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Debora S. Marks
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- affiliation: Harvard Medical School, Boston, MA, USA
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2020 – today
- 2024
- [c11]Pierre Glaser, Steffanie Paul, Alissa M. Hummer, Charlotte M. Deane, Debora Susan Marks, Alan Nawzad Amin:
Kernel-Based Evaluation of Conditional Biological Sequence Models. ICML 2024 - 2023
- [j11]Hanchen Wang
, Tianfan Fu, Yuanqi Du, Wenhao Gao
Scientific discovery in the age of artificial intelligence. Nat. 620(7972): 47-60 (2023) - [c10]Alan Nawzad Amin, Eli N. Weinstein, Debora Susan Marks:
A Kernelized Stein Discrepancy for Biological Sequences. ICML 2023: 718-767 - [c9]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 - [c8]Pascal Notin, Ruben Weitzman, Debora S. Marks, Yarin Gal:
ProteinNPT: Improving protein property prediction and design with non-parametric transformers. NeurIPS 2023 - [i5]Alan Nawzad Amin, Eli Nathan Weinstein, Debora Susan Marks:
Biological Sequence Kernels with Guaranteed Flexibility. CoRR abs/2304.03775 (2023) - 2022
- [j10]Mihaly Varadi
PDBe-KB: collaboratively defining the biological context of structural data. Nucleic Acids Res. 50(D1): 534-542 (2022) - [c7]Eli N. Weinstein, Alan Nawzad Amin, Will S. Grathwohl, Daniel Kassler, Jean Disset, Debora S. Marks:
Optimal Design of Stochastic DNA Synthesis Protocols based on Generative Sequence Models. AISTATS 2022: 7450-7482 - [c6]Pascal Notin
Tranception: Protein Fitness Prediction with Autoregressive Transformers and Inference-time Retrieval. ICML 2022: 16990-17017 - [c5]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 - [i4]Daniel Hesslow, Niccoló Zanichelli, Pascal Notin
RITA: a Study on Scaling Up Generative Protein Sequence Models. CoRR abs/2205.05789 (2022) - [i3]Pascal Notin, Mafalda Dias, Jonathan Frazer, Javier Marchena-Hurtado
Tranception: protein fitness prediction with autoregressive transformers and inference-time retrieval. CoRR abs/2205.13760 (2022) - 2021
- [c4]Eli N. Weinstein, Debora S. Marks:
A Structured Observation Distribution for Generative Biological Sequence Prediction and Forecasting. ICML 2021: 11068-11079 - [c3]Alan Nawzad Amin, Eli N. Weinstein, Debora S. Marks:
A generative nonparametric Bayesian model for whole genomes. NeurIPS 2021: 27798-27812
2010 – 2019
- 2019
- [j9]Thomas A. Hopf
The EVcouplings Python framework for coevolutionary sequence analysis. Bioinform. 35(9): 1582-1584 (2019) - [c2]John Ingraham, Adam J. Riesselman, Chris Sander, Debora S. Marks:
Learning Protein Structure with a Differentiable Simulator. ICLR 2019 - 2018
- [j8]Benjamin Schubert
Population-specific design of de-immunized protein biotherapeutics. PLoS Comput. Biol. 14(3) (2018) - 2017
- [c1]John Ingraham, Debora S. Marks:
Variational Inference for Sparse and Undirected Models. ICML 2017: 1607-1616 - [i2]Benjamin Schubert, Charlotta Schärfe, Pierre Dönnes, Thomas A. Hopf, Debora S. Marks, Oliver Kohlbacher:
Population-specific design of de-immunized protein biotherapeutics. CoRR abs/1706.09083 (2017) - 2015
- [j7]Richard R. Stein
Inferring Pairwise Interactions from Biological Data Using Maximum-Entropy Probability Models. PLoS Comput. Biol. 11(7) (2015) - 2014
- [j6]Mirco Michel, Sikander Hayat
PconsFold: improved contact predictions improve protein models. Bioinform. 30(17): 482-488 (2014) - [j5]László Kaján, Thomas A. Hopf, Matú Kala
FreeContact: fast and free software for protein contact prediction from residue co-evolution. BMC Bioinform. 15: 85 (2014) - [j4]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) - 2012
- [j3]Ashwini Jeggari
miRcode: a map of putative microRNA target sites in the long non-coding transcriptome. Bioinform. 28(15): 2062-2063 (2012) - 2011
- [i1]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 abs/1110.5091 (2011)
2000 – 2009
- 2008
- [j2]Doron Betel
The microRNA.org resource: targets and expression. Nucleic Acids Res. 36(Database-Issue): 149-153 (2008) - 2007
- [j1]Doron Betel
Computational Analysis of Mouse piRNA Sequence and Biogenesis. PLoS Comput. Biol. 3(11) (2007)
Coauthor Index
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