Lucy J. Colwell

Publication Activity (10 Years)

Years Active: 2009-2023
Publications (10 Years): 17

Top Topics

Protein Functional

Language Modeling

Top Venues

Nucleic Acids Res.

Publications

Lorna J. Richardson, Ben Allen, Germana Baldi, Martin Beracochea, Maxwell L. Bileschi, Tony Burdett, Josephine Burgin, Juan Caballero, Guy Cochrane, Lucy J. Colwell, Tom Curtis, Alejandra Escobar-Zepeda, Tatiana A. Gurbich, Varsha Kale, Anton I. Korobeynikov, Shriya Raj, Alexander b Rogers, Ekaterina A. Sakharova, Santiago Sanchez, Darren J. Wilkinson, Robert D. Finn
MGnify: the microbiome sequence data analysis resource in 2023. Nucleic Acids Res. 51 (D1) (2023)
Hirofumi Tsuruta, Hiroyuki Yamazaki, Ryota Maeda, Ryotaro Tamura, Jennifer N. Wei, Zelda E. Mariet, Poomarin Phloyphisut, Hidetoshi Shimokawa, Joseph R. Ledsam, Lucy J. Colwell, Akihiro Imura
AVIDa-hIL6: A Large-Scale VHH Dataset Produced from an Immunized Alpaca for Predicting Antigen-Antibody Interactions. NeurIPS (2023)
Typhaine Paysan-Lafosse, Matthias Blum, Sara Chuguransky, Tiago Grego, Beatriz Lázaro Pinto, Gustavo A. Salazar, Maxwell L. Bileschi, Peer Bork, Alan Bridge, Lucy J. Colwell, Julian Gough, Daniel H. Haft, Ivica Letunic, Aron Marchler-Bauer, Huaiyu Mi, Darren A. Natale, Christine A. Orengo, Arun Prasad Pandurangan, Catherine Rivoire, Christian J. A. Sigrist, Ian Sillitoe, Narmada Thanki, Paul D. Thomas, Silvio C. E. Tosatto, Cathy H. Wu, Alex Bateman
InterPro in 2022. Nucleic Acids Res. 51 (D1) (2023)
Hirofumi Tsuruta, Hiroyuki Yamazaki, Ryota Maeda, Ryotaro Tamura, Jennifer N. Wei, Zelda Mariet, Poomarin Phloyphisut, Hidetoshi Shimokawa, Joseph R. Ledsam, Lucy J. Colwell, Akihiro Imura
AVIDa-hIL6: A Large-Scale VHH Dataset Produced from an Immunized Alpaca for Predicting Antigen-Antibody Interactions. CoRR (2023)
Valérie de Crécy-Lagard, Rocio Amorin de Hegedus, Cecilia N. Arighi, Jill Babor, Alex Bateman, Ian Blaby, Crysten Blaby-Haas, Alan Bridge, Stephen K. Burley, Stacey Cleveland, Lucy J. Colwell, Ana Conesa, Christian Dallago, Antoine Danchin, Anita de Waard, Adam Deutschbauer, Raquel Dias, Yousong Ding, Gang Fang, Iddo Friedberg, John Gerlt, Joshua Goldford, Mark Gorelik, Benjamin M. Gyori, Christopher Henry, Geoffrey Hutinet, Marshall Jaroch, Peter D. Karp, Liudmyla Kondratova, Zhiyong Lu, Aron Marchler-Bauer, Maria Jesus Martin, Claire D. McWhite, Gaurav D. Moghe, Paul Monaghan, Anne Morgat, Christopher J. Mungall, Darren A. Natale, William C. Nelson, Seán I. O'Donoghue, Christine A. Orengo, Katherine H. O'Toole, Predrag Radivojac, Colbie Reed, Richard J. Roberts, Dmitri Rodionov, Irina A. Rodionova, Jeffrey DePons, Lana Saleh, Gloria M. Sheynkman, Françoise Thibaud-Nissen, Paul D. Thomas, Peter Uetz, David Vallenet, Erica Watson Carter, Peter Weigele, Valerie Wood, Elisha M. Wood-Charlson, Jin Xu
A roadmap for the functional annotation of protein families: a community perspective. Database J. Biol. Databases Curation 2022 (2022) (2022)
Krzysztof Marcin Choromanski, Valerii Likhosherstov, David Dohan, Xingyou Song, Andreea Gane, Tamás Sarlós, Peter Hawkins, Jared Quincy Davis, Afroz Mohiuddin, Lukasz Kaiser, David Benjamin Belanger, Lucy J. Colwell, Adrian Weller
Rethinking Attention with Performers. ICLR (2021)
David Dohan, Andreea Gane, Maxwell L. Bileschi, David Belanger, Lucy J. Colwell
Improving Protein Function Annotation via Unsupervised Pre-training: Robustness, Efficiency, and Insights. KDD (2021)
Richard A. Norman, Francesco Ambrosetti, Alexandre M. J. J. Bonvin, Lucy J. Colwell, Sebastian Kelm, Sandeep Kumar, Konrad Krawczyk
Computational approaches to therapeutic antibody design: established methods and emerging trends. Briefings Bioinform. 21 (5) (2020)
Benjamín Sánchez-Lengeling, Jennifer N. Wei, Brian K. Lee, Emily Reif, Peter Wang, Wesley Wei Qian, Kevin McCloskey, Lucy J. Colwell, Alexander B. Wiltschko
Evaluating Attribution for Graph Neural Networks. NeurIPS (2020)
Christof Angermüller, David Dohan, David Belanger, Ramya Deshpande, Kevin Murphy, Lucy J. Colwell
Model-based reinforcement learning for biological sequence design. ICLR (2020)
Christof Angermüller, David Belanger, Andreea Gane, Zelda Mariet, David Dohan, Kevin Murphy, Lucy J. Colwell, D. Sculley
Population-Based Black-Box Optimization for Biological Sequence Design. CoRR (2020)
Christof Angermüller, David Belanger, Andreea Gane, Zelda Mariet, David Dohan, Kevin Murphy, Lucy J. Colwell, D. Sculley
Population-Based Black-Box Optimization for Biological Sequence Design. ICML (2020)
Brandon Carter, Maxwell L. Bileschi, Jamie Smith, Theo Sanderson, Drew Bryant, David Belanger, Lucy J. Colwell
Critiquing Protein Family Classification Models Using Sufficient Input Subsets. J. Comput. Biol. 27 (8) (2020)
Krzysztof Choromanski, Valerii Likhosherstov, David Dohan, Xingyou Song, Jared Davis, Tamás Sarlós, David Belanger, Lucy J. Colwell, Adrian Weller
Masked Language Modeling for Proteins via Linearly Scalable Long-Context Transformers. CoRR (2020)
Krzysztof Choromanski, Valerii Likhosherstov, David Dohan, Xingyou Song, Andreea Gane, Tamás Sarlós, Peter Hawkins, Jared Davis, Afroz Mohiuddin, Lukasz Kaiser, David Belanger, Lucy J. Colwell, Adrian Weller
Rethinking Attention with Performers. CoRR (2020)
Kevin McCloskey, Ankur Taly, Federico Monti, Michael P. Brenner, Lucy J. Colwell
Using Attribution to Decode Dataset Bias in Neural Network Models for Chemistry. CoRR (2018)
Tiberiu Tesileanu, Lucy J. Colwell, Stanislas Leibler
Protein Sectors: Statistical Coupling Analysis versus Conservation. PLoS Comput. Biol. 11 (2) (2015)
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)
Lucy J. Colwell, Michael P. Brenner, Katharina Ribbeck
Charge as a Selection Criterion for Translocation through the Nuclear Pore Complex. PLoS Comput. Biol. 6 (4) (2010)
Lucy J. Colwell, Michael P. Brenner
Action Potential Initiation in the Hodgkin-Huxley Model. PLoS Comput. Biol. 5 (1) (2009)