Author

Jonathan Li

Arsenal Biosciences (United States)ORCID 0000-0003-0782-2077Unclaimed ORCID profile · follow to get notified of new preprints

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Jonathan Li1 paper

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Bioinformatics· 1 Systems Biology· 1

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Research Focus:benchmarking· 2 Assay:bulk RNA-seq· 1 Approach:contrastive learning· 1 Approach:deep learning· 1 Assay:DNA methylation· 1 Approach:experimental assay· 1 Organism:human· 1 Research Focus:perturbation response prediction· 1

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Aaron R. CooperiD· 1 shared Adam Barner· 1 shared Ajay PillaiiD· 1 shared Albert Lee· 1 shared Alexandra B. London· 1 shared Allyson J. MerrelliD· 1 shared Amaro N Taylor-WeineriD· 1 shared Andrea Fua· 1 shared

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2022-2025 · peak 1/yr

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10 top collaborators · 24 mutual co-author links

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Aaron R. CooperORCID

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2 papers

Recent·Most cited

BioinformaticsbioRxivPreprintDec 19, 2025

DINOcell: Learning Generalizable Perturbation Effects through Self-Distillation

Jonathan Li, Nilgun Tasdemir, Sofia Kyriazopoulou-Panagiotopoulou…·Amaro N Taylor-Weiner

DINOcell predicts cellular responses to perturbations using self-distillation in single-cell transcriptomics, outperforming baselines for single and combination gene effects.

DOI 10.64898/2025.12.16.694747

scRNA-seqdeep learning

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Systems BiologyCommunications BiologyPeer-reviewedOct 7, 2022

A LINCS microenvironment perturbation resource for integrative assessment of ligand-mediated molecular and phenotypic responses

Sean M. Gross, Mark A. Dane, Rebecca Lee Smith…·Laura M. Heiser

The paper presents a LINCS Microenvironment perturbation dataset cataloging transcriptional, proteomic, epigenomic, and phenotypic responses of MCF10A cells to six ligands, enabling integrative analysis of molecular and phenotypic changes.

35 citations

humanbulk RNA-seq

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