Samuel Oliveira, PhD
Research Assistant Professor
Boston University College of Engineering
Dept of Electrical and Computer Engineering




The Oliveira Lab investigates the emergence of microbial community complexity and their underlying interactions in varying environmental contexts and studies microbial community design principles and metrics to help build novel collective behaviors. We hope that breakthroughs in computational and synthetic biology methods will accelerate our knowledge of the links between genetic sequences and intercellular communication to study and engineer the spatiotemporal behavior of biological networks.
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One important goal is to develop innovative ways to shift microbiomes' metabolic state after interacting with desired external stimuli, e.g., heavy metals. Nevertheless, the increasing demand for testing and combining multiple cell types, mechanisms, topologies, and conditions requires the development of novel experimental methods.
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Our work explores novel ways to probe these interactions using massively parallel microscopy, microfluidic screening techniques, and control theory principles. These techniques use genetic engineering advancements, single-cell microscopy data and machine learning, dynamical modeling, and design optimization.

Lab's expertise includes High-throughput Screening and Characterization; Microfluidics Design and Fabrication; Lab Automation Workflows; Single-cell Microscopy; Designing Genetic Circuits; Computational Methods for Microscopy Data Analysis.
For further information, please visit www.oliveiralab.me

Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.

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  1. Landaverde L, McIntyre D, Robson J, Fu D, Ortiz L, Chen R, Oliveira SMD, Fan A, Barrett A, Burgay SP, Choate S, Corbett D, Doucette-Stamm L, Gonzales K, Hamer DH, Huang L, Huval S, Knight C, Landa C, Lindquist D, Lockard K, Macdowell TL, Mauro E, McGinty C, Miller C, Monahan M, Moore R, Platt J, Rolles L, Roy J, Schroeder T, Tolan DR, Zaia A, Brown RA, Waters G, Densmore D, Klapperich CM. Buildout and integration of an automated high-throughput CLIA laboratory for SARS-CoV-2 testing on a large urban campus. SLAS Technol. 2022 Oct; 27(5):302-311.View Related Profiles. PMID: 35718332; PMCID: PMC9212990; DOI: 10.1016/j.slast.2022.06.003;
     
  2. Jones TS, Oliveira SMD, Myers CJ, Voigt CA, Densmore D. Genetic circuit design automation with Cello 2.0. Nat Protoc. 2022 Apr; 17(4):1097-1113. PMID: 35197606; DOI: 10.1038/s41596-021-00675-2;
     
  3. Oliveira SMD, Densmor D. Hardware, Software, Wetware, Co-Design for Synthetic Biology. BioDesign Research. 2022. View Publication
  4. Oliveira SMD, Rocha LB, da Cunha MTR, Cintra MMM, Pinheiro NM, Mendonça AC. Effects of carboxytherapy on skin laxity. J Cosmet Dermatol. 2020 Nov; 19(11):3007-3013. PMID: 32091181; DOI: 10.1111/jocd.13337;
     
  5. Häkkinen A, Oliveira SMD, Neeli-Venkata R, Ribeiro AS. Transcription closed and open complex formation coordinate expression of genes with a shared promoter region. J R Soc Interface. 2019 Dec; 16(161):20190507. PMID: 31822223; PMCID: PMC6936044; DOI: 10.1098/rsif.2019.0507;
     
  6. Bahrudeen MNM, Chauhan V, Palma CSD, Oliveira SMD, Kandavalli VK, Ribeiro AS. Estimating RNA numbers in single cells by RNA fluorescent tagging and flow cytometry. J Microbiol Methods. 2019 Nov; 166:105745. PMID: 31654657; DOI: 10.1016/j.mimet.2019.105745;
     
  7. Oliveira SMD, Goncalves NSM, Kandavalli VK, Martins L, Neeli-Venkata R, Reyelt J, Fonseca JM, Lloyd-Price J, Kranz H, Ribeiro AS. Chromosome and plasmid-borne PLacO3O1 promoters differ in sensitivity to critically low temperatures. Sci Rep. 2019 Mar 14; 9(1):4486. PMID: 30872616; PMCID: PMC6418193; DOI: 10.1038/s41598-019-39618-z;
     
  8. Martins L, Neeli-Venkata R, Oliveira SMD, Häkkinen A, Ribeiro AS, Fonseca JM. SCIP: a single-cell image processor toolbox. Bioinformatics. 2018 Dec 15; 34(24):4318-4320. PMID: 29931314; DOI: 10.1093/bioinformatics/bty505;
     
  9. Neeli-Venkata R, Oliveira SMD, Martins L, Startceva S, Bahrudeen M, Fonseca JM, Minoia M, Ribeiro AS. The precision of the symmetry in Z-ring placement in Escherichia coli is hampered at critical temperatures. Phys Biol. 2018 May 18; 15(5):056002. PMID: 29717708; DOI: 10.1088/1478-3975/aac1cb;
     
  10. Goncalves NSM, Startceva S, Palma CSD, Bahrudeen MNM, Oliveira SMD, Ribeiro AS. Temperature-dependence of the single-cell variability in the kinetics of transcription activation in Escherichia coli. Phys Biol. 2018 Jan 24; 15(2):026007. PMID: 29182518; DOI: 10.1088/1478-3975/aa9ddf;
     
Showing 10 of 23 results. Show More

This graph shows the total number of publications by year, by first, middle/unknown, or last author.

Bar chart showing 23 publications over 9 distinct years, with a maximum of 4 publications in 2015 and 2018

YearPublications
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20193
20201
20223

2021 DOROTH DOT.AIR, Sao Paulo, Brazil: FINEP - Startup Seed Award
2020 DOROTH, Braskem, Sao Paulo, Brazil: Start-up Acceleration Award
2020 DOROTH, Open Innovation EMBRAPA-Soja, Paraná, Brazil: Start-up Acceleration Award
2019-2021 Sao Paulo Res. Found. (FAPESP), 1M BRL, Sao Paulo, Brazil: FAPESP Award, PIPE Fase-2
2019 DOROTH, SEVNA, Minas Gerais, Brazil: Startup Acceleration and Angel Investment Award
2019 Tampere University, Finland: Best Ph.D. Thesis Award
2017-2018 Väisälä Fund, Finnish Academy of Science, Tampere, Finland: Ph.D. Grant
2017 SmartLID, Sao Paulo City Foundation, Sao Paulo, Brazil: Best Idea for Innovative Product
2016 Väisälä Fund, Finnish Academy of Science, Tampere, Finland: Ph.D. Grant
2016 BIOTECHNO, the 8th International Conference, Lisbon, Portugal: Best Paper Award
2014 Tampere University, Finland: MSc degree with distinction
2013 DSP, TUT, Tampere, Finland: MSc. Thesis Grant

The Oliveira Lab investigates the emergence of microbial community complexity and their underlying interactions in varying environmental contexts and studies microbial community design principles and metrics to help build novel collective behaviors. We hope that breakthroughs in computational and synthetic biology methods will accelerate our knowledge of the links between genetic sequences and intercellular communication to study and engineer the spatiotemporal behavior of biological networks. One important goal is to develop innovative ways to shift microbiomes' metabolic state after interacting with desired external stimuli, e.g., heavy metals.

Many postdoctoral positions are available in microbiology, bioengineering, computational biology, and microfluidics. Please get in touch with Dr. Oliveira at smdo@bu.edu for more information.

Available to Mentor as: (Review Mentor Role Definitions):
  • Advisor
  • Education Mentor
  • Project Mentor
  • Research / Scholarly Mentor
Contact for Mentoring:
  • Email (see 'Contact Info')
  • Phone (see 'Contact Info')
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