TITLE: Bioinformatics and Systems Biology Graduate Student (2008-June 2014)
OFFICE: NSB 3209
EMAIL: mshokhir at ucsd.edu
B.S. Computer Science, Biochemistry and Molecular Biophysics, University of Arizona – 2008
I am interested in understanding how cell population dynamics are coordinated on the cellular and biochemical levels. A prime example, the mammalian immune response involves seemingly stochastic cellular decisions to respond, divide, and undergo programmed cell death. Understand how immune cells make decisions that result in an effective population response sheds light on the nature of multi-cellular biology and may provide insights into treating immune disorders and cancers. To this end, I have developed computational tools for describing cell population dynamics in terms of stochastic cellular processes, cell tracking software for quantifying time-lapse microscopy movies, performed single-cell RNAseq experiments, ran immunfluorescence studies, and constructed kinetic ODE models which incorporate the cell-cycle, apoptosis, and NFkB signaling. This has allowed me to characterize the responses of primary mouse B cells under diverse conditions in a multi-scale manner.
- Shokhirev MN and Alexander Hoffmann (2013) FlowMax: a computational tool for maximum likelihood deconvolution of CFSE time courses. PLoS One.
- Jiao B, Ma H, Shokhirev MN, Drung A, Yang Q, et al. (2012) Paternal RLIM/Rnf12 is a survival factor for milk-producing alveolar cells. Cell 149: 630-641.
- Grubisic I, Shokhirev MN, Orzechowski M, Miyashita O, Tama F (2010) Biased coarse-grained molecular dynamics simulation approach for flexible fitting of X-ray structure into cryo electron microscopy maps. J Struct Biol 169: 95-105.
- Berry RE, Shokhirev MN, Ho AY, Yang F, Shokhireva TK, et al. (2009) Effect of mutation of carboxyl side-chain amino acids near the heme on the midpoint potentials and ligand binding constants of nitrophorin 2 and its NO, histamine, and imidazole complexes. J Am Chem Soc 131: 2313-2327.
- Knipp M, Yang F, Berry RE, Zhang H, Shokhirev MN, et al. (2007) Spectroscopic and functional characterization of nitrophorin 7 from the blood-feeding insect Rhodnius prolixus reveals an important role of its isoform-specific N-terminus for proper protein function. Biochemistry 46: 13254-13268.
- Berry RE, Shokhireva T, Filippov I, Shokhirev MN, Zhang H, et al. (2007) Effect of the N-terminus on heme cavity structure, ligand equilibrium, rate constants, and reduction potentials of nitrophorin 2 from Rhodnius prolixus. Biochemistry 46: 6830-6843.
- Borunda, P.; Brewer, C.; Erten, C.; King, N.; Nation Z.; Shokhirev, M. (2005) GSPIM: Graphical Visualization Tool for MIPS Assembly Programming and Simulation. SIGCSE 2005.