Beyond Perfect Phylogeny: Multisample Phylogeny Reconstruction via ILP. - Paola Bonizzoni; Simone Ciccolella; Gianluca Della Vedova; Mauricio Soto Gomez (BCB, 2017)

Character-Based Phylogeny Construction and Its Application to Tumor Evolution. - Gianluca Della Vedova; Murray Patterson; Raffaella Rizzi; Mauricio Soto Gomez (CiE, 2017)

Modelling and Linking Company Data in the euBusinessGraph Platform. - Andrea Maurino; Anisa Rula; Bjørn Marius von Zernichow; Mauricio Soto Gomez; Brian Elvesæter; Dumitru Roman (DSMM@SIGMOD, 2019)

Does Relaxing the Infinite Sites Assumption Give Better Tumor Phylogenies? An ILP-Based Comparative Approach. - Paola Bonizzoni; Simone Ciccolella; Gianluca Della Vedova; Mauricio Soto Gomez (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

gpps: an ILP-based approach for inferring cancer progression with mutation losses from single cell data. - Simone Ciccolella; Mauricio Soto Gomez; Murray D. Patterson; Gianluca Della Vedova; Iman Hajirasouliha; Paola Bonizzoni (BMC Bioinform., 2020)

Inferring cancer progression from Single-Cell Sequencing while allowing mutation losses. - Simone Ciccolella; Camir Ricketts; Mauricio Soto Gomez; Murray Patterson; Dana Silverbush; Paola Bonizzoni; Iman Hajirasouliha; Gianluca Della Vedova (Bioinform., 2021)

Plastic: An Easy to Use and Modular Tool for Benchmarking Tumor Phylogeny Reconstruction Pipelines. - Akshay Juyal; Zahra Tayebi; Alexander Zelikovsky; Mauricio Soto Gomez; Simone Ciccolella; Gianluca Della Vedova; Murray Patterson (ICCABS, 2023)

A Meta-Graph for the Construction of an RNA-Centered Knowledge Graph. - Emanuele Cavalleri; Sara Bonfitto; Alberto Cabri; Jessica Gliozzo; Paolo Perlasca; Mauricio Soto Gomez; Gabriella Trucco; Elena Casiraghi; Giorgio Valentini; Marco Mesiti (IWBBIO (1), 2023)

Towards the Construction of an RNA-centered Knowledge Graph. - Emanuele Cavalleri; Sara Bonfitto; Alberto Cabri; Jessica Gliozzo; Paolo Perlasca; Mauricio Soto Gomez; Gabriella Trucco; Elena Casiraghi; Giorgio Valentini; Marco Mesiti (SEBD, 2023)

RNA-KG: An ontology-based knowledge graph for representing interactions involving RNA molecules. - Emanuele Cavalleri; Alberto Cabri; Mauricio Soto Gomez; Sara Bonfitto; Paolo Perlasca; Jessica Gliozzo; Tiffany J. Callahan; Justin T. Reese; Peter N. Robinson; Elena Casiraghi; Giorgio Valentini; Marco Mesiti (CoRR, 2023)

The promises of large language models for protein design and modeling. - Giorgio Valentini; Dario Malchiodi; Jessica Gliozzo; Marco Mesiti; Mauricio Soto Gomez; Alberto Cabri; Justin T. Reese; Elena Casiraghi; Peter N. Robinson (Frontiers Bioinform., 2023)

Three Metaheuristic Approaches for Tumor Phylogeny Inference: An Experimental Comparison. - Simone Ciccolella; Gianluca Della Vedova; Vladimir Filipovic; Mauricio Soto Gomez (Algorithms, 2023)

Initial achievements in relation extraction from RNA-focused scientific papers. - Emanuele Cavalleri; Mauricio Soto Gomez; Ali Pashaeibarough; Dario Malchiodi; J. Harry Caufield; Justin T. Reese; Christopher J. Mungall; Peter N. Robinson; Elena Casiraghi; Giorgio Valentini; Marco Mesiti (SEBD, 2024)

SPIREX: Improving LLM-based relation extraction from RNA-focused scientific literature using graph machine learning. - Emanuele Cavalleri; Mauricio Soto Gomez; Ali Pashaeibarough; Dario Malchiodi; J. Harry Caufield; Justin T. Reese; Chris Mungall; Peter N. Robinson; Elena Casiraghi; Giorgio Valentini; Marco Mesiti (VLDB Workshops, 2024)

Intrinsic-dimension analysis for guiding dimensionality reduction and data fusion in multi-omics data processing. - Jessica Gliozzo; Mauricio Soto Gomez; Valentina Guarino; Arturo Bonometti; Alberto Cabri; Emanuele Cavalleri; Justin T. Reese; Peter N. Robinson; Marco Mesiti; Giorgio Valentini; Elena Casiraghi (Artif. Intell. Medicine, 2025)

On recognizing graphs representing Persistent Perfect Phylogenies. - Paola Bonizzoni; Gianluca Della Vedova; Mauricio Soto Gomez; Gabriella Trucco (CoRR, 2025)