| A methodology for performing global uncertainty and sensitivity analysis in systems biology S Marino, IB Hogue, CJ Ray, DE Kirschner Journal of theoretical biology 254 (1), 178-196, 2008 | 2766 | 2008 |
| Synergy between individual TNF-dependent functions determines granuloma performance for controlling Mycobacterium tuberculosis infection JCJ Ray, JAL Flynn, DE Kirschner The Journal of Immunology 182 (6), 3706-3717, 2009 | 179 | 2009 |
| Stress‐response balance drives the evolution of a network module and its host genome C González, JCJ Ray, M Manhart, RM Adams, D Nevozhay, AV Morozov, ... Molecular systems biology 11 (8), 827, 2015 | 105 | 2015 |
| Bistable responses in bacterial genetic networks: designs and dynamical consequences A Tiwari, JCJ Ray, J Narula, OA Igoshin Mathematical biosciences 231 (1), 76-89, 2011 | 83 | 2011 |
| Adaptive Evolution of the Lactose Utilization Network in Experimentally Evolved Populations of Escherichia coli S Quan, JCJ Ray, Z Kwota, T Duong, G Balázsi, TF Cooper, RD Monds PLoS genetics 8 (1), e1002444, 2012 | 74 | 2012 |
| Adaptable functionality of transcriptional feedback in bacterial two-component systems JCJ Ray, OA Igoshin PLoS Comput Biol 6 (2), e1000676-e1000676, 2010 | 68 | 2010 |
| The timing of TNF and IFN-γ signaling affects macrophage activation strategies during Mycobacterium tuberculosis infection JCJ Ray, J Wang, J Chan, DE Kirschner Journal of theoretical biology 252 (1), 24-38, 2008 | 60 | 2008 |
| Non-transcriptional regulatory processes shape transcriptional network dynamics JCJ Ray, JJ Tabor, OA Igoshin Nature Reviews Microbiology 9 (11), 817-828, 2011 | 59 | 2011 |
| A novel metric reveals previously unrecognized distortion in dimensionality reduction of scRNA-Seq data SM Cooley, T Hamilton, SD Aragones, JCJ Ray, EJ Deeds Biorxiv, 689851, 2019 | 42 | 2019 |
| Cellular growth arrest and persistence from enzyme saturation JCJ Ray, ML Wickersheim, AP Jalihal, YO Adeshina, TF Cooper, ... PLoS Computational Biology 12 (3), e1004825, 2016 | 38 | 2016 |
| Interplay of gene expression noise and ultrasensitive dynamics affects bacterial operon organization JCJ Ray, OA Igoshin Public Library of Science 8 (8), e1002672, 2012 | 29 | 2012 |
| The effect of phospholipids and mucin on bacterial internalization in an enterocyte cell culture model N Usui, C Ray, H Okuyama, RA Drongowski, AG Coran, CM Harmon Ped Surg Int 15, 150-154, 1999 | 24 | 1999 |
| Amino acid positions subject to multiple co‐evolutionary constraints can be robustly identified by their eigenvector network centrality scores DJ Parente, JCJ Ray, L Swint‐Kruse Proteins: Structure, Function, and Bioinformatics, 2015 | 22 | 2015 |
| Diversity in lac Operon Regulation among Diverse Escherichia coli Isolates Depends on the Broader Genetic Background but Is Not Explained by Genetic … KN Phillips, S Widmann, HY Lai, J Nguyen, JCJ Ray, G Balázsi, ... Mbio 10 (6), 10.1128/mbio. 02232-19, 2019 | 15 | 2019 |
| Requirement for multiple activation signals by anti-inflammatory feedback in macrophages JCJ Ray, DE Kirschner Journal of theoretical biology 241 (2), 276-294, 2006 | 15 | 2006 |
| Computation by natural systems D Chu, M Prokopenko, JCJ Ray Interface Focus 8 (6), 20180058, 2018 | 6 | 2018 |
| Lineage space and the propensity of bacterial cells to undergo growth transitions A Bandyopadhyay, H Wang, JCJ Ray PLOS Computational Biology 14 (8), e1006380, 2018 | 6 | 2018 |
| Survival of phenotypic information during cellular growth transitions JCJ Ray ACS Synthetic Biology 5 (8), 810-816, 2016 | 5 | 2016 |
| A framework for evaluating edited cell libraries created by massively parallel genome engineering S Cawley, E Abbate, CG Abraham, S Alvarez, M Barber, S Bolte, J Bruand, ... bioRxiv, 2021.09. 23.458228, 2021 | 2 | 2021 |
| Signatures of antibiotic tolerance and persistence in response to divergent stresses H Wang, GW McElfresh, N Wijesuriya, A Podgorny, AD Hecht, JCJ Ray bioRxiv, 2023.02. 05.527212, 2023 | | 2023 |
Gábor BalázsiHenry Laufer Professor of Physical & Quantitative Biology, Stony Brook UniversityVerified email at stonybrook.edu
