# CisTransCell: Single-Cell Perturbation Prediction via Gene Function, Regulatory Control, and Cellular Context

arXiv: https://arxiv.org/abs/2606.13713 · HTML: https://mlsanity.com/paper/2606.13713/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 2 of its 8 references that are in the map.
- First posted on arXiv 10 Jun 2026.

## Builds on (most cited first, 2 of 2)

- [DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome](https://mlsanity.com/paper/2306.15006/) (2023)
- [PRESCRIBE: Predicting Single-Cell Responses with Bayesian Estimation](https://mlsanity.com/paper/2510.07964/) (2025)

## Built on by (most cited first, 1 of 1)

- [Modeling Cell-Cycle-Aware Single-Cell Drug Perturbation Responses](https://mlsanity.com/paper/2606.30695/) (2026)

## Abstract (arXiv)

Predicting cellular transcriptional responses to genetic perturbations is a central problem in single-cell biology, especially in the zero-shot setting where the perturbed gene or gene combination is unseen during training. A major difficulty is that perturbation effects are not determined by expression state alone: they depend on how the perturbed gene product influences other genes and proteins, how those downstream factors act on cis-regulatory elements, and which regulatory programs are active in the current cell state. To better capture this biological complexity, we propose CisTransCell, a cell-conditioned multi-modal framework for single-cell perturbation prediction that augments each gene with two complementary priors: a regulatory-sequence prior that captures how the gene is controlled, and a coding-sequence prior that captures what the gene product does. By integrating these priors with cellular expression state, CisTransCell models perturbation response as a cascade from gene function to regulatory control to downstream transcriptional change. Experiments on benchmark single-cell perturbation datasets show that CisTransCell achieves strong performance in zero-shot perturbation prediction.