Physics, programming, databases. Computational data generation and analyses.

For example... high-throughput docking and GBSA calculations for predicted protein-ligand binding; MD simulations of protein-ligand interactions; population of a large, searchable database of small-molecule descriptors -- 300+ descriptors (molecular weight, rotatable bonds, polar surface area...) each molecule, anticipating 60 billion+ virtual-library compounds.
 

University of California, Santa Cruz, B.A. Physics

University of California, Santa Cruz, B.A. Economics

Zemla, Adam; Allen, Jonathan; Kirshner, Daniel; Lightstone, Felice (2022) PDBspheres – a method for finding 3D similarities in local regions in proteins. NAR Genomics and Bioinformatics (forthcoming).

Dong H. Ahn, Xiaohua Zhang, Jeffrey Mast, Stephen Herbein, Francesco Di Natale, Dan Kirshner, Sam Ade Jacobs, Ian Karlin, Daniel J. Milroy, Bronis De Supinski, Brian Van Essen, Jonathan Allen, Felice Lightstone (2022) Scalable Composition and Analysis Techniques for Massive Scientific Workflows.  IEEE eScience 2022

G. A. Stevenson, D. Jones, H. Kim, W. F. D. Bennett, B. J. Bennion, M. Borucki, F. Bourguet, A. Epstein, M. Franco, B. Harmon, S. He, M. P. Katz, D. Kirshner, V. Lao, E. Y. Lau, J. Lo, K. McLoughlin, R. Mosesso, D. K. Murugesh, O. A. Negrete, E. A. Saada, B. Segelke, M. Stefan, M. W. Torres, D. Weilhammer, S. Wong, Y. Yang, A. Zemla, X. Zhang, F. Zhu, F. C. Lightstone, J. E. Allen (2021) High-throughput virtual screening of small molecule inhibitors for SARS-CoV-2 protein targets with deep fusion models, SC '21: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, Article No.: 74, 1–13.

Edmond Y. Lau, Oscar A. Negrete, W. F. Drew Bennett, Brian J. Bennion, Monica Borucki, Feliza Bourguet, Aidan Epstein, Magdalena Franco, Brooke Harmon, Stewart He, Derek Jones, Hyojin Kim, Daniel Kirshner, Victoria Lao, Jacky Lo, Kevin McLoughlin, Richard Mosesso, Deepa K. Murugesh, Edwin A. Saada, Brent Segelke, Maxwell A. Stefan, Garrett A. Stevenson, Marisa W. Torres, Dina R. Weilhammer, Sergio Wong, Yue Yang, Adam Zemla, Xiaohua Zhang, Fangqiang Zhu, Jonathan E. Allen, Felice C. Lightstone (2021) Discovery of Small-molecule Inhibitors of SARS-CoV-2 Proteins Using a Computational and Experimental Pipeline.  Frontiers in Molecular Biosciences 8, 644.

Derek Jones, Hyojin Kim, Xiaohua Zhang, Adam Zemla, Garrett Stevenson, W. F. Drew Bennett, Daniel Kirshner, Sergio E. Wong, Felice C. Lightstone, and Jonathan E. Allen (2021) Improved Protein–Ligand Binding Affinity Prediction with Structure-Based Deep Fusion Inference.  Journal of Chemical Information and Modeling 61, 4, 1583–1592.

Timothy S. Carpenter, Daniel A. Kirshner, Edmond Y. Lau, Sergio E. Wong, Jerome P. Nilmeier, and Felice C. Lightstone (2014).  A Method to Predict Blood-Brain Barrier Permeability of Drug-like Compounds Using Molecular Dynamics Simulations.  Biophys. J. (2014) 107(3), 630-641.

D. A. Kirshner, J. P. Nilmeier, and F. C. Lightstone (2013).  Catalytic Site Identification – A Web Server to Identify Catalytic Site Structural Matches Throughout PDB. Nucleic Acids Research, 41, W256-W265

J. P. Nilmeier, D. A. Kirshner, S. E. Wong, and F. C. Lightstone (2013).  Rapid Catalytic Template Searching as an Enzyme Function Prediction Procedure.  PLoS ONE, 8(5), e62535.

James J. Langham, Ann E. Cleves, Russell Spitzer, Daniel Kirshner, Ajay N. Jain (2009).   Physical Binding Pocket Induction for Affinity Prediction. Journal of Medicinal Chemistry.

Jake Gunn Glanville, Dan Kirshner, Nandini Krishnamurthy, and Kimmen Sjolander (2007).  Berkeley Phylogenomics Group Web Servers: Resources for structural phylogenomic analysis. Nucleic Acids Research; doi:10.1093/nar/gkm325.

Nandini Krishnamurthy, Duncan Brown, Dan Kirshner and Kimmen Sjölander (2006).  PhyloFacts: An online structural phylogenomic encyclopedia for protein functional and structural classification.  Genome Biology, 7:R83.

Daniel Kirshner (2001), Efficiency Gains From Value Pricing: Case Study of Sunol Grade” Transportation Research Record, No. 1747.

Daniel Kirshner, Barbara Barkovich, Kathy Treleven, and Robin Walther (1997).  A Cost-effective Renewables Policy Can Advance the Transition to Competition, The Electricity Journal, Vol. 10, No. 1.

Daniel Kirshner and Deborah Moore (1989).  The Effect of San Francisco Bay Water Quality on Adjacent Property Values. Journal of Environmental Management, 27.

Daniel Kirshner (1984).  Statistical Tests of Energy Savings Due to Voltage Reduction.  Institute of Electrical and Electronics Engineers Transactions, Vol. PAS‑103.

Daniel Kirshner (1980).  Some Non-explanations of Bicycle Stability, American Journal of Physics.

Daniel McFadden, Carlos Puig, and Daniel Kirshner (1979).  Determinants of the Long-Run Demand for Electricity.  Journal of the American Statistical Association.