BoYueGRN: Zero-shot causal discovery of directed gene regulatory networks from single-cell transcriptomes via amortized inference over synthetic structural causal models
BoYueGRN reframes directed GRN inference as a train-once, reuse-across-datasets paradigm, which opens the door to systematic, atlas-scale mapping of regulatory dynamics across human diseases.
Predicting single-gene knockout effects from wild-type single-cell RNA-seq data remains challenging when perturbation experiments are costly and existing approaches require knockout-specific model training. Here we introduce
Topology-Adjusted Knockout
(TAKO), a computationally efficient WT-only framework for single...
Hao Wang, Koji Oba· Frontiers in Bioinformatics· 0 citations
Sequence-to-function (S2F) deep learning models have become an important aid to decipher the genomic cis-regulatory code. However, current S2F models do not take the cellular trans-environment of transcription factors (TF) into account. Conversely, methods for gene regulatory network (GRN) inference often rely on heuri...
Gabriele Partel, Seppe De Winter, Vasilis Konstantakos et al.· bioRxiv· 0 citations
Perturb-seq prediction increasingly relies on either biological graph priors or single-cell foundation models, but their relative value is difficult to interpret when architectures, split definitions and graph sources vary simultaneously. We benchmarked STRING functional associations and Gene Ontology co-annotation aga...
Jie Ni, Xin-Ting Zhang, Ming-Yang Li et al.· Computational biology and ch...· 0 citations
NetMap is presented, a pipeline that jointly infers cell-level GRNs and clusters cells based on shared regulatory programs, combining state-of-the-art single-cell autoencoders and explainable artificial intelligence methods that outperforms existing methods on synthetic data with a known ground-truth GRN and is able to...
A. Hartebrodt, Mhaned Oubounyt, G. D. de Almeida et al.· bioRxiv· 0 citations
Virtual-cell models increasingly learn from large perturbation atlases, but their view of cis regulation remains limited to endogenous genes embedded in broad native regulatory contexts. Here we introduce Therna Biosciences’ Chronos platform and its first public dataset release, comprising two complementary modules of...
Timo Hagen, I. Liu, Ariana Nagainis et al.· bioRxiv· 0 citations
Gene regulatory network inference methods routinely disagree about individual edges, and practitioners resolve those conflicts by choosing one method or averaging them all. We ask whether the conflict can instead be arbitrated per edge. A gradient-boosted classifier is trained on the raw scores that ten inference metho...
I. Kendiukhov· Bio Systems· 0 citations
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