Publications

2026

• Nourreddine S, Doctor Y, Dailamy A, Lee YH, Hansen JN, Chinn R, Forget A, Polacco B, Muralidharan M, Sigaeva A, Sunder S, Pan E, Gao J, Chen JY, Clark T, Parker J, Obernier K, Metallo C, Ideker T, Lundberg E, Krogan N, Mali P. A genome-scale CRISPRi perturbation atlas of human induced pluripotent stem cells. Nat Biotechnol. 2026 Jul 1. doi: 10.1038/s41587-026-03199-w. Epub ahead of print. PMID: 42386990.
• Sun H, Kahnert K, Hansen JN, Leineweber W, Li M, Feng W, Ballllosera F, Axelsson U, Ouyang W, Lundberg E. Generative machine learning unlocks the first proteome-wide image of human cells. bioRxiv [Preprint]. 2026 May 13:2026.03.31.715748. doi: 10.64898/2026.03.31.715748. PMID: 41959450.
• Leineweber W, Tei R, Mäkiniemi A, Ting A, Lundberg E. Technologies to measure and modulate protein subcellular localization. Nat Rev Mol Cell Biol. 2026 Mar 19. doi: 10.1038/s41580-026-00957-1. Epub ahead of print. PMID: 41857183.
• Durant TJS, Lee SJ, Dudgeon S, Knight E, Nelson B, Young HP, Ohno-Machado L, Schulz WL. Quantum Machine Learning and Data Re-Uploading: Evaluation on Benchmark and Laboratory Medicine Datasets. Clinical Chemistry, 2026; hvaf192, doi: 10.1093/clinchem/hvaf192
• Sigaeva A, Hutchings C, Cesnik A, Lilley KS, Lundberg E. Subcellular localization as a driver of protein function. Nat Rev Mol Cell Biol. 2026. doi: 10.1038/s41580-026-00947-3. PMID: 41709002.

2025

• Lee YH, Doctor Y, Zhang Y, Kumar S, Rainaldi J, Pan E, Mali P. Multiplexed Pan Soluble Ligandome Assaying via OASIS. bioRxiv [Preprint]. 2025 Dec 23:2025.12.21.695830. doi: 10.64898/2025.12.21.695830. PMID: 41497589; PMCID: PMC12767521.
• Clayton EW, Rose S, Nebecker C, Novak L, Bensoussan Y, Chen Y, Collins BX, Cordes A, Evans BJ, Ferryman KS, Hurst S, Jiang X, Lee AY, McWeeney S, Parker J, Bélisle-Pipon J-C, Rosenthal E, Yin Z, Yracheta J, Malin BA, for the Bridge2AI Ethics Working Group. Biomedical data repositories require governance for artificial intelligence/machine learning applications at every step. JAMIA Open. 2025; 8(6): ooaf134. doi: 10.1093/jamiaopen/ooaf134.
• Stevens I, Pacia D, Hansen JN, Parker J, Payne-Foster P, Ideker T, Bélisle-Pipon JC, Ravitsky V. Towards the ethical development of functional genomics research. Trends Biotechnol. 2025 Oct 30:S0167-7799(25)00443-3. doi: 10.1016/j.tibtech.2025.10.015. Epub ahead of print. PMID: 41173722.
• Schaffer LV, Jain M, Nasser R, Sharan S, Ideker T. Unifying proteomic technologies with ProteinProjector. Bioinformatics Advances. 2025; vbaf266. doi: 10.1093/bioadv/vbaf266.
• Caufield H, Ghosh S, Kong SW, Parker J, Sheffield N, Patel B, Williams A, Clark T, Munoz-Torres MC. Standards in the Preparation of Biomedical Research Metadata: A Bridge2AI Perspective. arXiv. 2025; arXiv:2509.10432 [q-bio.OT]. doi: 10.48550/arXiv.2509.10432.
• Pacia DM, Stevens I, Ravitsky V, Parker JA, Ideker T, Clark T, Belisle-Pipon J-C. Ethical, Legal, and Social Implications of Functional Genomics Data Generation and Downstream AI Uses: An NIH Bridge2AI Initiative Qualitative Study. Hastings Center Qualitative Brief. Published online July 26, 2025. doi: 10.63293/7H54Rb.k.sj9vyj/YTVP3306.
• Lenkiewicz J, Churas C, Hu M, Qian G, Jain M, Levinson MA, Al Manir S, Qin Y, Fong D, Ono K, Chen J, Gao C, Pratt D, Parker JA, Clark T, Ideker T, Schaffer LV. Cell Mapping Toolkit: an end-to-end pipeline for mapping subcellular organization. Bioinformatics. 2025 Jun 2;41(6):btaf205. doi: 10.1093/bioinformatics/btaf205. PMID: 40489639; PMCID: PMC12161986.
• Rincon J, Pelletier AR, Gilliland D, Wang W, Wang D, Sankar BS, Scott-Sheldon L, Gebreab S, Hersh W, Rashidi P, Baxter S, Schulz W, Ideker T, Bensoussan Y, Boutros PC, Bui AAT, Walsh C, Watson KE, Ping P. Bridge2AI: Building A Cross-disciplinary Curriculum Towards AI-Enhanced Biomedical and Clinical Care. arXiv, 2505.14757. doi: 10.48550/arXiv.2505.14757
• Schaffer LV, Hu M, Qian G, Moon KM, Pal A, Soni N, Latham AP, Pontano-Vaites L, Tsai D, Mattson NM, Licon K, Bachelder R, Cesnik A, Gaur I, Le T, Leineweber W, Palar A, Pulido E, Qin Y, Zhao X, Churas C, Lenkiewicz J, Chen J, Ono K, Pratt D, Zage P, Echeverria I, Sali A, Harper JW, Gygi SP, Foster LJ, Huttlin EL, Lundberg E, Ideker T. Multimodal cell maps as a foundation for structural and functional genomics. Nature. 2025 Apr 9. doi: 10.1038/s41586-025-08878-3. Epub ahead of print. PMID: 40205054.
• Bélisle-Pipon JC, Ravitsky V. Consent Is Dead, Long Live Ethical Oversight: Integrating Ethically Sourced Data into Demonstrated Consent Models. Am J Bioeth. 2025; 25(4):112-115. doi: 10.1080/15265161.2025.2470657. Epub 2025 Apr 7. PMID: 40192687.
• Singhal A, Zhao X, Wall P, So E, Calderini G, Partin A, Koussa N, Vasanthakumari P, Narykov O, Zhu Y, Jones SE, Abbas-Aghababazadeh F, Kadambat Nair S, Bélisle-Pipon JC, Jayaram A, Parker BA, Yeung KT, Griffiths JI, Weil R, Nath A, Haibe-Kains B, Ideker T. The Hallmarks of Predictive Oncology. Cancer Discov. 2025 Feb 7;15(2):271–285. doi: 10.1158/2159-8290.CD-24-0760. PMID: 39760657.
• Xu J, Xie Q, Liu M, Sembay Z, Thaker S, Payne-Foster P, Chen JY, Ding Y. Decoding Patterns of Data Generation Teams for Clinical and Scientific Success: Insights from the Bridge2AI Talent Knowledge Graph. arXiv, 2501.09897. doi: 10.48550/arXiv.2501.09897
• Nasser R, Schaffer LV, Ideker T, Sharan R. An adversarial scheme for integrating multi-modal data on protein function. bioRxiv, 2025.01.16.633332. doi: 10.1101/2025.01.16.633332
• Al Manir S, Levinson MA, Niestroy J, Churas C, Parker JA, Clark T. FAIRSCAPE: An Evolving AI-readiness Framework for Biomedical Research. bioRxiv [Preprint]. 2025 Jan 5:2024.12.23.629818. doi: 10.1101/2024.12.23.629818. PMID: 39763764; PMCID: PMC11703166.
• Stevens I, Pacia D, Bélisle-Pipon J-C, Parker JA, Ideker T, Ravitsky V. The Ethics of Research at the Intersection of Functional Genomics and Artificial Intelligence. Hastings Center Issue Brief. Published online January 2025. doi: 10.63293/7H54Rb.k.sj9vyj/FGYA6097

2024

• Gupta A, Wefers Z, Kahnert K, Hansen JN, Leineweber WD, Cesnik A, Lu D, Axelsson U, Ballllosera Navarro F, Karaletsos T, Lundberg E. SubCell: Vision foundation models for microscopy capture single-cell biology. bioRxiv, 2024.12.06.627299. doi: 10.1101/2024.12.06.627299
• 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. Cell. 2024 Dec 12;187(25):7045–7063. doi: 10.1016/j.cell.2024.11.015. PMID: 39672099.
• Hu M, Alkhairy S, Lee I, Pillich RT, Fong D, Smith K, Bachelder R, Ideker T, Pratt D. Evaluation of large language models for discovery of gene set function. Nat Methods. 2025 Jan;22(1):82–91. doi: 10.1038/s41592-024-02525-x. Epub 2024 Nov 28. PMID: 39609565; PMCID: PMC11725441.
• Clark T, Caufield H, Parker JA, Al Manir S, Amorim E, Eddy J, Gim N, Gow B, Goar W, Haendel M, Hansen JN, Harris N, Hermjakob H, Joachimiak M, Jordan G, Lee IH, McWeeney SK, Nebeker C, Nikolov M, Shaffer J, Sheffield N, Sheynkman G, Stevenson J, Chen JY, Mungall C, Wagner A, Kong SW, Ghosh SS, Patel B, Williams A, Munoz-Torres MC. AI-readiness for Biomedical Data: Bridge2AI Recommendations. bioRxiv [Preprint]. 2024 Nov 24:2024.10.23.619844. doi: 10.1101/2024.10.23.619844. PMID: 39484409; PMCID: PMC11526931.
• Nourreddine S, Doctor Y, Dailamy A, Forget A, Lee YH, Chinn B, Khaliq H, Polacco B, Muralidharan M, Pan E, Zhang Y, Sigaeva A, Hansen JN, Gao J, Parker JA, Obernier K, Clark T, Chen JY, Metallo C, Lundberg E, Ideker T, Krogan N, Mali P. A Perturbation Cell Atlas of Human Induced Pluripotent Stem Cells. bioRxiv [Preprint]. 2024 Nov 4:2024.11.03.621734. doi: 10.1101/2024.11.03.621734. PMID: 39574586; PMCID: PMC11580897.
• Victor G, Bélisle-Pipon JC. Medical AI, Categories of Value Conflict, and Conflict Bypasses. Proceedings of the AAAI/ACM Conference on AI, Ethics, and Society, 7(1), 1482–1489. Published online October 16, 2024. doi: 10.1609/aies.v7i1.31740
• Rhim J, Gallois H, Ravitsky V, Bélisle-Pipon JC. Beyond Consent: The MAMLS in the Room. Am J Bioeth. 2024 Oct;24(10):85–88. doi: 10.1080/15265161.2024.2388737. Epub 2024 Sep 16. PMID: 39283388.
• Pacia DM, Ravitsky V, Hansen JN, Lundberg E, Schulz W, Bélisle-Pipon JC. Early AI Lifecycle Co-Reasoning: Ethics Through Integrated and Diverse Team Science. Am J Bioeth. 2024 Sep;24(9):86–88. doi: 10.1080/15265161.2024.2377106. Epub 2024 Sep 3. PMID: 39226006.
• Nasser R, Schaffer LV, Ideker T, Sharan R. Multi-modal contrastive learning of subcellular organization using DICE. Bioinformatics. 2024 Sep 1;40(Suppl 2):ii105–ii110. doi: 10.1093/bioinformatics/btae387. PMID: 39230695; PMCID: PMC11520230.
• Tong M, Palmer N, Dailamy A, Kumar A, Khaliq H, Han S, Finburgh E, Wing M, Hong C, Xiang Y, Miyasaki K, Portell A, Rainaldi J, Suhardjo A, Nourreddine S, Chew WL, Kwon EJ, Mali P. Robust genome and cell engineering via in vitro and in situ circularized RNAs. Nat Biomed Eng. 2025 Jan;9(1):109–126. doi: 10.1038/s41551-024-01245-z. Epub 2024 Aug 26. PMID: 39187662.
• Al Abir F, Chen JY. Mondrian Abstraction and Language Model Embeddings for Differential Pathway Analysis. bioRxiv [Preprint]. 2024 Aug 19:2024.04.11.589093. doi: 10.1101/2024.04.11.589093. PMID: 38659966; PMCID: PMC11042185.
• Cesnik A, Schaffer LV, Gaur I, Jain M, Ideker T, Lundberg E. Mapping the Multiscale Proteomic Organization of Cellular and Disease Phenotypes. Annu Rev Biomed Data Sci. 2024 Aug;7(1):369–389. doi: 10.1146/annurev-biodatasci-102423-113534. Epub 2024 Jul 24. PMID: 38748859; PMCID: PMC11343683.
• Durant TJS, Knight E, Nelson B, Dudgeon S, Lee SJ, Walliman D, Young HP, Ohno-Machado L, Schulz WL. A primer for quantum computing and its applications to healthcare and biomedical research. J Am Med Inform Assoc. 2024 Aug 1;31(8):1774–1784. doi: 10.1093/jamia/ocae149. PMID: 38934288; PMCID: PMC11258415.
• Ozturk K, Panwala R, Sheen J, Ford K, Payne N, Zhang DE, Hutter S, Haferlach T, Ideker T, Mali P, Carter H. Interface-guided phenotyping of coding variants in the transcription factor RUNX1 with SEUSS. Cell Rep. 2024 Jul 23;43(7):114436. doi: 10.1016/j.celrep.2024.114436. PMID: 37577681; PMCID: PMC10418284.
• Clark T, Parker J, Schaffer L, Obernier K, Al Manir S, Churas CP, Dailamy A, Doctor Y, Forget A, Hansen JN, Hu M, Lenkiewicz J, Levinson MA, Marquez C, Nourreddine S, Niestroy J, Pratt D, Qian G, Thaker S, Bélisle-Pipon JC, Brandt C, Chen J, Ding Y, Fodeh S, Krogan N, Lundberg E, Mali P, Payne-Foster P, Ratcliffe S, Ravitsky V, Sali A, Schulz W, Ideker T. Cell Maps for Artificial Intelligence: AI-Ready Maps of Human Cell Architecture from Disease-Relevant Cell Lines. bioRxiv [Preprint]. 2024 May 24:2024.05.21.589311. doi: 10.1101/2024.05.21.589311. PMID: 38826258; PMCID: PMC11142054.
• Victor G, Barbu A, Bélisle-Pipon JC. Moral Values in Medical AI: A Scoping Review. Research Square [preprint]. Published online May 16, 2024. doi: 10.21203/rs.3.rs-4391239/v1
• Hsu CY, Cox K, Xu J, Tan Z, Zhai T, Hu M, Pratt D, Chen T, Hu Z, Ding Y. Thought Graph: Generating Thought Process for Biological Reasoning. In Companion Proceedings of the ACM on Web Conference 2024 (pp. 537–540). Published online May 13, 2024. doi: 10.1145/3589335.3651572
• Hu M, Zhang X, Latham A, Šali A, Ideker T, Lundberg E. Tools for assembling the cell: Towards the era of cell structural bioinformatics. Pac Symp Biocomput. 2024;29:661–665. PMID: 38160316.

2023

• Victor G, Bélisle-Pipon JC, Ravitsky V. Generative AI, Specific Moral Values: A Closer Look at ChatGPT’s New Ethical Implications for Medical AI. Am J Bioeth. 2023 Oct;23(10):65–68. doi: 10.1080/15265161.2023.2250311. Epub 2023 Oct 9. PMID: 37812098; PMCID: PMC10575680.
• Brisson J, Bélisle-Pipon JC, Ravitsky V. Investigating the Influence of Artificial Intelligence on Adolescent Health: An Urgent Call to Action. J Adolesc Health. 2023 Oct;73(4):795. doi: 10.1016/j.jadohealth.2023.06.002. PMID: 37716717.
• Kumar A, He S, Mali P. Systematic discovery of transcription factors that improve hPSC-derived cardiomyocyte maturation via temporal analysis of bioengineered cardiac tissues. APL Bioeng. 2023 May 25;7(2):026109. doi: 10.1063/5.0137458. PMID: 37252678; PMCID: PMC10219684.
• Kratz A, Kim M, Kelly MR, Zheng F, Koczor CA, Li J, Ono K, Qin Y, Churas C, Chen J, Pillich RT, Park J, Modak M, Collier R, Licon K, Pratt D, Sobol RW, Krogan NJ, Ideker T. A multi-scale map of protein assemblies in the DNA damage response. Cell Syst. 2023 Jun 21;14(6):447–463.e8. doi: 10.1016/j.cels.2023.04.007. Epub 2023 May 22. PMID: 37220749; PMCID: PMC10330685.
• Ford K, Munson BP, Fong SH, Panwala R, Chu WK, Rainaldi J, Plongthongkum N, Arunachalam V, Kostrowicki J, Meluzzi D, Kreisberg JF, Jensen-Pergakes K, VanArsdale T, Paul T, Tamayo P, Zhang K, Bienkowska J, Mali P, Ideker T. Multimodal perturbation analyses of cyclin-dependent kinases reveal a network of synthetic lethalities associated with cell-cycle regulation and transcriptional regulation. Sci Rep. 2023 May 11;13(1):7678. doi: 10.1038/s41598-023-33329-2. PMID: 37169829; PMCID: PMC10175263.
• Booth BJ, Nourreddine S, Katrekar D, Savva Y, Bose D, Long TJ, Huss DJ, Mali P. RNA editing: Expanding the potential of RNA therapeutics. Mol Ther. 2023 Jun 7;31(6):1533–1549. doi: 10.1016/j.ymthe.2023.01.005. Epub 2023 Jan 7. PMID: 36620962; PMCID: PMC9824937.

2022

• Le T, Winsnes CF, Axelsson U, Xu H, Mohanakrishnan Kaimal J, Mahdessian D, Dai S, Makarov IS, Ostankovich V, Xu Y, Benhamou E, Henkel C, Solovyev RA, Banić N, Bošnjak V, Bošnjak A, Miličević A, Ouyang W, Lundberg E. Analysis of the Human Protein Atlas Weakly Supervised Single-Cell Classification competition. Nat Methods. 2022 Oct;19(10):1221–1229. doi: 10.1038/s41592-022-01606-z. Epub 2022 Sep 29. PMID: 36175767; PMCID: PMC9550622.