HIVbase: a PC/Windows-based software offering storage and querying power for locally held HIV-1 genetic, experimental and clinical data. - Susanna L. Lamers; Scott Beason; Luke Dunlap; Robert Compton; Marco Salemi (Bioinform., 2004)

Prediction of R5, X4, and R5X4 HIV-1 Coreceptor Usage with Evolved Neural Networks. - Susanna L. Lamers; Marco Salemi; Michael S. McGrath; Gary B. Fogel (IEEE ACM Trans. Comput. Biol. Bioinform., 2008)

QuRe: software for viral quasispecies reconstruction from next-generation sequencing data. - Mattia C. F. Prosperi; Marco Salemi (Bioinform., 2012)

Evolved neural networks for HIV-1 co-receptor identification. - Gary B. Fogel; Enoch S. Liu; Marco Salemi; Susanna L. Lamers; Michael S. McGrath (IEEE Congress on Evolutionary Computation, 2014)

HIV-associated neuropathogenesis: A systems biology perspective for modeling and therapy. - Susanna L. Lamers; Gary B. Fogel; David J. Nolan; Michael S. McGrath; Marco Salemi (Biosyst., 2014)

Baseline CD4+ T Cell Counts Correlates with HIV-1 Synonymous Rate in HLA-B*5701 Subjects with Different Risk of Disease Progression. - Melissa M. Norström; Nazle M. Veras; Wei Huang; Mattia C. F. Prosperi; Jennifer Cook; Wendy Hartogensis; Frederick M. Hecht; Annika C. Karlsoon; Marco Salemi (PLoS Comput. Biol., 2014)

Identification of dual-tropic HIV-1 using evolved neural networks. - Gary B. Fogel; Susanna L. Lamers; Enoch S. Liu; Marco Salemi; Michael S. McGrath (Biosyst., 2015)

Unexpected Predictors of Antibiotic Resistance in Housekeeping Genes of Staphylococcus Aureus. - Mattia Prosperi; Taj Azarian; Judith A. Johnson; Marco Salemi; Franco Milicchio; Marco Oliva (BCB, 2019)

New Insights into the Effect of Residue Mutations on the Rotavirus VP1 Function Using Molecular Dynamic Simulations. - Nabil Abid; Daniele Pietrucci; Marco Salemi; Giovanni Chillemi (J. Chem. Inf. Model., 2020)

Causal AI with Real World Data: Do Statins Protect from Alzheimer's Disease Onset? - Mattia Prosperi; Shantanu Ghosh; Zhaoyi Chen; Marco Salemi; Tianchen Lyu; Jinying Zhao; Jiang Bian 001 (ICMHI, 2021)

Transmission cluster characteristics of global, regional, and lineage-specific SARS-CoV-2 phylogenies. - Mattia Prosperi; Brittany Rife Magalis; Simone Marini; Marco Salemi (BIBM, 2022)

Dynamic Prediction of Non-Neutral SARS-Cov-2 Variants Using Incremental Machine Learning. - Giovanna Nicora; Simone Marini; Marco Salemi; Riccardo Bellazzi (MIE, 2022)

Optimizing viral genome subsampling by genetic diversity and temporal distribution (TARDiS) for phylogenetics. - Simone Marini; Carla Mavian; Alberto Riva; Mattia Prosperi; Marco Salemi; Brittany Rife Magalis (Bioinform., 2022)

ARCA: the interactive database for arbovirus reported cases in the Americas. - Maria V. Meneses; Alberto Riva; Marco Salemi; Carla Mavian (BMC Bioinform., 2023)

Sequencing Efforts and Epidemiological Trends: Analyzing SARS-CoV-2 Dynamics Across European Nations. - Simone Rancati; Daniele Pala; Simone Marini; Marco Salemi; Riccardo Bellazzi; Giovanna Nicora (BIBM, 2024)

Learning on Forecasting HIV Epidemic Based on Individuals' Contact Networks. - Chaoyue Sun; Yiyang Liu; Christina Parisi; Rebecca Fisk-Hoffman; Marco Salemi; Ruogu Fang; Brandi Danforth; Mattia Prosperi; Simone Marini (BIOSTEC (2), 2024)

Forecasting dominance of SARS-CoV-2 lineages by anomaly detection using deep AutoEncoders. - Simone Rancati; Giovanna Nicora; Mattia Prosperi; Riccardo Bellazzi; Marco Salemi; Simone Marini (Briefings Bioinform., 2024)

DeepDynaForecast: Phylogenetic-informed graph deep learning for epidemic transmission dynamic prediction. - Chaoyue Sun; Ruogu Fang; Marco Salemi; Mattia Prosperi; Brittany Rife Magalis (PLoS Comput. Biol., 2024)

What to consider when developing a new molecular HIV surveillance tool: Perspectives of key stakeholders working in HIV prevention and treatment. - Shantrel S. Canidate; Hannah R. Gracy; Sean McIntosh; Yiyang Liu; Rebecca Fisk-Hoffman; Shannon Rich; Carla Mavian; Robert L. Cook 002; Mattia Prosperi; Marco Salemi (ICHI, 2025)

SARITA: a large language model for generating the S1 subunit of the SARS-CoV-2 spike protein. - Simone Rancati; Giovanna Nicora; Laura Bergomi; Tommaso Mario Buonocore; Daniel M. Czyz; Enea Parimbelli; Riccardo Bellazzi; Marco Salemi; Mattia Prosperi; Simone Marini (Briefings Bioinform., 2025)