Publications

  1. H. Chung, T. D. Lieberman, S. O. Vargas, K. B. Flett, A. J. McAdam*, G.y P. Priebe*, R. Kishony*, “Diversification of the pathogen Stenotrophomonas maltophilia within the human lung”, Nature Communications 8 (2017).
  2. T. D. Lieberman, D. Wilson, R. Misra, L. L. Xiong, P. Moodley, T. Cohen*, R. Kishony*. “Genomic diversity in autopsy samples reveals within-host dissemination of HIV-associated M. tuberculosis”, Nature Medicine 22, 1470 (2016). 
  3. Y. Gerardin, M. Springer* & R. Kishony*. “A competitive trade-off limits the selective advantage of increased antibiotic production”, Nature Microbiology 1, 16175 (2016).
  4. E. D. Kelsic*, H. Chung*, N. Cohen, J. Park, H. H. Wang, R. Kishony, “RNA Structural Determinants of Optimal Codons Revealed by MAGE-Seq”, Cell Systems 3, 563 (2017). 
  5. M. Baym, T. D. Lieberman, E. D. Kelsic, R. Chait, R. Gross, I. Yelin, R. Kishony, “Spatiotemporal microbial evolution on antibiotic landscapes”, Science 353, 1147 (2016).
  6. L. K. Stone, M. Baym, T. D. Lieberman, R. Chait, J. Clardy, R. Kishony, “Compounds that select against the tetracycline resistance efflux pump”, Nature Chemical Biology12, 902 (2016). 
  7. E. Bairey, E. D. Kelsic, R. Kishony, “High-order species interactions shape ecosystem diversity”, Nature Communications 7 (2016). 
  8. E. D. Kelsic, K. Vetsigian*, R. Kishony*, “Evolutionary stability of microbial communities with antibiotic degrading species”, bioRxiv doi:10.1101/045732 (2016).
  9. R. Chait, A. C. Palmer, I. Yelin, R. Kishony. “Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments”. Nature Communications 7, 10333 (2016). 
  10. M. Baym*, L.K. Stone*, R. Kishony. “Multidrug evolutionary strategies to reverse antibiotic resistance”. Science 351, 40 (2016). {Review} 
  11. K. K. Wang, L. K. Stone, T. D Lieberman, M. Shavit, T. Baasov*, R. Kishony*, “A hybrid drug limits resistance by evading the action of the multiple antibiotic resistance pathway”. Molecular biology and evolution, 33, 492 (2015).
  12. E. D. Kelsic, J. Zhao, K. Vetsigian*, R. Kishony*. “Counteraction of antibiotic production and degradation generates stability in microbial communities”, Nature 521, 516 (2015).
  13. M. Baym*, S. Kryazhimskiy*, T. D. Lieberman*, H. Chung*, M. M. Desai#, and R. Kishony#. “Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes.”PLoS ONE: e0128036 (2015).
  14. A. C. Palmer, E. Toprak, M. H. Baym, S. Kim, A. Veres, S. Bershtein, R. Kishony.“Delayed commitment to evolutionary fate in antibiotic resistance fitness landscapes”, Nature Communications 6, 7385 (2015).
  15. A. M Selmecki, Y.E Maruvka, P.A Richmond, M. Guillet, N. Shoresh, A.L Sorenson, S. De, R. Kishony, F. Michor, R. Dowell, D. Pellman, “Polyploidy can drive rapid adaptation in yeast”, Nature 519, 349 (2015). 
  16. R. Kishony, J.J. Collins, “Editorial overview: Antimicrobials: grappling with the complexities of antibiotics and resistance”, Current Opinion Microbiology 21, v-vi. (2014). 
  17. S. Kim, T.D. Lieberman, R. Kishony, “Alternating antibiotic treatments constrain evolutionary paths to multidrug resistance”, PNAS 111, 14494 (2014). 
  18. A. C. Palmer, R. Kishony, “Opposing effects of target overexpression reveal drug mechanisms”, Nature Communications 5, 4296 (2014). 
  19. T. D. Lieberman, K. B. Flett, I. Yelin, T. R. Martin, A. J. McAdam*, G. P. Priebe*, R. Kishony*, “Genetic variation of a bacterial pathogen within individuals with cystic fibrosis provides a record of selective pressures”, Nature Genetics 46, 82 (2014). 
  20. D. Schultz, R. Kishony, “Optimization and control in bacterial Lag phase”, BMC Biology 2013, 11:120 {Commentary}
  21. A. C. Palmer, R. Kishony, “Understanding, predicting and manipulating the genotypic evolution of antibiotic resistance”, Nature Reviews Genetics, 14, 243 (2013). {Review} 
  22. E. Toprak, A. Veres, S. Yildiz, J. M. Pedraza, R. Chait, J. Paulsson, R. Kishony, “Building a morbidostat: an automated continuous-culture device for studying bacterial drug resistance under dynamically sustained drug inhibition”, Nature Protocols 8, 555 (2013).
  23. E. Toprak, A. C. Palmer, S. Kim, A. Veres, S. Bershtein, R. Kishony, “Evolution of Antibiotic Resistance through a Multi-Peaked Adaptive Landscape”, Biophysical Journal, 104, 660A (2013).
  24. Z. Yao, D. Kahne*, R. Kishony*, “Distinct single-cell morphological dynamics under beta-lactam antibiotics”, Molecular Cell, 48, 705 (2012).
  25. Z. Yao, R. M. Davis, R. Kishony, D. Kahne, N. Ruiz, “Regulation of cell size in response to nutrient availability by fatty acid biosynthesis in Escherichia coli”, PNAS, 109, E2561 (2012).
  26. Skurnik D, Davis MR Jr, Benedetti D, Moravec KL, Cywes-Bentley C, Roux D, Traficante DC, Walsh RL, Maira-Litrà n T, Cassidy SK, Hermos CR, Martin TR, Thakkallapalli EL, Vargas SO, McAdam AJ, Lieberman TD, Kishony R, Lipuma JJ, Pier GB, Goldberg JB, Priebe GP, “Targeting pan-resistant bacteria with antibodies to a broadly conserved surface polysaccharide expressed during infection”, Journal of Infectious Diseases 205, 1709 (2012).
  27. M. Ernebjerg and R. Kishony, “Distinct Growth Strategies of Soil Bacteria as Revealed by Large-Scale Colony Tracking”, Applied and Environmental Microbiology, 78, 1345 (2012).
  28. E. Toprak*, A. Veres*, J-B Michel, R. Chait, D. L Hartl, R. Kishony, “Evolutionary paths to antibiotic resistance under dynamically sustained drug selection”, Nature Genetics 44 (1), 101 (2012).
  29. R. Chait, K. Vetsigian & R. Kishony, “What counters antibiotic resistance in nature?”, Nature Chemical Biology 8, 2 (2012). {Perspective}
  30. T. D. Lieberman, J-B Michel, M. Aingaran, G. Potter-Bynoe, D. Roux, M. R. Davis Jr, D. Skurnik, N. Leiby, J. J. LiPuma, J. B. Goldberg, A. J. McAdam*, G. P. Priebe*, R. Kishony*, “Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes”, Nature Genetics 43,1275 (2011). [Selected for F1000; N&Vs by R. Lenski; Nature Reviews Microbiology; Science; The Scientist; Wall Street Journal; Boston Globe] 
  31. K. Bush, P. Courvalin , G. Dantas, J. Davies, B. Eisenstein, P. Huovinen, G.A. Jacob, R. Kishony, B.N Kreiswirth, E. Kutter, S.A Lerner, S. Levy, Lewis K, O. Lomovskaya, J.H. Miller, S. Mobashery, L.J Piddock, S. Projan, C.M. Thomas, A. Tomasz, P.M. Tulkens, T.R. Walsh, J.D. Watson, J. Witkowski, W. Witte, G. Wright, P. Yeh, H.I Zgurskaya, “Tackling antibiotic resistance”, Nature Reviews Microbiology 9, 894 (2011). {Perspective}
  32. K. Vetsigian, R. Jajoo, R. Kishony, “Structure and evolution of Streptomyces interaction networks in soil and in silico”, PLoS Biology 9, e1001184 (2011).
  33. R. Kishony and V. Hatzimanikatis, “Systems Biology: Editorial Review”, Current Opinion in Biotechnology 22, 1 (2011). {Editorial} 
  34. T. Bollenbach, R. Kishony, “Resolution of gene regulatory conflicts caused by combinations of antibiotics”, Molecular Cell 42, 413 (2011).
  35. M. Ernebjerg, R. Kishony, “Dynamic Phenotypic Clustering in Noisy Ecosystems”, PLoS Computational Biology, 7 (3): e1002017 (2011).
  36. R. Chait., S. Shrestha, A. Shah, J-B Michel, R. Kishony, “A differential drug screen for compounds that select against antibiotic resistance, PLoS ONE 5 (12): e15179 (2010).
  37. J. P. Torella, R. Chait, R. Kishony, “Optimal drug synergy in antimicrobial treatments”, PLoS Computational Biology 6 (6), e1000796 (2010).
  38. A. DeLuna, M. Springer, M. W. Kirschner, R. Kishony, “Need-based upregulation of protein levels in response to deletion of their duplicate genes”, PLoS Biology 8, e1000347 (2010).
  39. A. Palmer, E. Angelino, R. Kishony, “Chemical decay of an antibiotic inverts selection for resistance”, Nature Chemical Biology 6, 105 (2010).
  40. H-S Chung*, Z. Yao*, N. W. Goehring*, R. Kishony, J. Beckwith , D. Kahne, “Rapid β-lactam induced lysis requires successful assembly of the cell division machinery”, PNAS 106, 21872 (2009). [Selected for F1000]
  41. T. Bollenbach, R. Kishony, “Hydroxyurea triggers cellular responses that actively cause bacterial cell death”, Molecular Cell 36, 728 (2009).
  42. T. Bollenbach, S. Quan, R. Chait, and R. Kishony, “Non-optimal microbial response to antibiotics underlies suppressive drug interactions”, Cell 139, 707 (2009). [New England Journal of Medicine, Clinical implications of basic research, J. B. Xavier and C. Sander] 
  43. T. Bollenbach, R. Kishony, “Quiet gene circuit more fragile than its noisy peer”, Cell 139, 461 (2009). {N&V}
  44. J. G. Swoboda, T. C. Meredith, J. Campbell, S. Brown, T. Suzuki, T. Bollenbach, A. J. Malhowski, R. Kishony, M. S. Gilmore and S. Walker, “Discovery of a small molecule that blocks wall teichoic acid biosynthesis in Staphylococcus aureus”, ACS Chemical Biology 4, 875 (2009).
  45. P. Yeh, M. Hegreness, A. Presser, R. Kishony, “Drug interactions and the evolution of antibiotic resistance”, Nature Reviews Microbiology 7, 460 (2009).
  46. J.-B. Michel, P. Yeh, R. Chait, R. Moellering, R. Kishony, “Drug interactions modulate the potential for evolution of resistance”, PNAS 105, 14918 (2008). [Selected for F1000; PNAS “In this issue” Editorial] 
  47. M. Hegreness, N. Shoresh, D. Damian, D. Hartl, R. Kishony, “Accelerated evolution of resistance in multi-drug environments”, PNAS 105, 13977 (2008). [“Editor Choice”, Science] 
  48. N. Shoresh, M. Hegreness, R. Kishony, “Evolution exacerbates the paradox of the plankton”, PNAS 105, 12365 (2008).
  49. A. DeLuna, K. Vetsigian, N. Shoresh, M. Hegreness, M. Colón-González, S. Chao, R. Kishony,  “Exposing the fitness contribution of duplicated genes”, Nature Genetics 40, 676 (2008).
  50. S. Pearl, C. Gabay, R. Kishony, A. Oppenheim, N. Q. Balaban, “Nongenetic individuality in the host-phage interaction”, PLoS Biology 6(5): e120 (2008).
  51. A. Presser, M. B. Elowitz, M. Kellis, R. Kishony, “The evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network after duplication”, PNAS 105, 950 (2008).
  52. R. Chait, A. Craney and R. Kishony, “Antibiotic interactions that select against resistance”, Nature 446, 668 (2007). [Nature News by J. Whitfield] 
  53. T. Bollenbach, K. Vetsigian, R. Kishony, “Evolution and multilevel optimization of the genetic code”, Genome Research 17, 401 (2007).
  54. P. Yeh, R. Kishony, “Networks from drug-drug surfaces”, Molecular Systems Biology 3:85 (2007).  
  55. M. Hegreness, R. Kishony, “Analysis of genetic systems using experimental evolution and whole-genome sequencing”, Genome Biology 8:201 (2007). {Review} 
  56. P. Yeh, A. Tschumi, R. Kishony, “Functional classification of drugs by properties of their pair-wise interactions”, Nature Genetics 38, 489 (2006).
  57. M. Hegreness, N. Shoresh, D. Hartl, R. Kishony, “An equivalence principle for the incorporation of favorable mutations in asexual populations”, Science 311, p. 1615 (2006). [Selected for F1000] 
  58. E. Kussell, R. Kishony, N. Q. Balaban, and S. Leibler, “Bacterial persistence: a model of survival in changing environments”, Genetics 169: 1807-1814 (2005). [Selected for F1000] 
  59. D. Segrè, A. DeLuna, G. M. Church, R. Kishony, “Modular epistasis in yeast metabolism”, Nature Genetics 3, 77 (2005). [N&Vs by J. H. Moore; Editorial “From parts catalog to wiring diagram”; Research Highlight, Nature Reviews Genetics; Selected for F1000] 
  60. R. Kishony, S. Leibler, “Environmental stresses can alleviate the average deleterious effect of mutations”, Journal of Biology 2, p. 14 (2003). [Research news by P. Moore; Selected for F1000]
  61. R. Kishony, D. Shvarts, “Ignition condition and gain prediction for perturbed ICF targets”, Physics of Plasmas 8, 4925 (2001). 
  62. R. Kishony, E. Waxman, D. Shvarts, “Inertial confinement fusion ignition criteria, critical profiles and burn wave propagation using self-similar solutions”, Physics of Plasmas 4, 1385 (1997).

 

Last updated on June 2017