Prism algorithm:
PrismI.m – Segrè et al, “Modular epistasis in yeast metabolism”, Nature Genetics 3, 77 (2005)
PrismII.m – Yeh et al, “Functional classification of drugs by properties of their pair-wise interactions”, Nature Genetics 38, 489 (2006).
Supplementary Information:
Drug interactions and the evolution of antibiotic resistance
P. Yeh, M. Hegreness, A. Presser, R. Kishony, Nature Reviews Microbiology 7, 460 (2009).
Literature curated drug interaction network – Click to download
The Evolution of Bacteria on a “Mega-Plate” Petri Dish
Spatiotemporal microbial evolution on antibiotic landscapes
M. Baym, T. D. Lieberman, E. D. Kelsic, R. Chait, R. Gross, I. Yelin, R. Kishony, Science 353, 1147 (2016).
Supplementary Information:
Additivity of inhibitory effects in multi-drug combinations
D. Russ and R. Kishony. Nature Microbiology (2018).
Calculating microbial growth rate- Click to download
Predict microbial response to drug combinations- Click to download
Supplementary Information:
Personal clinical history predicts antibiotic resistance in urinary tract infections
I. Yelin, O. Snitser, G. Novich, R. Katz, O. Tal, M. Parizade, G. Chodick, G. Koren, V. Shalev, R. Kishony. Nature Medicine (2019).
Mathematical proof of optimality of the algorithm for drug choice- Click to download
Supplementary Information:
Escape mutations circumvent a tradeoff between resistance to a beta-lactam and resistance to a beta-lactamase inhibitor
D. Russ, F. Glaser, E. Shaer-Tamar, I. Yelin, M. Baym, E.D. Kelsic, C. Zampaloni, A. Haldimann, R. Kishony. Nature Communications (2020).
Scripts and growth data- Click to download
Supplementary Information:
Ubiquitous selection for mecA in community-associated MRSA across diverse chemical environments
O. Snitser, D. Russ, L.K Stone, K.K Wang, H. Sharir, N. Kozer, G. Cohen, H.M Barr, R. Kishony. Nature Communications (2020).
mecA chemical screen- Click to download
How-to
How to build a Macroscope: Go to link
How to build the MEGA-plate: Go to link
How to build the Morbidostat: Go to link
Inexpensive multiplexed library preparation for megabase-sized genomes: PDF