@ArcInstitute co-founder, @Stanford professor, @ThriveCapital investor | biology and ML research | 🇨🇦 prev @harvard @broadinstitute, Fast Grants
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Articles by Patrick D. Hsu
Predicting cellular responses to perturbation across diverse contexts with State
Keywords machine learning artificial intelligence transcriptomics single-cell RNA sequencing cell biology perturbation gene expression gene regulation systems biology Introduction Accurately predicting the impact of cellular perturbations at scale has the potential to reshape targeted therapies.
Virtual Cell Challenge 2026: Benchmarking zero-shot generalization across cellular contexts
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CommentaryOnline nowOpen access Affiliations & Notes 1Arc Institute, Palo Alto, CA, United States of America 2University of California, San Francisco, San Francisco, CA, United States of America Article Info Publication History: Published online August 26, 2026 DOI: 10.1016/j.cell.2026.08.004 External LinkAlso available on ScienceDirect External Link Copyright: © 2026 The Authors. Published by Elsevier Inc.
By Abhinav Adduri, Dave Burke, Joseph Caputo, Paul Datlinger, Alexander Dobin, Basak Eraslan, Patrick D. Hsu, Ben Hsu, Tony Hua, Julia Kazaks, Silvana Konermann, Dara E. Leto, Reshma Mehta, Usman Muzaffar, Brian Plosky, Chiara Ricci-Tam, Jeremy Sullivan, Michael Teng, Megan van Overbeek, Alden Woodrow, Daniel Serrano Verified, Alexander Atamian, Inna Averbukh, Jerika J. Barron, Beatrice Bevilacqua, Harry Bevir, Steven C. Boggess, Paul Bunk, Christopher Carpenter, Xiaolong Dong, Miles C. Duncan, Kevin CW Feng, Carmen Gallardo, Jesse Holt, Trinh Lam, Trịnh Lâm, NianZhen Li, Victor Li Verified, Gabriella E Martyn, Satoru Miura, Alexander A. Nevue, Charlene Pan, Khushali Patel, Akshaya Rajan, Sneha Rao, Lorena Saavedra, Nerea González, Ipek Tasan, Po-Yuan Tung, Sadie VanHorn, Rishi Verma, Hani Goodarzi, Rachel Senturia, Usha Adhikari, Will Agnew-Svoboda, Valeria Aizen, Dana Al-Azzeh, Yi-Chen Chih, Shawn Chizari, Gabriel Grenot, Malvenderjit Jagjit Singh, Emiliano Josue Hergenreder, Aarushi Kalaimani, David Lara Astiaso, Jonathan Lyda, Sanmati Nagesh, Harris Nami, Kheerthivasan Ramachandran, Ninad Ranadive, Kristen Seim, Tulsi Solanki, Ed Tuan, Tushita Wadhawan, Flora Yi, Nick Youngblut, Jamie Zaikov
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Cell Press
Verified
Memorial Plastic Surgery’s Dr. Patrick Hsu, Among America’s Best Plastic Surgeons in 2026
Houston, TX, August 14, 2026 --(PR.com)-- Memorial Plastic Surgery is proud to announce that Dr. Patrick Hsu, MD, FACS, has once again been recognized among America’s Best Plastic Surgeons by Newsweek. He has earned distinction in three core procedures: Tummy Tuck, Liposuction, and Breast Augmentation.
Structural mechanism governing the directionality of bridge recombination
Abstract Bridge recombinases from the IS110 family of transposons, such as IS621, associate with a bridge RNA (bRNA) to mediate programmable recombination between donor DNA and target DNA1,2. Although insertion is mediated by the recombinase–bRNA complex, it remains unknown how IS621 elements are excised from host genomes to form the circular DNA intermediates required for transposition.
A combinatorial domain screening platform reveals epigenetic effector interactions for transcriptional perturbation
Abstract Epigenetic regulation involves the coordinated interplay of diverse proteins. To systematically explore these combinations, we present COMBINE (combinatorial interaction exploration), a high-throughput platform that tests over 50,000 pairs of epigenetic effector domains up to 2,094 amino acids in length for their ability to modulate endogenous human gene transcription.
Generalist biological artificial intelligence in modeling the language of life
Abstract Generalist biological artificial intelligence (GBAI) represents a transformative approach to modeling the ‘language of life’—the flow of information from DNA to cellular function. This Review synthesizes rapid advances in biological AI to interpret and generate DNA, RNA, proteins and cellular systems. We chart a course toward comprehensive systems that can concurrently process and predict across these domains, performing several critical biological tasks simultaneously.
Genome modelling and design across all domains of life with Evo 2
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Abstract All of life encodes information with DNA. Although tools for genome sequencing, synthesis and editing have transformed biological research, we still lack sufficient understanding of the immense complexity encoded by genomes to predict the effects of many classes of genomic changes or to intelligently compose new biological systems.
By Garyk Brixi, Matthew Durrant, Jerome Ku, Mohsen Naghipourfar, Michael Poli, Gwanggyu Sun, Greg Brockman, Daniel Chang Verified, Alison Fanton, Gabriel Gonzalez, Samuel King, David Li, Aditi Merchant, Eric Nguyen, Chiara Ricci-Tam, David Romero Verified, Jonathan C. Schmok, Ali Taghibakhshi, Anton B. Vorontsov, Brandon Yang, Liv Gorton, Nam Nguyen, Nam Nguyễn, Nicholas Wang, Michael Pearce, Elana Simon, Etowah Adams, Zachary Amador, Euan A. Ashley, Stephen A. Baccus, Haoyu Dai, Steven Dillmann, Stefano Ermon, Daniel Guo, Michael H Herschl, Rajesh Ilango, Amy Lu Verified, Reshma Mehta, Mohammad Mofrad, Madelena Ng, Jaspreet Pannu, Christopher Ré, John St. John, Jeremy Sullivan, Ben Viggiano, Kevin Zhu, Greg Zynda, Patrick Collison, Patrick et John Collison, Anthony Costa, Tina Hernandez-Boussard, Eric Ho, Ming-Yu Liu, Thomas McGrath, Kimberly Powell, Sudarshan Pinglay, Dave Burke Verified, Hani Goodarzi, Patrick D. Hsu, Brian L. Hie, Myra Deng, Ken Janik, Joseph Tey, Daniel Balsam
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Nature
Verified
Virtual Cell Challenge: Toward a Turing test for the virtual cell
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Main text Rapid advances in single-cell technologies and high-throughput perturbational measurements have motivated renewed efforts to model cell behavior quantitatively. These “virtual cells” are expected to learn the relationship between cell state and function and are intended to predict the consequences of perturbations—such as a gene knockdown or the application of a drug—across cell types and cell contexts.
By Yusuf Roohani, Tony Hua, Lexi R. Bounds, Feiqiao B. Yu, Alexander Dobin, Noam Teyssier, Abhinav Adduri, Brian Plosky, Reshma Mehta, Benjamin Hsu, Jeremy Sullivan, Chiara Ricci-Tam, NianZhen Li, Luke A Gilbert, Silvana Konermann, Patrick D. Hsu, Hani Goodarzi, Dave Burke, Po-Yuan Tung, Alden Woodrow, Julia Kazaks
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Cell Press
Verified
How to build the virtual cell with artificial intelligence: Priorities and opportunities
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Keywords cell biology AI ML virtual cell Introduction The cell, the fundamental unit of life, is a wondrously intricate entity with properties and behaviors that challenge the limits of physical and computational modeling. Every cell is a dynamic and adaptive system in which complex behavior emerges from a myriad of molecular interactions. Some aspects are remarkably robust to perturbations, such as the elimination of genes or their replacement with homologs from different species.
By Charlotte Bunne, Yusuf Roohani, Yanay Rosen, Ankit Gupta, Xikun Zhang, Mohammed AlQuraishi, Patricia A. Brennan, Daniel B. Burkhardt, Andrea Califano, Jonah Cool, Abby Dernburg, Amy E. Herr, Eric J Horvitz, Patrick D. Hsu, Viren Jain, Gregory Johnson, Thomas Kalil, David Kelley, Shana O. Kelley, Anna Kreshuk, Tim Mitchison, Stephani Otte, Jay Shendure, Nicholas J Sofroniew, Fabian J. Theis, Christina V. Theodoris, Srigokul Upadhyayula, Bo Wang, Eric Xing, Serena Yeung-Levy, Marinka Zitnik, Theofanis Karaletsos, Aviv Regev, Emma Lundberg, Jure Leskovec, Stephen R. Quake, Marcel Roed, Theo Alexandrov, Kirsty Ewing, Matthias Haury, Marc Valer
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Cell Press
Verified
Sequence modeling and design from molecular to genome scale with Evo
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2 hours ago Here’s a straightforward list, in no certain order, of Mac apps that I’m currently using. Rocket for easy emoji access• Rocket Typist for expanding text snippets• Just Press Record for accessing recordings from iPhone on the Mac• Audio Hijack for recording podcast appearances and recording live …
By Eric Nguyen, Michael Poli, Matthew Durrant, Brian Kang, Dhruva Katrekar, Liam Bartie, Armin Thomas, Samuel King, Garyk Brixi, Jeremy Sullivan, Madelena Ng, Ashley Lewis, Stefano Ermon, Stephen A. Baccus, Tina Hernandez-Boussard, Christopher Ré, Patrick D. Hsu, Brian L. Hie, Aaron Lou, David K. Li Verified
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Flipboard
Structural mechanism of bridge RNA-guided recombination - Nature
Abstract Insertion sequence (IS) elements are the simplest autonomous transposable elements found in prokaryotic genomes1. We recently discovered that IS110 family elements encode a recombinase and a non-coding bridge RNA (bRNA) that confers modular specificity for target DNA and donor DNA through two programmable loops2.
Rethinking Software Pricing in the Era of AI
Jason Mendel, Patrick Hsu | November 15, 2023 Rethinking Software Pricing in the Era of AI This post originally appeared on our Condensing the Cloud Substack, read it in full here. Back To Blog A monthly newsletter to share new ideas, insights and introductions to help entrepreneurs grow their businesses. Subscribe
OpenCloud 2022: How to Navigate Stormy Markets and Other Tips for Cloud Founders
Much has changed since our first OpenCloud four years ago. We’ve lived through a global pandemic, a presidential election, intense geopolitical shifts and, most recently, a glum and inflationary macroeconomic outlook. The consistency and durability of cloud companies, however, have persisted since we first began reporting on the state of the OpenCloud, our term for the convergence of cloud-based infrastructure and open-source software.
Finally, Some Good News for Enterprise-Tech Startups: Battery Ventures Survey Finds Tech Spending Holding Steady, Even Increasing Despite Market Downturn - Battery Ventures
Technology startups of all stripes have been on edge lately as financial markets have whipsawed, and many investors have become more discerning about the companies they fund.
Rapid detection of SARS-CoV-2 RNA in saliva via Cas13 - Nature Biomedical Engineering
Abstract Rapid nucleic acid testing is central to infectious disease surveillance. Here, we report an assay for rapid COVID-19 testing and its implementation in a prototype microfluidic device. The assay, which we named DISCoVER (for diagnostics with coronavirus enzymatic reporting), involves extraction-free sample lysis via shelf-stable and low-cost reagents, multiplexed isothermal RNA amplification followed by T7 transcription, and Cas13-mediated cleavage of a quenched fluorophore.
Genome-wide bidirectional CRISPR screens identify mucins as host factors modulating SARS-CoV-2 infection - Nature Genetics
Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes a range of symptoms in infected individuals, from mild respiratory illness to acute respiratory distress syndrome. A systematic understanding of host factors influencing viral infection is critical to elucidate SARS-CoV-2–host interactions and the progression of Coronavirus disease 2019 (COVID-19).
What We Learned Doing Fast Grants
The COVID-19 pandemic isn’t over and it might yet kill more than ten million people worldwide. From the beginning, the institutional response has been lethargic. While officials (including, regrettably, prominent scientific officeholders) provided public assurances, the U.S. did virtually no surveillance sequencing in January or February, even as outbreaks took hold in China and Italy. The CDC botched the initial diagnostic test.
A plastic surgeon explains the dangers of the Brazilian butt lift
The Brazilian butt lift (BBL) is a procedure that enhances the buttocks through fat transfer. Excess fat is harvested from other areas of the body including the abdomen, hips, lower back and thighs through liposuction. BBL is a popular procedure for those seeking to enhance their bodies. However, with the recent reports of patient deaths from undergoing BBL, many have now labeled it as the most dangerous cosmetic procedure.
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