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%)

Resident Instruction

• 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 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

Research Topics

• Computational and Systems Biology

Chapters in Books

• Maslov, S., Sneppen, K., and Alon, U. (2003). Correlation Profiles and Circuit 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.

Selected Articles in Journals

• (*)(W)(D) Tong Wang, Ashish B. George, Sergei Maslov. "Higher-order interactions in auxotroph communities enhance their resilience to resource fluctuations." Cell Systems 17 (3) (2026).
• (*)(W) 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).
• (*)(W) Tarun Mahajan, Sergei Maslov. "Coarse-grained model of serial dilution dynamics in synthetic human gut microbiome." PLoS Computational Biology 21 (7): e1013222 (2025).
• (*)(W) 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).
• (*)(W) Angelo Miskalis, Shraddha Shirguppe, Jackson Winter, Gianna Elias, Devyani Swami, Ananthan Nambiar, Michelle Stilger, Wendy S. Woods, Nicholas Gosstola, Michael Gapinske, Alejandra Zeballos, Hayden Moore, Sergei Maslov, Thomas Gaj, Pablo Perez-Pinera. "SPLICER: a highly efficient base editing toolbox that enables in vivo therapeutic exon skipping." Nature Communications 15 (1): 10354 (2024).
• Tkachenko, A. V., Maslov, S., 2024. Emergence of catalytic function in prebiotic information-coding polymers. Elife 12, RP91397.
• 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, Veronika, 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.
• 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. Microbiol. Spectr. 12, e0253623.
• George A.B., Wang T., Maslov S. (2023) Functional universality 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
• Tkachenko, A. V. & Maslov, S. Emergence of catalytic function in prebiotic information-coding polymers. eLife 12, RP91397, doi:10.7554/elife.91397.1 (2023).
• 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 2021 12, 6661:6661-6612,  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). Elife 10, e68341, doi:10.7554/eLife.68341 (2021).   
• Tkachenko AV, Maslov S, Elbanna A, Wong GN, Weiner ZJ, Goldenfeld N. Persistent heterogeneity not short-term overdispersion determines herd immunity to COVID-19. PNAS, 118 (17) e2015972118; 
• 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). 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, May 1 2020, pp. 1-12
• 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) Microbial community structure predicted by the stable marriage problem. ISME Journal 12: 2823–2834.
• Goyal A, Maslov S (2018) Diversity, stability, and reproducibility in stochastically assembled microbial ecosystem, Phys. Rev. Lett., 120, 158102.
• Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, et al. (2018) The DOE Systems Biology Knowledgebase (KBase). Nature Biotechnology 36: 566–569;
• Tkachenko AV, Maslov S. Onset of natural selection in auto-catalytic 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).
• 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.:4258-4263.
• 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.

Pending Articles

• Wang, Z., Fu, Y., Goyal, A., Maslov, S., 2025. Fitness advantage of sequential metabolic strategies emerges from community interactions in strongly fluctuating environments. bioRxiv 2024.06.14.599039.
• 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).
• (W) Tarun Mahajan, Sergei Maslov. "noSpliceVelo infers gene expression dynamics without separating unspliced and spliced transcripts." bioRxiv 2024.08.08.607261 (2024).
• A.V. Tkachenko, B.M. Mognetti, Sergei Maslov. "Evolutionary chemical learning in dimerization networks." arXiv 2506.14006 (2025).
• (W) 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).
• (W) Elizabeth A. Thayer, G. Shipman, Joel Rivera-Cardona, Tarun Mahajan, Qi Wen Teo, J.S. Paez, et al., Sergei Maslov, Christopher B. Brooke. "Single-cell heterogeneity in interferon induction potential is heritable and governed by variation in cell state." bioRxiv 2025.12.09.693293 (2025).
• (W) Zihan Wang, Jacopo Grilli, Akshit Goyal, Sergei Maslov. "Resource ratio fluctuations drive the evolution of microbial metabolic strategies." bioRxiv 2025.12.18.695187 (2025).
• (W) 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 with Jasna Brujic, Oleg Gang, Arvind Murugan, Rebecca Shulman, Jack Szostak, Alexei and Tkachenko, 5/2025

Service on Campus Committees

• 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