Algorithms for the Constrained Perfect Phylogeny with Persistent Characters. - Paola Bonizzoni; Anna Paola Carrieri; Gianluca Della Vedova; Gabriella Trucco (CoRR, 2014)

When and How the Perfect Phylogeny Model Explains Evolution. - Paola Bonizzoni; Anna Paola Carrieri; Gianluca Della Vedova; Riccardo Dondi; Teresa M. Przytycka (Discrete and Topological Models in Molecular Biology, 2014)

Topological Signatures for Population Admixture. - Laxmi Parida; Filippo Utro; Deniz Yörükoglu; Anna Paola Carrieri; David Kuhn; Saugata Basu (RECOMB, 2015)

Fixed-parameter algorithms for scaffold filling. - Laurent Bulteau; Anna Paola Carrieri; Riccardo Dondi (Theor. Comput. Sci., 2015)

Host Phenotype Prediction from Differentially Abundant Microbes Using RoDEO. - Anna Paola Carrieri; Niina Haiminen; Laxmi Parida (CIBB, 2016)

Sampling ARG of multiple populations under complex configurations of subdivision and admixture. - Anna Paola Carrieri; Filippo Utro; Laxmi Parida (Bioinform., 2016)

Species-Driven Persistent Phylogeny. - Paola Bonizzoni; Anna Paola Carrieri; Gianluca Della Vedova; Raffaella Rizzi; Gabriella Trucco (Fundam. Informaticae, 2017)

A colored graph approach to perfect phylogeny with persistent characters. - Paola Bonizzoni; Anna Paola Carrieri; Gianluca Della Vedova; Raffaella Rizzi; Gabriella Trucco (Theor. Comput. Sci., 2017)

A Fast Machine Learning Workflow for Rapid Phenotype Prediction from Whole Shotgun Metagenomes. - Anna Paola Carrieri; Will P. M. Rowe; Martyn D. Winn; Edward O. Pyzer-Knapp (AAAI, 2019)

Utilizing stability criteria in choosing feature selection methods yields reproducible results in microbiome data. - Lingjing Jiang; Niina Haiminen; Anna Paola Carrieri; Shi Huang; Yoshiki Vazquez-Baeza; Laxmi Parida; Ho-Cheol Kim; Austin D. Swafford; Rob Knight 001; Loki Natarajan (CoRR, 2020)

AutoXAI4Omics: an automated explainable AI tool for omics and tabular data. - James Strudwick; Laura-Jayne Gardiner; Kate Denning-James; Niina Haiminen; Ashley Evans; Jennifer Kelly; Matthew Madgwick; Filippo Utro; Ed Seabolt; Christopher Gibson; Bharat Bedi; Daniel Clayton; et al. (Briefings Bioinform., 2024)