Resources
Application
evedesign
Accessible biosequence design with a unified framework.
Hopf et al., bioRxiv (2026)
Benchmark
ProteinGym
Large-scale benchmarks for protein fitness prediction and design.
Notin et al., NeurIPS (2023)
Benchmark
RNAGym
Large-scale benchmarks for RNA fitness and structure prediction.
Arora et al., bioRxiv (2025)
Application
EVcouplings
Predict evolutionary couplings, 3D structures and mutation effects from sequence alignments.
Hopf et al., Bioinformatics (2019)
Code
Marks Lab on GitHub
Source code for the lab’s models, benchmarks and analyses.
MLAB journal club
Machine Learning to Accelerate Biology (MLAB) is our open seminar series. Speakers present statistical and machine learning methods that solve, or could solve, biological problems, from protein design and structure to single-cell, whole-genome modeling and viral evolution. Talks are informal and questions are encouraged.
Join the mailing list Request to present
Past speakers 180
- 10/30/2026Arya Rao, Sabeti & Bhatia Labs
- 10/09/2026Nathaniel Blalock, Romero Lab
- 10/02/2026Jason Yang, Kulik and Jaakkola Labs
- 09/17/2026Sergio Garcia Busto, Marks & Lehner Labs
- 09/04/2026Ethan Eschbach, Marks Lab
- 07/31/2026Jishnu Das & Prabal Chhibbar, University of Pittsburgh, Das Lab
- 06/12/2026Soo-Jeong Kim, University of Cambridge
- 05/22/2026Constantin Ahlmann-Eltze, EMBL & UCL Cancer Institute
- 05/01/2026Maximilian Billmann, University of Bonn
- 04/24/2026David Ross, NIST
- 04/17/2026Amir Hossein Hosseini Akbarnejad and Marta Sallese, Lotfollahi Lab, Sanger Institute
- 04/03/2026Dominic Grisingher, Kortemme Lab, UCSF
- 03/27/2026Andrea Rubbi, Lotfollahi and Lio Labs, Sanger Institute
- 03/20/2026Lars Lorch, ETH Zürich
- 02/20/2026Greg Simond, NDPH - Oxford
- 02/06/2026Sam Sinai, Dyno
- 01/09/2026Sam Tipps, King Lab, University of Washington
- 11/21/2025Jiheum Park, Columbia University
- 11/19/2025Ekin Deniz Aksu, Vingron group - MPI
- 11/14/2025Chris Alexiev, Barzilay Lab, MIT
- 11/07/2025Emma Garcia, Liau Lab, Harvard Medical School
- 10/31/2025Arkadiusz (Arek) Sitek, MGH
- 10/24/2025Gabe Rocklin, Rocklin Lab, Northwestern University
- 10/17/2025Ben Orr, Kaiser Lab, University fo San Francisco
- 10/10/2025Aviv Spinner, The Align Foundation
- 10/03/2025Yu-Chen Cheng, Michor Lab, Dana Farber Institute
- 09/26/2025Jason Nomburg, Doudna Lab, UC Santa Barbara
- 09/12/2025Yuanqing Wang, Chodera Lab, Memorial Sloan Kettering Cancer Center
- 09/05/2025Ruth Johnson, Zitnik Lab, Harvard Medical School
- 08/15/2025Martin Pacesa, École Polytechnique Fédérale de Lausanne, Correia Group
- 08/07/2025Aleksandr N. Medvedev, Genomics AI
- 08/01/2025Yuan-Fei Pan, Fudan University
- 07/23/2025Joshua Pan, Google DeepMind
- 07/18/2025Kelly Brock, The Institute for Experiential AI, Northeastern University
- 06/27/2025Jean-Philippe Julien, University of Toronto & Sickkids Research Institute
- 06/13/2025Dominik Klein, Theis Lab, Helmholtz Munich
- 06/6/2025Charlie Pugh, Dias & Frazer Labs, CRG
- 05/23/2025Emek Demir, Oregon Health & Science University
- 05/16/2025Woody Ahern & Jason Yim, Baker lab & Jaakkola/Barzilay lab
- 05/09/2025Artem Shmatko, DFKZ & EMBL
- 05/02/2025Peter DeWeirdt, MIT, Laub Lab
- 04/25/2025Yu Xie & Jose Salvador Jimenez Luna, Microsoft Research AI for Science
- 04/11/2025Sukhwan Park, Seoul National University, Steinegger Lab
- 04/04/2025Sophie Vincoff, Duke University, Pratterjee Lab
- 03/28/2025Lea Bogensperger, University of Zurich, Krauthammer Lab
- 03/14/2025Ben Fry, Harvard Medical School, Polizzi Lab
- 03/07/2025Jonas Koeppel, University of Washington, Jay Shendure Lab
- 02/28/2025Core Francisco Park, Harvard University, Tanaka Lab
- 02/14/2025Gokul Gowry, Harvard medical School, Peng Yin Lab
- 02/21/2025Armita Nourmohammad, University of Washington
- 02/07/2025David Herreros, Universidad Autonoma de Madrid, CSIC, Carazo and Sorzano Labs
- 01/17/2025Amy Lu, UC Berkeley, Abbeel Lab
- 01/31/2025Maria Carreira, MIT, Davis Lab
- 12/13/2024Christopher Frank, Technische Universität München
- 12/05/2024Willow Coyote-Maestas, UC San Francisco, & Pranam Chatterjee, Duke University
- 11/22/2024Sidney Lisanza, University of Washington, Baker Lab
- 11/15/2024Katharina Waury, Vrije Universiteit Amsterdam
- 11/06/2024Sriram Garg, Max Planck Institute for Terrestrial Microbiology
- 11/01/2024Eli Weinstein, Columbia University, Blei Lab
- 10/25/2024Ziyi Zhou, Shanghai Jiao Tong University
- 10/18/2024Aaron Schmidt, Schmidt Lab
- 10/04/2024Agustinus Kristiadi, The Vector Institute
- 09/27/2024Robert Schmirler, Technical University of Munich
- 09/13/2024Wenhao Wu, University of Michigan
- 09/06/2024Jason Yang, California Institute of Technology, Arnold Group
- 08/30/2024Xiaojing Cong, Institut de Génomique Fonctionnelle
- 08/23/2024Jin Su, Westlake University
- 08/16/2024Sebastian Farquhar, Deepmind (formerly OATML)
- 08/09/2024Kaiyi Jiang, Abudayyeh-Gootenberg Lab
- 08/02/2024Jacob Rapp, Romero Lab
- 07/26/2024Mia Petljak, NYU Grossman Medical School
- 07/12/2024Pablo Gainza, Bruno Correia Lab
- 07/03/2024Alissa Hummer, Charlotte Deane Lab
- 06/14/2024Antoni Beltran Marques, Ben Lehner Lab
- 06/07/2024Nate Bennett, David Baker Lab
- 05/17/2024Jeff Ruffolo, Profluent
- 05/10/2024Kevin Yang, Microsoft Research New England
- 05/03/2024Tristan Bepler, Simons Machine Learning Center
- 04/19/2024Anthony Marchand, Bruno Correia Lab
- 04/26/2024Vikram Sundar and Boqiang Tu, Kevin Esvelt Lab
- 04/12/2024Luhuan Wu, David Blei Lab
- 04/05/2024Hannes Stark, Regina Barzilay Lab
- 03/22/2024Maria Brbic, Brbic Lab, EPFL
- 03/14/2024Weimin Wu, Zhihan Zhou, Han Liu, Northwestern
- 03/08/2024Sven Nelander, Nelander Lab, Uppsala University, Sweden
- 03/01/2024Soojung Yang, Rafael Gomez-Bombarelli Lab
- 02/16/2024Dawn Chen, Fei Chen Lab, Broad
- 02/09/2024Aleksandar Antanasijevic, Antanasijevic Lab, EPFL
- 01/26/2024Julie Forman-Kay, Forman-Kay Lab, University of Toronto
- 01/19/2024Gordon Rix, Chang Liu / Mo Khalil
- 01/12/2024Yuge Ji, Theis Lab, Helmholtz Munich, Munich, Germany
- 01/05/2024Michelle Li, Marinka Zitnik
- 12/15/2023Soojung Yang, Rafael Gomez-Bombarelli Lab
- 10/20/2023Perry Wasdin, Vanderbilt
- 10/06/2023Leonie Stockschläder, Berlin Institute of Health
- 08/25/2023Tobias Hegelund Olsen, Charlotte Dean Lab @ Oxford
- 08/11/2023Pierre Glaser, Arthur Gretton Lab @ UCL
- 07/21/2023Sunny and Annie Eom, Albany High School
- 06/30/2023Bowen Jing, Berger/Jaakkola Lab @ MIT
- 06/23/2023Sepehr Janghorbani, Gerard De Melo Lab @ Rutgers
- 06/16/2023Gonzalo Benegas, Song Lab @ UC Berkeley
- 06/02/2023Vikram Agarwal, @ Sanofi
- 05/26/2023Ellen Shrock, Church Lab @ Harvard Medical School
- 05/19/2023Vaibhav Mohanty, Ard Louis Group @ the University of Oxford
- 05/05/2023Zheming An, Sontag Lab @ Northeastern University
- 01/20/2023CradleBio Team, @ CradleBio
- 01/13/2023Rachapun Rotrattanadumrong, @ Okinawa Institute of Science and Technology
- 01/06/2023Michelle Li, @ Harvard Medical School
- 11/11/2022Dinko Franceschi, Broad Institute @ MIT
- 11/04/2022Feiran Li, @ Chalmers University
- 10/28/2022Alexander Cohen, Bjorkman Lab @ Caltech
- 10/21/2022Alex Li, @UCSF
- 10/14/2022Rachel Petherbridge, Higgin Lab @ MGH
- 09/30/2022Wengong Jin, CSAIL - MIT
- 09/23/2022Ameya Harmalkar; Roshan Rao, Jeffrey Gray Lab @ John Hopkins University
- 09/16/2022Haoran Sun, Hao-Min Zhou Lab
- 09/09/2022Japheth Gado, National Renewable Energy Laboratory
- 09/02/2022Justas Dauparas, Baker Lab @ UW
- 08/19/22Yuge Ji, Institute of Computational Biology @ Helmhotz Center Munich
- 08/12/22Jason Yim and Brian Trippe, @ MIT
- 07/29/22W Schneider, Y Yu, M Kass, Charlie Rice Lab @ The Rockefeller University
- 07/01/22Eeshit Vaishnav, @ MIT
- 06/24/22Hakhamanesh Mostafavi, @ Stanford University
- 06/17/22Martin Jankowiak, Broad Institute @ MIT
- 05/27/22Nick Polizzi, @ Harvard Medical School
- 05/13/22Juannan Zhou, @ University of Florida
- 05/06/22Samuel Stanton, Wilson Lab @ NYU
- 04/29/22A Faure, J Domingo, and J Schmiedel, @ The Center for Genomic Regulation
- 04/15/22Niloy Biswas, @ Harvard University
- 04/08/22Anubhav Sinha, @ MIT
- 03/25/22Karla Ilic Durdic, Weitz Lab @ Harvard University
- 03/18/22Chloe Hsu, @ UC Berkeley
- 03/11/22Marianna Cortese and Kjetil Bjornevik, @ Harvard School of Public Health
- 03/04/22Andrew Giessel, @ Moderna
- 02/11/22Ronen Mukamel, @ Harvard Medical School
- 02/04/22Sergei Kosakovsky-Pond, @ Temple University
- 01/28/22Yosuke Tanigawa, Kellis Lab @ MIT
- 01/21/22Luke O'Connor, Broad Institute @ MIT
- 01/14/22Lucas Janson, @ Harvard University
- 12/03/21Kate Dray, Leonard Lab @ Northwestern University
- 11/19/21Andy Keller, Welling Lab @ University of Amsterdam
- 11/12/21James Xue, Sabeti Lab @ Broad Institute
- 10/22/21Josh Pan, Hahn Lab @ Broad Institute, Dana-Farber Cancer Institute
- 10/15/21Connor Coley, @ MIT
- 9/17/21Luca Sesta, Pagnani Lab @ INFN, Sezione di Torino
- 9/10/21Ali Madani, @ Salesforce Research
- 7/30/21Peter Koo, @ Cold Spring Harbor Laboratory
- 7/23/21Joshua Meier, Facebook AI Research
- 7/2/21Antonio Khalil Moretti, Pe'er Lab @ Columbia University
- 6/25/21Alex Lee, Greene Lab @ UPenn
- 6/18/21Allie Greaney, Bloom Lab @ MIT
- 6/11/21Juan Angel Patiño-Galindo, Rabadan Lab @ Columbia University
- 6/4/21Lorin Crawford, @ Brown University
- 5/21/21Will Grathwohl, Duvenaud Lab @ University of Toronto
- 5/14/21Kaitlin Samocha, Hurles group @ Sanger Institute
- 5/7/21Romain Lopez, Nir Yosef and Michael I. Jordan's lab @ UC Berkeley
- 4/30/21Han Altae-Tran, Feng Zhang lab @ MIT
- 4/23/21Hattie Chung, Regev Lab @ Broad Institute
- 4/16/21Brian Trippe, Jason Ulirsch, Broderick lab, Finucane lab
- 4/9/21Tom Tropea, MIND inititiative collab with Alice Chen-Plotkin
- 3/12/21Anastasios Angelopoulos, Michael I. Jordan lab @ UC Berkeley
- 3/5/21Ellen Zhong, Brian Hie, Berger lab
- 2/19/21Georg Hochberg, Formerly Thornton Lab @ UChicago
- 2/12/21Anshul Kundaje, Kundaje lab @ Stanford
- 2/5/21Eric Wang, Ring lab @ Yale
- 1/29/21D Belanger, D Dohan, A Shanehsazzadeh, @ Google Brain
- 1/15/21Tomasz Kula, Formerly Elledge lab @ Harvard
- 11/20/20Evgenij Fiskin, @ Broad Institute
- 11/6/20Phase separation, In-house
- 10/30/20Yixin Wang, Michael I. Jordan lab @ UC Berkeley
- 10/23/20Yian Ma, @ UC San Diego
- 10/16/20Cedric Huchuan Xia, @ UPenn
- 9/25/20Max Shen, Regev lab @ Broad Institute
- 9/18/20Simon Dujardin and Caitlin Commins, Hyman lab @ Harvard
- 8/26/20Greg McInnes, @ Stanford
- 8/5/20Clara Wong-Fannjiang, Listgarden and Jordan lab @ UC Berkeley
- 7/29/20Karren Yang, Uhler lab @ MIT
- 7/22/20Jason Shepherd, Shepherd lab @ University of Utah
- 6/24/20A Rubinsteyn, B Vincent, C Smith, Rubinsteyn lab @ UNC Chapel Hill
- 6/17/20Martin Kampmann, Ruilin Tian, Kampmann lab @ UC San Francisco
Talks
-
Building and evaluating generative models of biological sequences, from proteins to whole genomes
Eli Weinstein · 2021 · MIA, Broad Institute
-
Estimation and testing with generative nonparametric Bayesian models
Alan Amin · 2021 · MIA, Broad Institute
-
Generative models of antibodies for functionally optimized library design
Jung-Eun (June) Shin · 2021 · MIA, Broad Institute
-
Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning
Jonathan Frazer & Mafalda Dias · 2021 · MIA, Broad Institute
-
EVcouplings: using evolution to determine structure and function
Thomas Hopf & Kelly Brock · 2020
-
Generative models from NLP for sequence data
Aaron Kollasch · 2019 · MIA, Broad Institute
-
Alignment-free models for protein and antibody design
Debora Marks · 2019 · MIA, Broad Institute
-
Learning protein structure with a differentiable simulator
John Ingraham · 2018 · MIA, Broad Institute
-
Generative models of biological sequence families
John Ingraham & Adam Riesselman · 2017 · MIA, Broad Institute
-
Structure and fitness from genomic sequences
Debora Marks · 2017 · MIA, Broad Institute
Earlier resources
- microRNA.orgPredicted microRNA targets and target downregulation scores, with experimentally observed expression patterns.
- Transmembrane protein 3D structuresPredicted structures for alpha-helical transmembrane proteins of unknown structure.
- Brain-expressed protein 3D structuresPredicted 3D structures of brain-expressed proteins.