Lucy J. Colwell

23 papers A* 6Journal 17

Year	Rank	Type	Title / Venue / Authors
2023	A*	`conf`	AVIDa-hIL6: A Large-Scale VHH Dataset Produced from an Immunized Alpaca for Predicting Antigen-Antibody Interactions. NeurIPS 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
2023	J	`jnl`	AVIDa-hIL6: A Large-Scale VHH Dataset Produced from an Immunized Alpaca for Predicting Antigen-Antibody Interactions. CoRR 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
2023	J	`jnl`	InterPro in 2022. Nucleic Acids Res. Typhaine Paysan-Lafosse, Matthias Blum, Sara Chuguransky, Tiago Grego, Beatriz Lázaro Pinto, Gustavo A. Salazar, Maxwell L. Bileschi, Peer Bork, Alan J. 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
2023	J	`jnl`	MGnify: the microbiome sequence data analysis resource in 2023. Nucleic Acids Res. 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
2022	J	`jnl`	A roadmap for the functional annotation of protein families: a community perspective. Database J. Biol. Databases Curation Valérie de Crécy-Lagard, Rocio Amorin de Hegedus, Cecilia N. Arighi, Jill Babor, Alex Bateman, Ian Blaby, Crysten Blaby-Haas, Alan J. 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 S. 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
2022	J	`jnl`	Meaningful machine learning models and machine-learned pharmacophores from fragment screening campaigns. CoRR Carl Poelking, Gianni Chessari, Christopher W. Murray, Richard J. Hall, Lucy J. Colwell, Marcel L. Verdonk
2021	A*	`conf`	Improving Protein Function Annotation via Unsupervised Pre-training: Robustness, Efficiency, and Insights. KDD David Dohan, Andreea Gane, Maxwell L. Bileschi, David Belanger, Lucy J. Colwell
2021	A*	`conf`	Rethinking Attention with Performers. ICLR 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
2020	J	`jnl`	Computational approaches to therapeutic antibody design: established methods and emerging trends. Briefings Bioinform. Richard A. Norman, Francesco Ambrosetti, Alexandre M. J. J. Bonvin, Lucy J. Colwell, Sebastian Kelm, Sandeep Kumar, Konrad Krawczyk
2020	J	`jnl`	Critiquing Protein Family Classification Models Using Sufficient Input Subsets. J. Comput. Biol. Brandon Carter, Maxwell L. Bileschi, Jamie Smith, Theo Sanderson, Drew Bryant, David Belanger, Lucy J. Colwell
2020	A*	`conf`	Evaluating Attribution for Graph Neural Networks. NeurIPS Benjamín Sánchez-Lengeling, Jennifer N. Wei, Brian K. Lee, Emily Reif, Peter Wang, Wesley Wei Qian, Kevin McCloskey, Lucy J. Colwell, Alexander B. Wiltschko
2020	J	`jnl`	Masked Language Modeling for Proteins via Linearly Scalable Long-Context Transformers. CoRR Krzysztof Choromanski, Valerii Likhosherstov, David Dohan, Xingyou Song, Jared Davis, Tamás Sarlós, David Belanger, Lucy J. Colwell, Adrian Weller
2020	A*	`conf`	Model-based reinforcement learning for biological sequence design. ICLR Christof Angermüller, David Dohan, David Belanger, Ramya Deshpande, Kevin Murphy, Lucy J. Colwell
2020	A*	`conf`	Population-Based Black-Box Optimization for Biological Sequence Design. ICML Christof Angermüller, David Belanger, Andreea Gane, Zelda Mariet, David Dohan, Kevin Murphy, Lucy J. Colwell, D. Sculley
2020	J	`jnl`	Population-Based Black-Box Optimization for Biological Sequence Design. CoRR Christof Angermüller, David Belanger, Andreea Gane, Zelda Mariet, David Dohan, Kevin Murphy, Lucy J. Colwell, D. Sculley
2020	J	`jnl`	Rethinking Attention with Performers. CoRR 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
2020	J	`jnl`	The Effect of Debiasing Protein-Ligand Binding Data on Generalization. J. Chem. Inf. Model. Vikram Sundar, Lucy J. Colwell
2019	J	`jnl`	Noisy, sparse, nonlinear: Navigating the Bermuda Triangle of physical inference with deep filtering. CoRR Carl Poelking, Yehia Amar, Alexei A. Lapkin, Lucy J. Colwell
2018	J	`jnl`	Using Attribution to Decode Dataset Bias in Neural Network Models for Chemistry. CoRR Kevin McCloskey, Ankur Taly, Federico Monti, Michael P. Brenner, Lucy J. Colwell
2015	J	`jnl`	Protein Sectors: Statistical Coupling Analysis versus Conservation. PLoS Comput. Biol. Tiberiu Tesileanu, Lucy J. Colwell, Stanislas Leibler
2011	J	`jnl`	3D Protein Structure Predicted from Sequence CoRR Debora S. Marks, Lucy J. Colwell, Robert P. Sheridan, Thomas A. Hopf, Andrea Pagnani, Riccardo Zecchina, Chris Sander
2010	J	`jnl`	Charge as a Selection Criterion for Translocation through the Nuclear Pore Complex. PLoS Comput. Biol. Lucy J. Colwell, Michael P. Brenner, Katharina Ribbeck
2009	J	`jnl`	Action Potential Initiation in the Hodgkin-Huxley Model. PLoS Comput. Biol. Lucy J. Colwell, Michael P. Brenner