Temperature-Dependent Model of Multi-step Transcription Initiation in Escherichia coli Based on Live Single-Cell Measurements. - Samuel M. D. Oliveira; Antti Häkkinen; Jason Lloyd-Price; Huy Tran; Vinodh Kandavalli; Andre S. Ribeiro (PLoS Comput. Biol., 2016)

Estimating Effects of Extrinsic Noise on Model Genes and Circuits with Empirically Validated Kinetics. - Samuel M. D. Oliveira; Mohamed N. M. Bahrudeen; Sofia Startceva; Andre S. Ribeiro (WIVACE, 2017)

Modeling and Engineering Promoters with Pre-defined RNA Production Dynamics in Escherichia Coli. - Samuel M. D. Oliveira; Mohamed N. M. Bahrudeen; Sofia Startceva; Vinodh Kandavalli; Andre S. Ribeiro (CMSB, 2018)

SCIP: a single-cell image processor toolbox. - Leonardo Martins; Ramakanth Neeli-Venkata; Samuel M. D. Oliveira; Antti Häkkinen; Andre S. Ribeiro; José M. Fonseca 001 (Bioinform., 2018)

Vespa: Logic-Level Constraint-Based Validation for Continuous-Flow Microfluidic Devices. - Yangruirui Zhou; Samuel M. D. Oliveira; Radhakrishna Sanka; David McIntyre; Douglas Densmore (IEEE Trans. Comput. Aided Des. Integr. Circuits Syst., 2025)