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).

Kussell E and Takeuchi N. Systems biology of ecological interactions across scales, Current Opinion in Systems Biology, 39:100532 (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).

Umetani M, Fujisawa M, Okura R, Nozoe T, Suenaga S, Nakaoka H, Kussell E, and Wakamoto Y. Observation of non-dormant persister cells reveals diverse modes of survival in antibiotic persistence, bioRxiv, 10.1101/2021.10.28.466227 (2022).

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