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...