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ZENODO
Software . 2025
License: CC BY
Data sources: ZENODO
ZENODO
Software . 2025
License: CC BY
Data sources: Datacite
ZENODO
Software . 2025
License: CC BY
Data sources: Datacite
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**DEPRECATED** Borzoi Human Model Predictor (Linder et al. 2025) using the Genomic API for Model Evaluation (GAME) Framework

Authors: Luthra, Ishika; Priyadarshi, Satyam;

**DEPRECATED** Borzoi Human Model Predictor (Linder et al. 2025) using the Genomic API for Model Evaluation (GAME) Framework

Abstract

This record provides a Predictor container for the Borzoi human model (Linder et al. 2025, Nature Genetics). Borzoi is a deep learning model that predicts cell-type and tissue-specific RNA-seq coverage directly from DNA sequence, enabling interpretation of genetic variants across multiple layers of gene regulation, including transcription, splicing, and polyadenylation. It is trained on human RNA-seq data from ENCODE (with 866 datasets across diverse biosamples, including cell lines and adult tissues) and Genotype-Tissue Expression (GTEx) data (with 2-3 replicates for each tissue, processed by the recount3 project). The training dataset also includes epigenomic datasets from the Enformer model, such as CAGE, DNase-seq, ATAC-seq, and ChIP-seq tracks. The Predictor container (borzoi_human_predictor.sif) includes: Predictor script for sequence processing and error handling. Integrated Borzoi model with its dependencies and borzoi-gpu conda environment created using borzoi_gpu_environment.yml. Baskerville and Borzoi packages, installed from local source copies of repositories (as of March 2025), which also contain helper scripts and 4 replicate model weights. Support scripts like: api_preprocessing_utils.py, error_message_functions_updated.py, predictor_help_message.json. NOTE: This container requires a GPU for execution because the Borzoi model relies on TensorFlow's GPU-accelerated operations. Running the container: Ensure Apptainer is intalled in the system the container is intended to run. Always run the Predictor first, so it can listen for incoming connections from Evaluators: apptainer run --containall --nv borzoi_human_predictor.sif HOST_IP HOST_PORT MATCHER_IP MATCHER_PORT Additional information about the GAME framework can be found on GitHub: Genomic API for Model Evaluation Borzoi Human Predictor-specific information, along with a sample Evaluator, can be found within the same repository: Borzoi Predictor Code repository for Borzoi models: Borzoi GitHub Paper can be found here: Linder, J., Srivastava, D., Yuan, H. et al. Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation. Nat Genet 57, 949–961 (2025). https://doi.org/10.1038/s41588-024-02053-6

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
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Average
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