Select publications

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

When predicting the function of microbial communities, simpler may be better (UChicago Biological Sciences News)

When more complex is simpler (The Source)

Bacteria could learn to predict the future (The Source)

Opinion: Microbiology Needs More Math (The Scientist Magazine)

Imagining a world without species: Theoretical physicist rethinks how we differentiate organisms on the microbial scale (Harvard SEAS News)

Resource competition: When communities collide (eLife)

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.

Y Zhao, OX Cordero, M Tikhonov. Linear-regression-based algorithms can succeed at identifying microbial functional groups despite the nonlinearity of ecological function. Preprint on bioRxiv.

RS McGee, G Kinsler, DA Petrov, M Tikhonov. Improving the accuracy of bulk fitness assays by correcting barcode processing biases. Preprint on bioRxiv.

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

Additional publications

K Crocker, KK Lee, M Chakraverti-Wuerthwein, Z Li, M Tikhonov, M Mani, K Gowda, S Kuehn. Environmentally-dependent interactions shape gene content in microbial communities. Nat Microbiol (accepted). 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.