Ray JCJ, Podgorny AR. 2020. Tasting the Terroir with Tsr. Biophys J 118(2):279-280 (commentary on Orr et al 2020) [journal]
Phillips KN, Widmann S, Lai H-Y, Nguyen J, Ray JCJ, Balázsi GB, Cooper TF. 2019. Diversity in lac Operon Regulation among Diverse Escherichia coli Isolates Depends on the Broader Genetic Background but Is Not Explained by Genetic Relatedness. mBio 10(6):e02232-19; DOI:10.1128/mBio.02232-19 [journal]
Cooley SM, Hamilton T, Ray JCJ, Deeds EJ. 2019 (updated 2020). A novel metric reveals previously unrecognized distortion in dimensionality reduction of scRNA-Seq data. bioRxiv https://doi.org/10.1101/689851 [bioRxiv]
Dominique Chu, Mikhail Prokopenko, J. Christian J. Ray. 2018. Computation by natural systems. Interface Focus. 8(6):20180058 [journal] [pdf]
McElfresh GW, Ray JCJ. 2018. Intergenerational Cellular Signal Transfer and Erasure. In: The interplay of thermodynamics and computation in natural and artificial systems. Wolpert D, Kempes C, Grochow J, Stadler P, editors. Santa Fe, NM: Santa Fe Institute Press. 16p. [pdf]
Bandyopadhyay A, Wang H, Ray JCJ. 2018. Lineage space and the propensity of bacterial cells to undergo growth transitions. PLoS Comput Biol 14(8):e1006380 [journal] [bioRxiv]
Wang H, Ray JCJ. 2017. Dynamical predictors of an imminent phenotypic switch in bacteria. Phys Biol 14(4):045007 (Special issue dedicated to the Tenth q-bio Conference) [journal] [bioRxiv]
Ray JCJ, Wickersheim ML, Jalihal AP, Adeshina YO, Cooper TF, Balázsi G. 2016. Cellular growth arrest and persistence from enzyme saturation. PLOS Comp Biol 12(3):e1004825 [journal] [pdf]
Ray JCJ. 2016. Survival of phenotypic information during cellular growth transitions. ACS Synth Biol 5(8):810-816 (Programmable Biology special issue) [journal] [pdf]
Parente DJ, Ray JCJ, Swint-Kruse L. 2015. Amino acid positions subject to multiple coevolutionary constraints can be robustly identified by their eigenvector network centrality scores. Proteins 83(12):2293-2306. doi:10.1002/prot.24948 [journal] [pdf]
González C, Ray JCJ, Manhart M, Adams RM, Nevozhay D, Morozov AV, and Balázsi, G. 2015. Stress-response balance drives the evolution of a network module and its host genome. Mol Sys Biol 11: 827. doi:10.15252/msb.20156185 [journal] [pdf]
Ray JCJ, and Igoshin OA. 2012. Interplay of Gene Expression Noise and Ultrasensitive Dynamics Affects Bacterial Operon Organization. PLOS Comput Biol 8(8): e1002672. doi:10.1371/journal.pcbi.1002672 [journal] [pdf]
Quan S, Ray JCJ, Kwota Z, Duong T, Balázsi G, Cooper TF, and Monds RD. 2012. Adaptive Evolution of the Lactose Utilization Network in Experimentally Evolved Populations of Escherichia coli. PLOS Genet 8(1): e1002444 (January 2012) doi:10.1371/journal.pgen.1002444 [journal] [pdf]
Ray JCJ, Tabor JJ, and Igoshin OA. 2011. Non-transcriptional regulatory processes shape transcriptional network dynamics. Nature Rev Microbiol 9, 817-828 (November 2011) doi:10.1038/nrmicro2667 [journal] [pdf]
Tiwari A, Ray JCJ, Narula J, and Igoshin OA. 2011. Bistable responses in bacterial genetic networks: Designs and dynamical consequences. Math Biosci 231(1):76-89. doi:10.1016/j.mbs.2011.03.004 [journal] [pdf]
Ray JCJ, and Igoshin OA. 2010. Adaptable Functionality of Transcriptional Feedback in Bacterial Two-Component Systems. PLOS Comput Biol 6(2): e1000676. doi:10.1371/journal.pcbi.1000676 [journal] [pdf]
Ray JCJ, Flynn JL, and Kirschner DE. 2009. Synergy between Individual TNF-Dependent Functions Determines Granuloma Performance for Controlling Mycobacterium tuberculosis Infection. J Immunol 182(6): 3706-3717. doi:10.4049/jimmunol.0802297 [journal] [pdf]
Ray JCJ, Wang J, Chan J, and Kirschner DE. 2008. The timing of TNF and IFN-gamma signaling affects macrophage activation strategies during Mycobacterium tuberculosis infection. J Theor Biol 252(1):24-38. doi:10.1016/j.jtbi.2008.01.010 [journal] [pdf]
Marino S, Hogue IB, Ray CJ, and Kirschner DE. 2008. A methodology for performing global uncertainty and sensitivity analysis in systems biology. J Theor Biol 254(1):178-196. doi:10.1016/j.jtbi.2008.04.011 [journal] [pdf]
Ray JCJ, and Kirschner DE. 2006. Requirement for multiple activation signals by anti-inflammatory feedback in macrophages. J Theor Biol 241(2):276-294. doi:10.1016/j.jtbi.2005.11.037 [journal] [pdf]
Usui N, Ray CJ, Drongowski RA, Coran AG, and Harmon CM. 1999. The effect of phospholipids and mucin on bacterial internalization in an enterocyte-cell culture model. Pediatr Surg Int 15(3-4):150-154. doi:10.1007/s003830050543 [journal] [pdf]