pivotal task often encountered in cancer research.

An analysis of data from the Sherlock-Lung study provides insight into the mutational processes that contribute to lung cancer in never smokers, and looks at the possible role of factors such as air pollution and passive smoking.

As of 20 May, the US Department of Agriculture (USDA) has confirmed highly pathogenic avian influenza (HPAI) in more than 173.1 million birds since the outbreak began in January 2022. The secretary of the US Department of Health and Human Services, Robert Kennedy Jr., has suggested allowing the unmitigated spread of HPAI in turkeys and chickens to identify surviving birds—a sentiment supported by Brooke Rollins, secretary of the USDA, which, along with state-level departments of agriculture, has jurisdiction over animal disease outbreaks (1)

Political interference and chaotic cuts to staff, programs and grants at the National Science Foundation are producing ‘devastating consequences’

With obesity afflicting over 44% of U.S. adults, Americans are sick, facing a chronic disease epidemic unlike anything we’ve ever seen before. Fortunately, we now have a powerful tool to address