"Fluctuograms" Reveal the Intermittent Intra-Protein Communication in Subtilisin Carlsberg and Correlate Mechanical Coupling with Co-Evolution. - Jordi Silvestre-Ryan; Yuchun Lin; Jhih-Wei Chu (PLoS Comput. Biol., 2011)

Consensus Decoding of Recurrent Neural Network Basecallers. - Jordi Silvestre-Ryan; Ian H. Holmes (AlCoB, 2018)

Machine Boss: rapid prototyping of bioinformatic automata. - Jordi Silvestre-Ryan; Yujie Wang; Mehak Sharma; Stephen Lin; Yolanda Shen; Shihab Dider; Ian H. Holmes (Bioinform., 2021)