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2020 – today
- 2022
[j41]Neeladri Sen
, Ivan Anishchenko, Nicola Bordin, Ian Sillitoe, Sameer Velankar, David Baker, Christine A. Orengo:
Characterizing and explaining the impact of disease-associated mutations in proteins without known structures or structural homologs. Briefings Bioinform. 23(4) (2022)- [j40]David Baker:
Book review: Patrick Lo, Robert Sutherland, Wei-En Hsu, Russ Girsberger, Stories and Lessons from the World's Leading Opera, Orchestra Librarians, and Music Archivists. J. Libr. Inf. Sci. 54(4): 818-819 (2022) - [j39]Johannes Linder, Alyssa La Fleur, Zibo Chen, Ajasja Ljubetic, David Baker, Sreeram Kannan, Georg Seelig:
Interpreting neural networks for biological sequences by learning stochastic masks. Nat. Mach. Intell. 4(1): 41-54 (2022) - [i1]Brian L. Trippe, Jason Yim, Doug Tischer, David Baker, Tamara Broderick, Regina Barzilay, Tommi S. Jaakkola:
Diffusion probabilistic modeling of protein backbones in 3D for the motif-scaffolding problem. CoRR abs/2206.04119 (2022) - 2021
- [j38]Brian Coventry, David Baker:
Protein sequence optimization with a pairwise decomposable penalty for buried unsatisfied hydrogen bonds. PLoS Comput. Biol. 17(3) (2021) - [c18]Luca Turchet, David Baker, Tony Stockman:
Musical Haptic Wearables for Synchronisation of Visually-impaired Performers: a Co-design Approach. IMX 2021: 20-27 - 2020
- [j37]Qi Wu, Zhenling Peng, Ivan Anishchenko, Qian Cong, David Baker, Jianyi Yang:
Protein contact prediction using metagenome sequence data and residual neural networks. Bioinform. 36(1): 41-48 (2020) - [j36]Julia Koehler Leman, Brian D. Weitzner, P. Douglas Renfrew, Steven M. Lewis, Rocco Moretti, Andrew M. Watkins, Vikram Khipple Mulligan, Sergey Lyskov, Jared Adolf-Bryfogle, Jason W. Labonte, Justyna Krys, RosettaCommons Consortium, Christopher Bystroff, William R. Schief, Dominik Gront, Ora Schueler-Furman, David Baker, Philip Bradley, Roland L. Dunbrack Jr., Tanja Kortemme, Andrew Leaver-Fay, Charlie E. M. Strauss, Jens Meiler, Brian Kuhlman, Jeffrey J. Gray, Richard Bonneau:
Better together: Elements of successful scientific software development in a distributed collaborative community. PLoS Comput. Biol. 16(5) (2020)
2010 – 2019
- 2019
- [j35]Zibo Chen, Scott E. Boyken, Mengxuan Jia, Florian Busch, David Flores-Solis, Matthew J. Bick, Peilong Lu, Zachary L. VanAernum, Aniruddha Sahasrabuddhe, Robert A. Langan, Sherry Bermeo, T. J. Brunette, Vikram Khipple Mulligan, Lauren P. Carter, Frank DiMaio, Nikolaos G. Sgourakis, Vicki H. Wysocki, David Baker:
Programmable design of orthogonal protein heterodimers. Nat. 565(7737): 106-111 (2019) - [j34]Daniel-Adriano Silva, Shawn Yu, Umut Y. Ulge, Jamie B. Spangler, Kevin M. Jude, Carlos Labão-Almeida, Lestat R. Ali, Alfredo Quijano-Rubio, Mikel Ruterbusch, Isabel Leung, Tamara Biary, Stephanie J. Crowley, Enrique Marcos, Carl D. Walkey, Brian D. Weitzner, Fátima Pardo Avila, Javier Castellanos, Lauren P. Carter, Lance J. Stewart, Stanley R. Riddell, Marion Pepper, Gonçalo J. L. Bernardes, Michael Dougan, K. Christopher Garcia, David Baker:
De novo design of potent and selective mimics of IL-2 and IL-15. Nat. 565(7738): 186-191 (2019) - [j33]Brian Koepnick, Jeff Flatten, Tamir Husain, Alex Ford, Daniel-Adriano Silva, Matthew J. Bick, Aaron Bauer, Gaohua Liu, Yojiro Ishida, Alexander Boykov, Roger D. Estep, Susan Kleinfelter, Toke Nørgård-Solano, Linda Wei, Foldit players, Gaetano T. Montelione, Frank DiMaio, Zoran Popovic, Firas Khatib, Seth Cooper, David Baker:
De novo protein design by citizen scientists. Nat. 570(7761): 390-394 (2019) - [j32]Robert A. Langan, Scott E. Boyken, Andrew H. Ng, Jennifer A. Samson, Galen Dods, Alexandra M. Westbrook, Taylor H. Nguyen, Marc J. Lajoie, Zibo Chen, Stephanie Berger, Vikram Khipple Mulligan, John E. Dueber, Walter R. P. Novak, Hana El-Samad, David Baker:
De novo design of bioactive protein switches. Nat. 572(7768): 205-210 (2019) - [j31]Andrew H. Ng, Taylor H. Nguyen, Mariana Gómez-Schiavon, Galen Dods, Robert A. Langan, Scott E. Boyken, Jennifer A. Samson, Lucas M. Waldburger, John E. Dueber, David Baker, Hana El-Samad:
Modular and tunable biological feedback control using a de novo protein switch. Nat. 572(7768): 265-269 (2019) - 2018
- [j30]Jiayi Dou, Anastassia A. Vorobieva, William Sheffler, Lindsey Doyle, Hahnbeom Park, Matthew J. Bick, Binchen Mao, Glenna W. Foight, Min-Yen Lee, Lauren A. Gagnon, Lauren P. Carter, Banumathi Sankaran, Sergey Ovchinnikov, Enrique Marcos, Po-Ssu Huang, Joshua C. Vaughan, Barry L. Stoddard, David Baker:
De novo design of a fluorescence-activating β-barrel. Nat. 561(7724): 485-491 (2018) - 2017
- [j29]Robert Kleffner, Jeff Flatten, Andrew Leaver-Fay, David Baker, Justin B. Siegel, Firas Khatib, Seth Cooper:
Foldit Standalone: a video game-derived protein structure manipulation interface using Rosetta. Bioinform. 33(17): 2765-2767 (2017) - [j28]Claudia Y. Janda, Luke T. Dang, Changjiang You, Junlei Chang, Wim de Lau, Zhendong A. Zhong, Kelley S. Yan, Owen Marecic, Dirk Siepe, Xingnan Li, James D. Moody, Bart O. Williams, Hans Clevers, Jacob Piehler, David Baker, Calvin J. Kuo, K. Christopher Garcia:
Surrogate Wnt agonists that phenocopy canonical Wnt and β-catenin signalling. Nat. 545(7653): 234-237 (2017) - [j27]Stefan Schoebel, Wei Mi, Alexander Stein, Sergey Ovchinnikov, Ryan E. Pavlovicz, Frank DiMaio, David Baker, Melissa G. Chambers, Huayou Su, Dongsheng Li, Tom A. Rapoport, Maofu Liao:
Cryo-EM structure of the protein-conducting ERAD channel Hrd1 in complex with Hrd3. Nat. 548(7667): 352-355 (2017) - [j26]Aaron Chevalier, Daniel-Adriano Silva, Gabriel J. Rocklin, Derrick R. Hicks, Renan Vergara, Patience Murapa, Steffen M. Bernard, Lu Zhang, Kwok-Ho Lam, Guorui Yao, Christopher D. Bahl, Shin-Ichiro Miyashita, Inna Goreshnik, James T. Fuller, Merika T. Koday, Cody M. Jenkins, Tom Colvin, Lauren P. Carter, Alan Bohn, Cassie M. Bryan, D. Alejandro Fernández-Velasco, Lance J. Stewart, Min Dong, Xuhui Huang, Rongsheng Jin, Ian A. Wilson, Deborah H. Fuller, David Baker:
Massively parallel de novo protein design for targeted therapeutics. Nat. 550(7674): 74-79 (2017) - 2016
- [j25]Richard D. Smith, Kelly L. Damm-Ganamet, James B. Dunbar Jr., Aqeel Ahmed, Krishnapriya Chinnaswamy, James Delproposto, Ginger Kubish, Christine E. Tinberg, Sagar D. Khare, Jiayi Dou, Lindsey Doyle, Jeanne A. Stuckey, David Baker, Heather A. Carlson:
CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge. J. Chem. Inf. Model. 56(6): 1022-1031 (2016) - [j24]Yang Hsia, Jacob B. Bale, Shane Gonen, Dan Shi, William Sheffler, Kimberly K. Fong, Una Nattermann, Chunfu Xu, Po-Ssu Huang, Rashmi Ravichandran, Sue Yi, Trisha N. Davis, Tamir Gonen, Neil P. King, David Baker:
Design of a hyperstable 60-subunit protein icosahedron. Nat. 535(7610): 136-139 (2016) - [j23]Gaurav Bhardwaj, Vikram Khipple Mulligan, Christopher D. Bahl, Jason M. Gilmore, Peta J. Harvey, Olivier Cheneval, Garry W. Buchko, Surya V. S. R. K. Pulavarti, Quentin Kaas, Alexander Eletsky, Po-Ssu Huang, William A. Johnsen, Per Greisen, Gabriel J. Rocklin, Yifan Song, Thomas W. Linsky, Andrew M. Watkins, Stephen A. Rettie, Xianzhong Xu, Lauren P. Carter, Richard Bonneau, James M. Olson, Evangelos A. Coutsias, Colin E. Correnti, Thomas Szyperski, David J. Craik, David Baker:
Accurate de novo design of hyperstable constrained peptides. Nat. 538(7625): 329-335 (2016) - [j22]Yang Hsia, Jacob B. Bale, Shane Gonen, Dan Shi, William Sheffler, Kimberly K. Fong, Una Nattermann, Chunfu Xu, Po-Ssu Huang, Rashmi Ravichandran, Sue Yi, Trisha N. Davis, Tamir Gonen, Neil P. King, David Baker:
Corrigendum: Design of a hyperstable 60-subunit protein icosahedron. Nat. 540(7631): 150 (2016) - [c17]Edgar Berdahl, Michael Blandino, David Baker, Daniel Shanahan:
An Approach for Using Information Theory to Investigate Continuous Control of Analog Sensors by Humans. Audio Mostly Conference 2016: 85-90 - [c16]David Baker, Anna Clements, Catherine Grout, Simon Kerridge, Valerie McCutcheon, Helen Newnham:
CASRAI-UK: Using the CASRAI Approach to Develop Standards for Communicating and Sharing Research Information in the UK. CRIS 2016: 100-103 - [c15]Ankit Agrawal, Jason Scott Mathias, David Baker, Alok N. Choudhary:
Identifying hotspots in five year survival electronic health records of older adults. ICCABS 2016: 1-6 - [c14]Ankit Agrawal, Jason Scott Mathias, David Baker, Alok N. Choudhary:
Five Year Life Expectancy Calculator for Older Adults. ICDM Workshops 2016: 1280-1283 - 2015
- [j21]T. J. Brunette, Fabio Parmeggiani, Po-Ssu Huang, Gira Bhabha, Damian C. Ekiert, Susan E. Tsutakawa, Greg L. Hura, John A. Tainer, David Baker:
Exploring the repeat protein universe through computational protein design. Nat. 528(7583): 580-584 (2015) - [j20]Lindsey Doyle, Jazmine Hallinan, Jill Bolduc, Fabio Parmeggiani, David Baker, Barry L. Stoddard, Philip Bradley:
Rational design of α-helical tandem repeat proteins with closed architectures. Nat. 528(7583): 585-588 (2015) - [j19]David Bednar, Koen Beerens, Eva Sebestova, Jaroslav Bendl, Sagar D. Khare, Radka Chaloupkova, Zbynek Prokop, Jan Brezovsky, David Baker, Jirí Damborský:
FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants. PLoS Comput. Biol. 11(11) (2015) - [c13]Zafer Aydin, David Baker, William Stafford Noble:
Constructing Structural Profiles for Protein Torsion Angle Prediction. BIOINFORMATICS 2015: 26-35 - [c12]Zafer Aydin, David Baker, William Stafford Noble:
Template Scoring Methods for Protein Torsion Angle Prediction. BIOSTEC (Selected Papers) 2015: 206-223 - 2014
- [j18]Bruno E. Correia, John T. Bates, Rebecca J. Loomis, Gretchen Baneyx, Chris Carrico, Joseph G. Jardine, Peter Rupert, Colin E. Correnti, Oleksandr Kalyuzhniy, Vinayak Vittal, Mary J. Connell, Eric Stevens, Alexandria Schroeter, Man Chen, Skye MacPherson, Andreia M. Serra, Yumiko Adachi, Margaret A. Holmes, Yuxing Li, Rachel E. Klevit, Barney S. Graham, Richard T. Wyatt, David Baker, Roland K. Strong, James E. Crowe Jr., Philip R. Johnson, William R. Schief:
Proof of principle for epitope-focused vaccine design. Nat. 507(7491): 201-206 (2014) - [j17]Neil P. King, Jacob B. Bale, William Sheffler, Dan E. McNamara, Shane Gonen, Tamir Gonen, Todd O. Yeates, David Baker:
Accurate design of co-assembling multi-component protein nanomaterials. Nat. 510(7503): 103-108 (2014) - [j16]Kuang-Yui M. Chen, Jiaming Sun, Jason S. Salvo, David Baker, Patrick Barth:
High-Resolution Modeling of Transmembrane Helical Protein Structures from Distant Homologues. PLoS Comput. Biol. 10(5) (2014) - [j15]Chris King, Esteban N. Garza, Ronit Mazor, Jonathan L. Linehan, Ira Pastan, Marion Pepper, David Baker:
Removing T-cell epitopes with computational protein design. Proc. Natl. Acad. Sci. USA 111(23): 8577-8582 (2014) - [c11]Brigitte Jörg, Thorsten Höllrigl, David Baker:
Harmonising and Formalising Research Administration Profiles CASRAI / CERIF. CRIS 2014: 95-102 - [c10]Laure Haak, David Baker, Thorsten Höllrigl:
CASRAI and ORCID: Putting the Pieces together to Collaboratively Support the Research Community. CRIS 2014: 284-288 - 2013
- [j14]Christine E. Tinberg, Sagar D. Khare, Jiayi Dou, Lindsey Doyle, Jorgen W. Nelson, Alberto Schena, Wojciech Jankowski, Charalampos G. Kalodimos, Kai Johnsson, Barry L. Stoddard, David Baker:
Computational design of ligand-binding proteins with high affinity and selectivity. Nat. 501(7466): 212-216 (2013) - 2012
- [j13]David Baker, Tom Costello:
Your Hollywood Guide to Antipatterns. IT Prof. 14(3): 64-63 (2012) - [j12]Michael D. Tyka, Kenneth Jung, David Baker:
Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers. J. Comput. Chem. 33(31): 2483-2491 (2012) - [c9]Laurel L. Haak, David Baker, Matthew A. Probus:
Creating a Data Infrastructure for Tracking Knowledge Flow. CRIS 2012 - 2011
- [j11]Firas Khatib, Seth Cooper, Michael D. Tyka, Kefan Xu, Ilya Makedon, Zoran Popovic, David Baker, Foldit players:
Algorithm discovery by protein folding game players. Proc. Natl. Acad. Sci. USA 108(47): 18949-18953 (2011) - [j10]Hartmut Boesch, David Baker, Brian Connor, David Crisp, Charles E. Miller:
Global Characterization of CO2 Column Retrievals from Shortwave-Infrared Satellite Observations of the Orbiting Carbon Observatory-2 Mission. Remote. Sens. 3(2): 270-304 (2011) - [c8]Seth Cooper, Firas Khatib, Ilya Makedon, Hao Lü, Janos Barbero, David Baker, James Fogarty, Zoran Popovic, Foldit players:
Analysis of social gameplay macros in the Foldit cookbook. FDG 2011: 9-14 - 2010
- [j9]Seth Cooper, Firas Khatib, Adrien Treuille, Janos Barbero, Jeehyung Lee, Michael Beenen, Andrew Leaver-Fay, David Baker, Zoran Popovic, Foldit players:
Predicting protein structures with a multiplayer online game. Nat. 466(7307): 756-760 (2010) - [c7]Seth Cooper, Adrien Treuille, Janos Barbero, Andrew Leaver-Fay, Kathleen Tuite, Firas Khatib, Alex Cho Snyder, Michael Beenen, David Salesin, David Baker, Zoran Popovic:
The challenge of designing scientific discovery games. FDG 2010: 40-47
2000 – 2009
- 2009
- [j8]Ruslan Sadreyev, Shuoyong Shi, David Baker, Nick V. Grishin:
Structure similarity measure with penalty for close non-equivalent residues. Bioinform. 25(10): 1259-1263 (2009) - [j7]Brian A. Kidd, David Baker, Wendy E. Thomas:
Computation of Conformational Coupling in Allosteric Proteins. PLoS Comput. Biol. 5(8) (2009) - [c6]June Clark, Bernice Baker, David Baker:
Getting eHealth into Basic Nursing Education: Report of the RCN Information in Nursing Project. Nursing Informatics 2009: 534-539 - 2008
- [j6]Srivatsan Raman, Bin Qian, David Baker, Ross C. Walker:
Advances in Rosetta protein structure prediction on massively parallel systems. IBM J. Res. Dev. 52(1-2): 7-18 (2008) - 2007
- [c5]Ben Blum, Michael I. Jordan, David Kim, Rhiju Das, Philip Bradley, David Baker:
Feature Selection Methods for Improving Protein Structure Prediction with Rosetta. NIPS 2007: 137-144 - 2006
- [j5]Matthew L. Baker, Wen Jiang, William J. Wedemeyer, Frazer J. Rixon, David Baker, Wah Chiu:
Ab Initio Modeling of the Herpesvirus VP26 Core Domain Assessed by CryoEM Density. PLoS Comput. Biol. 2(10) (2006) - [c4]Wenlong Li, Tao Wang, Eric Q. Li, David Baker, Li Jin, Steven Ge, Yurong Chen, Yimin Zhang:
Parallelization and performance characterization of protein 3D structure prediction of Rosetta. IPDPS 2006 - [c3]Ross C. Walker, Srivatsan Raman, David Baker:
Poster reception - High resolution, high throughput protein structure prediction using IBM Blue Gene supercomputers: predicting CASP targets in record time. SC 2006: 165 - 2004
- [j4]David E. Kim, Dylan Chivian, David Baker:
Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res. 32(Web-Server-Issue): 526-531 (2004) - [p1]Carol A. Rohl, Charlie E. M. Strauss, Kira M. S. Misura, David Baker:
Protein Structure Prediction Using Rosetta. Numerical Computer Methods, Part D 2004: 66-93 - 2000
- [j3]Edward C. Thayer, Chris Bystroff, David Baker:
Detection of Protein Coding Sequences Using a Mixture Model for Local Protein Amino Acid Sequence. J. Comput. Biol. 7(1-2): 317-327 (2000) - [c2]David Baker:
A whole new ballgame - supercomputing on two AA batteries (keynote session). MICRO 2000: 3
1990 – 1999
- 1999
- [j2]David Baker:
The multimedia librarian in the twenty-first century: the viewpoint of a university librarian. OCLC Syst. Serv. 15(1): 18-23 (1999) - 1992
- [j1]David Baker:
Resource Allocation in University Libraries. J. Documentation 48(1): 1-19 (1992) - [c1]David Baker, Russell F. Haddleton, Kevin G. Wika:
A Distributed Scheduling Simulation. HPDC 1992: 270-279
Coauthor Index
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