What do we do: modeling the evolution and immunology of pathogenes
Pathogens evolve rapidly to circumvent drug treatments and immune surveillance, which dramatically impacts public health. Research and treatment are complicated by high genetic diversity of some viruses within and across infected individuals, as well as their complex evolutionary mechanisms, including selection, random genetic drift, and temporal variation in a host environment. Moreover, many pathogens have a large number of linked sites approximately 102 -103 for HIV and hepatitis C virus (HCV) that evolve simultaneously and inter-dependently through two different effects, “epistasis” due to interaction between proteins and signaling network, and co-inheritance linkage (“clonal interference”). Our research is focused on developing mathematical tools that predict evolution of pathogens with strong linkage effects, including analytic and computational methods and estimators of evolutionary parameters from sequence data.
The last decade has seen explosive progress in mathematical modeling of microbial populations and high-fidelity sequencing. Taking advantage of these developments, my team will address evolution of microbes (yeast, bacteria) and viruses (HIV, influenza, polio, CHIKV, Dengue, HCV). Launching from my previous mathematical and applied studies, we are applying existing methods and models to study the viral evolution under time-dependent conditions, develop new mathematical techniques and improve existing phylogenetic tools, and identify some key factors of HIV pathogenesis. Our multi-disciplinary team fuses the recent mathematical discoveries with multiple-scale modeling and software tools. We are especially interested in the evolutionary effects of epistasis, recombination, and the theory of phylogenetic relationships in the presence of selection and the other factors. The project is designed to create significant clinical impact by fostering research into novel classes of drugs to control viral adaptation rate and achieve viral containment. Our software will facilitate personalized medicine and vaccine design against the pathogens escaping treatment and immune responses. The results are published and diffused in higher education and public presentations.
An example of a recent work
High-fidelity detection method of epistasis from DNA sequence samples
Pedruzzi & Rouzine, PLOS Pathogens 2021
A. The computer model of asexual evolution includes the factors of random mutation, selection, epistasis, and random genetic drift. Pairwise haplotype frequencies are averaged over an ensemble of independent simulation runs (populations). The strength of interactions, UFEij0, is calculated. The indirect links and the residual stochastic linkage disequilibrium are excluded by using triple-site haplotype frequencies, UFEij0.
B. Pre-set epistatic network for 50 sites. Real epistatic links are shown by green lines. The resulting indirect links are red lines. Some examples of stochastic linkage bonds are shown by blue lines. C-D. The network of strong ( UFE > 0.5 ) candidate epistatic interactions predicted (C) from a single population and (D) after averaging over 200 populations.
E. Scatter plot of 3-locus haplotype min(UFEij0) shown against UFEij for the pairs identified in (D). Dashed sector (green): Predicted direct interactions.
F. Predicted network accurately recapitulates the pre-set epistatic network.
- initial allele frequency 0.45,
- mutation rate per genome Ub = 0.07,
- fixed selection coefficient s = 0.1,
- epistatic strength E = 0.75.
Before 1995, Igor Rouzine worked in Condensed Matter Theoretical Physics, where he published 27 papers. Then he moved to the theory of evolution, application to viruses, and immunology of pathogens. Combining the methods of theoretical physics, population genetics, and epidemiology, he models mathematically the evolution, dynamics, and immunology of viruses. The aim is to understand and predict, with a mathematical precision, the systemic interaction between factors shaping evolution and dynamics of a pathogen. The modeling-style, commonly referred to as “biology-driven” or “bottom-up” approach, is designed to answer the questions “Why”, “How”, and “How much”, rather than merely describing data. PI worked on evolution and immunology of HIV, influenza virus, polio virus, vesicular stomatitis virus, and LCMV, and Plasmodium. The work was conducted in collaboration with virology and immunology laboratories in the USA (John Coffin at Tufts University, Boston, Leor Weinberger at the Gladstone Institute of Virology and Immunology, San Francisco, Raul Andino at UCSF, San Francisco, Rafi Ahmed at Georgia State University, Atlanta).
In 1999-2001, Igor published several papers, which detailed the basic mechanism of the rapid evolution of HIV in untreated patients and argued that it is due to the compensatory mutations of early CTL escape mutants, which prediction has been confirmed later. At the same time, he determined the relative role of stochastic effects and natural selection in HIV evolution. Later, he developed the first accurate theory of asexual evolution taking into account strong linkage effects existing between many evolving sites. Later, he showed that even rare recombination, which is the case for HIV, can accelerate evolution. His team then estimated the most important average parameters of HIV evolution, such as the average selection coefficient, the effective populations size, and the recombination rate.
Recently, Igor has proposed a model of primary HIV infection explaining the early formation of the latent HIV reservoir and proposing an evolutionary role for latency. He also investigated the stability and evolution of a virus in the presence of Defective Interference Particles and helped Leor Weinberger (Gladstone Institute) and Raul Andino (UCSF) to get NIH and DARPA grants on this topic . For all these tasks, Igor developed his own, custom-made mathematical approaches. In 2018, PI’s team published a paper explaining data on the evolution of influenza in the host population driven by immune response. They also developed a high-fidelity method of measuring the fitness landscape from viral sequence data, which is the most essential parameter for predicting viral adaptation.
1985 — M.S., Theor. Semicond. Physics, Electrical Engineering Institute, St. Petersburg, Russia
1988 — Ph.D., Theor. Semic. Physics, Ioffe Physico-Technical Institute, St. Petersburg, Russia
2017-2021 — Group Leader, Sorbonne Université (Pierre et Marie Curie), Laboratory of Computational and Quantitative Biology, Paris
2015-2017 — Specialist, Microbiology, University of California, San Francisco
2012-2015 — Staff Scientist, The Gladstone Institute of Virology and Immunology, San Francisco
2007-2011 — Research Associate Professor, Department of Molecular Biology and Microbiology, Tufts University, Boston
2001-2007 — Research Assistant Professor, Department of Molecular Biology and Microbiology, Tufts University, Boston
1996-2000 — Research Associate, Department of Molecular Biology and Microbiology, Tufts University, Boston
1993-1995 — Postdoctoral (Research) Associate, Department of Physics, University of California, Los Angeles
1990-1993 — Postdoctoral (Research) Associate, Theoretical Physics Institute, University of Minnesota, Minneapolis
1985-1990 — Researcher, Theoretical Department, A.F. Ioffe Physical Technical Institute, St. Petersburg, Russia
- English: fluent
- Russian: native
- French: advanced
- German: intermediate
- Italian: elementary
May 2016 — Pekin University, Center for Quantitative Biology, Bejing, China.
Oct-Nov 2015 — UPMC, Laboratory of Computational and Quantitative Biology, UMR 7238
CNRS- UPM, Paris, France
Oct-Dec 2011 — University of Cologne, Department of Physics, Germany
Aug-Sep 2011 — The Gladstone Institute of Virology and Immunology, San Francisco
June-July, 2011 — University of California at San Diego, Department of Chemistry and Biochemistry, La Jolla, CA, USA
Feb 2011 — Workshop on Microbial Evolution, KITP, University of California at Barbara, CA, USA
Mar, Jun-Aug 1995 — Harvard University, Department of Physics, Boston, USA
Apr-May, 1995 — Leiden University, Department of Physics, Leiden, Netherlands
- Computational and theoretical biology
- Dynamics and evolution of viruses
- Semiconductor Physics
Associations and service
2021-2022 — Organization Committee “QLife WS Quantitative Viral Dynamics Across Scales, March 21-25, 2022”
2021-now — Topic Editorial Board of Microorganisms
2018-2019 — Guest Editor of Pathogens
2006-2009 — Associate Editor of the Journal of Mathematical Analysis and Applications
2015-2017 — Member of the Society for Mathematical Biology
2013-2016 — Member of the American Mathematical Society
1990-1995 — Member of the American Physical Society
2017-2019 — Instructor in Evolution Modeling for third-year students of Sorbonne-Polytech, Paris
2013 — Adjunct Professor in Astronomy for business majors, University of San Francisco
1995 — Lecturer in Electricity and Magnetism for CS and EE majors, University of California at Los Angeles
2018-2020 — Public lectures at la Fête de la Science, Sorbonne Université Campus Pierre et Marie Curie, Paris, https://www.sorbonne-universite.fr/les-lois-de-la-selection-naturelle
Reviewer for international journals
AIDS Research Retroviruses
Bulletin of Mathematical Biology
Critical Reviews of Microbiology
Frontiers of Immunology
Inter. Journal of Molecular Sciences
Journal of Statistical Mechanics
Journal of Virology
Nucleic Acid Research
Proceed. of Nat. Acad. Sciences of USA
PLoS Computational Biology
Physical Review Letters
Physical Review B
Theoretical Population Biology
Reviewer for grants
|2020:||Vici grant proposal, Hague, Netherlands|
|2011:||NIH research grant proposal (R01)|
|2012:||NIH research grant proposal (R01)|
|2012:||Vienna Research Group grant proposal for Young Investigators|
ANR grant “Hosting high-level researchers”, $600,000 direct expenses
Grant DARPA-BAA-16-35–INTERCEPT, USA, $273 000
grant R21AI109611 from National Institutes of Health, $500,000 total
grant R01AI063926 from National Institutes of Health, USA, $1000,000 total
grant K25AI01811 from National Institutes of Health, USA, $600,000 total
Invited talks at seminars and conferences
|2021:||Seminar “Progression to AIDS and HIV controllers”, IAME, University de Paris, INSERM|
|2021:||Seminar “Progression to AIDS and HIV controllers”, University of Heidelberg, Germany|
|2020:||Seminar “Progression to AIDS and HIV controllers”, University of Montpelier, France|
|2019:||Nordita workshop “From Molecular Basis to Predictability and Control of Evolution”, Stockholm, Sweden.|
|2018:||3d IFOM Symposium “Evolution, Resistance, and Cancer”, IFOM, Milan, Italy.|
|2015:||5th Interdisciplinary Symposium “Genomics and Microbial Communities”, Institut de Biologie Paris-Seine, UPMC, Paris|
|2015:||Two seminars on the evolutionary role of HIV latency: Groupe de Travail math / bio, UPMC, Paris; Biophysique, Institut Curie, Paris|
|2015:||Seminar on the evolutionary role of HIV latency, IBM, Almaden Research Center, San Jose, CA|
|2014:||Seminar on modeling HIV evolution caused by the host immune response, IBM, Almaden, CA|
|2014:||Program “Evolution of Drug Resistance”, Kavli Institute of Theoretical Physics, University of California at Santa Barbara, CA|
|2014:||“Workshop on From Within-Host Dynamics to the Epidemiology of Infectious Disease”, Institute of Mathematical Biosciences, Columbus, Ohio|
|2014:||Seminar on therapeutic inteference particles, Institute of Biology, Paris Seine, UPMC, 2012: Workshop on Discrete and Topological Models in Molecular Biology and AMS special session on Discrete Models in Molecular Biology, University of Florida, Tampa, FL, USA|
|2011:||Seminar on modeling immune response against influenza, Department of Physics, University of Exeter, Exeter, UK|
|2011:||Workshop on Microbial Evolution, Kavli Institute for Theoretical Physics, University of California at Santa Barbara, Santa Barbara, CA, USA|
|2010:||Seminar on evolution theory, The National Evolutionary Synthesis Center, Duke University, Durham, NC, USA|
|2009:||International 3rd Eastern European and Central Asia AIDS Conference, Moscow, Russia|
|2007:||Workshop on Theoretical Immunology, University of Leuven, Belgium|
|2006:||Workshop on Mathematical Population Genetics, Edinburgh, UK|
|2006:||Seminar on evolution theory, Department of Evolution and Ecology, University of California at Davis, CA, USA|
|2006:||Two seminars on evolution theory and modeling HIV immunology, Department of Physics, University of California at San Diego, CA, USA|
|2005:||Seminar on modeling HIV immunology, Centre for Non-Linear Dynamics, Department of Physiology, McGill University, Montreal, Canada|
|2004:||Seminar on asexual evolution, Department of Biostatistics, University of California at Los Angeles, CA, USA|
|2004:||Seminar on evolution and dynamics of HIV at A.F. Ioffe Physical Technical Institute, St. Petersburg, Russia|
|2003:||Seminar in Genomics Center, Harvard University, Cambridge, MA, USA|
|2002:||Seminar on evolution theory of asexual populations, Department of Applied Mathematics, Massachusetts Technological Institute, Cambridge, MA, USA|
|2002:||Seminar on evolution theory of asexual populations, Department of Physics, Harvard University, Cambridge, MA, USA|
|1998:||Meeting on HIV Dynamics and Evolution, organized by University of California at San Diego|
|1995:||Seminar on antigenic escape of HIV from the immune response, Department of Microbiology, University of California, CA, USA|
Other presentations at conferences
|2021:||EEID Agropolis International (Université de Montpelier)|
|2021:||WIP ANRS AC41 (ANRS, Paris)|
|2021:||Alphy: Genomique evolutive (Université de Montpelier, Lyon, Grenoble)|
|2020:||Approche Interdisciplinaire de l’Evolution Moleculaire, Annual Meeting (CNRS INEE )|
|2012-2013:||4 informal seminars and 6 talks at the University of California at San Francisco|
|1996-2012:||20+ conferences including annual series:
Meeting on HIV evolution and dynamics (organized by UCSD, La Jolla, CA, USA)
Retroviruses (Cold Spring Harbor, NY)
Conference on Retroviruses and Opportunistic Infections
Keystone meetings at Keystone, Colorado, and Banff, Alberta, Canada
|1990-1995:||8-9 conferences including annual series:
Meeting of American Physical Society
Aspen Workshop on Condensed Matter Theory, Aspen, Colorado
Instruction of graduate and postdoctoral students
|2020:||Luis Pereira, postdoctoral associate, Sorbonne Université Campus Pierre et Marie Curie, Paris|
|2018:||Ayuna Barlukova, postdoctoral associate, Sorbonne Université Campus Pierre et Marie Curie, Paris|
|2017-2019:||Gabriele Pedruzzi, postdoctoral associate, Sorbonne Université Campus Pierre et Marie Curie, Paris|
|2014-2015:||Ariel Weinberger, collaborator and postdoctoral fellow at Harvard University|
|2013-2015:||Luke Rast, intern, Gladstone Institute of Virology and Immunology, University of California, San Francisco|
|2012:||Lisa Bishop, postdoctoral associate, Gladstone Institute of Virology and Immunology, University of California at San Francisco|
|2008-2012:||Rebecca Batorsky, graduate student, Department of Physics at Tufts University, Boston.|
|2006-2009:||Rinat Sergeev, postdoctoral associate, Department of Molecular Biology and Microbiology, Tufts University. (Current employment: Institute for Quantitative Social Science, Harvard University)|
|2007-2008:||Elena Gubankova, postdoctoral associate, Department of Molecular Biology and Microbiology, Tufts University|
|2003-2005:||Speranta Gheorghiu, postdoctoral associate, Department of Molecular Biology and Microbiology, Tufts University|
Collaboration with experimental teams
Raul Andino lab, Department of Microbiology and Immunology, University of California at San Francisco
Weinberger lab of Synthetic and Quantitative Virology, Gladstone Institute of Virology and Immunology, San Francisco
Coffin lab of Retrovirology, Department of Molecular Biology and Microbiology, Tufts University, Boston
John Coffin, Director (now Special Consultant), the HIV Drug Resistance Program at National Cancer Institute, NIH, Frederick, DC, USA
Novella lab of RNA virus evolution, College of Medicine, University of Toledo, Toledo, OH, USA
Rafi Ahmed, Director, Emory Vaccine Center, Atlanta, GA, USA
Results beyond the state-of-art
Rouzine* IM, Wakeley J, Coffin JM (2003) The solitary wave of asexual evolution. Proc Nat Acad Sci 100: 587-592
The first accurate mathematical analysis predicting the evolution rate of a population with a large number of linked loci in the absence of recombination.
Rouzine IM, Weinberger, AD, and Weinberger*, LS (2015) An evolutionary role for HIV latency in enhancing viral transmission. Cell 160, 1002–12
An evolutionary role for HIV latency is a Trojan horse effect during transmission.
Rouzine* IM, Coffin JM (2001) Transition between stochastic evolution and deterministic evolution in the presence of selection: general theory and application to virology [review]. Microbio Mol Bio Rev 65: 151-185
The classical stochastic theory of evolution 1930-1970 is reviewed and adapted for virology.
IM Rouzine (2020) An evolutionary model of progression to AIDS. Microorganisms 8, 1714
The first closed model of progression to AIDS is proposed based on gradual adaptation of HIV to a host is proposed.
Good BH, Rouzine IM, Balick DJ, Hallatschek O, and Desai* MM (2012) Distribution of fixed beneficial mutations and the rate of adaptation in asexual populations. Proc Natl Acad Sci U S A 109: 4950-4955
The traveling wave theory is generalized for the arbitrary distribution of mutational fitness effects.
Rouzine* IM and Rozhnova G (2018) Antigenic evolution of viruses in host populations. PLoS Pathogens 14, e1007291
A model of genetic evolution of a virus in a host population accumulating the immune memory connects epidemiology to immunology and the modern evolution theory. The predicted parameters are tested against data for influenza A.
Batorsky R, Kearney MF, Palmer SE, Maldarelli F, Rouzine* IM, Coffin JM (2011) Estimate of effective recombination rate and average selection coefficient for HIV in chronic infection. Proc Natl Acad Sci U S A 108: 5661
Rouzine* IM, Coffin JM (1999) Linkage disequilibrium test implies a large effective population number for HIV in vivo. Proc Nat Acad Sci 96: 10758-10763
The effective population size and the effective recombination rate of HIV are estimated correctly for the first time.
Rouzine* IM, Coffin JM (2005) Evolution of HIV under selection and weak recombination. Genetics 170: 7-18
Rouzine* IM, and Coffin, JM (2010) Many-site adaptation in the presence of infrequent recombination. Theor Pop Bio 77: 189-204
Recombination is incorporated in the modern multi-locus evolution theory
Rouzine* IM, Coffin JM (1999) Search for the mechanism of evolution in the pro gene of HIV in vivo. J Virol 73: 8167-8178.
The high diversity of HIV within and between infected individuals is explained as a result of compensatory mutations for the early escape mutations in CD8 T cell epitopes. The average value of the effective selection coefficient for HIV patient is estimated.
Rouzine* IM, McKenzie FE (2003) Link between immune response and parasite synchronization in malaria. Proc Nat Acad Sci 100: 3473-3478
Chaotic oscillations of parasitemia in malaria are predicted as a result of communication between different parasites in different phases of cell replication.
Rouzine IM. (2020) “Mathematical Models of Evolution. Volume 1: One-locus and multi-locus theory and recombination”, in series Mathematics and life sciences, De Gruyter, Berlin/Boston.
* Auteur correspondant
Rouzine* IM, Coffin JM (1999) Interplay between experiment and theory in development of a working model for HIV-1 population dynamics, in: Origin and Evolution of Viruses, eds. E.Domingo, R.Webster and J.Holland, Academic, London, 1999, pp.225-262.
Raikh* ME, Ruzin IM (1991) Transmittance fluctuations in randomly non-uniform barriers and incoherent mesoscopics, review, in: Mesoscopic Phenomena in Solids, eds. B.L.Altshuler, P.A.Lee and R.A.Webb. North Holland, Amsterdam, 1991, pp. 301-354.
Raikh* ME, Ruzin IM (1990) Distribution function of conductance of finite-size inhomogeneous barrier structures, in: Hopping and Related Phenomena, eds. H. Fritzsche and M. Pollak. World Scientific, Singapore, 1990, pp. 217-241.
Peer-reviewed publications (64 total)
Computational and theoretical biology
Pedruzzi G, Rouzine* IM (2021) An evolution-based high-fidelity method of epistasis measurement: theory and application to influenza. PLoS. Pathog. 17, e1009669. IF 6.2
Barlukova A, Rouzine* IM (2021) The evolutionary origin of the universal distribution of mutation fitness effect. PLoS Comp. Bio. 17, e1008822. IF 4.5
Rouzine IM (2020) An evolutionary model of progression to AIDS. Microorganisms 8, 1714 IF 4.2
Pedruzzi G, Rouzine IM * (2019) Epistasis detectably alters correlations between genomic sites in a narrow parameter window. PLoS ONE 14, e0214036. IF 2.7
Pedruzzi G, Barlukova A, Rouzine* IM (2018) Evolutionary footprint of epistasis. PLoS Computational Biology 14, e1006426. IF 4.5
Rouzine* IM, Rozhnova G (2018) Antigenic evolution of viruses in host populations. PLoS Pathogens 14, e1007291. IF 6.5
Lidsky PV, Andino R *, Rouzine IM (2017) Variability in viral pathogenesis: modeling the dynamic of acute and persistent infections. Current Opinion in Virology 23, 120-124. IF 5.6
Xiao Y, Rouzine IM, Bianco S, Acevedo A, Goldstein EF, Farkov, M, Andino M *. RNA recombination enhances adaptability and is required for virus spread and virulence (2016). Cell host & microbe 19 (4), 493-503. IF 17.9
LI Rast, IM Rouzine, G Rozhnova, L Bishop, AD, Weinberger*, LS. Conflicting selection pressures will constrain viral escape from interfering particles: principles for designing resistance-proof antivirals (2016). PLoS Computational Biology 12 (5), e1004799. IF 4.0
Rouzine, IM, Weinberger, AD, and Weinberger*, LS (2015) An evolutionary role for HIV latency in enhancing viral transmission. Cell 160, 1002–1012. IF 31.4
Razooky, BS, Pai, A, Aull, K, Rouzine, IM, and Weinberger*, LS (2015) A hardwired HIV latency program. Cell 160, 990–1001. IF 31.4
Batorsky, R, Sergeev, RA, Rouzine*, IM (2014) The route of HIV escape from immune response targeting multiple sites is determined by the cost-benefit tradeoff of escape mutations. PLoS Comp. Bio. 10, e1003878. IF 4.0
Rouzine IM, Razooky, BS, Weinberger*, LS (2014) Stochastic variability in HIV affects viral eradication. Proc Natl. Acad. Sci. U S A 111, 13251–13252. IF 9.5
Rouzine* IM, Coffin JM, Weinberger LS (2014) 15 years later: Hard and soft selection sweeps confirm a large population number for HIV in vivo. PLOS Genetics 10, e1004179. IF 5.5
Rouzine IM, Weinberger* LS (2013) Reply to ”Coadaptive stability of interfering particles with HIV-1 when there is an evolutionary conflict”. J Virol 87: 9960. IF 4.4
Rouzine IM, Weinberger* LS (2013) Design requirements for interfering particles to maintain co-adaptive stability with HIV-1. J Virol 87: 2081-2093. IF 4.4
Rouzine* IM, Weinberger LS (2013) The quantitative theory of within-host viral evolution [review]. J Stat Mech (2013) P01009
Good BH, Rouzine IM, Balick DJ, Hallatschek O, and Desai* MM (2012) Distribution of fixed beneficial mutations and the rate of adaptation in asexual populations. Proc Natl Acad Sci U S A 109: 4950-4955 IF 9.5
Batorsky R, Kearney MF, Palmer SE, Maldarelli F, Rouzine* IM, Coffin JM (2011) Estimate of effective recombination rate and average selection coefficient for HIV in chronic infection. Proc Natl Acad Sci U S A 108: 5661- IF 9.5
Rouzine*, IM, and Coffin, JM (2010) Many-site adaptation in the presence of infrequent recombination. Theor Pop Bio 77: 189-204
Sergeev, RA, Batorsky, RE, and Rouzine*, IM (2010) Model with two types of CTL regulation and experiments on CTL dynamics. J Theor Bio 263: 369-84.
Sergeev, RA, Batorsky, RE, and Rouzine*, IM (2010) Interpreting the effect of vaccination on steady state infection in animals challenged with simian immunodeficiency virus. J Theor Bio 263: 385-92.
Brunet*, E, Rouzine, IM, and Wilke, CO (2008) The stochastic edge in adaptive evolution. Genetics 179: 603-620 IF 3.8
Dutta, RN, Rouzine, IM, Smith, SD, Wilke, CO, and Novella*, IS (2008) Rapid adaptive amplification of preexisting variation in an RNA virus. J Virol 82: 4354-4362. IF 4.4
Rouzine*, IM, Brunet, E, and Wilke, CO (2008) The traveling-wave approach to asexual evolution: Muller’s ratchet and speed of adaptation. Theor Popul Biol 73: 24-46.
Rouzine* IM, Coffin JM (2007) Highly fit ancestors of partly sexual populations. Theor Pop Bio 71: 239-150.
Gheorghiu-Svirschevski S, Rouzine* IM, Coffin JM (2007) Increasing sequence correlations limits the efficiency of recombination in a multi-site evolution model. Mol Bio Evol 254: 574-586. IF 10.2
Rouzine* IM, Sergeev RA, Glushtsov AI (2006) Two types of cytotoxic lymphocyte regulation explain kinetics of immune response to human immunodeficiency virus. Proc Nat Acad Sci 103: 666-671 IF 9.5
Rouzine* IM, Coffin JM (2005) Evolution of HIV under selection and weak recombination. Genetics 170: 7-18 IF 3.8
Rouzine* IM, Murali-Krishna K, Ahmed R (2005) Generals die in friendly fire, or modeling immune response to HIV. J Comp Appl Math 184: 258-274. IF 1.4
Rouzine* IM, Wakeley J, Coffin JM (2003) The solitary wave of asexual evolution. Proc Nat Acad Sci 96: 587-592 IF 9.5
Rouzine* IM, McKenzie FE (2003) Link between immune response and parasite synchronization in malaria. Proc Nat Acad Sci 100: 3473-3478 IF 9.5
Rouzine* IM, Coffin JM (2001) Transition between stochastic evolution and deterministic evolution in the presence of selection: general theory and application to virology [review]. Microbio Mol Bio Rev 65: 151-185 IF 13.4
Rouzine* IM, Coffin JM (1999) Linkage disequilibrium test implies a large effective population number for HIV in vivo. Proc Nat Acad Sci 96: 10758-10763 IF 9.5
Rouzine* IM, Coffin JM (1999) Search for the mechanism of evolution in the pro gene of HIV in vivo. J Virol 73: 8167-8178 IF 4.4
Rouzine* IM, Coffin JM (1999) T cell turnover in SIV infection [comment]. Science 284: 555b IF 37.2
(Note spelling of name “Rouzine” as “Ruzin” from Cyrillic original name “Рузин”)
Cooper* NR, Halperin BI, Hu C, Ruzin IM Statistical properties of the low-temperature conductance peak heights for Corbino disks in the quantum Hall regime. Phys Rev B 1997; 55: 4551-
Cooper* NR, Halperin BI, Ruzin IM Thermoelectric response of an interacting two-dimensional electron gas in quantizing magnetic field. Phys Rev B 1997; 55: 2344-
Ruzin* IM, Cooper N, Halperin BI Non-universal behavior of finite quantum Hall systems as a result of weak macroscopic inhomogeneities. Phys Rev B 1996; 53: 1558-
Ruzin* I, Feng S Universal relation between longitudinal and transverse conductivities in quantum Hall effect. Phys Rev Lett 1995; 74: 154-
Dykhne AM, Ruzin* IM Theory of the fractional quantum Hall effect: The two-phase model. Phys Rev B 1994; 50: 2369-2379
Aleiner IL, Ruzin* IM Density of states of localized phonons in a pinned Wigner crystal. Phys Rev Lett 1994; 72: 1056-1060
Ruzin IM Hall transport in non-uniform two-dimensional conductors. Phys Rev B 1993; 47: 15727-15734
Ruzin* IM, Marianer S, Shklovskii BI Pinning of a two-dimensional Wigner crystal by charged impurities. Phys Rev B 1992: 46: 3999-4008
Ruzin IM, Chandrasekhar V, Levin EI, Glazman* LI Stochastic Coulomb blockade in a double-dot system. Phys Rev B 1992; 45: 13469-13478
Glazman LI, Ruzin IM, Shklovskii* BI Quantum transport and pinning of one-dimensional Wigner crystal. Phys Rev B 1992; 45: 8454-8463
Glazman* LI, Ruzin IM Metal-to-insulator crossover in mesoscopic wires [review]. Physica Scripta 1992; T42: 122-
Ruzin IM Fine structure of hopping conductance fluctuations in finite-size semiconductors. Phys Rev B 1991; 43: 11864-11872
SD Baranovskii, EI Levin, IM Ruzin, H Fritzsche, BI Shklovskii Computer simulation of energy relaxation and recombination of nonequilibriumelectrons in a disordered system with localized electronic states International Journal of Modern Physics C 1991; 2 : 220-222
Raikh ME, Ruzin* IM Size effect in the longitudinal hopping conduction of a narrow two-dimensional channel. Phys Rev B 1990; 42: 11203-11207
Ruzin IM, Shklovskii BI Theory of hopping conductivity due to long-wavelength excitation. Sov Phys Semicond 1989; 23: 1164-1167
Orlov AO, Raikh ME, Ruzin IM, Savchenko AK Statistical properties of mesoscopic conductivity fluctuations in a short-channel GaAs field-effect transistor. Sov Phys JETP 1989; 69: 1229-1236
Baranovskii SD, Fritzsche H, Levin EI, Ruzin IM, Shklovskii BI Theory of low-temperature photoconductivity and photoluminescence in amorphous semiconductors. Sov Phys JETP 1989; 69: 773-782
Raikh ME, Ruzin IM Fluctuations of the hopping conductance of one-dimensional systems. Sov Phys JETP 1989; 68: 642-647
Orlov AO, Raikh ME, Ruzin IM, Savchenko AK Distribution function of hopping conductance fluctuations of a short GaAs field- effect transistor channel. Solid State Communic 1989; 72: 169-172
Raikh ME, Ruzin IM, Shklovskii BI Influence of localized states in a barrier on a fluctuation tunnel current flowing across a metal-semiconductor contact. Sov Phys Semicond 1988; 22: 1254-1257
Raikh ME, Ruzin IM Mesoscopic behavior of the transverse hopping conductivity of an amorphous film. Sov Phys Semicond 1988; 22: 799-805
Levin EI, Ruzin IM, Shklovskii BI Transverse hopping conductivity of amorphous films in strong electric fields. Sov Phys Semicond 1988; 22: 401-408
Raikh ME, Ruzin IM Transparency fluctuations in randomly inhomogeneous barriers of finite area. Sov Phys JETP 1987; 65: 1273-1282
Tartakovskii AV, Fistul MV, Raikh ME, Ruzin IM Hopping conductivity of metal-semiconductor-metal contacts. Sov Phys Semicond 1987; 21: 370-373
Raikh ME, Ruzin IM Temperature dependence of fluctuation excess currents flowing across a metal-semiconductor contact. Sov Phys Semicond 1987; 21: 283-285
Raikh ME, Ruzin IM Mesoscopic behavior of the temperature dependence of the transverse hopping conductivity of an amorphous film. JETP Lett 1986; 43: 563-565
Gerbstein* YuM, Ruzin IM, Chudnovskii FA Fractal dimensionality of silver dendrites in the two-dimensional ionically conducting system Ag-AgI-Ag. Sov Phys Solid State 1986; 28: 1073-1074
Raikh* ME, Ruzin IM Fluctuation mechanism of excess tunnel currents in reverse-biased p-n– junctions. Sov Phys Semicond 1985; 19: 745-750