SKLab @ UCSD

Ardell S*, Martsul A*, Johnson M, Kryazhimskiy S†. Environment-independent distribution of mutational effects emerges from microscopic epistasis (2023). bioRxiv.

Venkataram S, Kuo H, Hom E, Kryazhimskiy S† (2023). Mutualism-enhancing mutations dominate early adaptation in a microbial community. Nature Eco Evo 7: 143–154.

Ardell S, Kryazhimskiy S† (2021). The population genetics of collateral resistance and sensitivity. eLife 10:e73250

Kryazhimskiy S (2021). Emergence and propagation of epistasis in metabolic networks. eLife 10:e60200

*Equal contribution; †Corresponding author; bold = SKLAB members

Ardell S*, Martsul A*, Johnson M, Kryazhimskiy S†. Environment-independent distribution of mutational effects emerges from microscopic epistasis (2023). bioRxiv.

Kuo H, Kryazhimskiy S†. A Bayesian filtering method for estimating the fitness effects of beneficial mutations in barcode-lineage tracking experiments. In preparation.

Kim M, Ardell S, Kryazhimskiy S†. The dynamics of adaptation of modular organisms. In preparation.

*Equal contribution; †Corresponding author(s); bold = Current or former SKLAB members

Venkataram S, Kryazhimskiy S† (2023). Evolutionary repeatability of emergent properties of ecological communities. Phil Trans R Soc B 378: 20220047.

Venkataram S*, Johnson M*, Kryazhimskiy S† (2023). Best practices in designing, sequencing and identifying barcodes for lineage tracking. J Mol Evol 91: 263–280.

Venkataram S, Kuo H, Hom E, Kryazhimskiy S† (2023). Mutualism-enhancing mutations dominate early adaptation in a microbial community. Nature Eco Evo 7: 143–154.

Ardell S, Kryazhimskiy S† (2021). The population genetics of collateral resistance and sensitivity. eLife 10:e73250

Iranmehr A, Stobdan T, Zhou D, Zhao H, Kryazhimskiy S, Bafna V, Haddad GG (2021). Multiple mechanisms drive genomic adaptation to extreme O2 levels in Drosophila melanogaster. Nat Commun 12: 997

Kryazhimskiy S (2021). Emergence and propagation of epistasis in metabolic networks. eLife 10:e60200

Venkataram S, Monasky R, Sikaroodi SH, Kryazhimskiy S*,†, Kaçar B*,† (2020). Evolutionary stalling and a limit on the power of natural selection to improve a cellular module. Proc Natl Acad Sci USA 117: 18582–18590

Jerison ER, Nguyen Ba AN, Desai MM†, Kryazhimskiy S† (2020). Chance and necessity in the pleiotropic consequences of adaptation for budding yeast. Nat Ecol Evol. 4: 601–611

Johnson MS, Martsul A, Kryazhimskiy S†, Desai MM† (2019). Higher fitness yeast genotypes are less robust to deleterious mutations. Science 366: 490–493 (Perspective by Craig R. Miller)

Fisher KJ, Kryazhimskiy S†, Lang GI† (2019). Detecting beneficial variants and genetic interactions using parallel evolution in experimental populations. Phil Trans B 374: 20180237

Rojas Echenique JI, Kryazhimskiy S, Nguyen Ba AN, Desai MM (2019). Modular epistasis and the compensatory evolution of gene deletion mutants. PLoS Genet 15: e1007958

Jerison ER*, Kryazhimskiy S*, Mitchell J, Bloom JS, Kruglyak L, Desai MM (2017). Genetic variation in adaptability and pleiotropy in budding yeast. eLife 6: 27167

Neverov AD*, Kryazhimskiy S*, Plotkin JB, Bazykin GA (2015). Coordinated evolution of influenza A surface proteins. PLoS Genet 11: e1005404

Baym M*, Kryazhimskiy S*, Lieberman T*, Chung H*, Desai MM, Kishony R (2015). Inexpensive multiplexed library preparation for megabase-sized genomes. PLoS One 10: e0128036

Jerison ER, Kryazhimskiy S, Desai MM (2014). Pleiotropic consequences of adaptation across gradations of environmental stress in budding yeast. arXiv:1409.7839

Kryazhimskiy S*,†, Rice DP, Jerison ER, Desai MM† (2014). Global epistasis makes adaptation predictable despite sequence-level stochasticity. Science 344: 1519–1522 (Covered in Quanta Magazine)

Feder AF*,  Kryazhimskiy S*, Plotkin JB (2014). Identifying signatures of selection in time-series allele-frequency data. Genetics 196: 509–522

Pennings P, Kryazhimskiy S, Wakeley J (2014). Loss and recovery of genetic diversity in adapting populations of HIV. PLoS Genetics 10: e1004000 (Perspective by Rouzine, Coffin, Weinberger) 

Kryazhimskiy S, Desai MM (2014). Refining a key metabolic innovation in Escherichia coli. Proc Natl Acad Sci USA 111: 2056–2057

Kryazhimskiy S, Rice DP, Desai MM (2012). Population subdivision and adaptation in asexual populations of Saccharomyces cerevisiae. Evolution 66: 1931–1941

de Silva S*,†, Ranjeewa AD, Kryazhimskiy S*,† (2011). The dynamics of social networks among female Asian elephants. BMC Ecol 11:17 (Covered in Science Now; New York Times)

Kryazhimskiy S, Draghi JA, Plotkin JP (2011). In evolution, the sum is less than its parts. Science 332: 1160–1161

Kryazhimskiy S, Dushoff J, Bazykin GA, Plotkin JB (2011). Prevalence of epistasis in the evolution of influenza A surface proteins. PLoS Genet 7: e1001301 (Research highlight in Nat Rev Genet)

Vishnoi A, Kryazhimskiy S, Bazykin GA, Hannenhalli S, Plotkin JB (2010). Young proteins experience more variable selection pressure than old proteins. Genome Res 20: 1574–1581

Kryazhimskiy S*, Tkačik G*, Plotkin JB (2009). The dynamics of adaptation on correlated fitness landscapes. Proc Natl Acad Sci USA 106: 18638–18643

Roy S, Vandenberghe LH, Kryazhimskiy S, Grant R, Calcedo R, Yuan X, Keough M, Sandhu A, Wang Q, Medina-Jaszek CA, Plotkin JB, Wilson JM (2009). Isolation and characterization of adenoviruses persistently shed from the gastrointestinal tract of non-human primates. PLoS Pathog 5: e1000503

Kryazhimskiy S, Plotkin JB (2008). The population genetics of dN/dS. PLoS Genet 4: e1000304 (Research highlight in Nat Rev Genet)

Kryazhimskiy S†, Bazykin GA, Plotkin JB, Dushoff J (2008). Directionality in the evolution of influenza A haemagglutinin. Proc R Soc B 275: 2455–2464

Kryazhimskiy S†, Bazykin GA, Dushoff J (2008). Natural selection for nucleotide usage at synonymous and non-synonymous sites in the influenza A genes. J Virol 82: 4938–4945

Kryazhimskiy S†, Dieckmann U, Levin SA, Dushoff J (2007). On state-space reduction in multi-strain pathogen models, with an application to antigenic drift in influenza A. PLoS Comp Biol 3: e159

Logginov AS, Mayorov AS, Kryazhimskiy SA (2005). Modeling of the characteristics of the ring resonator selective optical elements by solving the wave equation (in Russian), Radiotehnika 1

Butuzov VF, Kryazhimskiy SA, Nedel'ko IV (2004). On global domain of attraction of a step-like contrast structure in the critical case. J Comp Math and Math Phys 44: 1410–1431

Butuzov VF, Kryazhimskiy SA, Nedel'ko IV (2004). Global domain of attraction of stable step-like contrast structures in Dirichlet problem. J Comp Math and Math Phys 44: 985−1006

*Equal contribution; †Corresponding author; bold = SKLAB members