Facile: a command-line network compiler for systems biology. - Fernando Siso-Nadal; Julien F. Ollivier; Peter S. Swain (BMC Syst. Biol., 2007)

Scalable Rule-Based Modelling of Allosteric Proteins and Biochemical Networks. - Julien F. Ollivier; Vahid Shahrezaei; Peter S. Swain (PLoS Comput. Biol., 2010)

Trade-Offs and Constraints in Allosteric Sensing. - Bruno M. C. Martins; Peter S. Swain (PLoS Comput. Biol., 2011)

The Fidelity of Dynamic Signaling by Noisy Biomolecular Networks. - Clive G. Bowsher; Margaritis Voliotis; Peter S. Swain (PLoS Comput. Biol., 2013)

Ultrasensitivity in Phosphorylation-Dephosphorylation Cycles with Little Substrate. - Bruno M. C. Martins; Peter S. Swain (PLoS Comput. Biol., 2013)

Optimally designed vs intuition-driven inputs: the study case of promoter activity modelling. - Lucia Bandiera; Varun Kothamachu; Eva Balsa-Canto; Peter S. Swain; Filippo Menolascina (CDC, 2018)

Morphologically constrained and data informed cell segmentation of budding yeast. - Elco Bakker; Peter S. Swain; Matthew M. Crane (Bioinform., 2018)

Multiple nutrient transporters enable cells to mitigate a rate-affinity tradeoff. - Luis Fernando Montaño-Gutierrez; Kevin Correia; Peter S. Swain (PLoS Comput. Biol., 2022)

Analysing and meta-analysing time-series data of microbial growth and gene expression from plate readers. - Luis Fernando Montaño-Gutierrez; Nahuel Manzanaro Moreno; Iseabail L. Farquhar; Yu Huo; Lucia Bandiera; Peter S. Swain (PLoS Comput. Biol., 2022)

Nunchaku: optimally partitioning data into piece-wise contiguous segments. - Yu Huo; Hongpei Li; Xiao Wang; Xiaochen Du; Peter S. Swain (Bioinform., 2023)