Debora S. Marks

Publication Activity (10 Years)

Years Active: 2007-2023
Publications (10 Years): 13

Top Topics

Scientific Discovery

Amino Acid Residues

Top Venues

PLoS Comput. Biol.

Publications

Hanchen Wang, Tianfan Fu, Yuanqi Du, Wenhao Gao, Kexin Huang, Ziming Liu, Payal Chandak, Shengchao Liu, Peter Van Katwyk, Andreea Deac, Anima Anandkumar, Karianne Bergen, Carla P. Gomes, Shirley Ho, Pushmeet Kohli, Joan Lasenby, Jure Leskovec, Tie-Yan Liu, Arjun Manrai, Debora S. Marks, Bharath Ramsundar, Le Song, Jimeng Sun, Jian Tang, Petar Velickovic, Max Welling, Linfeng Zhang, Connor W. Coley, Yoshua Bengio, Marinka Zitnik
Scientific discovery in the age of artificial intelligence. Nat. 620 (7972) (2023)
Pascal Notin, Aaron Kollasch, Daniel Ritter, Lood van Niekerk, Steffanie Paul, Han Spinner, Nathan J. Rollins, Ada Shaw, Rose Orenbuch, Ruben Weitzman, Jonathan Frazer, Mafalda Dias, Dinko Franceschi, Yarin Gal, Debora S. Marks
ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design. NeurIPS (2023)
Pascal Notin, Ruben Weitzman, Debora S. Marks, Yarin Gal
ProteinNPT: Improving protein property prediction and design with non-parametric transformers. NeurIPS (2023)
Pascal Notin, Mafalda Dias, Jonathan Frazer, Javier Marchena-Hurtado, Aidan N. Gomez, Debora S. Marks, Yarin Gal
Tranception: Protein Fitness Prediction with Autoregressive Transformers and Inference-time Retrieval. ICML (2022)
Eli N. Weinstein, Alan Nawzad Amin, Jonathan Frazer, Debora S. Marks
Non-identifiability and the Blessings of Misspecification in Models of Molecular Fitness. NeurIPS (2022)
Daniel Hesslow, Niccoló Zanichelli, Pascal Notin, Iacopo Poli, Debora S. Marks
RITA: a Study on Scaling Up Generative Protein Sequence Models. CoRR (2022)
Mihaly Varadi, Stephen Anyango, David R. Armstrong, John M. Berrisford, Preeti Choudhary, Mandar S. Deshpande, Nurul Nadzirin, Sreenath Nair, Lukás Pravda, Ahsan Tanweer, Bissan Al-Lazikani, Claudia Andreini, Geoffrey J. Barton, David Bednar, Karel Berka, Tom L. Blundell, Kelly Brock, José María Carazo, Jirí Damborský, Alessia David, Sucharita Dey, Roland L. Dunbrack Jr., Juan Fernández-Recio, Franca Fraternali, Toby J. Gibson, Manuela Helmer-Citterich, David Hoksza, Thomas A. Hopf, David Jakubec, Natarajan Kannan, Radoslav Krivák, Manjeet Kumar, Emmanuel D. Levy, Nir London, José Ramón Macías, Mallur Srivatsan Madhusudhan, Debora S. Marks, Lennart Martens, Stuart A McGowan, Jake E. McGreig, Vivek Modi, R. Gonzalo Parra, Gerardo Pepe, Damiano Piovesan, Jaime Prilusky, Valeria Putignano, Leandro G. Radusky, Pathmanaban Ramasamy, Atilio O. Rausch, Nathalie Reuter, Luis A. Rodriguez, Nathan J. Rollins, Antonio Rosato, Pawel Rubach, Luis Serrano, Gulzar Singh, Petr Skoda, Carlos Oscar Sánchez Sorzano, Jan Stourac, Joanna I. Sulkowska, Radka Svobodová Vareková, Natalia Tichshenko, Silvio C. E. Tosatto, Wim F. Vranken, Mark N. Wass, Dandan Xue, Daniel Zaidman, Janet M. Thornton, Michael J. E. Sternberg, Christine A. Orengo, Sameer Velankar
PDBe-KB: collaboratively defining the biological context of structural data. Nucleic Acids Res. 50 (D1) (2022)
Pascal Notin, Mafalda Dias, Jonathan Frazer, Javier Marchena-Hurtado, Aidan N. Gomez, Debora S. Marks, Yarin Gal
Tranception: protein fitness prediction with autoregressive transformers and inference-time retrieval. CoRR (2022)
John Ingraham, Adam J. Riesselman, Chris Sander, Debora S. Marks
Learning Protein Structure with a Differentiable Simulator. ICLR (2019)
Thomas A. Hopf, Anna G. Green, Benjamin Schubert, Sophia Mersmann, Charlotta Schärfe, John Ingraham, Ágnes Tóth-Petróczy, Kelly Brock, Adam J. Riesselman, Perry Palmedo, Chan Kang, Robert P. Sheridan, Eli J. Draizen, Christian Dallago, Chris Sander, Debora S. Marks
The EVcouplings Python framework for coevolutionary sequence analysis. Bioinform. 35 (9) (2019)
Benjamin Schubert, Charlotta Schärfe, Pierre Dönnes, Thomas A. Hopf, Debora S. Marks, Oliver Kohlbacher
Population-specific design of de-immunized protein biotherapeutics. PLoS Comput. Biol. 14 (3) (2018)
Benjamin Schubert, Charlotta Schärfe, Pierre Dönnes, Thomas A. Hopf, Debora S. Marks, Oliver Kohlbacher
Population-specific design of de-immunized protein biotherapeutics. CoRR (2017)
John Ingraham, Debora S. Marks
Variational Inference for Sparse and Undirected Models. ICML (2017)
Richard R. Stein, Debora S. Marks, Chris Sander
Inferring Pairwise Interactions from Biological Data Using Maximum-Entropy Probability Models. PLoS Comput. Biol. 11 (7) (2015)
Yana Gofman, Charlotta Schärfe, Debora S. Marks, Turkan Haliloglu, Nir Ben-Tal
Structure, Dynamics and Implied Gating Mechanism of a Human Cyclic Nucleotide-Gated Channel. PLoS Comput. Biol. 10 (12) (2014)
Mirco Michel, Sikander Hayat, Marcin J. Skwark, Chris Sander, Debora S. Marks, Arne Elofsson
PconsFold: improved contact predictions improve protein models. Bioinform. 30 (17) (2014)
László Kaján, Thomas A. Hopf, Matú Kala, Debora S. Marks, Burkhard Rost
FreeContact: fast and free software for protein contact prediction from residue co-evolution. BMC Bioinform. 15 (2014)
Ashwini Jeggari, Debora S. Marks, Erik Larsson
miRcode: a map of putative microRNA target sites in the long non-coding transcriptome. Bioinform. 28 (15) (2012)
Debora S. Marks, Lucy J. Colwell, Robert P. Sheridan, Thomas A. Hopf, Andrea Pagnani, Riccardo Zecchina, Chris Sander
3D Protein Structure Predicted from Sequence CoRR (2011)
Doron Betel, Manda Wilson, Aaron Gabow, Debora S. Marks, Chris Sander
The microRNA.org resource: targets and expression. Nucleic Acids Res. 36 (Database-Issue) (2008)
Doron Betel, Robert P. Sheridan, Debora S. Marks, Chris Sander
Computational Analysis of Mouse piRNA Sequence and Biogenesis. PLoS Comput. Biol. 3 (11) (2007)