Towards a computational model of the colonic crypt with a realistic, deformable geometry. - Sara-Jane Nicole Dunn (2011)

A Two-Dimensional Model of the Colonic Crypt Accounting for the Role of the Basement Membrane and Pericryptal Fibroblast Sheath. - Sara-Jane Dunn; Paul L. Appleton; Scott A. Nelson; Inke S. Näthke; David Gavaghan; James M. Osborne (PLoS Comput. Biol., 2012)

Chaste: An Open Source C++ Library for Computational Physiology and Biology. - Gary R. Mirams; Christopher J. Arthurs; Miguel O. Bernabeu; Rafel Bordas; Jonathan Cooper; Alberto Corrias; Yohan Davit; Sara-Jane Dunn; Alexander G. Fletcher; Daniel G. Harvey; Megan E. Marsh; James M. Osborne; et al. (PLoS Comput. Biol., 2013)

Ten Simple Rules for Effective Computational Research. - James M. Osborne; Miguel O. Bernabeu; Maria Bruna; Ben Calderhead; Jonathan Cooper; Neil Dalchau; Sara-Jane Dunn; Alexander G. Fletcher; Robin Freeman; Derek Groen; Bernhard Knapp; Greg J. McInerny; et al. (PLoS Comput. Biol., 2014)

Switching Gene Regulatory Networks. - Yoli Shavit; Boyan Yordanov; Sara-Jane Dunn; Christoph M. Wintersteiger; Youssef Hamadi; Hillel Kugler (IPCAT, 2015)

Algebraic Polynomial-based Synthesis for Abstract Boolean Network Analysis. - Peter Backeman; Christoph M. Wintersteiger; Boyan Yordanov; Sara-Jane Dunn (SMT@IJCAR, 2016)

Automated Synthesis and Analysis of Switching Gene Regulatory Networks. - Yoli Shavit; Boyan Yordanov; Sara-Jane Dunn; Christoph M. Wintersteiger; Tomoki Otani; Youssef Hamadi; Frederick J. Livesey; Hillel Kugler (Biosyst., 2016)

Biological computation (keynote). - Sara-Jane Dunn (CGO, 2018)

Formal Analysis of Network Motifs. - Hillel Kugler; Sara-Jane Dunn; Boyan Yordanov (CMSB, 2018)

Automated Reasoning for the Synthesis and Analysis of Biological Programs. - Sara-Jane Dunn; Boyan Yordanov (Automated Reasoning for Systems Biology and Medicine, 2019)

Formal Analysis of Network Motifs Links Structure to Function in Biological Programs. - Sara-Jane Dunn; Hillel Kugler; Boyan Yordanov (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

An SMT-Based Framework for Reasoning About Discrete Biological Models. - Boyan Yordanov; Sara-Jane Dunn; Colin Gravill; Hillel Kugler; Christoph M. Wintersteiger (ISBRA, 2022)

DiscoGen: Learning to Discover Gene Regulatory Networks. - Nan Rosemary Ke; Sara-Jane Dunn; Jörg Bornschein; Silvia Chiappa; Mélanie Rey; Jean-Baptiste Lespiau; Albin Cassirer; Jane X. Wang; Theophane Weber; David G. T. Barrett; Matthew M. Botvinick; Anirudh Goyal; et al. (CoRR, 2023)

The Reasoning Engine: A Satisfiability Modulo Theories-Based Framework for Reasoning About Discrete Biological Models. - Boyan Yordanov; Sara-Jane Dunn; Colin Gravill; Himanshu Arora; Hillel Kugler; Christoph M. Wintersteiger (J. Comput. Biol., 2023)