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Biology subjects

Eagle, A.

Publications and source records attributed to Eagle, A..

3 recordsLinked to original sources

B-REAL: A keypoint-less behavior platform for offline classification and real-time detection

Two obstacles limit automated behavior analysis in neuroethology: the burden of first training pose estimation models, and the inability to identify behavior quickly enough for real-time classification that could trigger stimuli, drug delivery, or environmental manipulations. Here we present B-REAL, a pose-free classifier that maps raw video to behavior faster than video frames are recorded, even on a CPU. Given substantially less training data, B-REAL matched or surpassed established methods trained on full benchmark rodent or fly datasets, particularly on rare and even single-frame behaviors. Pretraining on unlabeled video further improves its accuracy without slowing inference or training time. In closed loop, rewarding mice for B-REAL-detected grooming more than doubled their performance of grooming bouts. B-REAL thus makes closed-loop behavioral experiments practical with minimal annotation and standard hardware.

neuroscience↗

Zebrafish Information Network, the knowledgebase for Danio rerio research

The Zebrafish Information Network (ZFIN, zfin.org) is the central repository for zebrafish genetic and genomic data. ZFIN expertly curates, integrates, and displays zebrafish data including genes, alleles, human disease models, gene expression, phenotype, gene function, orthology, morpholino, CRISPR, TALEN, and antibodies. ZFIN makes zebrafish research data Findable, Accessible, Interoperable, and Reusable (FAIR) through nomenclature, curatorial and annotation activities, web interfaces, and data downloads. ZFIN is a founding member of the Alliance of Genome Resources, providing zebrafish data for integration into the cross species platform as well as contributing to model organism data harmonization efforts.

genetics↗

Integrative annotation of genomic features reveal functional elements and epigenetic landscapes in the developing zebrafish

Zebrafish, a popular model for embryonic development and for modelling human diseases, has so far lacked a systematic functional annotation programme akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium and created the first central repository to store and process zebrafish developmental functional genomic data. Our Data Coordination Center (https://danio-code.zfin.org) combines a total of 1,802 sets of unpublished and reanalysed published genomics data, which we used to improve existing annotations and show its utility in experimental design. We identified over 140,000 cis-regulatory elements in development, including novel classes with distinct features dependent on their activity in time and space. We delineated the distinction between regulatory elements active during zygotic genome activation and those active during organogenesis, identifying new aspects of how they relate to each other. Finally, we matched regulatory elements and epigenomic landscapes between zebrafish and mouse and predict functional relationships between them beyond sequence similarity, extending the utility of zebrafish developmental genomics to mammals.

developmental biology↗