Tag

Genomics

All articles tagged with #genomics

science15 days ago•2 min saved

Sharks May Not Form a True Family, New Genomic Study Suggests

A Yale-led study analyzed whole genomes from 48 shark-relatives and found conflicting signals: some DNA segments point to all sharks sharing a common ancestor, while others suggest species like frilled and cow sharks are closer to rays, implying sharks may not constitute a natural, exclusive group. The researchers estimate sharks emerged around 300 million years ago, offering new insights into early jawed vertebrate evolution; the study is awaiting publication.

via BBC Science Focus Magazine|

#cartilaginous-fishes #evolution #genomics

science19 days ago•4 min saved

Genomic Split Reveals Tokara Leaf Warbler as a New Japanese Bird Species

Genome sequencing revealed the Tokara Leaf Warbler (Phylloscopus tokaraensis) as a distinct species from Ijima's Leaf Warbler, marking Japan's first new bird species identification since 1982. Despite near-identical appearance, differences in songs and genetics justified the split, highlighting conservation concerns for small-island populations.

via The Daily Galaxy|

#conservation #genomics #ijimas-leaf-warbler

science21 days ago•6 min saved

David Botstein, Architect of Gene Mapping, Dies at 83

David Botstein, a pioneering molecular biologist who developed a gene-mapping approach using DNA marker variations and helped enable the human-genome project, died at 83 from Parkinson’s disease. His work bridged genetics and sequencing, guiding discoveries of disease genes and advancing interdisciplinary science education during stints at MIT, Genentech, Stanford, Princeton, and Calico.

via The New York Times|

#botstein #gene-mapping #genetics

science28 days ago•7 min saved

Cat Cancer Map Reveals Shared Genetic Drivers with Humans and Dogs

An international study published in Science maps the first large-scale genetic landscape of domestic-cat cancers, revealing shared driver genes with humans and dogs—most notably FBXW7 in feline mammary tumors—and suggesting cross-species insights for prevention and therapy; preliminary data also hint that FBXW7 mutations influence chemotherapy responses, and a public data resource has been released to advance feline oncology and its relevance to human cancer under a One Medicine approach.

via SciTechDaily|

#cancer #cats #cross-species

science29 days ago•187 min saved

Wildflowers' rapid genetics save California’s scarlet monkeyflower from drought

During California’s 2012–2015 megadrought, scarlet monkeyflowers (Mimulus cardinalis) declined dramatically, but a multi-site genomic study found rapid, genome-wide genetic changes that helped some populations recover, a phenomenon called evolutionary rescue. The research, spanning 55 wild populations over eight years, shows drought-driven selection and suggests that genetic diversity and habitat connectivity are crucial for resilience as climate change intensifies, while also highlighting that some populations avoided extinction by evolving fast enough to persist.

via CNN|

#climate-change #drought-adaptation #evolutionary-rescue

science29 days ago•6 min saved

Genomes unsettle the shark family tree, blurring lines with rays

Genome analysis of sharks, rays, and relatives suggests sharks may be paraphyletic: Hexanchiformes appear on a distinct lineage from the rest, implying rays and skates may share shark-like origins and challenging the idea of a single, unified shark group.

via Nature|

#genomics #hexanchiformes #phylogeny

science1 month ago•85 min saved

Sorghum pangenome reveals hidden diversity to boost trait discovery

A 33-member sorghum pangenome and a 1,984-genotype diversity panel expand beyond the BTx623 reference to capture extensive structural variation and presence–absence variation. The study annotates genes with RNA-seq, identifies large-scale variants, and uses a fast k-mer genotyping approach to map complex alleles at loci like SH1 and the dhurrin biosynthetic cluster. By linking genomic diversity to traits such as drought tolerance, biomass, and leaf chemistry, the work provides a framework to accelerate trait discovery and breeding across global sorghum germplasm.

via Nature|

#breeding #genomics #pangenome

science1 month ago•11 min saved

Cat Cancers Mirror Human Cancers, Guiding Cross-Species Therapies

A large study sequencing 1,000 cancer-associated genes in 500 cat tumors finds striking similarities with human cancers: TP53 is the most commonly mutated gene in both species, cat mammary cancers show about 50% PIK3CA mutations, and RAS mutations are less common in cats. Because cat cancers arise spontaneously in the same environment as people, they offer a valuable cross-species model for understanding cancer biology and testing targeted therapies, aided by veterinary biobanks and open data that can accelerate translational research for both cats and humans.

via The Conversation|

#cancer #cats #genomics

technology1 month ago•10 min saved

Open-Source Evo 2 AI Maps Genome Features Across Life

Ars Technica reports Evo 2, an open-source large genome model trained on 8.8 trillion bases from bacteria, archaea, eukaryotes, and related viruses, enabling it to identify genes, regulatory DNA, and splice sites without task-specific tuning. Built on a StripedHyena 2 CNN, Evo 2 underwent two training stages—short, feature-rich segments then long-range sequences—and was released with model weights, training/inference code, and the OpenGenome2 dataset. While it shows strong genome-annotation capabilities and can recognize features across domains and some mutation effects, its ability to design functional new proteins remains unproven and early tests of regulatory sequence activity yielded only modest results. The researchers anticipate many possible uses and further specialization, with the code and data open for community exploration.

via Ars Technica|

#artificial-intelligence #evo-2 #genomics

science1 month ago•76 min saved

Evo 2: An Open-Source AI for Genome-Scale Prediction and Design Across Life

Evo 2 is a large, open biological foundation model trained on 9 trillion base pairs across all life, with a 1‑million‑token context, available in 7B and 40B sizes. It predicts mutational effects on DNA, RNA and proteins without task-specific fine-tuning, can generate genome-scale sequences and chromatin-accessibility designs, and supports exon–intron annotation and variant-effect prediction across diverse species. The model and data (OpenGenome2) are fully open-source, with training/inference code and tools (Evo Designer, Evo Mech Interp), plus safety safeguards such as virus-data exclusions to mitigate misuse.

via Nature|

#artificial-intelligence #bioinformatics #genome-design

technology1 month ago•5 min saved

Illumina outlines 18-month NovaSeq X upgrades to boost quality, throughput and speed

Illumina announced an 18‑month roadmap for the NovaSeq X system featuring a Q70 quality score, a 40% output increase to 35 billion reads, and 30% faster runtimes (14B reads in 20–22 hours). The plan adds staggered starts, new flow cells and DRAGEN software to broaden multiomics, oncology and genetics applications. Rollout will span all NovaSeq X installations (~890 systems) and aims to enable higher-quality data at lower cost, advancing oncology, MRD testing and rare-disease research.

via Illumina|

#genomics #high-throughput-sequencing #illumina

science1 month ago•2 min saved

Cats Mirror Human Breast Cancer, Paving Cross-Species Treatment Paths

A Science study analyzing nearly 500 feline tumors from five countries across 13 cancer types finds genetic similarities with human cancers, notably FBXW7 mutations in feline mammary tumors that mirror aggressive human cases; two chemotherapy drugs show promise against these tumors in cats, suggesting a potential path for new treatments in humans and enabling faster veterinary testing—highlighting cats as a valuable model for cancer biology and shared environmental factors.

via CTV News|

#breast-cancer #cancer-research #cats

science2 months ago•5 min saved

Comb Jellies Crown the Earliest Split in the Animal Family Tree

New research used chromosome-level gene-order analysis to compare 14 gene groups in comb jellies, sea sponges, and closely related single-celled relatives. The patterns show conserved gene positions in comb jellies and non-animal relatives but greater genomic rearrangement in sponges, identifying comb jellies as the earliest animal branch and the sister lineage to all other animals, prompting a rethink of how key animal features evolved.

via Indian Defence Review|

#comb-jellies #evolution #genomics

science2 months ago•6 min saved

DeepMind AI maps noncoding DNA to solve undiagnosed rare diseases

At the Undiagnosed Hackathon, DeepMind's AlphaGenome was used to predict how noncoding DNA mutations affect gene activity, helping researchers tie variants to 29 undiagnosed conditions and illustrating AI’s potential to illuminate the genome’s dark matter for hundreds of millions with undiagnosed rare diseases.

via Nature|

#ai #alphagenome #genomics

genomics2 months ago•11 min saved

Biobank DNA leftovers unlock secrets of Epstein–Barr virus

Researchers show that non-human DNA discarded during whole-genome sequencing can be repurposed to detect and quantify Epstein–Barr virus DNA in human cells, using a method described by Nyeo et al. in Nature. This population-scale approach lets biobanks reveal persistent EBV DNA and its links to complex diseases, turning sequencing byproducts into a new source of epidemiological insight.

via Nature|

#biobanks #epstein-barr-virus #genomics