Kishony Lab - Publications


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).

A. C. Palmer, R. Kishony
Understanding, predicting and manipulating the genotypic evolution of antibiotic resistance
Nature Reviews Genetics, 14, 243 (2013) (pdf).

Z. Yao, D. Kahne, R. Kishony
Distinct single-cell morphological dynamics under beta-lactam antibiotics
Molecular Cell, 48, 705 (2012) (pdf).

Z. Yao, R. M. Davis, R. Kishon, D. Kahne, N. Ruiz
Regulation of cell size in response to nutrient availability by fatty acid biosynthesis in Escherichia coli
PNAS, 109, E2561 (2012).

Skurnik D, Davis MR Jr, Benedetti D, Moravec KL, Cywes-Bentley C, Roux D, Traficante DC, Walsh RL, Maira-Litràn 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
J. Infect Dis., 205, 1709 (2012).

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).

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). (pdf)

R. Chait, K. Vetsigian, R. Kishony
What counters antibiotic resistance in nature?
Nature Chemical Biology 8, 2 (2012). (pdf)

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 (4), 1275 (2011). (pdf)

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). (pdf)

K. Vetsigian, R. Jajoo, R. Kishony
Structure and evolution of Streptomyces interaction networks in soil and in silico
PLoS Biology 9, e1001184 (2011). (pdf)

R. Kishony and V. Hatzimanikatis
Systems Biology: Editorial Review
Current Opinion in Biotechnology 22, 1 (2011). (pdf)

T. Bollenbach, R. Kishony
Resolution of Gene Regulatory Conflicts Caused by Combinations of Antibiotics
Molecular Cell 42 (4), 413 (2011). (pdf)

M. Ernebjerg, R. Kishony
Dynamic Phenotypic Clustering in Noisy Ecosystems
PLoS Computational Biology 7 (3): e1002017 (2011). (pdf)

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)

J. P. Torella, R. Chait, R. Kishony
Optimal Drug Synergy in Antimicrobial Treatments
PLoS Computational Biology 6 (6), e1000796 (2010). (pdf)

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)

A. C. Palmer, E. Angelino, R. Kishony
Chemical decay of an antibiotic inverts selection for resistance
Nature Chemical Biology 6, 105 (2010). (pdf)

H. S. Chung*, Z. Yao*, N. W. Goehring*, R. Kishony, J. Beckwith, D. Kahne
Rapid b-lactam-induced lysis requires successful assembly of the cell division machinery
PNAS 106, 21872 (2009). (PubMed)

T. Bollenbach, R. Kishony
Hydroxyurea Triggers Cellular Responses that Actively Cause Bacterial Cell Death Molecular Cell 36, 728 (2009). [Preview] (pdf)

T. Bollenbach, S. Quan, R. Chait, R. Kishony
Nonoptimal Microbial Response to Antibiotics Underlies Suppressive Drug Interactions
Cell 139, 707 (2009). (pdf)

T. Bollenbach, R. Kishony
Quiet gene circuit more fragile than its noisy peer
Cell 139, 460 (2009). [Preview] (PubMed)

J. G. Swoboda, T.C. Meredith, J. Campbell, S. Brown, T. Suzuki, T. Bollenbach, A. J. Malhowski, R. Kishony, M. S. Gilmore, S. Walker
Discovery of a small molecule that blocks wall teichoic acid biosynthesis in Staphylococcus aureus
ACS Chem Biol 4, 875 (2009). (PubMed)

P. J. Yeh, M. J. Hegreness, R. A. Presser Aiden, R. Kishony
Drug interactions and the evolution of antibiotic resistance
Nature Reviews Microbiology 7, 460 (2009). (pdf, Supplementary Material: Literature curated drug network)

J.-B. Michel*, P. J. Yeh*, R. Chait, R. C. Moellering, R. Kishony
Drug interactions modulate the potential for evolution of resistance
PNAS 105, 14918 (2008). (pdf)

M. Hegreness*, N. Shoresh*, D. Damian, D. Hartl, R. Kishony
Accelerated evolution of resistance in multi-drug environments
PNAS 105, 13977 (2008). (pdf)

N. Shoresh*, M. Hegreness*, R. Kishony
Evolution exacerbates the paradox of the plankton
PNAS 105, 12365 (2008). (pdf)

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)

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)

R. Chait, A. Craney, R. Kishony
Antibiotic interactions that select against resistance
Nature 446, 668 (2007). (pdf)

T. Bollenbach, K. Vetsigian, R. Kishony
Evolution and multilevel optimization of the genetic code
Genome Research 17, 401 (2007). [Perspective] (pdf)

P. Yeh, R. Kishony
Networks from drug-drug surfaces
Molecular Systems Biology 3, 85 (2007). [News & Views] (pdf)

M. Hegreness, R. Kishony
Analysis of genetic systems using experimental evolution and whole-genome sequencing
Genome Biology 8, 201 (2007). [Mini-Review] (pdf)

P. Yeh, A. Tschumi, R. Kishony
Functional classification of drugs by properties of their pair-wise interactions
Nature Genetics 38, 489 (2006). (pdf)

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). (pdf)

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

D. Segrè, A. DeLuna, G. M. Church, R. Kishony
Modular epistasis in yeast metabolism
Nature Genetics 3, 77 (2005). (pdf)

R. Kishony, S. Leibler
Environmental stresses can alleviate the average deleterious effect of mutations
Journal of Biology 2, p. 14 (2003). (pdf)