Google Scholar profile

Selected publications in peer-reviewed journals

• Biswas, K., Mitrophanov, A. Y., Sahu, S., Sullivan, T., Southon, E., Nousome, D., Reid, S., Narula, S., Smolen, J., Sengupta, T., Riedel-Topper, M., Kapoor, M., Babbar, A., Stauffer, S., Cleveland, L., Tandon, M., Malys, T., and Sharan, S. K. (2023) Sequencing-based functional assays for classification of BRCA2 variants in mouse ES cells. Cell Rep Methods 3: 100628 [Article]
• Sahu, S., Sullivan, T. L., Mitrophanov, A. Y., Galloux, M., Nousome, D., Southon, E., Caylor, D., Mishra, A. P., Evans, C. N., Clapp, M. E., Burkett, S., Malys, T., Chari, R., Biswas, K., and Sharan, S. K. (2023) Saturation genome editing of 11 codons and exon 13 of BRCA2 coupled with chemotherapeutic drug response accurately determines pathogenicity of variants. PLOS Genet 19: e1010940 [Article]
• Pandkar, M. R., Raveendran, A., Biswas, K., Mutnuru, S. A., Mishra, J., Samaiya, A., Malys, T., Mitrophanov, A. Y., Sharan, S. K., and Shukla, S. (2023) PKM2 dictates the poised chromatin state of PFKFB3 promoter to enhance breast cancer progression. NAR Cancer 5: zcad032 [Article]
• Mitrophanov, A. Y., Vandyck, K., and Tanaka, K. A. (2022) Thrombin generation in trauma patients: how do we navigate through Scylla and Charybdis? Curr Anesthesiol Rep 12: 308-319 [Article]
• Grover, S. P., Bendapudi, P. K., Yang, M., Merrill-Skoloff, G., Govindarajan, V., Mitrophanov, A. Y., and Flaumenhaft, R. (2020) Injury measurements improve interpretation of thrombus formation data in the cremaster arteriole laser-induced injury model of thrombosis. J Thromb Haemost 18: 3078-3085 [Article]
• Mitrophanov, A. Y., Merrill-Skoloff, G., Grover, S. P., Govindarajan, V., Kolanjiyil, A., Hariprasad, D. S., Unnikrishnan, G., Flaumenhaft, R., and Reifman, J. (2020) Injury length and arteriole constriction shape clot growth and blood-flow acceleration in a mouse model of thrombosis. Arterioscler Thromb Vasc Biol 40: 2114-2126 [Article]
• Mitrophanov, A. Y., Szlam, F., Sniecinski, R. M., Levy, J. H., and Reifman, J. (2020) Controlled multifactorial coagulopathy: effects of dilution, hypothermia, and acidosis on thrombin generation in vitro. Anesth Analg 130: 1063-1076 [Article]
• Mitrophanov, A. Y., Govindarajan, V., Zhu, S., Li, R., Lu, Y., Diamond, S. L., and Reifman, J. (2019) Microfluidic and computational study of structural properties and resistance to flow of blood clots under arterial shear. Biomech Model Mechanobiol 18: 1461-1474 [Article]
• Nagaraja, S., Chen, L., DiPietro, L. A., Reifman, J., and Mitrophanov, A. Y. (2019) Predictive approach identifies molecular targets and interventions to restore angiogenesis in wounds with delayed healing. Front Physiol 10: 636 [Article]
• Hobbs, S., Reynoso, M., Geddis, A. V., Mitrophanov, A. Y., and Matheny, R. W. (2018) LPS-stimulated NF-kB p65 dynamic response marks the initiation of TNF expression and transition to IL-10 expression in RAW 264.7 macrophages. Physiol Rep 6: e13914 [Article]
• Govindarajan, V., Zhu, S., Li, R., Lu, Y., Diamond, S. L., Reifman, J., and Mitrophanov, A. Y. (2018) Impact of tissue factor localization on blood clot structure and resistance under venous shear. Biophys J 114: 978-991 [Article]
• Nagaraja, S., Chen., L., DiPietro, L. A., Reifman, J., and Mitrophanov, A. Y. (2018) Computational analysis identifies putative prognostic biomarkers of pathological scarring in skin wounds. J Transl Med 16: 32 [Article]
• Chen, L., Nagaraja, S., Zhou, J., Zhao, Y., Fine, D., Mitrophanov, A. Y., Reifman, J., and DiPietro, L. A. (2017) Wound healing in Mac-1 deficient mice. Wound Rep Reg 25: 366-376 [PDF]
• Mitrophanov, A. Y., Szlam, F., Sniecinski, R. M., Levy, J. H., and Reifman, J. (2017) In response to “Clinical and practical aspects of restoring thrombin generation in acute coagulopathic bleeding.” Anesth Analg 124: 702 [PDF]
• Mitrophanov, A. Y., Szlam, F., Sniecinski, R. M., Levy, J. H., and Reifman, J. (2017) In response to “If the goal is balance, why not fresh frozen plasma?” Anesth Analg 124: 699-700 [PDF]
• Nagaraja, S., Chen, L., Zhou, J., Zhao, Y., Fine, D., DiPietro, L. A., Reifman, J., and Mitrophanov, A. Y. (2017) Predictive analysis of mechanistic triggers and mitigation strategies for pathological scarring in skin wounds. J Immunol 198: 832-841 [PDF]
• Mitrophanov, A. Y., Szlam, F., Sniecinski, R. M., Levy, J. H., and Reifman, J. (2016) A step toward balance: thrombin generation improvement via procoagulant factor and antithrombin supplementation. Anesth Analg 123: 535-546 [PDF]
• Govindarajan, V., Rakesh, V., Reifman, J., and Mitrophanov, A. Y. (2016) Computational study of thrombus formation and clotting factor effects under venous flow conditions. Biophys J 110: 1869-1885 [Article]
• Tomaiuolo, M., Kottke, M., Matheny, R. W., Reifman, J., and Mitrophanov, A. Y. (2016) Computational identification and analysis of signaling subnetworks with distinct functional roles in the regulation of TNF production. Mol BioSyst 12: 826-838 [Article]
• Nagaraja, S., Reifman, J., and Mitrophanov, A. Y. (2015) Computational identification of mechanistic factors that determine the timing and intensity of the inflammatory response. PLOS Comput Biol 11: e1004460 [Article]
• Mitrophanov, A. Y., Rosendaal, F. R., and Reifman, J. (2015) Mechanistic modeling of the effects of acidosis on thrombin generation. Anesth Analg 121: 278-288 [Article]
• Mitrophanov, A. Y., Wolberg, A. S., and Reifman, J. (2014) Kinetic model facilitates analysis of fibrin generation and its modulation by clotting factors: implications for hemostasis-enhancing therapies. Mol BioSyst 10: 2347-2357 [PDF]
• Nagaraja, S., Wallqvist, A., Reifman, J., and Mitrophanov, A. Y. (2014) Computational approach to characterize causative factors and molecular indicators of chronic wound inflammation. J Immunol 192: 1824-1834 [Article]
• Mitrophanov, A. Y., Rosendaal, F. R., and Reifman, J. (2013) Computational analysis of the effects of reduced temperature on thrombin generation: the contributions of hypothermia to coagulopathy. Anesth Analg 117: 565-574 [Article]
• Mitrophanov, A. Y., Rosendaal, F. R., and Reifman, J. (2012) Therapeutic correction of thrombin generation in dilution-induced coagulopathy: computational analysis based on a data set of healthy subjects. J Trauma Acute Care Surg 73: S95-S102 [PDF]
• Mitrophanov, A. Y., Rosendaal, F. R., and Reifman, J. (2012) Computational analysis of intersubject variability and thrombin generation in dilutional coagulopathy. Transfusion 52: 2475-2486 [PDF]
• Mitrophanov, A. Y. and Reifman, J. (2011) Kinetic modeling sheds light on the mode of action of recombinant factor VIIa on thrombin generation. Thrombosis Res 128: 381-390 [PDF]
• Mitrophanov, A. Y., Hadley, T. J., and Groisman, E. A. (2010) Positive autoregulation shapes response timing and intensity in two-component signal transduction systems. J Mol Biol 401: 671-680 [PDF]
• Mitrophanov, A. Y. and Groisman, E. A. (2010) Response acceleration in post-translationally regulated genetic circuits. J Mol Biol 396: 1398-1409 [PDF]
• Mitrophanov¹, A. Y., Jewett¹, M. W., Hadley, T. J., and Groisman, E. A. (2008) Evolution and dynamics of regulatory architectures controlling polymyxin B resistance in enteric bacteria. PLOS Genet 4: e1000233 [Article]
  ¹Equal authorship
• Mitrophanov, A. Y. and Groisman, E. A. (2008) Signal integration in bacterial two-component regulatory systems. Genes Dev 22: 2601-2611 [Article]
• Mitrophanov, A. Y. and Groisman, E. A. (2008) Positive feedback in cellular control systems. Bioessays 30: 542-555 [PDF]
• Kato¹, A., Mitrophanov¹, A. Y., and Groisman, E. A. (2007) A connector of two-component regulatory systems promotes signal amplification and persistence of expression. Proc Natl Acad Sci USA 104: 12063-12068 [Article]
  ¹Equal authorship
• Mitrophanov, A. Y., Churchward, G., and Borodovsky, M. (2007) Control of Streptococcus pyogenes virulence: modeling of the CovR/S signal transduction system. J Theor Biol 246: 113-128 [PDF]
• Mitrophanov, A. Y. and Borodovsky, M. (2007) Convergence of the TKF91 model and biological sequence length evolution. Math Biosci 209: 470-485 [PDF]
• Mitrophanov, A. Yu. and Borodovsky, M. (2006) Statistical significance in biological sequence analysis. Brief Bioinform 7: 2-24 [Article]
• Mitrophanov, A. Yu. (2006) Stability estimates for finite homogeneous continuous-time Markov chains. Theory Probab Appl 50: 319-326 [PDF]
• Mitrophanov, A. Yu. (2005) Sensitivity and convergence of uniformly ergodic Markov chains. J Appl Probab 42: 1003-1014 [PDF]
• Mitrophanov, A. Yu., Lomsadze, A., and Borodovsky, M. (2005) Sensitivity of hidden Markov models. J Appl Probab 42: 632-642 [PDF]
• Mitrophanov, A. Yu. (2005) Ergodicity coefficient and perturbation bounds for continuous-time Markov chains. Math Inequal Appl 8: 159-168 [PDF]
• Mitrophanov, A. Yu. (2004) The spectral gap and perturbation bounds for reversible continuous-time Markov chains. J Appl Probab 41: 1219-1222 [PDF]
• Mitrophanov, A. Yu. (2004) Reversible Markov chains and spanning trees. Math Scientist 29: 107-114 [PDF] [The journal's web page]
• Mitrophanov, A. Yu. (2004) Note on Zeifman's bounds on the rate of convergence for birth-death processes. J Appl Probab 41: 593-596 [PDF]
• Mitrophanov, A. Yu. (2003) Stability and exponential convergence of continuous-time Markov chains. J Appl Probab 40: 970-979 [PDF]
• Evseeva, N. V., Tkachenko, O. V., Lobachev, Yu. V., Mitrophanov, A. Yu., Djatchouk, T. I., and Shchyogolev, S. Yu. (2002) Studies on the embryogenic processes in the in vitro culture of wheat somatic tissues by using a proliferative antigen of initial cells. Wheat Information Service 94: 1-4 [PDF]
• Mitrophanov, A. Yu. (2001) Stochastic Markov models for the process of binary complex formation and dissociation. Mat Model 13 (9): 101-109
  [Math-Net.Ru entry] [PDF] [Author's English translation in PDF]
  

Other publications

Thought leadership, research-community building, scientific outreach

• Mitrophanov, A. Y. (2023) Statistics, stochastics, and data science for systems biology. IMS Bulletin 52(7): 19-20 [PDF] [HTML]
• Mitrophanov, A. Y. (2022) Quantitative perturbation theory for stochastic processes. IMS Bulletin 51(6): 10-11 [PDF] [HTML]

Some relevant works by other people