L1 · Network-informed inverse design heuristics

Inverse design fidelity

Level 1 · Network-informed inverse design heuristics

Uses source–target comparison and static network influence; still no predicted post-intervention state.

u^{⋆} = ar g u max H (u; G, P_{S}, P_{T})

The level's compact mathematical form.

Methods at this level

11 methods

Sorted by publication year, oldest first.

CellNet

Cahan et al. · 2014 · Cell

Canonical Level 1 method. Reconstructs cell-type-specific GRNs from expression data and prioritizes regulators whose perturbation is expected to restore the target network.

I D T

Code Repro 4/4 FAIR 3/5

Mogrify

Rackham OJ et al. · 2016 · Nature genetics

Transdifferentiation, the process of converting from one cell type to another without going through a pluripotent state, has great promise for regenerative medicine.

Code

SeesawPred

Hartmann A et al. · 2018 · Scientific reports

Cellular differentiation is a complex process where a less specialized cell evolves into a more specialized cell.

Code Repro 4/4 FAIR 1/5

ANANSE

Xu Q et al. · 2021 · Nucleic acids research

Proper cell fate determination is largely orchestrated by complex gene regulatory networks centered around transcription factors.

I T

Code Repro 4/4 FAIR 3/5

Taiji-reprogram

Wang J et al. · 2021 · NAR genomics and bioinformatics

Cellular reprogramming is a promising technology to develop disease models and cell-based therapies.

I T

Code Repro 2/4 FAIR 0/5

TRANSDIRE

Eguchi R et al. · 2022 · Bioinformatics (Oxford, England)

MOTIVATION: Direct reprogramming involves the direct conversion of fully differentiated mature cell types into various other cell types while bypassing an intermediate pluripotent state (e.g. induced pluripotent stem…

Code Repro 3/4 FAIR 1/5

scANANSE

Smits JGA et al. · 2023 · F1000Research

The recent development of single-cell techniques is essential to unravel complex biological systems.

Code Repro 4/4 FAIR 3/5

CANDiT

Sinha S et al. · 2025 · Cell reports. Medicine

Reactivating lineage commitment to differentiate, and hence eliminate, cancer stem cells (CSCs) remains a therapeutic challenge.

Code Repro 2/4 FAIR 0/5

SwitchTFI

Martini P et al. · 2025 · Genome biology

Many methods exist that infer cell differentiation trajectories from single-cell RNA sequencing data, but only few determine which mechanisms drive the inferred differentiation dynamics.

Code Repro 4/4 FAIR 4/5

TRAPT

Zhang G et al. · 2025 · Nature communications

It is challenging to identify regulatory transcriptional regulators (TRs), which control gene expression via regulatory elements and epigenomic signals, in context-specific studies on the onset and progression of…

Code Repro 4/4 FAIR 4/5

Atlas-guided

Chung HK et al. · 2026 · Nature

CD8+ T cells differentiate into diverse states that shape immune outcomes in cancer and chronic infection1-4.

Code Repro 4/4 FAIR 1/5

Other levels

Target-feature discovery

Proxy inverse design

Explicit model-based inverse intervention