CV

Education

Ph.D. Applied Mathematics, minor in Biochemistry, University of Arizona
M.S. Applied Mathematics, University of Arizona
B.A. Natural Science concentration in Chemistry, cum laude, Simon’s Rock College of Bard

Employment Experience

Senior Lecturer, Biological Sciences Collegiate Division, University of Chicago.
Lecturer, Biological Sciences Collegiate Division, University of Chicago.
CIBM Postdoctoral Trainee, Dept. of Biochemistry, University of Wisconsin.
Graduate Teaching Assistant, Mathematics Department, University of Arizona.
Staff Research Assistant, Los Alamos National Lab, Los Alamos, NM, USA.
Applications Chemist, Millipore Corp., Bedford, MA, USA.

Teaching Experience

University of Chicago

Introduction to quantitative modeling for biology (regular and advanced)
Mathematical methods for biological sciences I and II (and formerly III)
Multiscale modeling of biological systems I
Numbers on drugs (no longer teaching)

University of Arizona

Introduction to statistics
Mathematics in modern society
Elements of calculus

Other teaching

Biomedical Informatics Course: NLM-sponsored biannual week-long course; Marine Biology Lab (2013-14) and Augusta University, GA (2014–present)
School of Molecular and Theoretical Biology: three-week summer school for high school students, Pushchino, Russia
Mini-course on Markov Models in Biology: week-long seminar at Centre for Genomic Regulation, PRBB, Barcelona, Spain

Publications

Books

D.A. Kondrashov. Quantifying Life: A Symbiosis of Computation, Mathematics, and Biology. Chicago: University of Chicago Press, 2016.

Peer-reviewed publications

12. Kondrashov DA and Kondrashov FA. Topological features of rugged fitness landscapes in sequence space. Trends in Genetics, 31: 24-33 (2015) (cover article)
11. Kondrashov DA. Using normal mode analysis in teaching mathematical modeling to biology students. Mathematical Modeling of Natural Phenomena, 6: 278-294 (2011)
10. Bitto E, Bingman CA, Bittova L, Kondrashov DA, Bannen RM, Fox BG, Markley JL, and Phillips GN, Jr. Structure of human J-type co-chaperone HscB reveals a tetracysteine metal binding domain. Journal of Biological Chemistry, 283: 30184-30192 (2008)
9. Kondrashov DA, Zhang W, Aranda R IV, Stec B, and Phillips GN, Jr. Sampling of the native conformational ensemble of myoglobin via structures in different crystalline environments. Proteins, 70: 353-362 (2008)
8. Bitto E, Bingman CA, Kondrashov DA, McCoy JG, Bannen RM, Wesenberg GE, Phillips GN, Jr. Structure and dynamics of γ–SNAP: Insight into flexibility of proteins from the SNAP family. Proteins, 70: 93-104 (2008)
7. DiMaio F, Kondrashov DA, Bitto E, Soni A, Bingman CA, Phillips GN, Jr., Shavlik JW. Creating protein models from electron-density maps using particle-filtering methods. Bioinformatics, 23: 2851-2858 (2007)
6. Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN, Jr. Ensemble refinement of X-ray crystal structures of proteins: validation and application. Structure, 15: 1040-1050 (2007)
5. Kondrashov DA and Montfort WR. Nonequilibrium dynamics simulations of nitric oxide release: comparative study of nitrophorin and myoglobin. Journal of Physical Chemistry B, 111: 9244-9252 (2007) (cover article)
4. McCoy JG, Bitto E, Bingman CA, Wesenberg GE, Bannen RM, Kondrashov DA, Phillips GN, Jr. Structure and dynamics of UDP-glucose pyrophosphorylase from Arabidopsis thaliana with bound UDP-glucose and UTP. Journal of Molecular Biology, 366: 830-841 (2007)
3. Kondrashov DA, Van Wynsberghe AW, Bannen RM, Cui Q and Phillips GN, Jr. Protein structural variation in computational models and crystallographic data. Structure, 15: 169-177 (2007) (highlighted article); correction here
2. Kondrashov DA, Cui Q, and Phillips GN, Jr. Optimization and evaluation of a coarse-grained model of protein motion using X-ray crystal data. Biophysical Journal, 91: 2760-2767 (2006)
1. Kondrashov DA, Roberts SA, Weichsel A, and Montfort WR. Protein functional cycle viewed at atomic resolution: conformational change and mobility in nitrophorin 4 as a function of pH and NO binding. Biochemistry, 43: 13637-13647 (2004)

Mentoring

Thesis advisor for Alanna Gary, B.S. in Biology 2017 (expected)

Service

Reviewer: Letters in Biomathematics, PLoS Computational Biology, Biophysical Journal, Proteins, Biopolymers, Journal of Biological Physics, Workshop on Algorithms in Bioinformatics 2008
Member of search and reappointment committees at University of Chicago
External reviewer for faculty promotion at other institutions
Session organizer: SIAM annual meeting, Minneapolis, MN July 2012
Session organizer: Symposium on Biomathematics and Ecology: Education and Research (BEER), Portland, OR, December 2011
Outreach speaker: Science Chicago seminars for Chicago public school students and teachers, October 2008
Co-organizer: Steenbock Symposium on Protein Dynamics, University of Wisconsin, May 2006.
Organizer: Workshop for high school students on mathematics and biology, University of Arizona, November 2003.
Organizer: Graduate Mathematics Day, University of Arizona, May 2001.
Volunteer tutor: Berkshire Farm Center and Services for Youth, Canaan, NY, 1995-96.

Honors and Awards

  • NSF postdoctoral fellowship, Institute for Mathematics and its Applications for 2007-08 Year on Mathematics and Molecular and Cellular Biology (declined)
  • Travel award to ISMB/ECCB 2007 Vienna, Austria
  • Faculty of 1000 recommended paper, “Optimization and evaluation of a coarse- grained model of protein motion using X-ray crystal data"
  • 2005–2007 CIBM postdoctoral fellowship, NLM-supported Computation and Informatics in Biology and Medicine program, University of Wisconsin - Madison
  • 2004 Graduate fellowship, BIO5 Institute, University of Arizona
  • 1999-2003 NSF IGERT predoctoral fellowship, Biology, Mathematics, and Physics Initiative, University of Arizona
  • Graduate fellowship, Mathematics Department, University of Arizona