Publications

My Google Scholar Profile

 PREPRINTS

• Daniel W. Swartz*, Hyunseok Lee*, Mehran Kardar, Kirill S. Korolev, New sector morphologies emergefrom anisotropic colony growth, arXiv:2405.19478 (2024)

• Ilija Dukovski, Lauren Golden*, Jing Zhang, Melisa Osborne, Daniel Segr`e, and Kirill S. Korolev, Biophysical metabolic modeling of complex bacterial colony morphology, bioRxiv (2024)

• Louis Brezin* and Kirill S. Korolev, Mechanically-driven growth and competition in a Voronoi model of tissues, arXiv:2405.07899 (2024)

• Zhenjun Hu, Dileep Kishore, Yan Wang, Gabriel Birzu, Charles DeLisi, Kirill S. Korolev, Daniel Segrè, A resource for the comparison and integration of heterogeneous microbiome networks (bioRxiv).

PUBLICATIONS

2023

• Daniel W. Swartz*, Hyunseok Lee*, Mehran Kardar, Kirill S. Korolev, Interplay between morphology and competition in two-dimensional colony expansion, Physical Review E 108, L032301 (2023)

• Dileep Kishore*, Gabriel Birzu*, Zhenjun Hu, Charles DeLisi, Kirill S. Korolev, and Daniel Segr`e, Infer-ring microbial co-occurrence networks from amplicon data: a systematic evaluation, mSystems 8:e00961-22 (2023)

• Ashish B. George and Kirill S. Korolev, Ecological landscapes guide the assembly of optimal microbial communities, PLoS Computational Biology19(1): e1010570 (2023).

2022

• Hyunseok Lee, Jeff Gore, and Kirill S. Korolev, Slow expanders invade by forming dented fronts in microbial colonies, PNAS 119(1), e2108653119 (2022)

• Alexander Golden, Ilija Dukovski, Daniel Segre, and Kirill S Korolev, Growth instabilities shape morphology and genetic diversity of cellular aggregates, Physical Biology, (2022).

2021

• Gabriel Birzu, Oskar Hallatschek, and Kirill S. Korolev, Genealogical structure changes as range expansions transition from pushed to pulled, PNAS118 (34) e2026746118 (2021).

• Ilija Dukovski, Djordje Bajić, Jeremy M Chacón, Michael Quintin, Jean CC Vila, Snorre Sulheim, Alan R Pacheco, David B Bernstein, William J Rieh, Kirill S Korolev, Alvaro Sanchez, William R Harcombe, Daniel Segrè, Computation Of Microbial Ecosystems in Time and Space (COMETS), Nature Protocols 16, 5030–5082 (2021).

2020

• Keisuke Ishihara, Ashish B. George, Ryan Cornelius, and Kirill S. Korolev, Traveling fronts in self-replicating persistent random walks with multiple internal states, New Journal of Physics 22(8) 083034 (2020).

2019  

• Saurabh Gandhi, Kirill S. Korolev, Jeff Gore, Cooperation mitigates diversity loss in a spatially expanding microbial population, PNAS 116(47), 23582-23587 (2019).

        Highlighted in a commentary by Mark Lewis: Feasting yeast and the sweetness of diversity in PNAS.

• Gabriel Birzu, Sakib Matin, Oskar Hallatschek, and Kirill S. Korolev, Genetic drift in range expansions is very sensitive to density feedback in dispersal and growth, Ecology Letters 22, 1817-1827 (2019).

• Ching-Hao Wang, Sakib Matin, Ashish B. George, and Kirill S. Korolev, Pinned, locked, pushed, and pulled traveling waves in structured environments, Theoretical Population Biology 127, 102-119 (2019).

• Maxime Deforet, Carlos Carmona-Fontaine, Kirill S. Korolev, and Joao B. Xavier, Evolution at the edge of expanding populations, American Naturalist 194(3), 291-305 (2019).

• Robert Marsland III, Wenping Cui, Joshua Goldford, Alvaro Sanchez, Kirill S. Korolev, and Pankaj Mehta, Available energy fluxes drive a phase transition in the diversity, stability, and functional structure of microbial communities, PLoS Computational Biology 15(2): e1006793 (2019).

2018 

• Gabriel Birzu, Oskar Hallatschek, and Kirill S. Korolev, Fluctuations uncover a distinct class of traveling waves, PNAS 115, E3645-E3654 (2018).

• Rajita Menon, Vivek Ramanan, and Kirill S. Korolev, Interactions between species introduce spurious associations in microbiome studies, PLoS Computational Biology 14(1): e1005939 (2018).

• Ashish B. George and Kirill S. Korolev, Chirality provides a direct fitness advantage and facilitates intermixing in cellular aggregates, PLoS Computational Biology 14(12): e1006645 (2018).

• Mina Nazari, Xiaoqing Li, Mohammad Amin Alibakhshi, Haojie Yang, Kathleen Souza, Christopher Gillespie, Suryaram Gummuluru, Björn M. Reinhard, Kirill S. Korolev, Lawrence D. Ziegler, Qing Zhao, Meni Wanunu, Shyamsunder Erramilli, Femtosecond Photonic Viral Inactivation Probed Using Solid-State Nanopores, Nano Futures 2, 045005 (2018).

• Mohammad I. El Mouzan, Harland S. Winter, Assad A. Assiri, Kirill S. Korolev, Ahmad A. Al Sarkhy, Scot E. Dowd, Mohammad A. Al Mofarreh, and Rajita Menon, Microbiota profile in new-onset pediatric Crohn’s disease: data from a non-Western population, BMC Gut Pathogens 10, 49 (2018).

• Mohammad I El Mouzan, Kirill S. Korolev, Mohammad A Al Mofarreh, Rajita Menon, Harland S Winter, Ahmad A Al Sarkhy, Scot E Dowd, Ahmad M Al Barrag, and Asaad A Assiri, Fungal dysbiosis predicts the diagnosis of pediatric Crohn’s disease, WJG 24(39): 4510-4516 (2018).

2017 

• Ana B. Pavel and Kirill S. Korolev, Genetic load makes cancer cells more sensitive to common drugs: evidence from Cancer Cell Line Encyclopedia, Scientific Reports 7, 1938 (2017).

• Liselotte Jauffred, Rebecca M. Vejborg, Kirill S. Korolev, Stanley Brown, and Lene B. Oddershede, Chirality in microbial biofilms is mediated by close interactions between the cell surface and the substratum, ISME Journal 11, 1688-1701 (2017).

• Mohammad El Mouzan, Feng Wang, Mohammad Al Mofarreh, Rajita Menon, Ahmad Al Barrag, Kirill S. Korolev, Ahmad Al Sarkhy, Mona Al Asmi, Yassin Hamed, Anjum Saeed, Scot Dowd, Asaad Assiri, and Harland Winter, Fungal Microbiota Profile in Newly-diagnosed Treatment-naïve Children with Crohn disease, Journal of Crohn’s and Colitis 11(5), 586-592 (2017).

2016

• Keisuke Ishihara, Kirill S. Korolev, Timothy J. Mitchison, Physical basis of large microtubule aster growth, eLife e19145 (2016).

            Video abstract

• Saurabh R. Gandhi, Eugene A. Yurtsev, Kirill S. Korolev and Jeff Gore, Range expansions transition from pulled to pushed waves as growth becomes more cooperative in an experimental microbial population, PNAS 113, 6923 (2016).

             Highlighted in a PNAS Commentary by Mark Lewis: Finding the sweet spot for invasion theory.

• Feng Wang, Jess L. Kaplan, Benjamin D. Gold, …, Towia A. Libermann, Harland S. Winter, and Kirill S. Korolev, Detecting Microbial Dysbiosis Associated with Pediatric Crohn Disease Despite the High Variability of the Gut Microbiota, Cell Reports 14, 945-955 (2016).

2015

• Kirill S. Korolev, Evolution arrests invasions of cooperative populations, Physical Review Letters 115, 208104 (2015).

            Highlighted in APS Physics, Focus: Evolution sometimes slows things down.

• Rajita Menon and Kirill S. Korolev, Public good diffusion limits microbial mutualism, Physical Review Letters 114, 168102 (2015).

            Highlighted in APS Physics, Synopsis: Microbes share, but not too much.

• Lei Dai, Kirill S. Korolev, and Jeff Gore, Relation between stability and resilience determines the performance of early warning signals under different environmental drivers, PNAS 112, 10056 (2015).

 2014

• Christopher D. McFarland, Leonid A. Mirny, and Kirill S. Korolev, Tug-of-war between driver and passenger mutations in cancer and other adaptive processes, PNAS 111, 15138 (2014).

            Highlighted in Editor’s Choice in Science.

• Kirill S. Korolev, Joao B. Xavier, and Jeff Gore, Turning ecology and evolution against cancer, Nature Reviews Cancer 14, 371 (2014).

            Highlighted in MIT News.

• Peter D. Freese, Kirill S. Korolev, Jose I. Jimenez, and Irene A. Chen, Genetic Drift Suppresses Bacterial Conjugation in Spatially Structured Populations, Biophysical Journal 106, 944 (2014).

 2013

• Manoshi S. Datta, Kirill S. Korolev, Ivana Cvijovic, Carmel Dudley, and Jeff Gore, Range expansion promotes cooperation in an experimental microbial metapopulation, PNAS 110, 7354 (2013).

             Highlighted in Quanta Magazine and Wired.com.

• Lei Dai, Kirill S. Korolev, and Jeff Gore, Slower recovery in space before collapse of connected populations, Nature 496, 355 (2013).

            Highlighted in Nature News and Views, Science News, and MIT News.

• Kirill S. Korolev, The fate of cooperation during range expansions, PLoS Computational Biology 9, e1002994 (2013).

• Christopher D. McFarland, Kirill S. Korolev, Gregory V. Kryukov, Shamil Sunyaev,  and Leonid A. Mirny, The impact of deleterious passenger mutations on cancer progression, PNAS 110, 2910 (2013).

            Highlighted in Nature Reviews Cancer and MIT News.

• • Maxim O. Lavrentovich, Kirill S. Korolev, and David R. Nelson, Radial Domani-Kinzel models with mutation and selection, Physical Review E 87, 012103 (2013).

2012

• Lei Dai, Daan Vorselen, Kirill S. Korolev, Jeff Gore, Generic indicators for loss of resilience before tipping point leading to population collapse, Science336, 1175 (2012).

           Highlighted on yeastgenome.org: Yeast on the Brink and in Condensed Matter Journal Club.

• Kirill S. Korolev, Melanie J. I. Muller, Nilay Karahan, Andrew W. Murray, Oskar Hallatschek, and David R. Nelson, Selective sweeps in growing microbial colonies,  Physical Biology 9, 026008 (2012).

2011

• Kirill S. Korolev, Joao B. Xavier, David R. Nelson, and Kevin R. Foster, A quantitative test of population genetics using spatiogenetic patterns in bacterial colonies,  The American Naturalist 178, 538 (2011).

• Kirill S. Korolev and David R. Nelson, Competition and cooperation in one-dimensional stepping-stone models,  Physical Review Letters 107, 088103 (2011).

2005 – 2010

• Kirill S. Korolev, Mikkel Avlund, Oskar Hallatschek, and David R. Nelson, Genetic demixing and evolution in linear stepping stone models, Reviews of Modern Physics 82, 1691 (2010).

            Highlighted in Nature Physics: Dimensional Analysis.

• Oskar Hallatschek and Kirill S. Korolev, Fisher waves in the strong noise limit,  Physical Review Letters 103, 108103 (2009).

• Kirill S. Korolev and David R. Nelson, Defect-mediated emulsification in two dimensions,  Physical Review E 77, 051702 (2008).

• L.S. Uspenskaya, Kirill S. Korolev, and P.N. Yarykin, Peculiarity of magnetization relaxation in finite size superconductors,  Physica C 423:181-9 (2005).