| ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules A Leaver-Fay, M Tyka, SM Lewis, OF Lange, J Thompson, R Jacak, ... Methods in enzymology 487, 545-574, 2011 | 1937 | 2011 |
| Improving physical realism, stereochemistry, and side‐chain accuracy in homology modeling: Four approaches that performed well in CASP8 E Krieger, K Joo, J Lee, J Lee, S Raman, J Thompson, M Tyka, D Baker, ... Proteins: Structure, Function, and Bioinformatics 77 (S9), 114-122, 2009 | 1418 | 2009 |
| Inceptionism: Going deeper into neural networks A Mordvintsev, C Olah, M Tyka Google research blog 20 (14), 5, 2015 | 734 | 2015 |
| Algorithm discovery by protein folding game players F Khatib, S Cooper, MD Tyka, K Xu, I Makedon, Z Popović, D Baker, ... Proceedings of the National Academy of Sciences 108 (47), 18949-18953, 2011 | 636 | 2011 |
| Structure prediction for CASP8 with all‐atom refinement using Rosetta S Raman, R Vernon, J Thompson, M Tyka, R Sadreyev, J Pei, D Kim, ... Proteins: Structure, Function, and Bioinformatics 77 (S9), 89-99, 2009 | 592 | 2009 |
| Relaxation of backbone bond geometry improves protein energy landscape modeling P Conway, MD Tyka, F DiMaio, DE Konerding, D Baker Protein science 23 (1), 47-55, 2014 | 366 | 2014 |
| Alternate states of proteins revealed by detailed energy landscape mapping MD Tyka, DA Keedy, I André, F DiMaio, Y Song, DC Richardson, ... Journal of molecular biology 405 (2), 607-618, 2011 | 356 | 2011 |
| High-precision automated reconstruction of neurons with flood-filling networks M Januszewski, J Kornfeld, PH Li, A Pope, T Blakely, L Lindsey, ... Nature methods 15 (8), 605-610, 2018 | 355 | 2018 |
| Refinement of protein structures into low-resolution density maps using rosetta F DiMaio, MD Tyka, ML Baker, W Chiu, D Baker Journal of molecular biology 392 (1), 181-190, 2009 | 319 | 2009 |
| NMR structure determination for larger proteins using backbone-only data S Raman, OF Lange, P Rossi, M Tyka, X Wang, J Aramini, G Liu, ... Science 327 (5968), 1014-1018, 2010 | 309 | 2010 |
| Structure prediction for CASP7 targets using extensive all‐atom refinement with Rosetta@ home R Das, B Qian, S Raman, R Vernon, J Thompson, P Bradley, S Khare, ... Proteins: Structure, Function, and Bioinformatics 69 (S8), 118-128, 2007 | 274 | 2007 |
| Combined covalent-electrostatic model of hydrogen bonding improves structure prediction with Rosetta MJ O¢Meara, A Leaver-Fay, MD Tyka, A Stein, K Houlihan, F DiMaio, ... Journal of chemical theory and computation 11 (2), 609-622, 2015 | 245 | 2015 |
| Scientific benchmarks for guiding macromolecular energy function improvement A Leaver-Fay, MJ O'Meara, M Tyka, R Jacak, Y Song, EH Kellogg, ... Methods in enzymology 523, 109-143, 2013 | 244 | 2013 |
| Deepdream-a code example for visualizing neural networks A Mordvintsev, C Olah, M Tyka Google Research 2 (5), 2015 | 148 | 2015 |
| Principles for computational design of binding antibodies D Baran, MG Pszolla, GD Lapidoth, C Norn, O Dym, T Unger, S Albeck, ... Proceedings of the National Academy of Sciences 114 (41), 10900-10905, 2017 | 140 | 2017 |
| AbDesign: An algorithm for combinatorial backbone design guided by natural conformations and sequences GD Lapidoth, D Baran, GM Pszolla, C Norn, A Alon, MD Tyka, ... Proteins: Structure, Function, and Bioinformatics 83 (8), 1385-1406, 2015 | 109 | 2015 |
| Inceptionism: Going deeper into neural networks, 2015 A Mordvintsev, C Olah, M Tyka URL https://research. googleblog. com/2015/06/inceptionism-going-deeper-into …, 2015 | 103 | 2015 |
| Automated reconstruction of a serial-section EM Drosophila brain with flood-filling networks and local realignment PH Li, LF Lindsey, M Januszewski, M Tyka, J Maitin-Shepard, T Blakely, ... Microscopy and Microanalysis 25 (S2), 1364-1365, 2019 | 90 | 2019 |
| Structure‐guided forcefield optimization Y Song, M Tyka, A Leaver‐Fay, J Thompson, D Baker Proteins: Structure, Function, and Bioinformatics 79 (6), 1898-1909, 2011 | 66 | 2011 |
| An efficient, path-independent method for free-energy calculations MD Tyka, AR Clarke, RB Sessions The Journal of Physical Chemistry B 110 (34), 17212-17220, 2006 | 57 | 2006 |
