Select publications

RS McGee, G Kinsler, DA Petrov, M Tikhonov. Improving the accuracy of bulk fitness assays by correcting barcode processing biases. Mol Biol Evol, msae152. Open access.

A Skwara, K Gowda, M Yousef, J Diaz-Colunga, AS Raman, A Sanchez, M Tikhonov, S Kuehn (2023). Statistically learning the functional landscape of microbial communities. Nat Ecol Evol 7: 1823-33. Preprint on bioRxiv.

J Moran, M Tikhonov (2022). Defining coarse-grainability in a model of structured microbial ecosystems. PRX 12: 021038. Open access.

J Bergelson, M Kreitman, DA Petrov, A Sanchez, M Tikhonov (2021). Functional biology in its natural context: A search for emergent simplicity. eLife 10: e67646 (equal contribution of all authors). Open access.

JE Goldford*, N Lu*, D Bajic, S Estrela, M Tikhonov, A Sanchez-Gorostiaga, D Segre, P Mehta, and A Sanchez (2018). Emergent simplicity in microbial community assembly. Science 361 (6401): 469-74. Preprint on bioRxiv (*equal contribution).

M Tikhonov and R Monasson (2017). Collective phase in resource competition in a highly diverse ecosystem. PRL 118 (4): 048103. Preprint at arXiv:1609.01270.

In the media

Tikhonov wins NSF CAREER award (Ampersand, Washington University in St Louis; 2024)
When predicting the function of microbial communities, simpler may be better (UChicago Biological Sciences News; 2023)
When more complex is simpler (The Source, Washington University in St Louis; 2022)
Bacteria could learn to predict the future (The Source, Washington University in St Louis; 2021)
Opinion: Microbiology Needs More Math (The Scientist Magazine; 2017)
Imagining a world without species (Harvard SEAS News; 2017)
Resource competition: When communities collide (eLife; 2016)

Preprints

J Moran, M Tikhonov. Emergent predictability in microbial ecosystems. Preprint on arXiv.

A Goyal, M Tikhonov. Energy-ordered resource stratification as an agnostic signature of life. Preprint on arXiv.

KK Lee, S Liu, K Crocker, DR Huggins, M Tikhonov, M Mani, S Kuehn. Functional phases encode the response of the soil microbiome to environmental change. Preprint on bioRxiv.

F Yu, M Tikhonov. Generalized end-product feedback circuit senses high dimensional environmental fluctuations. Preprint on arXiv.

Additional publications

Y Zhao, OX Cordero, M Tikhonov. Linear-regression-based algorithms can succeed at identifying microbial functional groups despite the nonlinearity of ecological function. PLOS Comp Biol 20(11): e1012590. (open access)

K Crocker, KK Lee, M Chakraverti-Wuerthwein, Z Li, M Tikhonov, M Mani, K Gowda, S Kuehn (2024). Environmentally dependent interactions shape patterns in gene content across natural microbiomes. Nat Microbiol DOI: 10.1038/s41564-024-01752-4. Preprint on bioRxiv.

BD Knapp, L Willis, C Gonzalez, H Vashistha, JJ Touma, M Tikhonov, J Ram, H Salman, JE Elias, KC Huang. Metabolomic rearrangement controls the intrinsic microbial response to temperature changes. Nat Microbiol (accepted). Preprint on bioRxiv.

J Diaz-Colunga, A Skwara, K Gowda, R Diaz-Uriarte, M Tikhonov, D Bajic, A Sanchez (2023). Global epistasis on fitness landscapes. Philos Trans R Soc B 378 (1877): 20220053. Preprint on arXiv.

J Díaz-Colunga, N Lu, A Sanchez-Gorostiaga, CY Chang, HS Cai, JE Goldford, M Tikhonov, and A Sánchez (2022). Top-down and bottom-up cohesiveness in microbial community coalescence. PNAS 119 (6): e2111261119.

S Landmann, CM Holmes, M Tikhonov (2021). A simple regulatory architecture allows learning the statistical structure of a changing environment. eLife 10: e67455. Open access.

J Moran, D Finlay, M Tikhonov (2021). Improve it or lose it: Evolvability cost of competition for expression. PRE 103 (6): 062402. Preprint on arXiv.

M Tikhonov, S Kachru, and DS Fisher (2020). A model for the interplay between plastic tradeoffs and evolution in changing environments. PNAS 117 (16): 8934-40. Open access.

C Strandkvist, P Chvykov, M Tikhonov (2020). Metric flow naturally encodes question-dependent emergence of effective theories in complex systems. Preprint on arXiv.

S Mukherjee, M Jemielita, V Stergioula, M Tikhonov, and BL Bassler (2019). Photosensing and quorum sensing are integrated to control Pseudomonas aeruginosa collective behaviors. PLOS Biology 17 (12): e3000579 (open access).

Y Guo, M Tikhonov, and MP Brenner (2018). Local growth rules can maintain metabolically efficient spatial structure throughout growth. PNAS 115 (14): 3593-98.

M Tikhonov and R Monasson (2018). Innovation rather than improvement: a solvable high-dimensional model highlights the limitations of scalar fitness. J Stat Phys 172 (1): 74. Open view access; preprint also available at arXiv:1708.05453.

M Tikhonov (2017). Theoretical microbial ecology without species. PRE 96: 032410. Preprint at arXiv:1504.02550. 

ED Sonnenburg, SA Smits, M Tikhonov, SK Higginbottom, NS Wingreen, and JL Sonnenburg (2016). Diet-induced extinctions in the gut microbiota compound over generations. Nature 529 (7585): 212. Available at Harvard DASH.

M Tikhonov (2016). Community-level cohesion without cooperation. eLife 5: e15747. Open access. 

M Tikhonov and W Bialek (2016). Complexity of generic biochemical circuits: topology versus strength of interactions. Phys Biol 13 (6): 066012, featured article. Preprint at arXiv:1308.0317.

M Tikhonov, RW Leach, and NS Wingreen (2015). Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution. ISME J 9 (1): 68. Preprint at arXiv:1312.0570.

M Tikhonov, SC Little, and T Gregor (2015). Only accessible information is useful: insights from gradient-mediated patterning. R Soc Open Sci 2 (11): 150486 (open access). 

SC Little*, M Tikhonov*, and T Gregor (2013). Precise developmental gene expression arises from globally stochastic transcriptional activity. Cell 154 (4): 789 (*equal contribution; open archive). 

HG Garcia, M Tikhonov, A Lin, and T Gregor (2013). Quantitative imaging of transcription in living Drosophila embryos links polymerase activity to patterning. Curr Biol 23 (21): 2140 (open archive). 

AM Popov, MA Tikhonov, OV Tikhonova, and EA Volkova (2009). Comparative analysis of the strong-field ionization of a quantum system with the Coulomb and short-range potentials. Laser Physics 19 (2): 191. 

A Kapustin and M Tikhonov (2009). Abelian duality, walls and boundary conditions in diverse dimensions. JHEP 2009 (11) 006 (open access).

AM Popov, MA Tikhonov, OV Tikhonova, and EA Volkova (2008). Hydrogen atom in a strong laser field: Numerical simulation versus Keldysh-type theories. Laser Physics 18 (5): 568. 

EA Volkova, AM Popov, MA Tikhonov, and OV Tikhonova (2007). Atom under an intense laser pulse: Stabilization effect and strong-field approximation. JETP 105 (3): 526.