| Wisdom of crowds for robust gene network inference D Marbach, JC Costello, R Küffner, NM Vega, RJ Prill, DM Camacho, ... Nature methods 9 (8), 796-804, 2012 | 1873 | 2012 |
| Next-generation machine learning for biological networks DM Camacho, KM Collins, RK Powers, JC Costello, JJ Collins Cell 173 (7), 1581-1592, 2018 | 957 | 2018 |
| A complex human gut microbiome cultured in an anaerobic intestine-on-a-chip S Jalili-Firoozinezhad, FS Gazzaniga, EL Calamari, DM Camacho, ... Nature biomedical engineering 3 (7), 520-531, 2019 | 718 | 2019 |
| The Mycobacterium tuberculosis regulatory network and hypoxia JE Galagan, K Minch, M Peterson, A Lyubetskaya, E Azizi, L Sweet, ... Nature 499 (7457), 178-183, 2013 | 496 | 2013 |
| Antibiotic-Induced Bacterial Cell Death Exhibits Physiological and Biochemical Hallmarks of Apoptosis DJ Dwyer, DM Camacho, MA Kohanski, JM Callura, JJ Collins Molecular Cell, 2012 | 433 | 2012 |
| The origin of correlations in metabolomics data D Camacho, A de la Fuente, P Mendes Metabolomics 1 (1), 53-63, 2005 | 332 | 2005 |
| Fungicidal Drugs Induce a Common Oxidative-Damage Cellular Death Pathway P Belenky, D Camacho, JJ Collins Cell Reports, 2013 | 204 | 2013 |
| Directed differentiation of human induced pluripotent stem cells into mature kidney podocytes and establishment of a Glomerulus Chip S Musah, N Dimitrakakis, DM Camacho, GM Church, DE Ingber Nature protocols 13 (7), 1662-1685, 2018 | 172 | 2018 |
| Species-specific enhancement of enterohemorrhagic E. coli pathogenesis mediated by microbiome metabolites A Tovaglieri, A Sontheimer-Phelps, A Geirnaert, R Prantil-Baun, ... Microbiome 7, 1-21, 2019 | 134 | 2019 |
| Functional characterization of bacterial sRNAs using a network biology approach SR Modi, DM Camacho, MA Kohanski, GC Walker, JJ Collins Proceedings of the National Academy of Sciences 108 (37), 15522-15527, 2011 | 129 | 2011 |
| Sequence-to-function deep learning frameworks for engineered riboregulators JA Valeri, KM Collins, P Ramesh, MA Alcantar, BA Lepe, TK Lu, ... Nature communications 11 (1), 5058, 2020 | 103 | 2020 |
| Deep-Learning Resources for Studying Glycan-Mediated Host-Microbe Interactions D Bojar, RK Powers, DM Camacho, JJ Collins Cell Host & Microbe 29 (1), 132-144. e3, 2021 | 80* | 2021 |
| Central role for RNase YbeY in Hfq-dependent and Hfq-independent small-RNA regulation in bacteria SP Pandey, JA Winkler, H Li, DM Camacho, JJ Collins, GC Walker BMC genomics 15, 1-16, 2014 | 68 | 2014 |
| Comparison of Reverse‐Engineering Methods Using an in Silico Network D CAMACHO, P VERA LICONA, P MENDES, R LAUBENBACHER Annals of the New York Academy of Sciences 1115 (1), 73-89, 2007 | 58 | 2007 |
| A systems biology study of two distinct growth phases of Saccharomyces cerevisiae cultures AM Martins, D Camacho, J Shuman, W Sha, P Mendes, V Shulaev Current Genomics 5 (8), 649-663, 2004 | 53 | 2004 |
| Modelling and simulation for metabolomics data analysis P Mendes, D Camacho, A de la Fuente Biochemical Society Transactions 33 (6), 1427-1429, 2005 | 47 | 2005 |
| Nutritional deficiency in an intestine-on-a-chip recapitulates injury hallmarks associated with environmental enteric dysfunction A Bein, CW Fadel, B Swenor, W Cao, RK Powers, DM Camacho, ... Nature Biomedical Engineering 6 (11), 1236-1247, 2022 | 42 | 2022 |
| Systems biology strikes gold DM Camacho, JJ Collins Cell 137 (1), 24-26, 2009 | 36 | 2009 |
| Harnessing colon chip technology to identify commensal bacteria that promote host tolerance to infection FS Gazzaniga, DM Camacho, M Wu, MF Silva Palazzo, ALM Dinis, ... Frontiers in Cellular and Infection Microbiology 11, 638014, 2021 | 34 | 2021 |
| BioAutoMATED: An end-to-end automated machine learning tool for explanation and design of biological sequences JA Valeri, LR Soenksen, KM Collins, P Ramesh, G Cai, R Powers, ... Cell Systems 14 (6), 525-542. e9, 2023 | 21 | 2023 |
James J CollinsMIT; Wyss Institute, Harvard; Broad Institute of MIT & HarvardVerified email at mit.edu