Publications

Alpha protein kinase 3 gene therapy restores heart function in mouse and human models of cardiomyopathy

McNamara JW, Keen EB, Sutton R, She Y, Huckstep H, Le LHH, Mehdiabadi NR, Venkatesh MS, Griffen B, Mills RJ, Theodoris CV, Hudson JE, Titmarsh DM, Humphrey SJ, Porrello ER, Elliott DA

Nature Cardiovascular Research, 19 Aug 2026

The Landscape of Single-Cell Foundation Models: Design Principles, Applications, and Open Challenges

Jiang S*, Fang Z*, Zhang Y, Zhang X, Kalfon J, Wang W, Fu X, Patel A, Rizvi S, Lu YR, He S, Wang Y, Ying K, Pao-Huang P, Lu Y, Xu W, Wang M, Miao Z, Lin J, Ding J, Wang ZJ, Ouyang W, Chen T, Yu G, Li M, Ma J, Wang F, Xie Y, Tang J, Rabadan R, van Dijk D, Xie P, He P, Fox EB, Song L, Theis FJ, Xing E, Theodoris CV#, Qiu X#, Ding J#

Preprints.org, 18 Aug 2026 (*co-first authors, #co-corresponding authors) (Review)

Senescent microglia with shortened telomeres secrete soluble DLK1 to induce aging-associated hypomyelination and neuronal dysfunction

Liu B, Mahoney M, Feng Y, Telpoukhovskaia M, Giani AM, Torres ER, Zhan L, Ye P, Zhu J, Foxe NR, Zhu D, Tong X, Srivastava D, Theodoris CV, Gong S, Zhao M, Fan L, Gan L

Neuron, 11 Aug 2026

Agentic Laboratories of the Future: Towards World Models for Scientific Discovery

Fu K, Lyu L, Li S, Huang S, Xu S, Zheng J, Liu X, Liu S, Barbone G, Liu Y, Fan LJ, Zhu Y, Davis M, Jiang K, Yang S, Kuang X, Luo Y, Dominici F, Curtis C, Qiu X, Abadie A, Uhler C, Tang M, Wu JC, Li J, Toettcher J, Avalos JL, Rojansky R, Zhao H, Ioannidis JPA, Rand B, Lundberg E, Rosen AS, Liu Z, Kelley S, Xiong C, Engelhardt BE, Montine T, Theodoris CV, Pollard KS, Li F, Zhang X, Peng T, Basov D, Qian X, Xing E, Yazdani A, Leskovec J, Shah N, Bao Z, Perona P, Wu S, Brangwynne C, Cong L, Wang M

Preprints.org, 4 Aug 2026 (Perspective)

A male infant with a novel heterogeneous nuclear ribonucleoprotein H1 variant, bilateral cataracts, dysplastic thumbs, and severe airway malacia

Thakral A, Theodoris CV, Wallerstein R

Clinical Dysmorphology, 1 July 2026

Proteomics Uncovers Cryptic JPH2 Loss in Paediatric Dilated Cardiomyopathy

Smith-Diaz CC, Iaprintsev V, Huckstep H, Macciocca IM, Piers AT, Henden N, Bryen S, Stewart N, Butters A, Baker AM, Catto L, Kemp L, King I, Le LHH, Elliott DA, Watt KI, Mathew J, Justo R, Richardson E, Simons C, Landstrom AP, Theodoris CV, Deveson IW, MacArthur DG, Konstantinov IE, Weintraub RG, Porrello ER, Humphrey SJ, Ingles J

medRxiv, 17 Jun 2026

Discovery of candidate therapeutic targets with Geneformer

Zhang Y, Venkatesh MS, and Theodoris CV

Nature Protocols, 23 Apr 2026

Temporal AI model predicts drivers of cell state trajectories across human aging

Gómez Ortega J*, Nadadur RD*, Kunitomi A, Kothen-Hill S, Wagner JUG, Kurtoglu SD, Kim B, Reid MM, Lu T, Washizu K, Zanders L, Chen H, Zhang Y, Ancheta S, Lichtarge S, Johnson WA, Thompson C, Phan DM, Combes AJ, Yang AC, Tadimeti N, Dimmeler S, Yamanaka S, Alexanian M#, Theodoris CV#

bioRxiv, 1 Apr 2026 (*co-first authors, #co-corresponding authors)

Scaling and quantization of large-scale foundation model enables resource-efficient predictions in network biology

Chen C*, Venkatesh MS*, Gómez Ortega J, Mahesh SV, Nandi TN, Madduri RK, Pelka K†, Theodoris CV†#

Nature Computational Science, 27 Mar 2026 (*co-first authors, †co-senior authors, #corresponding author)

Interpolating perturbations across contexts

Chen H and Theodoris CV

Nature Computational Science, 15 Oct 2025 (News & Views)

Precision medicine: Crossing the biomedical scales with AI

Israni S, Bader GD, Baranzini SE, Capra JA, Sirota M, Theodoris CV, and Ye CJ

The Journal of Precision Medicine: Health and Disease, 18 June 2025 (Perspective)

AI learns from chromatin data to uncover gene interactions

Brozek A and Theodoris CV

Nature, 8 Jan 2025 (News & Views)

How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities

Bunne C, Roohani Y, Rosen Y, Gupta A, Zhang X, Roed M, Alexandrov T, AlQuraishi M, Brennan P, Burkhardt DB, Califano A, Cool J, Dernburg AF, Ewing K, Fox EB, Haury M, Herr AE, Horvitz E, Hsu PD, Jain V, Johnson GR, Kalil T, Kelley DR, Kelley SO, Kreshuk A, Mitchison T, Otte S, Shendure J, Sofroniew NJ, Theis F, Theodoris CV, Upadhyayula S, Valer M, Wang B, Xing E, Yeung-Levy S, Zitnik M, Karaletsos T, Regev A, Lundberg E, Leskovec J, Quake SR

Cell, 12 Dec 2024 (Perspective)

Learning the language of DNA

Theodoris CV

Science, 14 Nov 2024 (News & Views)

Perspectives on benchmarking foundation models for network biology

Theodoris CV

Quantitative Biology, 14 July 2024 (Perspective)

Current opinions on large cellular models

Hao M, Wei L, Yang F, Yao J#, Theodoris CV#, Wang B#, Li X#, Yang G#, Zhang X#

Quantitative Biology, 1 Jul 2024 (#co-corresponding authors) (Perspective)

Interpretable model of CRISPR-Cas9 enzymatic reactions

Wen DJ and Theodoris CV

Nature Computational Science, 14 Dec 2023 (News & Views)

Race, Ethnicity, and Ancestry in Clinical Pathways: A Framework for Evaluation

Rosen RH, Epee-Bounya A, Curran D, Chung S, Hoffman R, Lee L, Marcus C, Mateo C, Miller J, Nereim C, Silberholz E, Shah S, Theodoris CV, Wardell H, Winn A, Toomey S, Finkelstein JA, Ward V, Starmer A

Pediatrics, 1 Dec 2023

Theodoris CV#, Xiao L, Chopra A, Chaffin MD, Al Sayed ZR, Hill MC, Mantineo H, Brydon EM, Zeng Z, Liu XS, Ellinor PT#

Transfer learning enables predictions in network biology

Nature, 31 May 2023 (#co-corresponding authors)

MIRA: joint regulatory modeling of multimodal expression and chromatin accessibility in single cells

Lynch AW*, Theodoris CV*, Long HW, Brown M, Liu XS, Meyer CA

Nature Methods, 06 Sep 2022 (*co-first authors)

Network-based screen in iPSC-derived cells reveals therapeutic candidate for heart valve disease

Theodoris CV, Zhou P, Liu L, Zhang Y, Nishino T, Huang Y, Kostina A, Ranade SS, Gifford CA, Uspenskiy V, Malashicheva A, Ding S, Srivastava D

Science, 12 Feb 2021

Long telomeres protect against age-dependent cardiac disease caused by NOTCH1 haploinsufficiency

Theodoris CV, Mourkioti F, Huang Y, Ranade SS, Liu L, Blau HM, Srivastava D