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Simone Marini

State University System of Florida

24H-index
131Paper Count
3.1KCitation Count
Published Papers 39
Publication Date
SARITA: a large language model for generating the S1 subunit of the SARS-CoV-2 spike protein
err2025-07-01
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errOAAI
errRancati, Simone; Nicora, Giovanna; Bergomi, Laura; Buonocore, Tommaso Mario; Czyz, Daniel M.; Parimbelli, Enea; Bellazzi, Riccardo; Salemi, Marco; Prosperi, Mattia; Marini, Simone
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Leveraging large language models to predict antibiotic resistance in Mycobacterium tuberculosis
err2025-07-01
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errOAAI
errTestagrose, Conrad; Pandey, Sakshi; Serajian, Mohammadali; Marini, Simone; Prosperi, Mattia; Boucher, Christina
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Forecasting dominance of SARS-CoV-2 lineages by anomaly detection using deep AutoEncoders
err2024-10-24
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errOAAI
errRancati, Simone; Nicora, Giovanna; Prosperi, Mattia; Bellazzi, Riccardo; Salemi, Marco; Marini, Simone
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Oral Cannabidiol Treatment Is Associated with an Anti-Inflammatory Gene Expression Signature in Myeloid Cells of People Living with HIV
err2024-08-01
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PREAI
errMarini, Simone; Huber, Amanda; Cash, Melanie N.; Salemi, Marco; Cook, Robert L.; Borsa, Paul; Mavian, Carla N.
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Bacterial DnaK reduces the activity of anti-cancer drugs cisplatin and 5FU
err2024-03-12
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errBenedetti, Francesca; Mongodin, Emmanuel F.; Badger, Jonathan H.; Munawwar, Arshi; Cellini, Ashley; Yuan, Weirong; Silvestri, Giovannino; Kraus, Carl N.; Marini, Simone; Rathinam, Chozha V.; Salemi, Marco; Tettelin, Herve; Gallo, Robert C.; Zella, Davide
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Machine Learning Prediction and Phyloanatomic Modeling of Viral Neuroadaptive Signatures in the Macaque Model of HIV-Mediated Neuropathology
err2023-04-13
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errRamirez-Mata, Andrea S.; Ostrov, David; Salemi, Marco; Marini, Simone; Magalis, Brittany Rife
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The K-mer antibiotic resistance gene variant analyzer (KARGVA)
err2023-03-07
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errOAAI
errMarini, Simone; Boucher, Christina; Noyes, Noelle; Prosperi, Mattia
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MEGARes and AMR++, v3.0: an updated comprehensive database of antimicrobial resistance determinants and an improved software pipeline for classification using high-throughput sequencing
err2022-11-16
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errOAAI
errBonin, Nathalie; Doster, Enrique; Worley, Hannah; Pinnell, Lee J.; Bravo, Jonathan E.; Ferm, Peter; Marini, Simone; Prosperi, Mattia; Noyes, Noelle; Morley, Paul S.; Boucher, Christina
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Macrophage TGF-β signaling is critical for wound healing with heterotopic ossification after trauma
err2022-10-24
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errOAAI
errPatel, Nicole K.; Nunez, Johanna H.; Sorkin, Michael; Marini, Simone; Pagani, Chase A.; Strong, Amy L.; Hwang, Charles D.; Li, Shuli; Padmanabhan, Karthik R.; Kumar, Ravi; Bancroft, Alec C.; Greenstein, Joey A.; Nelson, Reagan; Rasheed, Husain A.; Livingston, Nicholas; Vasquez, Kaetlin; Huber, Amanda K.; Levi, Benjamin
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Macrophage-mediated PDGF Activation Correlates With Regenerative Outcomes Following Musculoskeletal Trauma
err2022-09-15
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PREAI
errChowdary, Ashish R.; Maerz, Tristan; Henn, Dominic; Hankenson, Kurt D.; Pagani, Chase A.; Marini, Simone; Gallagher, Katherine; Aguilar, Carlos A.; Tower, Robert J.; Levi, Benjamin
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AMR-meta: a k-mer and metafeature approach to classify antimicrobial resistance from high-throughput short-read metagenomics data
err2022-05-18
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errMarini, Simone; Oliva, Marco; Slizovskiy, Ilya B.; Das, Rishabh A.; Noyes, Noelle Robertson; Kahveci, Tamer; Boucher, Christina; Prosperi, Mattia
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Low-frequency variants in mildly symptomatic vaccine breakthrough infections presents a doubled-edged sword
err2022-04-13
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errOAAI
errMagalis, Brittany R.; Mavian, Carla; Tagliamonte, Massimiliano; Rich, Shannan N.; Cash, Melanie; Riva, Alberto; Loeb, Julia C.; Norris, Michael; Amador, David M.; Zhang, Yanping; Shapiro, Jerne; Starostik, Petr; Marini, Simone; Myers, Paul; Ostrov, David A.; Lednicky, John A.; Morris, J. Glenn, Jr.; Lauzardo, Michael; Salemi, Marco
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Early Emergence Phase of SARS-CoV-2 Delta Variant in Florida, US
err2022-04-06
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errOAAI
errCella, Eleonora; Ali, Sobur; Schmedes, Sarah E.; Magalis, Brittany Rife; Marini, Simone; Salemi, Marco; Blanton, Jason; Azarian, Taj
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Severe Acute Respiratory Syndrome Coronavirus 2 Delta Vaccine Breakthrough Transmissibility in Alachua County, Florida
err2022-03-10
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errOAAI
errMagalis, Brittany Rife; Rich, Shannan; Tagliamonte, Massimiliano S.; Mavian, Carla; Cash, Melanie N.; Riva, Alberto; Marini, Simone; Amador, David Moraga; Zhang, Yanping; Shapiro, Jerne; Horine, Amelia; Starostik, Petr; Pieretti, Maura; Vega, Samantha; Lacombe, Ana Paula; Salinas, Jessica; Stevenson, Mario; Myers, Paul; Morris, J. Glenn; Lauzardo, Michael; Prosperi, Mattia; Salemi, Marco
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Towards routine employment of computational tools for antimicrobial resistance determination via high-throughput sequencing
err2022-02-25
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errOAAI
errMarini, Simone; Mora, Rodrigo A.; Boucher, Christina; Noyes, Noelle Robertson; Prosperi, Mattia
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NGF-TrkA signaling dictates neural ingrowth and aberrant osteochondral differentiation after soft tissue trauma
err2021-08-16
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errOAAI
errLee, Seungyong; Hwang, Charles; Marini, Simone; Tower, Robert J.; Qin, Qizhi; Negri, Stefano; Pagani, Chase A.; Sun, Yuxiao; Stepien, David M.; Sorkin, Michael; Kubiak, Carrie A.; Visser, Noelle D.; Meyers, Carolyn A.; Wang, Yiyun; Rasheed, Husain A.; Xu, Jiajia; Miller, Sarah; Huber, Amanda K.; Minichiello, Liliana; Cederna, Paul S.; Kemp, Stephen W. P.; Clemens, Thomas L.; James, Aaron W.; Levi, Benjamin
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Novel Lineage-Tracing System to Identify Site-Specific Ectopic Bone Precursor Cells
err2021-03-01
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errOAAI
errPagani, Chase A.; Huber, Amanda K.; Hwang, Charles; Marini, Simone; Padmanabhan, Karthik; Livingston, Nicholas; Nunez, Johanna; Sun, Yuxiao; Edwards, Nicole; Cheng, Yu-Hao; Visser, Noelle; Yu, Pauline; Patel, Nicole; Greenstein, Joseph A.; Rasheed, Husain; Nelson, Reagan; Kessel, Karen; Vasquez, Kaetlin; Strong, Amy L.; Hespe, Geoffrey E.; Song, Jane Y.; Wellik, Deneen M.; Levi, Benjamin
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