Marks, Debora Susan

18 publications

ICLRW 2025 AI-Guided Data-Scarce Engineering of RfxCas13d to Create a Cell Selection Tool Aviv Spinner, Ayush Noori, Debora Susan Marks, George Church, Lisa Maria Riedmayr

ICML 2025 Protriever: End-to-End Differentiable Protein Homology Search for Fitness Prediction Ruben Weitzman, Peter Mørch Groth, Lood Van Niekerk, Aoi Otani, Yarin Gal, Debora Susan Marks, Pascal Notin

ICLRW 2025 Protriever: End-to-End Differentiable Protein Homology Search for Fitness Prediction Ruben Weitzman, Peter Mørch Groth, Aoi Otani, Debora Susan Marks, Yarin Gal, Pascal Notin

ICLRW 2025 RNAGym: Benchmarks for RNA Fitness and Structure Prediction Rohit Arora, Murphy Angelo, Christian Andrew Choe, Aaron W Kollasch, Fiona Qu, Courtney A. Shearer, Ruben Weitzman, Artem Gazizov, Sarah Gurev, Erik Xie, Debora Susan Marks, Pascal Notin

ICLRW 2025 Residue-Level Text Conditioning for Protein Language Model Mutation Effect Prediction Dan Berenberg, Nate Gruver, Alan Nawzad Amin, Peter Mørch Groth, Leo Chen, Harsh R. Srivastava, Pascal Notin, Debora Susan Marks, Andrew Gordon Wilson, Kyunghyun Cho, Richard Bonneau

ICLRW 2025 Sequence-Based Protein Models for the Prediction of Mutations Across Priority Viruses Sarah Gurev, Noor Youssef, Navami Jain, Debora Susan Marks

NeurIPSW 2024 Alignment-Based and Protein Foundation Models for Viral Evolution, Vaccines and Vectors Sarah Gurev, Noor Youssef, Navami Jain, Debora Susan Marks

ICMLW 2024 Augmenting Evolutionary Models with Structure-Based Retrieval Yining Huang, Zuobai Zhang, Jian Tang, Debora Susan Marks, Pascal Notin

ICLRW 2024 Future-Proof Vaccine Design with a Generative Model of Antibody Cross-Reactivity Sarah Gurev, Noor Youssef, Hannah Rivka Pierce-Hoffman, Debora Susan Marks

ICMLW 2024 Future-Proof Vaccine Design with a Generative Model of Antibody Cross-Reactivity Noor Youssef, Sarah Gurev, Hannah Rivka Pierce-Hoffman, Alexander A Cohen, Luis F Caldera, Pamela J Bjorkman, Debora Susan Marks

ICLRW 2024 How Well Do Generative Protein Models Generate? Han Spinner, Aaron W Kollasch, Debora Susan Marks

ICML 2024 Kernel-Based Evaluation of Conditional Biological Sequence Models Pierre Glaser, Steffanie Paul, Alissa M Hummer, Charlotte Deane, Debora Susan Marks, Alan Nawzad Amin

ICML 2023 A Kernelized Stein Discrepancy for Biological Sequences Alan Nawzad Amin, Eli N Weinstein, Debora Susan Marks

NeurIPSW 2022 Designing Proteins Using Sparse Data Ada Shaw, Jung-Eun Shin, Nicole Nisha Thadani, Alan Nawzad Amin, Debora Susan Marks

NeurIPSW 2022 Designing and Evolving Neuron-Specific Proteases Han Spinner, Colin Hemez, Julia McCreary, David Ruchien Liu, Debora Susan Marks

NeurIPSW 2022 Kernelized Stein Discrepancies for Biological Sequences Alan Nawzad Amin, Eli N Weinstein, Debora Susan Marks

NeurIPSW 2022 TranceptEVE: Combining Family-Specific and Family-Agnostic Models of Protein Sequences for Improved Fitness Prediction Pascal Notin, Lood Van Niekerk, Aaron W Kollasch, Daniel Ritter, Yarin Gal, Debora Susan Marks

NeurIPSW 2022 scPerturb: Information Resource for Harmonized Single-Cell Perturbation Data Tessa Durakis Green, Stefan Peidli, Ciyue Shen, Torsten Gross, Joseph Min, Samuele Garda, Jake P. Taylor-King, Debora Susan Marks, Augustin Luna, Nils Blüthgen, Chris Sander