Simone Marini

Simone Marini,

Assistant Professor

Department: Department of Epidemiology
Business Phone: (352) 294-8951
Business Email: simone.marini@ufl.edu

About Simone Marini

Teaching Profile

Courses Taught
2020,2022-2024
PHC7083 Artificial Intelligence and Data Science for Epidemiology and Population Health
2021-2025
PHC7199 Topics in Precision Medicine and Public Health Informatics
2022
PHC6941 MPH Applied Practice Experience

Research Profile

Areas of Interest
  • Antimicrobial Resistance
  • Data Integration
  • HIV
  • Inflammation
  • Machine Learning
Open Researcher and Contributor ID (ORCID)

0000-0002-5704-3533

Publications

2024
Bacterial DnaK reduces the activity of anti-cancer drugs cisplatin and 5FU.
Journal of translational medicine. 22(1) [DOI] 10.1186/s12967-024-05078-x. [PMID] 38475767.
2024
Forecasting dominance of SARS-CoV-2 lineages by anomaly detection using deep AutoEncoders.
bioRxiv : the preprint server for biology. [DOI] 10.1101/2023.10.24.563721. [PMID] 37961168.
2024
OCTOPUS: Disk-based, Multiplatform, Mobile-friendly Metagenomics Classifier.
bioRxiv : the preprint server for biology. [DOI] 10.1101/2024.03.15.585215. [PMID] 38559026.
2024
Oral Cannabidiol Treatment Is Associated with an Anti-Inflammatory Gene Expression Signature in Myeloid Cells of People Living with HIV.
Cannabis and cannabinoid research. [DOI] 10.1089/can.2023.0139. [PMID] 38252549.
2024
Scalable de novo classification of antibiotic resistance of Mycobacterium tuberculosis
Bioinformatics. 40(Supplement_1):i39-i47 [DOI] 10.1093/bioinformatics/btae243. [PMID] 38940175.
2023
4. Skeletal Muscle in Inbred Mice Exhibits Divergent Hypoxia and Angiogenesis Transcriptome Expression as Compared to Humans in Aging
Plastic and Reconstructive Surgery Global Open. 11(5 Suppl)
2023
Machine Learning Prediction and Phyloanatomic Modeling of Viral Neuroadaptive Signatures in the Macaque Model of HIV-Mediated Neuropathology.
Microbiology spectrum. 11(2) [DOI] 10.1128/spectrum.03086-22. [PMID] 36847516.
2023
Macrophage-mediated PDGF Activation Correlates With Regenerative Outcomes Following Musculoskeletal Trauma.
Annals of surgery. 278(2):e349-e359 [DOI] 10.1097/SLA.0000000000005704. [PMID] 36111847.
2023
MEGARes and AMR++, v3.0: an updated comprehensive database of antimicrobial resistance determinants and an improved software pipeline for classification using high-throughput sequencing
Nucleic Acids Research. 51(D1):D744-D752 [DOI] 10.1093/nar/gkac1047. [PMID] 36382407.
2023
Optimizing Dynamic Antibiotic Treatment Strategies against Invasive Methicillin-Resistant Staphylococcus Aureus Infections using Causal Survival Forests and G-Formula on Statewide Electronic Health Record Data.
Proceedings of machine learning research. 218:98-115 [PMID] 37854935.
2023
Oral CBD treatment is associated to an anti-inflammatory gene expression signature in myeloid cells of people living with HIV
medRxiv.
2023
The K-mer antibiotic resistance gene variant analyzer (KARGVA).
Frontiers in microbiology. 14 [DOI] 10.3389/fmicb.2023.1060891. [PMID] 36960290.
2022
AMR-meta: a k-mer and metafeature approach to classify antimicrobial resistance from high-throughput short-read metagenomics data
GigaScience. 11 [DOI] 10.1093/gigascience/giac029. [PMID] 35583675.
2022
Assessing putative bias in prediction of anti-microbial resistance from real-world genotyping data under explicit causal assumptions.
Artificial intelligence in medicine. 130 [DOI] 10.1016/j.artmed.2022.102326. [PMID] 35809965.
2022
Dynamic prediction of non-neutral SARS-Cov-2 variants using incremental machine learning
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2022
Dynamic Prediction of Non-Neutral SARS-Cov-2 Variants Using Incremental Machine Learning.
Studies in health technology and informatics. 294:654-658 [DOI] 10.3233/SHTI220550. [PMID] 35612170.
2022
Early emergence phase of SARS-CoV-2 Delta variant in Florida (preprint)
.
2022
Early Emergence Phase of SARS-CoV-2 Delta Variant in Florida, US.
Viruses. 14(4) [DOI] 10.3390/v14040766. [PMID] 35458495.
2022
Identification of Social and Racial Disparities in Risk of HIV Infection in Florida using Causal AI Methods
.
2022
Identification of Social and Racial Disparities in Risk of HIV Infection in Florida using Causal AI Methods.
Proceedings. IEEE International Conference on Bioinformatics and Biomedicine. 2022:2934-2939 [DOI] 10.1109/bibm55620.2022.9995662. [PMID] 36865610.
2022
Joint Application of the Target Trial Causal Framework and Machine Learning Modeling to Optimize Antibiotic Therapy: Use Case on Acute Bacterial Skin and Skin Structure Infections due to Methicillin-resistant Staphylococcus aureus
arXiv preprint arXiv:2207.07458.
2022
KARGAMobile: Android app for portable, real-time, easily interpretable analysis of antibiotic resistance genes via nanopore sequencing.
Frontiers in bioengineering and biotechnology. 10 [DOI] 10.3389/fbioe.2022.1016408. [PMID] 36324897.
2022
Low-frequency variants in mildly symptomatic vaccine breakthrough infections presents a doubled-edged sword.
Journal of medical virology. 94(7):3192-3202 [DOI] 10.1002/jmv.27726. [PMID] 35307848.
2022
Macrophage TGF-β signaling is critical for wound healing with heterotopic ossification after trauma
JCI Insight. 7(20) [DOI] 10.1172/jci.insight.144925. [PMID] 36099022.
2022
Moving from predicting hospital deaths by antibiotic-resistant bloodstream bacteremia toward actionable risk reduction using machine learning on electronic health records.
AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science. 2022:274-283 [PMID] 35854723.
2022
Optimizing viral genome subsampling by genetic diversity and temporal distribution (TARDiS) for phylogenetics.
Bioinformatics (Oxford, England). 38(3):856-860 [DOI] 10.1093/bioinformatics/btab725. [PMID] 34672334.
2022
Phylogenetic-informed graph deep learning to classify dynamic transmission clusters in infectious disease epidemics
bioRxiv.
2022
Predicting emerging SARS-CoV-2 variants of concern through a One Class dynamic anomaly detection algorithm.
BMJ health & care informatics. 29(1) [DOI] 10.1136/bmjhci-2022-100643. [PMID] 36593658.
2022
Severe Acute Respiratory Syndrome Coronavirus 2 Delta Vaccine Breakthrough Transmissibility in Alachua County, Florida.
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. 75(9):1618-1627 [DOI] 10.1093/cid/ciac197. [PMID] 35271704.
2022
Towards routine employment of computational tools for antimicrobial resistance determination via high-throughput sequencing.
Briefings in bioinformatics. 23(2) [DOI] 10.1093/bib/bbac020. [PMID] 35212354.
2022
Transmission cluster characteristics of global, regional, and lineage-specific SARS-CoV-2 phylogenies
.
2022
Transmission cluster characteristics of global, regional, and lineage-specific SARS-CoV-2 phylogenies.
IEEE International Conference on Bioinformatics and Biomedicine workshops. IEEE International Conference on Bioinformatics and Biomedicine. 2022:2940-2944 [DOI] 10.1109/bibm55620.2022.9995364. [PMID] 36780250.
2021
Artificial Intelligence in Medicine: 19th International Conference on Artificial Intelligence in Medicine, AIME 2021, Virtual Event, June 15–18, 2021, Proceedings
. 12721
2021
Beneath the surface: hyper-connectivity between caudate and salience regions in ADHD fMRI at rest
European Child \& Adolescent Psychiatry. 30
2021
Brain tissue transcriptomic analysis of SIV-infected macaques identifies several altered metabolic pathways linked to neuropathogenesis and poly (ADP-ribose) polymerases (PARPs) as potential therapeutic targets.
Journal of neurovirology. 27(1):101-115 [DOI] 10.1007/s13365-020-00927-z. [PMID] 33405206.
2021
Do local curriculum scores correlate with national residency test results? A pluriannual, nationwide survey of Italian Medical Universities
Italian Journal of Medicine. 15(2) [DOI] 10.4081/itjm.2021.1470.
2021
DYNAMITE: a phylogenetic tool for identification of dynamic transmission epicenters
bioRxiv.
2021
Earliest detection to date of SARS-CoV-2 in Florida: Identification together with influenza virus on the main entry door of a university building, February 2020
PLOS ONE. 16(1) [DOI] 10.1371/journal.pone.0245352. [PMID] 33439885.
2021
Exploring Prediction of Antimicrobial Resistance Based on Protein Solvent Accessibility Variation.
Frontiers in genetics. 12 [DOI] 10.3389/fgene.2021.564186. [PMID] 33552147.
2021
Fast and exact quantification of motif occurrences in biological sequences.
BMC bioinformatics. 22(1) [DOI] 10.1186/s12859-021-04355-6. [PMID] 34537012.
2021
Karga: Multi-platform toolkit for k-mer-based antibiotic resistance gene analysis of high-throughput sequencing data
.
2021
KARGA: Multi-platform Toolkit for k-mer-based Antibiotic Resistance Gene Analysis of High-throughput Sequencing Data.
… IEEE-EMBS International Conference on Biomedical and Health Informatics. IEEE-EMBS International Conference on Biomedical and Health Informatics. 2021 [DOI] 10.1109/bhi50953.2021.9508479. [PMID] 34447942.
2021
NGF-TrkA signaling dictates neural ingrowth and aberrant osteochondral differentiation after soft tissue trauma.
Nature communications. 12(1) [DOI] 10.1038/s41467-021-25143-z. [PMID] 34400627.
2021
Novel lineage-tracing system to identify site-specific ectopic bone precursor cells
Stem Cell Reports. 16(3)
2021
Optimizing viral genome subsampling by genetic diversity and temporal distribution (TARDiS) for phylogenetics
bioRxiv.
2021
SARS-CoV-2 Delta vaccine breakthrough transmissibility in Alachua, Florida
medRxiv.
2021
SARS-CoV-2 Delta vaccine breakthrough transmissibility in Alachua, Florida (preprint)
.
2021
SARS-CoV-2 infection of BNT162b2 (mRNA)-vaccinated individuals is not restricted to variants of concern or high-risk exposure environments
medRxiv.
2021
The colors of our brain: an integrated approach for dimensionality reduction and explainability in fMRI through color coding (i-ECO)
Brain Imaging and Behavior.
2020
A snapshot of SARS-CoV-2 genome availability up to 30th March, 2020 and its implications
bioRxiv.
2020
A Snapshot of SARS-CoV-2 Genome Availability up to April 2020 and its Implications: Data Analysis
JMIR Public Health and Surveillance. 6(2) [DOI] 10.2196/19170. [PMID] 32412415.
2020
Activin A does not drive post-traumatic heterotopic ossification.
Bone. 138 [DOI] 10.1016/j.bone.2020.115473. [PMID] 32553795.
2020
Authors’ Reply to: Errors in Tracing Coronavirus SARS-CoV-2 Transmission Using a Maximum Likelihood Tree. Comment on “A Snapshot of SARS-CoV-2 Genome Availability up to April 2020 and its Implications: Data Analysis”
JMIR Public Health and Surveillance. 6(4) [DOI] 10.2196/24661. [PMID] 33174844.
2020
Brain tissue transcriptomic analysis of SIV-infected macaques identifies Poly (ADP-ribose) polymerases (PARPs) as potential biomarkers for neuropathogenesis.
.
2020
Comparative Study of Salivary, Duodenal, and Fecal Microbiota Composition Across Adult Celiac Disease.
Journal of clinical medicine. 9(4) [DOI] 10.3390/jcm9041109. [PMID] 32294965.
2020
Correction: A Snapshot of SARS-CoV-2 Genome Availability up to April 2020 and its Implications: Data Analysis
JMIR Public Health and Surveillance. 6(3) [DOI] 10.2196/22853. [PMID] 32776889.
2020
Differing impacts of global and regional responses on SARS-CoV-2 transmission cluster dynamics (preprint)
.
2020
Differing impacts of global and regional responses on SARS-CoV-2 transmission cluster dynamics.
bioRxiv : the preprint server for biology. [DOI] 10.1101/2020.11.06.370999. [PMID] 33173870.
2020
Endogenous CCN family member WISP1 inhibits trauma-induced heterotopic ossification
JCI Insight. 5(13) [DOI] 10.1172/jci.insight.135432. [PMID] 32484792.
2020
Identifying The Myeloid Subpopulation Responsible For Tissue Fibrosis Across Organ Systems Via Machine Learning Parameterization And Predictive Transcriptomics
Plastic and Reconstructive Surgery–Global Open. 8(4S)
2020
Immobilization after injury alters extracellular matrix and stem cell fate
Journal of Clinical Investigation. 130(10):5444-5460 [DOI] 10.1172/jci136142.
2020
Nerve Growth Factor Derives From Pericytes And Smooth Muscle Cells After Extremity Trauma
Plastic and Reconstructive Surgery Global Open. 8(4 Suppl)
2020
Perivascular Fibro-Adipogenic Progenitor Tracing during Post-Traumatic Osteoarthritis
The American Journal of Pathology. 190(9):1909-1920 [DOI] 10.1016/j.ajpath.2020.05.017. [PMID] 32533926.
2020
Post-Traumatic Limb Immobilization Alters Mesenchymal Stem Cell Fate
Plastic and Reconstructive Surgery Global Open. 8(4 Suppl)
2020
Regaining perspective on SARS-CoV-2 molecular tracing and its implications
medRxiv.
2020
Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable.
Proceedings of the National Academy of Sciences of the United States of America. 117(23):12522-12523 [DOI] 10.1073/pnas.2007295117. [PMID] 32381734.
2020
Small molecule inhibition of non-canonical (TAK1-mediated) BMP signaling results in reduced chondrogenic ossification and heterotopic ossification in a rat model of blast-associated combat-related lower limb trauma.
Bone. 139 [DOI] 10.1016/j.bone.2020.115517. [PMID] 32622875.
2020
The hierarchic treatment of marine ecological information from spatial networks of benthic platforms
Sensors. 20(6)
2020
The role of neutrophil extracellular traps and TLR signaling in skeletal muscle ischemia reperfusion injury.
FASEB journal : official publication of the Federation of American Societies for Experimental Biology. 34(12):15753-15770 [DOI] 10.1096/fj.202000994RR. [PMID] 33089917.
2020
Tuning Macrophage Phenotype to Mitigate Skeletal Muscle Fibrosis
The Journal of Immunology. 204(8):2203-2215 [DOI] 10.4049/jimmunol.1900814. [PMID] 32161098.
2019
A Semi-supervised Learning Approach for Pan-Cancer Somatic Genomic Variant Classification
Artificial Intelligence in Medicine. 42-46 [DOI] 10.1007/978-3-030-21642-9_7.
2019
A semi-supervised learning approach for pan-cancer somatic genomic variant classification
.
2019
Disruption of Neutrophil Extracellular Traps (NETs) Links Mechanical Strain to Post-traumatic Inflammation.
Frontiers in immunology. 10 [DOI] 10.3389/fimmu.2019.02148. [PMID] 31708911.
2019
Mesenchymal VEGFA induces aberrant differentiation in heterotopic ossification.
Bone research. 7 [DOI] 10.1038/s41413-019-0075-6. [PMID] 31840004.
2019
MTGO-SC, A Tool to Explore Gene Modules in Single-Cell RNA Sequencing Data.
Frontiers in genetics. 10 [DOI] 10.3389/fgene.2019.00953. [PMID] 31649730.
2019
Protease target prediction via matrix factorization
Bioinformatics. 35(6):923-929 [DOI] 10.1093/bioinformatics/bty746.
2019
Toward more accurate prediction of caspase cleavage sites: a comprehensive review of current methods, tools and features.
Briefings in bioinformatics. 20(5):1669-1684 [DOI] 10.1093/bib/bby041. [PMID] 29860277.
2018
A Comprehensive Roadmap of Murine Spermatogenesis Defined by Single-Cell RNA-Seq.
Developmental cell. 46(5):651-667.e10 [DOI] 10.1016/j.devcel.2018.07.025. [PMID] 30146481.
2018
A variant within the FTO confers susceptibility to diabetic nephropathy in Japanese patients with type 2 diabetes
PloS one. 13(12)
2018
Machine Learning Methods to Predict Diabetes Complications.
Journal of diabetes science and technology. 12(2):295-302 [DOI] 10.1177/1932296817706375. [PMID] 28494618.
2018
MTGO: PPI Network Analysis Via Topological and Functional Module Identification.
Scientific reports. 8(1) [DOI] 10.1038/s41598-018-23672-0. [PMID] 29615773.
2018
Patient similarity for precision medicine: A systematic review
Journal of biomedical informatics. 83
2018
Risk factors for the development of micro-vascular complications of type 2 diabetes in a single-centre cohort of patients.
Diabetes & vascular disease research. 15(5):424-432 [DOI] 10.1177/1479164118780808. [PMID] 29911415.
2017
A short review of methods for Caspase cleavage site prediction
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2017
Dscam1 web server: online prediction of Dscam1 self- and hetero-affinity.
Bioinformatics (Oxford, England). 33(12):1879-1880 [DOI] 10.1093/bioinformatics/btx039. [PMID] 28137710.
2017
Exploring Wound-Healing Genomic Machinery with a Network-Based Approach.
Pharmaceuticals (Basel, Switzerland). 10(2) [DOI] 10.3390/ph10020055. [PMID] 28635674.
2017
MTopGO: a tool for module identification in PPI Networks
.
2016
A Data Fusion Approach to Enhance Association Study in Epilepsy
PLOS ONE. 11(12) [DOI] 10.1371/journal.pone.0164940. [PMID] 27984588.
2016
A network-based data integration approach to support drug repurposing and multi-target therapies in triple negative breast cancer
PloS one. 11(9)
2016
Data Fusion for cleavage target prediction
PeerJ PrePrints.
2016
Learning T2D Evolving Complexity from EMR and Administrative Data by Means of Continuous Time Bayesian Networks.
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2016
“Noisy beets”: impact of phenotyping errors on genomic predictions for binary traits in Beta vulgaris
Plant Methods. 12
2015
A Dynamic Bayesian Network model for long-term simulation of clinical complications in type 1 diabetes.
Journal of biomedical informatics. 57:369-76 [DOI] 10.1016/j.jbi.2015.08.021. [PMID] 26325295.
2015
A Genomic Data Fusion Framework to Exploit Rare and Common Variants for Association Discovery
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2015
Developing a parsimonius predictor for binary traits in sugar beet (Beta vulgaris)
Molecular breeding. 35
2015
PaPI: pseudo amino acid composition to score human protein-coding variants.
BMC bioinformatics. 16 [DOI] 10.1186/s12859-015-0554-8. [PMID] 25928477.
2014
Improvement of Dscam homophilic binding affinity throughout Drosophilaevolution
BMC Evolutionary Biology. 14(1)
2013
The role of SwrA, DegU and P(D3) in fla/che expression in B. subtilis.
PloS one. 8(12) [DOI] 10.1371/journal.pone.0085065. [PMID] 24386445.
2011
In silico protein-protein interaction prediction with sequence alignment and classifier stacking
Current Protein and Peptide Science. 12(7)
AMR-meta: a $\{$$\backslash$em k$}$-mer and metafeature approach to classify
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Grants

May 2024 ACTIVE
Recurrence of Cholera in Haiti: Exploration of Contributing Factors and Intervention Strategies
Role: Co-Investigator
Funding: NATL INST OF HLTH NIAID
Jul 2022 ACTIVE
A Phylodynamic Artificial Intelligence framework to predict evolution of SARS-CoV-2 variants of concern in Immunocompromised persons with HIV (PhAI-CoV)
Role: Co-Investigator
Funding: NATL INST OF HLTH NIAID
Jun 2021 – Aug 2022
Expanding genomic surveillance and epidemiology capacity in Central Florida and Southeastern US
Role: Co-Investigator
Funding: THE ROCKEFELLER FOU

Education

PhD, Bioengineering
2012 · The Hong Kong University of Science and Technology
MSc, Biomedical Engineering
2007 · University of Pavia
BSc, Biomedical Engineering
2004 · University of Pavia

Contact Details

Phones:
Business:
(352) 294-8951
Emails:
Addresses:
Business Mailing:
Box 100231
Dept. of Epidemiology
GAINESVILLE FL 32611
Business Street:
Box 100231
Dept. of Epidemiology
GAINESVILLE FL 32611