Sergei Maslov

For More Information

• Sergei Maslov's group webpage

Education

• Stony Brook University PhD 1996 Theoretical statistical physics

Academic Positions

• 2015- Full Professor and Bliss Faculty Scholar at the Department of Bioengineering, University of Illinois at Urbana-Champaign (100%)
• 2015- Full Professor and Bliss Faculty Scholar at the Department of Physics, University of Illinois at Urbana-Champaign (0%)

Documents

• Ecosystem network (top). Epistasis in protein-language models (bottom)

Other Professional Employment

• 9/2016 - present. Affiliate at the Computing, Environment, at the Computing, Environment and Life Sciences (CELS) directorate, Argonne National Laboratory, IL, USA
• 9/2025 - present Affiliate Member, NSF-Simons National Institute for Theory and Mathematics in Biology (NITMB), Chicago, Illinois, United States

Resident Instruction

• Spring 2018: BIOE 310, Computational Tools for Biological Data. A junior class teaching probability and statistics for bioengineers with applications in systems biology and genomics. 
• Fall 2020: BIOE 505, Computational Bioengineering. A core first year graduate class teaching probability and statistics for bioengineering graduate students with applications in systems biology and genomics.
• Spring 2021: BIOE 310, Computational Tools for Biological Data. A junior class teaching probability and statistics for bioengineers with applications in systems biology and genomics. 
• Fall 2021: BIOE 505, Computational Bioengineering. A core first year graduate class teaching probability and statistics for bioengineering graduate students with applications in systems biology and genomics.
• Fall 2022: BIOE 505, Computational Bioengineering. A core first year graduate class teaching probability and statistics for bioengineering graduate students with applications in systems biology and genomics.
• Spring 2023: BIOE 310, Computational Tools for Biological Data. A junior class teaching probability and statistics for bioengineers with applications in systems biology and genomics. 
• Fall 2023: BIOE 505, Computational Bioengineering. A core first year graduate class teaching probability and statistics for bioengineering graduate students with applications in systems biology and genomics.
• Spring 2024: BIOE 310, Computational Tools for Biological Data. A junior class teaching probability and statistics for bioengineers with applications in systems biology and genomics. 
• Fall 2024: BIOE 505, Computational Bioengineering. A core first year graduate class teaching probability and statistics for bioengineering graduate students with applications in systems biology and genomics. 24 students
• Spring 2025: BIOE 310, Computational Tools for Biological Data. A junior class teaching probability and statistics for bioengineers with applications in systems biology and genomics. 140 students
• Fall 2025: BIOE 505, Computational Bioengineering. A core first year graduate class teaching probability and statistics for bioengineering graduate students with applications in systems biology and genomics.
• Spring 2026: BIOE 310, Computational Tools for Biological Data. A junior class teaching probability and statistics for bioengineers with applications in systems biology and genomics. 

Research Interests

• Machine Learning
• Single Cell and Spatial Transcriptomics
• Human Gut Microbiome
• Phage-Bacterial Interactions
• Microbial Ecology & Evolution

Research Topics

• Computational and Systems Biology

Chapters in Books

• Maslov, S., Sneppen, K., and Alon, U. (2003). Correlation profiles and motifs in complex networks, an invited book chapter in the "Handbook of Graphs and Networks", S. Bornholdt, and H.-G. Schuster, (eds.), Wiley-VCH, Weinheim, pp. 168-198.

Selected Articles in Journals

• Tkachenko AV, Mognetti BM, Maslov S (2026) Evolutionary chemical learning in dimerization networks. Phys. Rev. E 114(3):035404.
• Thayer EA, Shipman G, Rivera-Cardona J, Mahajan T, Teo QW, Paez JS, Lederer J, Chen J, Wu NC, Maslov S, Brooke CB (2026) Single-cell heterogeneity in interferon induction potential is heritable and governed by variation in cell state. Cell Systems 101676.
• Wang Z, Fu Y, Goyal A, Maslov S (2026) Fitness advantage of sequential metabolic strategies emerges from community interactions in strongly fluctuating environments. PLoS Comput Biol 22(5):e1014277.
• Tong Wang, Ashish B. George, Sergei Maslov. "Higher-order interactions in auxotroph communities enhance their resilience to resource fluctuations." Cell Systems 17 (3): 101491 (2026).
• Joel Rivera-Cardona, Tarun Mahajan, Elizabeth A. Thayer, Neeharika R. Kakuturu, Qi Wen Teo, Joseph Lederer, Elizabeth F. Rowland, Kyle Heimburger, Jiayi Sun, Cera A. McDonald, Clayton K. Mickelson, Ryan A. Langlois, Nicholas C. Wu, Olgica Milenkovic, Sergei Maslov, Christopher B. Brooke. "Intrinsic OASL expression governs heterogeneity in interferon induction during influenza A virus infection." Proceedings of the National Academy of Sciences 123 (1): e2509560123 (2026).
• Tarun Mahajan, Sergei Maslov. "Coarse-grained model of serial dilution dynamics in synthetic human gut microbiome." PLoS Computational Biology 21 (7): e1013222 (2025).
• Tong Wang, Hannah D. Holscher, Sergei Maslov, Frank B. Hu, Scott T. Weiss, Yang-Yu Liu. "Predicting metabolite response to dietary intervention using deep learning." Nature Communications 16 (1): 815 (2025).
• Tkachenko, A. V., Maslov, S., 2024. Emergence of catalytic function in prebiotic information-coding polymers. Elife 12, RP91397. doi:10.7554/eLife.91397
• Nambiar, A., Pan, C., Rana, V., Cheraghchi, M., Ribeiro, J., Maslov, S., Milenkovic, O., 2024. Semi-quantitative group testing for efficient and accurate qPCR screening of pathogens with a wide range of loads. BMC Bioinform. 25, 195.
• Nambiar, A., Forsyth, J.M., Liu, S., Maslov, S., 2024. DR-BERT: A protein language model to annotate disordered regions. Structure 32, 1260-1268 e3.
• Miskalis, A., Shirguppe, S., Winter, J., Elias, G., Swami, D., Nambiar, A., Stilger, M., Woods, W.S., Gosstola, N., Gapinske, M., Zeballos, A., Moore, H., Maslov, S., Gaj, T., Perez-Pinera, P., 2024. SPLICER: a highly efficient base editing toolbox that enables in vivo therapeutic exon skipping. Nat. Commun. 15, 10354.
• Dubinkina, V., Bhogale, S., Hsieh, P.-H., Dibaeinia, P., Nambiar, A., Maslov, S., Yoshikuni, Y., Sinha, S., 2024. A transcriptomic atlas of acute stress response to low pH in multiple Issatchenkia orientalis strains. Microbiology Spectrum 12, e02536-23.
• George A.B., Wang T., Maslov S. (2023) Functional convergence in slow-growing microbial communities arises from thermodynamic constraints. ISME J. 2023 Sep;17(9):1482-1494. PubMed Central PMCID: PMC10432562.
• Fridman Y., Wang Z., Maslov S., Goyal A. (2022) Fine-scale diversity of microbial communities due to satellite niches in boom and bust environments, PLoS Comp Bio 18(12): e1010244. https://doi.org/10.1371/journal.pcbi.1010244
• Wang T, Wang X-W, Lee-Sarwar KA, Litonjua AA, Weiss ST, Sun Y, Maslov S, Liu YY. Predicting metabolomic profiles from microbial composition through neural ordinary differential equations. Nat Mach Intell. 2023; 1–10. https://doi.org/10.1038/s42256-023-00627-3
• Nambiar A, Dubinkina V, Liu S, Maslov S. FUN-PROSE: A deep learning approach to predict condition-specific gene expression in fungi. PLoS Comput Biol 19(11): e1011563 (2023) https://doi.org/10.1371/journal.pcbi.1011563
• Nambiar A, Liu S, Heflin M, Forsyth JM, Maslov S, Hopkins M, Ritz A. Transformer Neural Networks for Protein Family and Interaction Prediction Tasks. J Comput Biol. 2022. https://doi.org/10.1089/cmb.2022.0132
• Wang Z, Goyal A, Dubinkina V, George A, Wang T, Fridman Y, Maslov S. Complementary resource preferences spontaneously emerge in diauxic microbial communities. Nature Communications 12:6661,  DOI:10.1038/s41467-021-27023-y (2021).
• Tkachenko AV, Maslov S, Wang T, Elbanna A, Wong GN, Goldenfeld N. [co-first and co-corresponding author] (2021). Stochastic social behavior coupled to COVID-19 dynamics leads to waves, plateaus, and an endemic state. Elife 10, e68341, doi:10.7554/eLife.68341 (2021).
• Tkachenko AV, Maslov S, Elbanna A, Wong GN, Weiner ZJ, Goldenfeld N. Time-dependent heterogeneity leads to transient suppression of the COVID-19 epidemic, not herd immunity. PNAS 118(17):e2015972118 (2021).
• Kudella PW, Tkachenko AV, Salditt A, Maslov S, Braun D. Structured sequences emerge from random pool when replicated by templated ligation. Proceedings of the National Academy of Sciences. 2021 Feb 23;118(8):e2018830118. https://doi.org/10.1073/pnas.2018830118
• Goyal, A., Wang, T., Dubinkina, V. , Maslov S. Ecology-guided prediction of cross-feeding interactions in the human gut microbiome. Nat Commun 12, 1335 (2021). https://doi.org/10.1038/s41467-021-21586-6
• Wong GN, Weiner ZJ, Tkachenko AV, Elbanna A, Maslov S, Goldenfeld N. Modeling COVID-19 dynamics in Illinois under nonpharmaceutical interventions. Physical Review X. 2020 Nov 16;10(4):041033
• Ping D, Wang T, Fraebel DT, Maslov S, Sneppen K and Kuehn S (2020) [co-corresponding author] Hitchhiking, collapse, and contingency in phage infections of migrating bacterial populations. ISME Journal 14:2007-2018
• Wang T, Goyal A, Dubinkina V, Maslov S (2019) [corresponding author] Evidence for a multi-level trophic organization of the human gut microbiome. PLoS Comp Biol 15(12): e1007524. Selected for PLoS Comp Bio press release.
• Dubinkina V, Fridman Y, Pandey PP, Maslov S (2019) [corresponding author] Multistability and regime shifts in microbial communities explained by competition for essential nutrients. eLife 8:e49720; Selected for eLife digest cover article.
• Maslov S, Sneppen K (2019) Regime Shifts in a Phage-Bacterium Ecosystem and Strategies for Its Control. mSystems 4, e00470-19. Editor’s pick.
• Goyal A, Dubinkina V, Maslov S (2018) Multiple stable states in microbial communities explained by the stable marriage problem. ISME Journal 12: 2823–2834.
• Goyal A, Maslov S (2018) Diversity, stability, and reproducibility in stochastically assembled microbial ecosystems. Phys. Rev. Lett., 120, 158102.
• Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, et al. (2018) KBase: The United States Department of Energy Systems Biology Knowledgebase. Nature Biotechnology 36: 566–569;
• Tkachenko AV, Maslov S. Onset of natural selection in populations of autocatalytic heteropolymers (2018) J Chem Phys. 149, 134901
• Tkachenko AV & Maslov S (2015) Spontaneous emergence of autocatalytic information-coding polymers. J Chem Phys 143(4):045102.
• Maslov S & Sneppen K (2015) Well-temperate phage: optimal bet-hedging against local environmental collapses. Sci Rep 5:10523.
• Maslov S & Sneppen K (2015) Diversity Waves in Collapse-Driven Population Dynamics. PLoS Comput Biol 11(9):e1004440.
• Dixit PD, Pang TY, Studier FW, & Maslov S (2015) Recombinant transfer in the basic genome of Escherichia coli. Proc Natl Acad Sci U S A 112(29):9070-9075.
• Pang TY & Maslov S (2013) Universal distribution of component frequencies in biological and technological systems. Proc. Natl. Acad. Sci. U. S. A. 110(15):6235-6239.
• Dixit PD & Maslov S (2013) Evolutionary Capacitance and Control of Protein Stability in Protein-Protein Interaction Networks. PLoS Computational Biology 9(4):e1003023.
• Grilli J, Bassetti B, Maslov S, & Lagomarsino MC (2012) Joint scaling laws in functional and evolutionary categories in prokaryotic genomes. Nucleic Acids Res. 40(2):530-540.
• Heo M, Maslov S, & Shakhnovich E (2011) Topology of protein interaction network shapes protein abundances and strengths of their functional and nonspecific interactions. Proc. Natl. Acad. Sci. U. S. A. 108(10):4258-4263.
• Maslov S (2009) Power laws in chess. Physics 2:97.
• Studier FW, Daegelen P, Lenski RE, Maslov S, & Kim JF (2009) Understanding the differences between genome sequences of Escherichia coli B strains REL606 and BL21(DE3) and comparison of the E. coli B and K-12 genomes. Journal of molecular biology 394(4):653-680.
• Maslov S, Krishna S, Pang TY, & Sneppen K (2009) Toolbox model of evolution of prokaryotic metabolic networks and their regulation. Proc Natl Acad Sci U S A 106(24):9743-9748.
• Maslov S & Sneppen K (2002) Specificity and stability in topology of protein networks. Science 296(5569):910-913.
• Maslov S & Zhang YC (1998) Optimal investment strategy for risky assets. Int. J. Theor. Appl. Finance 1(3):377-387.

Articles in Conference Proceedings

• Strey HH, Mujica-Parodi L, Amgalan A, Maslov S (2015) Measuring social networks using proximity sensors. Proceedings of the 12th International Conference and Expo on Emerging Technologies for a Smarter World (CEWIT 2015), IEEE, article 7338168.
• Wang D, Pan E, Fang G, Kumari S, He F, Ware D, Maslov S, Gerstein M (2013) Comparative network analysis of gene co-expression networks reveals the conserved and species-specific functions of cell-wall related genes between Arabidopsis and Poplar. Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics (ACM-BCB 2013), pp. 689-690.

Pending Articles

• Wang, Z., Goyal, A. & Maslov, S. The ecological consequences of microbial metabolic strategies in fluctuating environments. bioRxiv, 2023.2007.2024.550395, doi:10.1101/2023.07.24.550395 (2023).
• Tarun Mahajan, Sergei Maslov. "noSpliceVelo infers gene expression dynamics without separating unspliced and spliced transcripts." bioRxiv 2024.08.08.607261 (2024).
• Ananthan Nambiar, S.B. Littlefield, C. Cuellar, R. Khorana, Sergei Maslov. "Protein Language Models Capture Structural and Functional Epistasis in a Zero-Shot Setting." bioRxiv 2025.09.14.676130 (2025).
• Zihan Wang, Jacopo Grilli, Akshit Goyal, Sergei Maslov. "Resource ratio fluctuations drive the evolution of microbial metabolic strategies." bioRxiv 2025.12.18.695187 (2025).
• Ananthan Nambiar, Kaushik Karambelkar, A. Athreya, A.M. Allen, K.N. Lazaridis, et al., Sergei Maslov. "ML-Guided GWAS Reveals Genetic Architectures for MASLD for Overweight and Lean Individuals in the All of Us Cohort." medRxiv 2025.12.18.25342567 (2025).

Journal Editorships

• Associate Editor, PLoS Computational Biology, 9/2019-present
• Editorial board member of Biology Direct Journal, 10/2005-present

Other Scholarly Activities

• One of two founding members of the COVID-19 modeling team at the University of Illinois at Urbana-Champaign. The team developed an agent-based model of COVID-19 epidemics on the UIUC campus. This model was used to advise the university leadership on testing frequency, scheduling, and mitigation measures such as, e.g., a temporary ban on student parties.
• One of two founding members of the COVID-19 modeling team for the office of the Governor of Illinois. Between April 2020 and July 2021, the modeling team provided weekly modeling predictions such as the likelihood to exceed hospital capacity in each of the 11 regions of the state.

Conferences Organized or Chaired

• International workshop "Mathematics of the Origin of Life and Self-Organized Complexity", NSF-Simons National Institute for Theory and Mathematics in Biology (NITMB) in Chicago, co-organized by Sergei Maslov, Jasna Brujic, Oleg Gang, Arvind Murugan, Rebecca Shulman, Jack Szostak, Alexei Tkachenko, 5/2025

Service on College Committees

• Grainger College of Engineering Executive Committee 2025-present

Service on Campus Committees

• Peer Reviewer, Campus Research Board, University of Illinois Urbana-Champaign (2025-2026)
• Math Bio Faculty Search Committee. Department of Mathematics, 2022

Honors

• University of Illinois Presidential Award and Medallion (2021)
• American Institute for Medical and Biological Engineering (AIMBE) fellow (2021)
• American Physical Society Fellow (2020)
• Bliss Faculty Scholar at University of Illinois at Urbana-Champaign (2014)
• Presidential Early Career Award for Scientists & Engineers (PECASE) (2002)

Recent Courses Taught

• BIOE 310 - Comp Tools Bio Data
• BIOE 505 (CSE 505) - Computational Bioengineering