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. How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities. arXiv, 18 Sep 2024.

Chen C*, Venkatesh MS*, Gómez Ortega J, Mahesh SV, Nandi TN, Madduri RK, Pelka K†, Theodoris CV†#. Quantized multi-task learning for context-specific representations of gene network dynamics. bioRxiv, 16 Aug 2024. (*co-first authors, †co-senior authors, #corresponding author)

Theodoris CV. Perspectives on benchmarking foundation models for network biology. Quantitative Biology, 14 July 2024.

Hao M, Wei L, Yang F, Yao J#, Theodoris CV#, Wang B#, Li X#, Yang G#, Zhang X#. Current opinions on large cellular models. Quantitative Biology, 1 Jul 2024. (#co-corresponding authors)

Wen DJ and Theodoris CV. Interpretable model of CRISPR-Cas9 enzymatic reactions. Nature

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

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

Lynch AW*, Theodoris CV*, Long HW, Brown M, Liu XS, Meyer CA. MIRA: joint regulatory modeling of multimodal expression and chromatin accessibility in single cells. Nat Methods, 06 Sep 2022. (*co-first authors)

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. Network-based screen in iPSC-derived cells reveals therapeutic candidate for heart valve disease. Science, 12 Feb 2021.

Theodoris CV, Mourkioti F, Huang Y, Ranade SS, Liu L, Blau HM, Srivastava D. Long telomeres protect against age-dependent cardiac disease caused by NOTCH1 haploinsufficiency. J Clin Invest, 20 March 2017.

Barruet E, Morales BM, Lwin W, White MP, Theodoris CV, Kim H, Urrutia A, Wong SA, Srivastava D, Hsiao EC. The ACVR1 R206H mutation found in fibrodysplasia ossificans progressiva increases human induced pluripotent stem cell-derived endothelial cell formation and collagen production through BMP-mediated SMAD1/5/8 signaling. Stem Cell Res Ther, 20 Mar 2017.

White MP, Theodoris CV, Liu L, Collins WJ, Blue KW, Lee JH, Meng X, Robbins RC, Ivey KN, Srivastava D. NOTCH1 regulates matrix gla protein and calcification gene networks in human valve endothelium.  J Mol Cell Cardiol, 12 Apr 2015.

Theodoris CV, Li M, White MP, Liu L, He D, Pollard KS, Bruneau BG, Srivastava D. Human disease modeling reveals integrated transcriptional and epigenetic mechanisms of NOTCH1 haploinsufficiency. Cell. 12 Mar 2015.

Smith J, Kraemer E, Liu H, Theodoris CV, Davidson EH. A Spatially Dynamic Cohort of Regulatory Genes in the Endomesodermal Gene Network of the Sea Urchin Embryo. Developmental Biology, 15 Jan 2008.

Smith J, Theodoris CV, Davidson EH. A gene regulatory network subcircuit drives a dynamic pattern of gene expression. Science, 2 Nov 2007.