A basic analysis toolkit for biological sequences. - Raffaele Giancarlo; Alessandro Siragusa; Enrico Siragusa; Filippo Utro (Algorithms Mol. Biol., 2007)

Computational cluster validation for microarray data analysis: experimental assessment of Clest, Consensus Clustering, Figure of Merit, Gap Statistics and Model Explorer. - Raffaele Giancarlo; Davide Scaturro; Filippo Utro (BMC Bioinform., 2008)

A Tutorial on Computational Cluster Analysis with Applications to Pattern Discovery in Microarray Data. - Raffaele Giancarlo; Davide Scaturro; Filippo Utro (Math. Comput. Sci., 2008)

Textual data compression in computational biology: a synopsis. - Raffaele Giancarlo; Davide Scaturro; Filippo Utro (Bioinform., 2009)

The Three Steps of Clustering in the Post-Genomic Era: A Synopsis. - Raffaele Giancarlo; Giosuè Lo Bosco; Luca Pinello; Filippo Utro (CIBB, 2010)

Functional Information, Biomolecular Messages and Complexity of BioSequences and Structures. - Raffaele Giancarlo; Davide Corona; Valeria Di Benedetto; Alessandra Gabriele; Filippo Utro (Structure Discovery in Biology: Motifs, Networks & Phylogenies, 2010)

Speeding up the Consensus Clustering methodology for microarray data analysis. - Raffaele Giancarlo; Filippo Utro (Algorithms Mol. Biol., 2011)

IRiS: Construction of ARG networks at genomic scales. - Asif Javed; Marc Pybus; Marta Melé; Filippo Utro; Jaume Bertranpetit; Francesc Calafell; Laxmi Parida (Bioinform., 2011)

Algorithms for Internal Validation Clustering Measures in the Post Genomic Era - Filippo Utro (CoRR, 2011)

Stability-Based Model Selection for High Throughput Genomic Data: An Algorithmic Paradigm. - Raffaele Giancarlo; Filippo Utro (ICARIS, 2012)

GenomicTools: a computational platform for developing high-throughput analytics in genomics. - Aristotelis Tsirigos; Niina Haiminen; Erhan Bilal; Filippo Utro (Bioinform., 2012)

ARG-based genome-wide analysis of cacao cultivars. - Filippo Utro; Omar Cornejo; Donald Livingstone; Juan Motamayor; Laxmi Parida (BMC Bioinform., 2012)

The Chromatin Organization of an Eukaryotic Genome : Sequence Specific+ Statistical=Combinatorial (Extended Abstract) - Davide Corona; Valeria Di Benedetto; Raffaele Giancarlo; Filippo Utro (CoRR, 2012)

Textual data compression in computational biology: Algorithmic techniques. - Raffaele Giancarlo; Davide Scaturro; Filippo Utro (Comput. Sci. Rev., 2012)

Algorithmic paradigms for stability-based cluster validity and model selection statistical methods, with applications to microarray data analysis. - Raffaele Giancarlo; Filippo Utro (Theor. Comput. Sci., 2012)

Genetic History of Populations: Limits to Inference. - Daniel E. Platt; Filippo Utro; Marc Pybus; Laxmi Parida (Models and Algorithms for Genome Evolution, 2013)

Efficient in silico Chromosomal Representation of Populations via Indexing Ancestral Genomes. - Niina Haiminen; Filippo Utro; Claude Lebreton; Pascal Flament; Zivan Karaman; Laxmi Parida (Algorithms, 2013)

A methodology to assess the intrinsic discriminative ability of a distance function and its interplay with clustering algorithms for microarray data analysis. - Raffaele Giancarlo; Giosuè Lo Bosco; Luca Pinello; Filippo Utro (BMC Bioinform., 2013)

Sum of parts is greater than the whole: inference of common genetic history of populations. - Filippo Utro; Marc Pybus; Laxmi Parida (BMC Genom., 2013)

Compressive biological sequence analysis and archival in the era of high-throughput sequencing technologies. - Raffaele Giancarlo; Simona E. Rombo; Filippo Utro (Briefings Bioinform., 2014)

Effect of sampling on the extent and accuracy of the inferred genetic history of recombining genome. - Daniel E. Platt; Filippo Utro; Laxmi Parida (Comput. Biol. Chem., 2014)

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

Epigenomic k-mer dictionaries: shedding light on how sequence composition influences in vivo nucleosome positioning. - Raffaele Giancarlo; Simona E. Rombo; Filippo Utro (Bioinform., 2015)

ValWorkBench: An open source Java library for cluster validation, with applications to microarray data analysis. - Raffaele Giancarlo; Davide Scaturro; Filippo Utro (Comput. Methods Programs Biomed., 2015)

Bayesian versus data driven model selection for microarray data. - Raffaele Giancarlo; Giosuè Lo Bosco; Filippo Utro (Nat. Comput., 2015)

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

The intrinsic combinatorial organization and information theoretic content of a sequence are correlated to the DNA encoded nucleosome organization of eukaryotic genomes. - Filippo Utro; Valeria Di Benedetto; Davide F. V. Corona; Raffaele Giancarlo (Bioinform., 2016)

A Quantitative and Qualitative Characterization of k-mer Based Alignment-Free Phylogeny Construction. - Filippo Utro; Daniel E. Platt; Laxmi Parida (CIBB, 2017)

Foreword: Algorithms, Strings and Theoretical Approaches in the Big Data Era - Special Issue in Honor of the 60th Birthday of Professor Raffaele Giancarlo. - Simona E. Rombo; Filippo Utro (Theor. Comput. Sci., 2017)

Simultaneous Phasing of Multiple Polyploids. - Laxmi Parida; Filippo Utro (CIBB, 2018)

Essential Simplices in Persistent Homology and Subtle Admixture Detection. - Saugata Basu; Filippo Utro; Laxmi Parida (WABI, 2018)

In vitro versus in vivo compositional landscapes of histone sequence preferences in eucaryotic genomes. - Raffaele Giancarlo; Simona E. Rombo; Filippo Utro (Bioinform., 2018)

Dark-matter matters: Discriminating subtle blood cancers using the darkest DNA. - Laxmi Parida; Claudia Haferlach; Kahn Rhrissorrakrai; Filippo Utro; Chaya Levovitz; Wolfgang Kern; Niroshan Nadarajah; Sven Twardziok; Stephan Hutter; Manja Meggendorfer; Wencke Walter; Constance Baer; et al. (PLoS Comput. Biol., 2019)

Linear Time Algorithms to Construct Populations Fitting Multiple Constraint Distributions at Genomic Scales. - Enrico Siragusa; Niina Haiminen; Filippo Utro; Laxmi Parida (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

DNA combinatorial messages and Epigenomics: The case of chromatin organization and nucleosome occupancy in eukaryotic genomes. - Raffaele Giancarlo; Simona E. Rombo; Filippo Utro (Theor. Comput. Sci., 2019)

Computation Cluster Validation in the Big Data Era. - Raffaele Giancarlo; Filippo Utro (Encyclopedia of Bioinformatics and Computational Biology (1), 2019)

Impact of Clinical and Genomic Factors on COVID-19 Disease Severity. - Sanjoy Dey; Aritra Bose; Subrata Saha; Prithwish Chakraborty; Mohamed F. Ghalwash; Filippo Utro; Aldo Guzmán-Sáenz; Kenney Ng; Jianying Hu; Laxmi Parida; Daby Sow (AMIA, 2021)

Multiple Loci Selection with Multi-Way Epistasis in Coalescence with Recombination. - Aritra Bose; Filippo Utro; Daniel E. Platt; Laxmi Parida (Algorithms, 2021)

Lesion Shedding Model: unraveling site-specific contributions to ctDNA. - Kahn Rhrissorrakrai; Filippo Utro; Chaya Levovitz; Laxmi Parida (Briefings Bioinform., 2023)

Hybrid Quantum-Classical Graph Neural Networks for Tumor Classification in Digital Pathology. - Anupama Ray; Dhiraj Madan; Srushti Patil; Pushpak Pati; Maria Anna Rapsomaniki; Aviwe Kohlakala; Thembelihle Rose Dlamini; Stephanie Julia Muller; Kahn Rhrissorrakrai; Filippo Utro; Laxmi Parida (QCE, 2024)

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)

How quantum computing can enhance biomarker discovery. - Frederik F. Flöther; Daniel Blankenberg; Maria Demidik; Karl Jansen; Raga Krishnakumar; Rajiv Krishnakumar; Nouamane Laanait; Laxmi Parida; Carl Y. Saab; Filippo Utro (Patterns, 2025)

Quantum Doubly Stochastic Transformers. - Jannis Born; Filip Skogh; Kahn Rhrissorrakrai; Filippo Utro; Nico Wagner; Aleksandros Sobczyk (CoRR, 2025)

Quantum Ensembling Methods for Healthcare and Life Science. - Kahn Rhrissorrakrai; Kathleen E. Hamilton; Prerana Bangalore Parthsarathy; Aldo Guzmán-Sáenz; Tyler Alban; Filippo Utro; Laxmi Parida (CoRR, 2025)

Enhanced Prediction of CAR T-Cell Cytotoxicity with Quantum-Kernel Methods. - Filippo Utro; Meltem Tolunay; Kahn Rhrissorrakrai; Tanvi P. Gujarati; Jie Shi; Sara Capponi; Mirko Amico; Nathan Earnest-Noble; Laxmi Parida (CoRR, 2025)