Studying Irreversible Transitions in a Model of Cell Cycle Regulation. - Paolo Ballarini; Tommaso Mazza; Alida Palmisano; Attila Csikász-Nagy (PASM@EPEW, 2008)

Analyzing various models of Circadian Clock and Cell Cycle coupling. - Attila Csikász-Nagy; Adrien Fauré; Roberto Larcher; Paola Lecca; Ivan Mura; Ferenc Jordán; Alida Palmisano; Alessandro Romanel; Sean Sedwards; Heike Siebert; Sylvain Soliman; Denis Thieffry; et al. (Formal Methods in Molecular Biology, 2009)

On the Parameter Inference in Chaotic Chemical Systems. - Paola Lecca; Alida Palmisano (EMS, 2009)

From ODES to Language-Based, Executable Models of Biological Systems. - Alida Palmisano; Ivan Mura; Corrado Priami (Pacific Symposium on Biocomputing, 2009)

A new probabilistic generative model of parameter inference in biochemical networks. - Paola Lecca; Alida Palmisano; Corrado Priami; Guido Sanguinetti (SAC, 2009)

Deducing Chemical Reaction Rate Constants and Their Regions of Confidence from Noisy Measurements of Time Series of Concentration. - Paola Lecca; Alida Palmisano; Corrado Priami (UKSim, 2009)

Coding Biological Systems in a Stochastic Framework - The Case Study of Budding Yeast Cell Cycle. - Alida Palmisano (BIOINFORMATICS, 2010)

Modelling and Inference Strategies for Biological Systems. - Alida Palmisano (2010)

Multistate Model Builder (MSMB): a flexible editor for compact biochemical models. - Alida Palmisano; Stefan Hoops; Layne T. Watson; Thomas C. Jones Jr; John J. Tyson; Clifford A. Shaffer (BMC Syst. Biol., 2014)

JigCell Run Manager (JC-RM): a tool for managing large sets of biochemical model parametrizations. - Alida Palmisano; Stefan Hoops; Layne T. Watson; Thomas C. Jones Jr; John J. Tyson; Clifford A. Shaffer (BMC Syst. Biol., 2015)

OpenGeneMed: a portable, flexible and customizable informatics hub for the coordination of next-generation sequencing studies in support of precision medicine trials. - Alida Palmisano; Yingdong Zhao; Ming-Chung Li; Eric C. Polley; Richard M. Simon (Briefings Bioinform., 2017)

JigCell Model Connector: building large molecular network models from components. - Thomas C. Jones Jr; Stefan Hoops; Layne T. Watson; Alida Palmisano; John J. Tyson; Clifford A. Shaffer (Simul., 2018)

TPWshiny: an interactive R/Shiny app to explore cell line transcriptional responses to anti-cancer drugs. - Peter Zhang; Alida Palmisano; Ravindra Kumar; Ming-Chung Li; James H. Doroshow; Yingdong Zhao (Bioinform., 2022)