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3 papers · ranked by Valyu relevance

01
BbioRxiv7 Sep 2026
BOTANIC-1: a series of long-context plant genomic foundation models in the agentic era
Amélie Barozet, Vincent Cabeli, Jean Ogier du Terrail, Alexey Rukhovich + 6 more
The development of climate-resilient crops would be greatly accelerated by models able to reason directly over plant genomic sequences and to pinpoint trait-associated regions or loci. Anticipating the impact of DNA base changes (variants) remains challenging, and understanding regulatory mechanisms is still an active…
61relevance
02
BbioRxiv6 Sep 2026
gVCF2CNV: a scalable pipeline for CNV detection from whole-genome sequencing data
Mame Seynabou Diop, Florian Bénitière, Kuldeep Kumar, Benjamin Clark + 5 more
Copy-number variants (CNVs) contribute to human disease and population trait variation. CNV detection from large whole-genome sequencing cohorts remains computationally demanding, as most methods require BAM or CRAM files. Genomic VCF (gVCF) files are smaller, routinely generated by standard variant-calling workflows…
58relevance
03
BbioRxiv8 Sep 2026
scFLAME: a unified generative model for interpretable clustering, hierarchical structure discovery and marker-gene identification in single-cell RNA-seq data
Jackie Rao, Muntadher Jihad, Giulia Biffi, Paul D.W. Kirk
Identifying cell types from single-cell RNA sequencing (scRNA-seq) data typically requires several separate and often uninterpretable steps: dimensionality reduction, batch-correction, clustering, marker-gene identification and the discovery of finer-grained structure. Here we introduce scFLAME (single-cell Factor…
56relevance

Results for Python parallelization

BOTANIC-1: a series of long-context plant genomic foundation models in the agentic era

gVCF2CNV: a scalable pipeline for CNV detection from whole-genome sequencing data

scFLAME: a unified generative model for interpretable clustering, hierarchical structure discovery and marker-gene identification in single-cell RNA-seq data

BOTANIC-1: a series of long-context plant genomic foundation models in the agentic era

gVCF2CNV: a scalable pipeline for CNV detection from whole-genome sequencing data

scFLAME: a unified generative model for interpretable clustering, hierarchical structure discovery and marker-gene identification in single-cell RNA-seq data