Diogo M. Camacho

Looking for patterns in biological data.

Google Scholar Profile

Peer-reviewed Publications

  • Valeri, JA, Soenksen, LR, Collins, KM, Ramesh, P, Cai, G, Powers, R, Angenent–Mari, NA, Camacho, DM, Wong, F, Lu, TK, Collins, JJ (2023), BioAutoMATED: An end-to-end automated machine learning tool for explanation and design of biological sequences, Cell Systems, 14, 525 PubMed
  • Sperry, MM, Novak, R, Keshari, V, Dinis, ALM, Cartwright, MJ, Camacho, DM, ParĂ©, JF, Super, M, Levin, M, Ingber, DE (2022), Enhancers of host immune tolerance to bacterial infection discovered using linked computational and experimental approaches, Adv Sci PubMed
  • Gazzaniga, FS, Camacho, DM, Wu, M, Palazzo, MFS, Dinis, ALM, Grafton, FN, Cartwright, MJ, Super, M, Kasper, DL, Ingber, DE (2021), Harnessing Colon Chip technology to identify commensal bacteria that promote host tolerance to infection, Frontiers in Cellular and Infection Microbiology, 11, 105 PubMed
  • Bein, A, ,Fadel, CW, Swenor, B, Cao, W, Powers, RK, Camacho, DM, Naziripour, A, Parsons, AW, LoGrande, NT, Sharma, S, Kim, S, Jalili-Firoozinezhad, S, Grant, J, Breault, DT, Iqbal, J, Ali, A, Denson, LA, Moore, SR, Prantil-Baun, R, Goyal, G, Ingber, DE (2022), Nutritional deficiency recapitulates intestinal injury associated with environmental enteric dysfunction in patient-derived Organ Chips, Nature Biomed Eng PubMed
  • Bojar, D, Powers, RK, Camacho, DM, Collins, JJ (2020), Deep-Learning Resources for Studying Glycan-Mediated Host-Microbe Interactions, Cell Host & Microbe, 29, 132-144 PubMed
  • Valeri, J, Collins, KM, Ramesh, P, Alcantar, M, Lepe, BA, Lu, TK, Camacho, DM (2020), Sequence-to-function deep learning frameworks for engineered riboregulators, Nature Communications, 11, 5058 PubMed
  • Jalili-Firoozinezhad, S, Gazzaniga, FS, Calamari, EL, Camacho, DM, Fadel, C, Nestor, B, Cronce, MJ, Tovaglieri, A, Levy, O, Gregory, KE, Breault, DT, Cabral, JMS, Kasper, DL, Novak, R, Ingber, DE (2019), A complex human gut microbiome cultured in an anaerobic intestine-on-a-chip, Nature Biomedical Engineering, 3, 520-531 PubMed
  • Tovaglieri, A, Sontheimer-Phelps, A, Geirnaert, A, Prantil-Baun, R, Camacho, DM, Chou, DB, Jalili-Firoozinezhad, S, de Wouters, T, Kasendra, M, Super, M, Cartwright, M, Richmond, CA, Breault, DT, Lacroix, C, Ingber, DE (2019), Species-specific enhancement of enterohemorrhagic E. coli pathogenesis mediated by microbiome metabolites, Microbiome, 7, 43 PubMed
  • Camacho, DM, Collins, KM, Powers, RK, Costello, JC, Collins, JJ (2018), Next-generation machine learning for biological networks, Cell, 173, 1581-1592 PubMed
  • Musah, S, Dimitrakakis, N, Camacho, DM, Church, GM, Ingber, DE (2018), Directed differentiation of human induced pluripotent stem cells into mature kidney podocytes and establishment of a Glomerulus Chip, Nature Protocols, 13, 1662-1685 PubMed
  • Paandey, SP, Winkler, JA, Li, H, Camacho, DM, Collins, JJ, Walker, GC (2014), Central role for RNase YbeY in Hfq-dependent and Hfq-independent small-RNA regulation in bacteria, BMC Genomics, 15, 121 PubMed
  • Galagan, JE, Minch, K, Peterson, M, Lyubetskya, A, Azzizi, E, Sweet, L, Gomes, A, Rustad, T, Dolganov, G, Glotova, I, Abeel, T, Mawhinney, C, Kennedy, A, Allard, R, Brabant, W, Krueger, A, Jaini, S, Honda, B, Yu, W-H, Hickey, M, Zucker, J, Garay, C, Weiner, B, Sisk, P, Stolte, C, Winkler, J, Van de Peer, Y, Iazzetti, P, Camacho, D, Dreyfuss, J, Liu, Y, Dorhoi, A, Mollenkopf, H-J, Drogaris, P, Lamontagne, J, Zhou, Y, Piquenot, J, Park, ST, Raman, S, Kaufmann, S, Mohney, R, Chelsky, D, Moody, B, Sherman, D, Schoolnik, G (2013), The Mycobacterium tuberculosis regulatory network and hypoxia, Nature, 499, 178-183 PubMed
  • Belenky, P, Camacho, D, Collins, JJ (2013), Fungicidal drugs induce a common oxidative-damage cellular death pathway, Cell Reports, 3, 350-358 PubMed
  • Marbach, D, Costello, JC, Kuffner, R, Vega, N, Prill, RJ, Camacho, DM, Allison, KR, the DREAM5 Consortium, Kellis, M, Collins, JJ, Stolovitzky, G (2012), Wisdom of crowds for robust gene network inference, Nature Methods, 9, 796-804 PubMed
  • Dwyer, DJ, Camacho, DM, Callura, JM, Kohanski, MA, Collins, JJ (2011), Antibiotic-induced bacterial cell death exhibits physiological and biochemical hallmarks of apoptosis, Molecular Cell, 46, 561-572 PubMed
  • Modi, SR, Camacho, DM, Kohanski, MA, Collins, JJ (2011), Functional characterization of bacterial sRNAs using a network biology approach, Proc. Natl. Acad. Sci. USA, 108, 15522-15527 PubMed
  • Camacho, DM, Collins, JJ (2009), Systems biology strikes gold, Cell, 137, 24-26 PubMed
  • Camacho, D, Vera-Licona, P, Laubenbacher, R, Mendes, P (2007), Comparison of existing reverse engineering methods by use of an in silico system, Ann. N. Y. Acad. Sci., 1115, 73-89 PubMed
  • Mendes, P, Camacho, D, de la Fuente, A (2005), Modelling and simulation for metabolomics data analysis, Biochem. Soc. Trans., 33, 1427-1429 PubMed
  • Camacho, D, de la Fuente, A, Mendes, P (2005), The origin of correlations in metabolomics data, Metabolomics, 1, 53-63 Link
  • Martins, AM, Camacho, D, Shuman, J, Sha, W, Mendes, P, Shulaev, V (2004), A systems biology study of two distinct growth phases of Saccharomyces cerevisiae cultures, Curr. Genomics, 5, 649-663 Link

Patents

  • Methods for detecting cellular transitions (US Provisional, 63/612,266)
  • Disease detection systems and methods (US Providional, 63/612,320)
  • Systems and methods for predicting compounds associated with transcriptional signatures (US Non-provisional, 18/539,190; International PCT, PCT/US2023/083922)
  • Contrastive systems and methods (US Non-provisional, 18/539,204; International PCT, PCT/US2023/083934)
  • Complex Human Gut Microbiome Cultured in an Anaerobic Human Gut-on-A-Chip (US20240002808A1)
  • Riboregulators and methods of use thereof (International PCT, PCT/US2020/064695)
  • Compositions and methods for treating fungal infections (WO2014130922A1)

Awards and Grants

  • Molecular circuits in the hematopoietic stem cell niche (NIH) (2020)
    Role: co-Investigator
    Award: $415,000

  • Synergistic Discovery and Design (DARPA) (2017)
    Role: co-PI
    Award: $2,000,000