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Recent advances in machine learning and large-scale biological data collections have revived the prospect of building a virtual cell, a computational model of cellular behavior that could accelerate biological discovery.
Reciprocal rank fusion outperforms condorcet and individual rank learning methods
Gordon V Cormack, Charles LA Clarke, and Stefan Buettcher · 2009
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A theoretical analysis of ndcg type ranking measures
Yining Wang, Liwei Wang, Yuanzhi Li, Di He, and Tie-Yan Liu · 2013
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Genetic screens in human cells using the crispr-cas9 system
Tim Wang, Jenny J Wei, David M Sabatini, and Eric S Lander · 2014
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Deep sets
Manzil Zaheer, Satwik Kottur, Siamak Ravanbakhsh, Barnabas Poczos, Russ R Salakhutdinov, and Alexander J Smola · 2017
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The biogrid database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions
Rose Oughtred, Jennifer Rust, Christie Chang, Bobby-Joe Breitkreutz, Chris Stark, Andrew Willems, Lorrie Boucher, Genie Leung, Nadine Kolas, Frederick Zhang, et al · 2021
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Mapping information-rich genotype-phenotype landscapes with genome-scale perturb-seq
Joseph M Replogle, Reuben A Saunders, Angela N Pogson, Jeffrey A Hussmann, Alexander Lenail, Alina Guna, Lauren Mascibroda, Eric J Wagner, Karen Adelman, Gila Lithwick-Yanai, et al · 2022
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Phenotypic drug discovery: recent successes, lessons learned and new directions
Fabien Vincent, Arsenio Nueda, Jonathan Lee, Monica Schenone, Marco Prunotto, and Mark Mercola · 2022
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Rxrx1: A dataset for evaluating experimental batch correction methods
Maciej Sypetkowski, Morteza Rezanejad, Saber Saberian, Oren Kraus, John Urbanik, James Taylor, Ben Mabey, Mason Victors, Jason Yosinski, Alborz Rezazadeh Sereshkeh, et al · 2023
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How to build the virtual cell with artificial intelligence: Priorities and opportunities
Charlotte Bunne, Yusuf Roohani, Yanay Rosen, Ankit Gupta, Xikun Zhang, Marcel Roed, Theo Alexandrov, Mohammed AlQuraishi, Patricia Brennan, Daniel B Burkhardt, et al · 2024
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scgpt: toward building a foundation model for single-cell multi-omics using generative ai
Haotian Cui, Chloe Wang, Hassaan Maan, Kuan Pang, Fengning Luo, Nan Duan, and Bo Wang · 2024
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scperturb: harmonized single-cell perturbation data
Stefan Peidli, Tessa D Green, Ciyue Shen, Torsten Gross, Joseph Min, Samuele Garda, Bo Yuan, Linus J Schumacher, Jake P Taylor-King, Debora S Marks, et al · 2024
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Disentanglement of single-cell data with biolord
Zoe Piran, Niv Cohen, Yedid Hoshen, and Mor Nitzan · 2024
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Gpqa: A graduate-level google-proof q&a benchmark
David Rein, Betty Li Hou, Asa Cooper Stickland, Jackson Petty, Richard Yuanzhe Pang, Julien Dirani, Julian Michael, and Samuel R Bowman · 2024
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Predicting transcriptional outcomes of novel multigene perturbations with gears
Yusuf Roohani, Kexin Huang, and Jure Leskovec · 2024
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Deepseekmath: Pushing the limits of mathematical reasoning in open language models
Zhihong Shao, Peiyi Wang, Qihao Zhu, Runxin Xu, Junxiao Song, Xiao Bi, Haowei Zhang, Mingchuan Zhang, YK Li, Yang Wu, et al · 2024
Cited alongside, same era.
Perturbench: Benchmarking machine learning models for cellular perturbation analysis
Yan Wu, Esther Wershof, Sebastian M Schmon, Marcel Nassar, Błażej Osiński, Ridvan Eksi, Zichao Yan, Rory Stark, Kun Zhang, and Thore Graepel · 2024
Cited alongside, same era.
gpt-oss-120b & gpt-oss-20b model card
Sandhini Agarwal, Lama Ahmad, Jason Ai, Sam Altman, Andy Applebaum, Edwin Arbus, Rahul K Arora, Yu Bai, Bowen Baker, Haiming Bao, et al · 2025
Cited alongside, same era.
Gepa: Reflective prompt evolution can outperform reinforcement learning
Lakshya A Agrawal, Shangyin Tan, Dilara Soylu, Noah Ziems, Rishi Khare, Krista Opsahl-Ong, Arnav Singhvi, Herumb Shandilya, Michael J Ryan, Meng Jiang, et al · 2025
Cited alongside, same era.
Virtual cell challenge: Toward a turing test for the virtual cell
Yusuf H Roohani, Tony J Hua, Po-Yuan Tung, Lexi R Bounds, Feiqiao B Yu, Alexander Dobin, Noam Teyssier, Abhinav Adduri, Alden Woodrow, Brian S Plosky, et al · 2025
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Openevolve: an open-source evolutionary coding agent, 2025
Asankhaya Sharma · 2025
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Aaditya Singh, Adam Fry, Adam Perelman, Adam Tart, Adi Ganesh, Ahmed El-Kishky, Aidan McLaughlin, Aiden Low, AJ Ostrow, Akhila Ananthram, et al · 2025
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Virtual crispr: Can llms predict crispr screen results?
Steven Song, Abdalla Abdrabou, Asmita Dabholkar, Kastan Day, Pavan Dharmoju, Jason Perera, Volodymyr Kindratenko, and Aly Khan · 2025
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Contextualizing biological perturbation experiments through language
Menghua Wu, Russell Littman, Jacob Levine, Lin Qiu, Tommaso Biancalani, David Richmond, and Jan-Christian Huetter · 2025
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Systematic discovery of crispr-boosted car t cell immunotherapies
Paul Datlinger, Eugenia V Pankevich, Cosmas D Arnold, Nicole Pranckevicius, Jenny Lin, Daria Romanovskaia, Moritz Schaefer, Francesco Piras, Anne-Christine Orts, Amelie Nemc, et al · 2025
Cited alongside, same era.
A new era of intelligence with gemini 3, Nov 2025
Google · 2025
Cited alongside, same era.
Biomni: A general-purpose biomedical ai agent
Kexin Huang, Serena Zhang, Hanchen Wang, Yuanhao Qu, Yingzhou Lu, Yusuf Roohani, Ryan Li, Lin Qiu, Gavin Li, Junze Zhang, et al · 2025
Cited alongside, same era.
Benchmarking large language models on multiple tasks in bioinformatics nlp with prompting
Jiyue Jiang, Pengan Chen, Jiuming Wang, Dongchen He, Ziqin Wei, Liang Hong, Licheng Zong, Sheng Wang, Qinze Yu, Zixian Ma, et al · 2025
Cited alongside, same era.
Virus-like particles enable targeted gene engineering and pooled crispr screening in primary human myeloid cells
Hyuncheol Jung, Pascal Devant, Carter Ching, Mineto Ota, Jennifer Hamilton, Zachary Steinhart, Wayne Ngo, Luis Sandoval, Jae Hyung Jung, Da Xu, et al · 2025
Cited alongside, same era.
Gene-embedding-based prediction and functional evaluation of perturbation expression responses with presage
Russell Littman, Jacob Levine, Sepideh Maleki, Yongju Lee, Vladimir Ermakov, Lin Qiu, Alexander Wu, Kexin Huang, Romain Lopez, Gabriele Scalia, et al · 2025
Cited alongside, same era.
Bixbench: a comprehensive benchmark for llm-based agents in computational biology
Ludovico Mitchener, Jon M Laurent, Alex Andonian, Benjamin Tenmann, Siddharth Narayanan, Geemi P Wellawatte, Andrew White, Lorenzo Sani, and Samuel G Rodriques · 2025
Cited alongside, same era.
Alphaevolve: A coding agent for scientific and algorithmic discovery
Alexander Novikov, Ngân Vũ, Marvin Eisenberger, Emilien Dupont, Po-Sen Huang, Adam Zsolt Wagner, Sergey Shirobokov, Borislav Kozlovskii, Francisco JR Ruiz, Abbas Mehrabian, et al · 2025
Cited alongside, same era.
Later among the works it cites.
scbasecount: an ai agent-curated, uniformly processed, and continually expanding single cell data repository
Nicholas D Youngblut, Christopher Carpenter, Jaanak Prashar, Chiara Ricci-Tam, Rajesh Ilango, Noam Teyssier, Silvana Konermann, Patrick D Hsu, Alexander Dobin, David P Burke, et al · 2025
Later among the works it cites.
Genome-scale perturb-seq in primary human cd4+ t cells maps context-specific regulators of t cell programs and human immune traits
Ronghui Zhu, Emma Dann, Jun Yan, Justine Reyes Retana, Ryunosuke Goto, Reese C Guitche, Lillian K Petersen, Mineto Ota, Jonathan K Pritchard, and Alexander Marson · 2025
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Genome-wide single-cell perturbation screens with viperturb-seq
Alexandra Bradu, John D Blair, Isabella N Grabski, Isabella Mascio, Junsuk Lee, Cecilia McCormick, and Rahul Satija · 2026
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Rational design of synthetic proteins using a genome-scale crispr screen
Wells H Burrell, Simon J Mueller, Zharko Daniloski, P Duffy Doyle Jr, Anne B Rovsing, Christopher James, Max Drabkin, Chien-Yu Chou, Hei Yu Annika So, Lyla Katgara, et al · 2026
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Incompressible knowledge probes: Estimating black-box llm parameter counts via factual capacity
Bojie Li · 2026
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Qwen3.5: Towards native multimodal agents, February 2026
Qwen Team · 2026
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Scaling large language models for next-generation single-cell analysis
Syed Asad Rizvi, Daniel Levine, Aakash Patel, Shiyang Zhang, Eric Wang, Curtis Jamison Perry, Ivan Vrkic, Nicole Mayerli Constante, Zirui Fu, Sizhuang He, et al · 2026
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Glm-5: from vibe coding to agentic engineering
Aohan Zeng, Xin Lv, Zhenyu Hou, Zhengxiao Du, Qinkai Zheng, Bin Chen, Da Yin, Chendi Ge, Chengxing Xie, Cunxiang Wang, et al · 2026
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