- updated resume

DMC.Rmd

@@ -141,6 +141,15 @@ Senior Research Scientist, Computational Sciences Center of Emphasis \hfill _Jan
  - Performed analysis of genetic data (genome-wide and metabolome-wide) from large sets of patient cohorts
  - Implemented network inference tools for the analysis of large-scale data sets
  - Involved in project decision-making process for the characterization of toxicology patterns of drugs and drug candidates
+
+ **<span style="font-size:1em;">Howard Hughes Medical Institute @ Boston University</span>** \hfill _Boston, MA_  
+Post-doctoral Fellow \hfill _July 2007 - January 2011_ 
+
+- Developed a network inference algorithm for identification of regulatory architectures of pathways
+- Identified a novel mechanism of action for antifungal drugs using transcriptomics and metabolomics data
+- Identified and characterized the small RNA regulatory network in bacterial systems using gene expression data
+- Performed data analysis of gene expression data and metabolomics data in bacterial and fungal systems
+- Consulted in the implementation and usage of inference algorithms across platforms for biotechnology/pharmaceutical companies in the Boston area
 
 
 # Awards and Grants
@@ -229,14 +238,15 @@ co-PI \hfill _9/1/17_
 #   )
 ```
 
+ - Ramesh, P, **Camacho, DM**, Collins, JJ (2019), Nu-speak: A language framework for RNA biology, _Proc. Natl. Acad. Sci. USA_ (_submitted_)
  - Bojar, D, **Camacho, DM**, Collins, JJ (2019), Using natural language processing to learn the language of glycans, _Nature communications_ (_submitted_)
  - Valeri, J, Collins, KM, Lepe, BA, Lu, TK, **Camacho, DM** (2019), A convolutional neural network for interpretable prediction and redesign of toehold switches, _Nature communications_ (_submitted_)
  - 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](https://www.ncbi.nlm.nih.gov/pubmed/31086325)]
  - 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](https://www.ncbi.nlm.nih.gov/pubmed/30890187)]
  - **Camacho, DM**, Collins, KM, Powers, RK, Costello, JC, Collins, JJ (2018), Next-generation machine learning for biological networks, _Cell_, 173, 1581-1592 [[PubMed](https://www.ncbi.nlm.nih.gov/pubmed/29887378)]
  - 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](https://www.ncbi.nlm.nih.gov/pubmed/29995874)]
  - 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](https://www.ncbi.nlm.nih.gov/pubmed/24511998)]
- - 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](https://www.ncbi.nlm.nih.gov/pubmed/23823726)]
+ - 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](https://www.ncbi.nlm.nih.gov/pubmed/23823726)]
  - Belenky, P, **Camacho, D**, Collins, JJ (2013), Fungicidal drugs induce a common oxidative-damage cellular death pathway, _Cell Reports_, 3, 350-358 [[PubMed](https://www.ncbi.nlm.nih.gov/pubmed/23416050)]
  - 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](https://www.ncbi.nlm.nih.gov/pubmed/22796662)]
  - 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](https://www.ncbi.nlm.nih.gov/pubmed/22633370)]
@@ -249,6 +259,7 @@ co-PI \hfill _9/1/17_
 
 
 # Patents
+ - Soenksen, LR, **Camacho, DM**, Collins, KM, Angenent-Mari, NM, Garruss, AS, Collins, JJ, Church, GM, Method for deep learning for RNA synthetic biology (_submitted_)
  - Collins, JJ, Belenky, P, **Camacho, DM** (2015), Compositions and methods for treating fungal infections, WO2014130922A1 [[Link](https://patents.google.com/patent/WO2014130922A1/en)]
 
 # References