Pollack D, Nozoe T, and Kussell E. Proteolytic stability and aggregation in a key metabolic enzyme of bacteria, Proceedings of the National Academy of Sciences USA, 121:e2301458121 (2024).

Hobson-Gutierrez S and Kussell E. Evolutionary advantage of cell size control, arXiv, 2303.08042 (2023).

Preska Steinberg A, Silander OK, and Kussell E. Correlated substitutions reveal SARS-like coronaviruses recombine frequently with a diverse set of structure gene pools, Proceedings of the National Academy of Sciences USA, 120:e2206945119 (2023).

Featured in PNAS Commentary “It takes a village to build a virus”, 120:e2219052120 (2023).

Yamauchi S, Nozoe T, Okura R, Kussell E, and Wakamoto Y. A unified framework for measuring selection on cellular lineages and traits, eLife, 11:e72299 (2022).

Preska Steinberg A, Lin M, and Kussell E. Core genes can have higher recombination rates than accessory genes within global microbial populations, eLife, 11:e78533 (2022).

Skanata A and Kussell E.  Ecological memory preserves phage resistance mechanisms in bacteria, Nature Communications, 12:6817 (2021).

Umetani M, Fujisawa M, Okura R, Nozoe T, Suenaga S, Nakaoka H, Kussell E, and Wakamoto Y. Actively growing cells are the predominant persisters in exponential phase of Escherichia coli, bioRxiv, 10.1101/2021.10.28.466227 (2021).

Skanata A and  Kussell E. ‘Memory and adaptation in time-varying environments’ in Roadmap article on time-varying environments by Murugan et al., Physical Biology, 18:041502(2021).

Lin WH, Kussell E, Young LS, Jacobs-Wagner C. Origin of exponential growth in nonlinear reaction networks, Proceedings of the National Academy of Sciences USA, 117:27795 (2020).

Nozoe T and Kussell E. Cell-cycle heritability and localization phase transition in growing populations, Physical Review Letters, 125:268103 (2020).

Lin M and Kussell E.  Inferring bacterial recombination rates from large scale sequencing datasets, Nature Methods, 16:199-204 (2019).

Moxon R and Kussell E.  The impact of bottlenecks on microbial survival, variation and phenotypic switching in host-pathogen interactions.  Evolution, 71:2803 (2017)

Nozoe T, Kussell E, and Wakamoto Y.  Inferring fitness landscapes and selection on phenotypic states from single-cell genealogical data. PLoS Genetics, 13:e1006653 (2017).

Lin M and Kussell E. Correlated mutations and homologous recombination within bacterial populations. Genetics, 205:891-917 (2017).  

Featured as a Genetics Issue Highlight.

Qian L and Kussell E. Genome-wide motif statistics are shaped by DNA binding proteins over evolutionary timescales. Physical Review X, 6:041009 (2016).

Featured in “ Focus: Evolution Thins Out Distracting DNA”, Physics, 9:119 (2016)

Skanata A and Kussell E. Evolutionary phase transitions in random environments. Physical Review Letters, 117:038104 (2016). 

Lin W-H and Kussell E. Complex interplay of physiology and selection in the emergence of antibiotic resistance. Current Biology, 26:1486 (2016). 

Hashimoto M, Nozoe T, Nakaoka H, Okura R, Akiyoshi S, Kaneko K, Kussell E, and Wakamoto Y.  Noise-driven growth rate gain in clonal cellular populations. Proceedings of the National Academy of Sciences USA, 113:3251-3256 (2016).

Pleska M, Qian L, Okura R, Bergmiller T, Wakamoto Y, Kussell E, and Guet CC. Bacterial autoimmunity due to a restriction-modification system. Current Biology, 26:1-6 (2016). 

Featured in “Damage limitation after friendly fire”, Nature Reviews Microbiology, 14:130 (2016).

Lambert G and Kussell E.  Quantifying selective pressures driving bacterial evolution using lineage analysis. Physical Review X, 5:011016 (2015). 

Featured in “Viewpoint: History is Written by the Survivors”, Physics, 8:14 (2015).

Lin W-H, Rocco MJ, Bertozzi-Villa, A and Kussell E.  Populations adapt to fluctuating selection using derived and ancestral allelic diversity. Evolution, 69:1448-1460 (2015).

Lambert G and Kussell E.  Memory and fitness optimization of bacteria under fluctuating environments. PLoS Genetics, 77:102602 (2014).

Included in collection: PLoS Genetics Top 10%.

Kussell E and Vucelja M.  Non-equilibrium physics and evolution–adaptation, extinction, and ecology: A Key Issues review. Reports on Progress in Physics, 77:192602 (2014).

Kussell E.  Evolution in microbes. Annual Reviews of Biophysics, 42:493-514 (2013).

Qian L and Kussell E.  Evolutionary dynamics of restriction site avoidance. Physical Review Letters, 108:158105 (2012).

Sood R, Johnston R, and Kussell E.  Stochastic de-repression of rhodopsins in single photoreceptors of the fly retina. PLoS Computational Biology, 8(2):e1002357 (2012).

Lin W and Kussell E.  Evolutionary pressures on simple sequence repeats in prokaryotic coding regions. Nucleic Acids Research, 40:2399-2413 (2012).

Wakamoto Y, Grosberg AY, and Kussell E.  Optimal lineage principle for age-structured populations. Evolution, 66:115-134 (2011).

Birnbaum K and Kussell E.  Measuring cell identity in noisy biological systems. Nucleic Acids Research, 39: 9093-9107 (2011).

Johnston R, Otake Y, Sood P, Vogt N, Behnia R, Vasiliauskas D, McDonald E, Xie B, Cook T, Gebelstein B, Kussell E, Nagakoshi H, and Desplan C .  Interlocked feedforward loops ensure robust rhodopsin expression in the Drosophila eye. Cell, 145:956–968 (2011).

Leibler S and Kussell E.  Individual histories and selection in heterogeneous populations. Proceedings of the National Academy of Sciences USA, 107:13183-13188 (2010).

Featured in “Learning from history”, Nature Methods, 7:673 (2010).

Kussell E, Leibler S, and Grosberg AY.  Polymer-population mapping and localization in the space of phenotypes. Physical Review Letters, 97:068101 (2006).

Kussell E and Leibler S.  Phenotypic diversity, population growth, and information in fluctuating environments. Science, 309: 2075-2078 (2005).

Featured in “Perspective: Making Sense of Evolution in an Uncertain World”, Science, 309:5743 (2005).

Kussell E, Kishony R, Balaban NQ, and Leibler S.  Bacterial persistence: a model of survival in changing environments. Genetics, 169: 1807-1814 (2005).

Kussell E.  The designability hypothesis and protein evolution. Protein and Peptide Letters, 12: 111-116 (2005).

Kussell E, Shimada J, and Shakhnovich EI.  Side-chain dynamics and protein folding. Proteins, 52: 303-321 (2003).

Kussell E and Shakhnovich EI.  Glassy dynamics of side-chain ordering in a simple model of protein folding. Physical Review Letters, 89: 168101 (2002).

Kussell E, Shimada J, and Shakhnovich EI.  A structure-based method for derivation of all-atom potentials for protein folding. Proc Natl Acad Sci USA, 99: 5343-5348 (2002).

Kussell E, Shimada J, and Shakhnovich EI.  Excluded volume in protein side-chain packing. Journal of Molecular Biology, 311: 183-193 (2001).

Shimada J, Kussell E, and Shakhnovich EI.  The folding thermodynamics and kinetics of crambin using an all-atom Monte Carlo simulation. Journal of Molecular Biology, 308: 79-95 (2001).

Kussell E and Shakhnovich EI.  Analytical approach to the protein design problem. Physical Review Letters, 83:4437-4440 (1999).

Vendruscolo M, Kussell E, and Domany E.  Recovery of protein structure from contact maps. Folding and Design, 2:295-306 (1997).