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Samuel Oliveira

Samuel Oliveira, Ph.D.

About Professor Oliveira


PDF Version, August 2023


Dr. Oliveira is an Assistant Professor in the Nanoengineering department. His lab investigates the emergence of microbial community complexity, their underlying interactions, and synthetic microbial communities’ design principles. His team applies breakthroughs in computational and synthetic biology methods to improve our knowledge of the links between genetic sequences, intercellular communication, and programmable spatiotemporal behaviors of biological networks. Ultimately, the lab applies this knowledge to build novel collective behaviors, such as micro-bio factories of valuable industry products or “smart” biosensors for agriculture and environmental problems. He is engaged in the SemiSynBio community as a member of the Engineering Biology Research Consortium (EBRC), the most renowned SynBio academic competition named Internationally Genetically Engineered Machine (iGEM) for exposing young interdisciplinary engineers to intensive research opportunities, and Boston University’s Outreach Program STEM Pathways for engaging high schoolers and undergrads in STEM careers.

Selected Publications

S.M.D. Oliveira and D. Densmore (2022) Hardware, Software, Wetware, Co-Design for Synthetic Biology. BioDesign Research. 2022(9794510), 15. DOI: 10.34133/2022/9794510

T.S. Jones, S.M.D. Oliveira, C.J. Myers, C.A. Voigt, and D. Densmore (2022) Genetic Circuit Design Automation with Cello 2.0. Nature Protocols. 17: 1097–1113. DOI: 10.1038/s41596-021-00675-2

S.M.D. Oliveira, N.S.M. Goncalves, L. Martins, R. Neeli-Venkata, J. Reyelt, J.M. Fonseca, J. Lloyd-Price, H. Kranz, and A.S. Ribeiro (2019) Chromosome and plasmid-borne pLacO3O1 promoters differ in sensitivity to critically low temperatures. Scientific Reports, 9:4486. DOI: 10.1038/s41598-019-39618-z

S.M.D. Oliveira, A. Häkkinen, J. Lloyd-Price, H. Tran, V. Kandavalli, and A.S. Ribeiro (2017) Temperature-Dependent Model of Multi-Step Transcription Initiation in Escherichia coli Based on Live Single-Cell Measurements. PLoS Computational Biology, 12(10): e1005174. DOI: 10.1371/journal.pcbi.1005174

S.M.D. Oliveira et al. (2016) Increased cytoplasm viscosity hampers aggregate polar segregation in Escherichia coli. Molecular Microbiology, 99(4):686-699. DOI: 10.1111/mmi.13257

S.M.D. Oliveira, J.G. Chandraseelan, A. Häkkinen, N.S.M. Goncalves, O. Yli-Harja, S. Startceva, and A.S. Ribeiro (2015) Single-cell kinetics of the Repressilator when inserted into a single-copy plasmid. Molecular Biosystems, 11:1939-1945. DOI: 10.1039/C5MB00012B

J. Mäkelä, M. Kandhavelu, S.M.D. Oliveira, J.G. Chandraseelan, J. Lloyd-Price, J. Peltonen, O. Yli-Harja, and A.S. Ribeiro (2013) In vivo single-molecule kinetics of activation and subsequent activity of the arabinose promoter. Nucleic Acids Research, 5:1-9. DOI: 10.1093/nar/gkt350 (complete list:

Honors & Awards

  • National Science Foundation, Collaborative Research (#2211040), Technical Leader, $1,4M, Boston-Greensboro, USA (2023-2025).
  • PIPE FASE-2 and PIPE-INVEST FAPESP Awards, Startup Doroth, $0,5M, Sao Paulo, Brazil (2019-2022).
  • The 2nd Best AgriTech Startup Award, AgriShow Summit, Startup Doroth, Ribeirao Preto, BrazilStartup
  • Startup Acceleration Award, Open Innovation EMBRAStartup, Startup Doroth, Paraná, Brazil (2020).
  • Best Ph.D. Thesis Award, Functionality of Genetic Circuits at Fluctuating Temperatures, Tampere University, Tampere, Finland (2020).
  • PhD Study Funds at Tampere University, Väisälä Fund, Finnish Academy of Science, Tampere, Finland (2016-2019).
  • University of Sao Paulo State Exchange Program Scholarship and Scientific Initiation Grants by FAPESP, Assis, Brazil (2008-2011).

Classes Taught

NANO 781 – Introduction to Synthetic Biology

NANO 782 – Techniques in Synthetic Biology

NANO 706 – Systems and Computational Biology

NANO 881 – Nano and Synthetic Biology

NANO 853 – Nano Bio Electronics Laboratory

Scholarly & Professional Keywords

Bioengineering, Synthetic Microbial Communities, Live Interspecies Dynamics, Co-design Environment of Hardware, Software, and Wetware tools.