Reference-free genome phasing is vital for understanding allele inheritance and the impact of single-molecule DNA variation on phenotypes. To achieve thorough phasing across homozygous or repetitive r...

Google AI, in collaboration with the UC Santa Cruz Genomics Institute, has introduced DeepPolisher, a cutting-edge deep learning tool designed to substantially improve the accuracy of genome assemblies by correcting base-level errors. Its notable efficacy was recently demonstrated in advancing the Human Pangenome Reference, a major milestone in genomics research. The Challenge of Accurate Genome Assembly A reference genome is an essential foundation for understanding genetic diversity, heredity, disease mechanisms, and evolutionary biology.

For many years, machine learning-based ab initio gene finding approaches have been the central components of eukaryotic genome annotation pipelines, and they remain so today. The reliance on these app...

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We investigate the internal mechanisms used by Claude 3.5 Haiku — Anthropic's lightweight production model — in a variety of contexts, using our circuit tracing methodology.

Eight faculty from UC Davis are among 471 scientists, engineers and innovators newly elected as fellows of the American Association for the Advancement of Science, the society announced today (March 2...

a simple tool for listing conda environments with descriptions - rrwick/condaenvlist

Gene duplication and subsequent paralogue diversification are major obstacles to genotype-to-phenotype predictability.

A foundation model learns transcriptional regulatory syntax from chromatin accessibility and sequence data across a range of cell types to predict gene expression and transcription factor interactions...

Balanced mating type polymorphisms offer a distinct window into the forces shaping sexual reproduction strategies. Multiple hermaphroditic genera in Juglandaceae, including walnuts (Juglans) and hicko...

Gene Info: a custom GPT that takes a list of gene symbols and provides summary information, gene ontology terms, and provides contextual information like pathway or disease involvement.

Aligning genomes into common coordinates is central to pangenome analysis and construction, but it is also computationally expensive. Multi-sequence maximal unique matches (multi-MUMs) are guideposts ...

Plant nucleotide-binding, leucine-rich repeat (NLR) immune receptors recognize pathogen effectors and activate defense. NLR genes can be non-functional in distantly related plants (restricted taxonomi...

Scientists are using ever more sophisticated AI algorithms trained on vast, unlabeled datasets to develop models that can ‘interpret’ biological data to help guide biomolecule design.

Epigenetic inheritance can be influenced by environmental conditions and somatic inputs originating from different tissues. Such transgenerational inheritance is reversable as it does not lead to muta...

An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms

Population genetics notes. Contribute to cooplab/popgen-notes development by creating an account on GitHub.

Background Centromeres depend on chromatin containing the conserved histone H3 variant CENP-A for function and inheritance, while the role of centromeric DNA repeats remains unclear. Retroelements are...

Authors, websites, and apps can use action intent links to implement "Share on Bluesky" buttons, or similar in-app actions. Logged-in users will be directed to the corresponding action view in the Blu...

Abstract. Reference sequences and annotations serve as the foundation for many lines of research today, from organism and sequence identification to provid

Scientific Data - Chromosome-level genome assembly of banaba (Lagerstroemia speciosa L.)

A pangenome analysis of 76 wild and domesticated barley accessions in combination with short-read sequence data of 1,315 barley genotypes indicates that allelic diversity at structurally complex loci ...