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 (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 (2016) PDF
  3. Y. Gerardin, M. Springer* & R. Kishony*. A competitive trade-off limits the selective advantage of increased antibiotic production. Nature Microbiology (2016)
  4. E. D. Kelsic*, H. Chung*, N. Cohen, J. Park, H. H. Wang#, R. Kishony#, “Optimal codon choice throughout a gene revealed by MAGE-Seq”, Cell Systems (2016).
  5. M. Baym, T. D. Lieberman, E. D. Kelsic, R. Chait, R. Gross, I. Yelin, R. Kishony, “Spatiotemporal microbial evolution on antibiotic landscapes”, Science (2016). PDF
  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 Biology (2016). PDF
  7. Bairey, E., Kelsic, E.D. and Kishony, R. “High-order species interactions shape ecosystem diversity”. Nature Communications, 7. (2016) PDF
  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 (2016).
  10. Baym, M.*, Stone, L.*, Kishony, R. “Multi-drug evolutionary strategies to reverse antibiotic resistance”, Science 351, 40 (2016).  PDF
  11. Wang, K. K., Stone, L. K., Lieberman, T. D., Shavit, M., Baasov, T.*, & Kishony, R.*, “A hybrid drug limits resistance by evading the action of the multiple antibiotic resistance pathway”. Molecular biology and evolution, msv243 (2015).
  12. E. D. Kelsic, J. Zhao, K. Vetsigian*, R. Kishony*, “Counteraction of antibiotic production and degradation stabilizes microbial communities”, Nature 521, 516 (2015). PDFClarification
  13. M. Baym, S. Kryazhimskiy, T. D. Lieberman, H. Chung, M. M. Desai*, R. Kishony*, “Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes”, PLoS ONE 10(5): e0128036 (2015).
  14. A. C. Palmer, E. Toprak, M. 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 (2015).  PDF
  16. R. Kishony, J. J. Collins, “Editorial overview: Antimicrobials: grappling with the complexities of antibiotics and resistance”, Current Opinion Microbiology 21 (2014). PDF
  17. S. Kim, T. D. Lieberman, R. Kishony, “Alternating antibiotic treatments constrain evolutionary paths to multidrug resistance”, PNAS 111 (2014). PDF
  18. A. C. Palmer, R. Kishony, “Opposing effects of target overexpression reveal drug mechanisms”, Nature Communications 5, 4296 (2014). PDF
  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). [N&Vs by M. G. Surette; Nature Research Highlights] PDF
  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} PDF
  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). PDF
  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). PDF
  24. Z. Yao, D. Kahne*, R. Kishony*, “Distinct single-cell morphological dynamics under beta-lactam antibiotics”, Molecular Cell, 48, 705 (2012). PDF
  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. Ernebjerga and R. Kishony, “Distinct Growth Strategies of Soil Bacteria as Revealed by Large-Scale Colony Tracking”, Applied and Environmental Microbiology, 78, 1345 (2012). PDF
  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). [N&Vs by M. Elowitz; Science; The Scientist; New Scientist, BBC Horizon, 60 Minutes Australia] PDF
  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] PDF
  31. Bush K, Courvalin P, Dantas G, Davies J, Eisenstein B, Huovinen P, Jacoby GA, Kishony R, Kreiswirth BN, Kutter E, Lerner SA, Levy S, Lewis K, Lomovskaya O, Miller JH, Mobashery S, Piddock LJ, Projan S, Thomas CM, Tomasz A, Tulkens PM, Walsh TR, Watson JD, Witkowski J, Witte W, Wright G, Yeh P, Zgurskaya HI, “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). PDF
  33. R. Kishony and V. Hatzimanikatis, “Systems Biology: Editorial Review”, Current Opinion in Biotechnology 22, 1 (2011). {Editorial} PDF
  34. T. Bollenbach, R. Kishony, “Resolution of gene regulatory conflicts caused by combinations of antibiotics”, Molecular Cell 42, 413 (2011). [N&Vs by Elowitz; “Editor Choice” in Science] PDF
  35. M. Ernebjerg, R. Kishony, “Dynamic Phenotypic Clustering in Noisy Ecosystems”, PLoS Computational Biology, 7 (3): e1002017 (2011). PDF
  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). PDF
  37. J. P. Torella, R. Chait, R. Kishony, “Optimal drug synergy in antimicrobial treatments”, PLoS Computational Biology 6 (6), e1000796 (2010). PDF
  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). PDF
  39. A. Palmer, E. Angelino, R. Kishony, “Chemical decay of an antibiotic inverts selection for resistance”, Nature Chemical Biology 6, 105 (2010). [N&Vs by G. Wright] PDF
  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).  {N&V}
  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] PDF
  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). PDF
  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] PDF
  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] PDF
  48. N. Shoresh, M. Hegreness, R. Kishony, “Evolution exacerbates the paradox of the plankton”, PNAS 105, 12365 (2008). PDF
  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). PDF
  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). PDF
  52. R. Chait, A. Craney and R. Kishony, “Antibiotic interactions that select against resistance”, Nature 446, 668 (2007). [Nature News by J. Whitfield] PDF
  53. T. Bollenbach, K. Vetsigian, R. Kishony, “Evolution and multilevel optimization of the genetic code”, Genome Research 17, 401 (2007). PDF
  54. P. Yeh, R. Kishony, “Networks from drug-drug surfaces”, Molecular Systems Biology 3:85 (2007).  [N&V] PDF
  55. M. Hegreness, R. Kishony, “Analysis of genetic systems using experimental evolution and whole-genome sequencing”, Genome Biology 8:201 (2007). {Review} PDF
  56. P. Yeh, A. Tschumi, R. Kishony, “Functional classification of drugs by properties of their pair-wise interactions”, Nature Genetics 38, 489 (2006). [N&Vs by Schmatz & Friend] PDF
  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] PDF
  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] PDF
  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] PDF
  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] PDF
  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 January 2017