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Publications

2024

  • K.O. Osiro, N. Hashemi, J. Brango-Vanegas, S.M.D. Oliveira, and O.L. Franco (2024) Emerging peptide-based technology for biofilm control Expert Opinion on Biological Therapy. doi:10.1080/14712598.2024.2430623

  • K.A. Walp, Y.H. Patel, W. Alsadoun, H.L. Gordon, H. Rastaghi, S.M.D. Oliveira (2024) A Continuous, Low-Flow, and Multiplexing Pumping System for Microfluidics Applications. BioRxiv. doi:10.1101/2024.08.16.608339

  • Y. Zhou, S.M.D. Oliveira, R. Sanka, D. McIntyre, and D. Densmore (2024) Vespa: Logic-level Constraint-based Validation for Continuous-Flow Microfluidic Devices. IEEE TCAD. doi:10.1109/TCAD.2024.3435706

  • S. Dash, R. Jagadeesan, I.S.C. Baptista, V. Chauhan, V. Kandavalli, S.M.D. Oliveira, and A.S. Ribeiro (2024) A library of reporters of the global regulators of gene expression of Escherichia coli. mSystems. doi:10.1128/msystems.00065-24

Selected (2014-2023)

  • 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

  • B.L.B. Almeida, M.N.M. Bahrudeen, V. Chauhan, S. Dash, V. Kandavalli, A. Häkkinen, J. Lloyd-Price, C.S.D. Palma, I.S.C. Baptista, A. Gupta, J. Kesseli, E. Dufour, O.P. Smolander, M. Nykter, P. Auvinen, H.T. Jacobs, S.M.D. Oliveira and A. S. Ribeiro (2022) The transcription factor network of E. coli steers global responses to shifts in RNAP concentration. Nucleic Acids Research. doi:10.1101/2022.03.07.483226

  • 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. doi:10.5281/zenodo.4676314

  • L. Landaverde, D. McIntyre, J. Robson, D. Fu, L. Ortiz, R. Chen, S.M.D. Oliveira, et al. (2022) Buildout and Integration of an Automated High-Throughput CLIA Laboratory for SARS-CoV-2 Testing on a Large Urban Campus. SLAS Technology. doi:10.1016/j.slast.2022.06.003.

  • 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) Plasmid and chromosome-integrated genes differ in sensitivity to critically low temperatures. Scientific Reports, 9:4486. doi:10.1038/s41598-019-39618-z

  • L. Martins, R. Neeli-Venkata, S.M.D. Oliveira, A. Häkkinen, A.S. Ribeiro, and J.M. Fonseca (2018) SCIP: a single-cell image processor toolbox. Bioinformatics, 34(24):4318-4320. doi:10.1093/bioinformatics/bty505

  • 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. *Equal contribution. doi:10.1371/journal.pcbi.1005174

  • 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

  • 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

  • J. Lloyd-Price, S. Startceva, V. Kandavalli, J.G. Chandraseelan, N. Goncalves, S.M.D Oliveira, A. Häkkinen, and A.S. Ribeiro (2016) Dissecting the stochastic transcription initiation process in live Escherichia coli. DNA Research, 23(3):203-214. doi:10.1093/dnares/dsw009

  • A. Gupta, J. Lloyd-Price, R. Neeli-Venkata, S.M.D. Oliveira, and A.S. Ribeiro (2014) In vivo kinetics of segregation and polar retention of MS2-GFP-RNA complexes in Escherichia coli. Biophysical Journal, 106:1828-1937. doi:10.1016/j.bpj.2014.03.035

  • 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

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