Climate Sciences, Ocean Biogeochemistry

Yankovsky, Elizabeth, Mengyang Zhou, Michael Tyka, Scott Bachman, David Ho, Alicia Karspeck, and Matthew Long. 2024. “Impulse Response Functions as a Framework for Quantifying Ocean-Based Carbon Dioxide Removal. [Preprint]”

Tyka, Michael D. 2024. “Efficiency Metrics for Ocean Alkalinity Enhancement Under Responsive and Prescribed Atmosphere Conditions.” EGUsphere 2024: 1–18. [Preprint]

Zhou, Mengyang, Michael Tyka, David Ho, Elizabeth Yankovsky, Scott Bachman, Thomas Nicholas, Alicia Karspeck, and Matthew Long. 2024b. “Mapping the Global Variation in the Efficiency of Ocean Alkalinity Enhancement for Carbon Dioxide Removal.” Nat. Clim. Change. [Preprint] [Interactive]

Tyka, Michael D, Christopher Van Arsdale, and John C Platt. 2022. “CO 2 Capture by Pumping Surface Acidity to the Deep Ocean.” Energy & Environmental Science 15 (2): 786–98. [Fulltext]

He, Jing, and Michael D Tyka. 2023. “Limits and Co 2 Equilibration of Near-Coast Alkalinity Enhancement.” Biogeosciences 20 (1): 27–43. [Fulltext]

Bach, Lennart T, David T Ho, Philip W Boyd, and Michael D Tyka. 2023. “Toward a Consensus Framework to Evaluate Air–Sea Co2 Equilibration for Marine Co2 Removal.” Limnology and Oceanography Letters 8 (5): 685–91. [Fulltext]

Jin, Shijian, Michael Tyka, Cristian Rodriguez Martinez, Christopher Davis, Christopher Van Arsdale, and Antonio Papania-Davis. 2024. “Negative Emission Enabled by Combining Ocean Alkalinity Enhancement and Waste Concrete Upcycling.” [Preprint]

Rackley, Steve A, Tingzhen Ming, Wei Li, Michael Tyka, Adrienne Sewel, Diarmaid Clery, George Dowson, et al. 2023. “Negative Emissions Technologies for Climate Change Mitigation.” Elsevier.

Shaw, Cody, Mallory Ringham, Xi Lu, Brendan Carter, Matthew Eisaman, and Mike Tyka. 2022. “Understanding the Kinetics of Electrochemically Derived Magnesium Hydroxide for Ocean Alkalinity Enhancement.” In AGU Fall Meeting Abstracts, 2022:GC32I–0713.

Tyka, Michael, and Mengyang Zhou. 2024. “Differences in Calculated Oae-Efficiency Between the Cesm2/Marbl and Ecco-Darwin Circulation Models.” AGU24.

Protein Structure, Biophysics, Biochemistry

Baran, Dror, M Gabriele Pszolla, Gideon D Lapidoth, Christoffer Norn, Orly Dym, Tamar Unger, Shira Albeck, Michael D Tyka, and Sarel J Fleishman. 2017. “Principles for Computational Design of Binding Antibodies.” Proceedings of the National Academy of Sciences 114 (41): 10900–10905.

Conway, Patrick, Michael D Tyka, Frank DiMaio, David E Konerding, and David Baker. 2014. “Relaxation of Backbone Bond Geometry Improves Protein Energy Landscape Modeling.” Protein Science 23 (1): 47–55.

Das, Rhiju, Bin Qian, Srivatsan Raman, Robert Vernon, James Thompson, Philip Bradley, Sagar Khare, et al. 2007. “Structure Prediction for Casp7 Targets Using Extensive All-Atom Refinement with Rosetta@ Home.” Proteins: Structure, Function, and Bioinformatics 69 (S8): 118–28.

DiMaio, Frank, Michael D Tyka, Matthew L Baker, Wah Chiu, and David Baker. 2009. “Refinement of Protein Structures into Low-Resolution Density Maps Using Rosetta.” [Journal of Molecular Biology 392 (1):181–90.] (https://www.sciencedirect.com/science/article/abs/pii/S0022283609008341?via%3Dihub)

Khatib, Firas, Seth Cooper, Michael D Tyka, Kefan Xu, Ilya Makedon, Zoran Popović, David Baker, and Foldit Players. 2011. “Algorithm Discovery by Protein Folding Game Players.” Proceedings of the National Academy of Sciences 108 (47): 18949–53. [PDF]

Krieger, Elmar, Keehyoung Joo, Jinwoo Lee, Jooyoung Lee, Srivatsan Raman, James Thompson, Mike Tyka, David Baker, and Kevin Karplus. 2009. “Improving Physical Realism, Stereochemistry, and Side-Chain Accuracy in Homology Modeling: Four Approaches That Performed Well in Casp8.” Proteins: Structure, Function, and Bioinformatics 77 (S9): 114–22.

Lapidoth, Gideon D, Dror Baran, Gabriele M Pszolla, Christoffer Norn, Assaf Alon, Michael D Tyka, and Sarel J Fleishman. 2015. “Abdesign: A N Algorithm for Combinatorial Backbone Design Guided by Natural Conformations and Sequences.” Proteins: Structure, Function, and Bioinformatics 83 (8): 1385–1406.PDF

Leaver-Fay, Andrew, Matthew J O’meara, Mike Tyka, Ron Jacak, Yifan Song, Elizabeth H Kellogg, James Thompson, et al. 2013. “Scientific Benchmarks for Guiding Macromolecular Energy Function Improvement.” In Methods in Enzymology, 523:109–43. Academic Press. PDF

Leaver-Fay, Andrew, Michael Tyka, Steven M Lewis, Oliver F Lange, James Thompson, Ron Jacak, Kristian Kaufman, et al. 2011a. “Rhiju Das, Jens Meiler, Tanja Kortemme, Jeffrey J. Gray, Brian Kuhlman, David Baker, and Philip Bradley. Rosetta3: An Object-Oriented Software Suite for the Simulation and Design of Macromolecules.” Methods in Enzymology 487: 545–74. PDF

O’Meara, Matthew J, Andrew Leaver-Fay, Michael D Tyka, Amelie Stein, Kevin Houlihan, Frank DiMaio, Philip Bradley, et al. 2015. “Combined Covalent-Electrostatic Model of Hydrogen Bonding Improves Structure Prediction with Rosetta.” Journal of Chemical Theory and Computation 11 (2): 609–22. PDF

Wang, Chu, Robert Vernon, Oliver Lange, Michael Tyka, and David Baker. 2010. Prediction of Structures of Zinc-Binding Proteins Through Explicit Modeling of Metal Coordination Geometry. Protein Science 19 (3): 494–506. PDF

Raman, Srivatsan, Oliver F Lange, Paolo Rossi, Michael Tyka, Xu Wang, James Aramini, Gaohua Liu, et al. 2010. “NMR Structure Determination for Larger Proteins Using Backbone-Only Data.” Science 327 (5968): 1014–8. [PDF]

Raman, Srivatsan, Robert Vernon, James Thompson, Michael Tyka, Ruslan Sadreyev, Jimin Pei, David Kim, et al. 2009a. “Prediction Report.” Proteins 77 (9): 89–99. Fulltext

Wang, Ray Yu-Ruei, Yan Han, Kristina Krassovsky, William Sheffler, Michael Tyka, and David Baker. 2011. “Modeling Disordered Regions in Proteins Using Rosetta.” PloS One 6 (7): e22060. Fulltext

Song, Yifan, Michael Tyka, Andrew Leaver-Fay, James Thompson, and David Baker. 2011. “Structure-Guided Forcefield Optimization.” Proteins: Structure, Function, and Bioinformatics 79 (6): 1898–1909.Fulltext

Tyka, Michael D, Anthony R Clarke, and Richard B Sessions. 2006. “An Efficient, Path-Independent Method for Free-Energy Calculations.” The Journal of Physical Chemistry B 110 (34): 17212–20.PDF

Tyka, Michael D, Kenneth Jung, and David Baker. 2012. “Efficient Sampling of Protein Conformational Space Using Fast Loop Building and Batch Minimization on Highly Parallel Computers.” Journal of Computational Chemistry 33 (31): 2483–91.PDF

Tyka, Michael D, Daniel A Keedy, Ingemar André, Frank DiMaio, Yifan Song, David C Richardson, Jane S Richardson, and David Baker. 2011. “Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping.” Journal of Molecular Biology 405 (2): 607–18.PDF

Tyka, Michael D, Richard B Sessions, and Anthony R Clarke. 2007. “Absolute Free-Energy Calculations of Liquids Using a Harmonic Reference State.” The Journal of Physical Chemistry B 111 (32): 9571–80.PDF

Neuroscience, Machine Learning

Januszewski, Michał, Jörgen Kornfeld, Peter H Li, Art Pope, Tim Blakely, Larry Lindsey, Jeremy Maitin-Shepard, Mike Tyka, Winfried Denk, and Viren Jain. 2018. “High-Precision Automated Reconstruction of Neurons with Flood-Filling Networks.” Nature Methods 15 (8): 605–10. PDF

Li, Peter H, Larry F Lindsey, Michał Januszewski, Mike Tyka, Jeremy Maitin-Shepard, Tim Blakely, and Viren Jain. 2019. “Automated Reconstruction of a Serial-Section Em Drosophila Brain with Flood-Filling Networks and Local Realignment.” Microscopy and Microanalysis 25 (S2): 1364–5. [Preprint]

Alexander, Mordvintsev, Olah Christopher, and Tyka Mike. 2015. “Inceptionism: Going Deeper into Neural Networks.” Google Research Blog 2015. [Link]

Sathanur, Arun V, Miao Sui, Vikram Jandhyala, Michael D Tyka, and Nicole A Deflaux. 2014. “Simulating Context-Driven Activity Cascades in Online Social Networks on the Google Exacycle Platform.” In 2014 Ieee International Conference on Systems, Man, and Cybernetics (Smc), 1388–91. IEEE.