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. Oliveira SMD, Densmore D. Hardware, Software, and Wetware Codesign Environment for Synthetic Biology. Biodes Res. 2022; 2022:9794510. PMID: 37850136
  2. 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;
  3. 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;
  4. Oliveira SMD, Densmor D. Hardware, Software, Wetware, Co-Design for Synthetic Biology. BioDesign Research. 2022. View Publication
  5. 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;
  6. 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;
  7. 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;
  8. 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;
  9. 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;
  10. 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;
Showing 10 of 24 results. Show More

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

Bar chart showing 3 publications over 3 distinct years, with a maximum of 1 publications in 2015 and 2018 and 2022


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 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')