Simone Marini

Also affiliated with University of Florida, University of Florida Health Science Center, Florida College

Biochemistry, Genetics and Molecular BiologyMedicine

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 2%percentile

3.9Author DataRank

Indexed papers

3in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 3 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

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(2022)10.1093/nar/gkac1047

Top 7%

3.4DataRank

Top 7%206 citations

Enrique Doster, Hannah Worley, Lee J. Pinnell, Jonathan E. Bravo, Peter Ferm +6 more

Papers

Driven by 33 papers — median percentile 55. Top paper: “MEGARes and AMR++, v3.0: an updated comprehensive database of antimicrobial resistance determinants and an improved software pipeline for classification using high-throughput sequencing”.

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(2022)10.1093/nar/gkac1047

Top 7%

3.4DataRank

Top 7%206 citations

Enrique Doster, Hannah Worley, Lee J. Pinnell, Jonathan E. Bravo, Peter Ferm +6 more

Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable

Proceedings of the National Academy of Sciences(2020)10.1073/pnas.2007295117

N/A

0.665DataRank · unranked

83 citations

Sergei L. Kosakovsky Pond, Simone Marini, Brittany Rife Magalis, Anne–Mieke Vandamme, Simon Dellicour +31 more

Immobilization after injury alters extracellular matrix and stem cell fate

Journal of Clinical Investigation(2020)10.1172/jci136142

N/A

0.654DataRank · unranked

77 citations

Nicole Patel, Chase A. Pagani, Simone Marini, Karthik Padmanabhan, Daniel L. Matera +16 more

The role of neutrophil extracellular traps and TLR signaling in skeletal muscle ischemia reperfusion injury

The FASEB Journal(2020)10.1096/fj.202000994rr

N/A

0.553DataRank · unranked

39 citations

Charles Hwang, Simone Marini, Chase A. Pagani, Philip Spreadborough, Cassie J. Rowe +12 more

Novel Lineage-Tracing System to Identify Site-Specific Ectopic Bone Precursor Cells

Stem Cell Reports(2021)10.1016/j.stemcr.2021.01.011

N/A

0.533DataRank · unranked

34 citations

Amanda K. Huber, Charles Hwang, Simone Marini, Karthik Padmanabhan, Nicholas Livingston +18 more

Perivascular Fibro-Adipogenic Progenitor Tracing during Post-Traumatic Osteoarthritis

American Journal Of Pathology(2020)10.1016/j.ajpath.2020.05.017

N/A

0.505DataRank · unranked

28 citations

Ching-Yun Hsu, Yiyun Wang, Jiajia Xu, Masnsen Cherief, Simone Marini +6 more

Macrophage-mediated PDGF Activation Correlates With Regenerative Outcomes Following Musculoskeletal Trauma

Annals of Surgery(2022)10.1097/sla.0000000000005704

N/A

0.442DataRank · unranked

18 citations

Tristan Maerz, Dominic Henn, Kurt D. Hankenson, Chase A. Pagani, Simone Marini +5 more

The K-mer antibiotic resistance gene variant analyzer (KARGVA)

Frontiers in Microbiology(2023)10.3389/fmicb.2023.1060891

Top 45%

0.413DataRank

Top 45%10 citations

Christina Boucher, Noelle Noyes, Mattia Prosperi, Simone Marini

SARITA: a large language model for generating the S1 subunit of the SARS-CoV-2 spike protein

Briefings in Bioinformatics(2025)10.1093/bib/bbaf384

N/A

0.330DataRank · unranked

8 citations

Giovanna Nicora, Laura Bergomi, Tommaso Mario Buonocore, Daniel M. Czyż, Enea Parimbelli +5 more

Novel insights on unraveling dynamics of transmission clusters in outbreaks using phylogeny-based methods

Infection Genetics and Evolution(2024)10.1016/j.meegid.2024.105661

N/A

0.208DataRank · unranked

3 citations

Alberto Riva, Simone Marini, Marco Salemi, Mattia Prosperi, Brittany Rife Magalis

The K -mer Antibiotic Resistance Gene Variant Analyzer (KARGVA)

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.08.12.503773

Top 78%

0.104DataRank

Top 78%1 citations

Christina Boucher, Noelle Noyes, Mattia Prosperi, Simone Marini

Forecasting dominance of SARS-CoV-2 lineages by anomaly detection using deep AutoEncoders

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.24.563721

N/A

0.104DataRank · unranked

1 citations

Giovanna Nicora, Mattia Prosperi, Riccardo Bellazzi, Marco Salemi, Simone Marini +1 more

Machine Learning Prediction and Phyloanatomic Modeling of Viral Neuroadaptive Signatures in the Macaque Model of HIV-Mediated Neuropathology

Microbiology Spectrum(2023)10.1128/spectrum.03086-22

N/A

0.104DataRank · unranked

1 citations

David A. Ostrov, Marco Salemi, Simone Marini, Brittany Rife Magalis, Andrea S. Ramirez-Mata

Assessing putative bias in prediction of anti-microbial resistance from real-world genotyping data under explicit causal assumptions

Artificial Intelligence in Medicine(2022)10.1016/j.artmed.2022.102326

N/A

0DataRank · unranked

9 citations

Christina Boucher, Jiang Bian, Simone Marini, Mattia Prosperi

AMR-meta: a k-mer and metafeature approach to classify antimicrobial resistance from high-throughput short-read metagenomics data

GigaScience(2022)10.1093/gigascience/giac029

N/A

0DataRank · unranked

18 citations

Marco Antônio Oliva, Ilya B. Slizovskiy, Rishabh A Das, Noelle Noyes, Tamer Kahveci +3 more

KARGAMobile: Android app for portable, real-time, easily interpretable analysis of antibiotic resistance genes via nanopore sequencing

Frontiers in Bioengineering and Biotechnology(2022)10.3389/fbioe.2022.1016408

N/A

0DataRank · unranked

7 citations

Simone Marini, Christina Boucher, Jaimé Ruiz, Mattia Prosperi, Alexander Barquero

Machine learning prediction and phyloanatomic modeling of viral neuroadaptive signatures in the macaque model of HIV-mediated neuropathology

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.06.17.496109

N/A

0DataRank · unranked

0 citations

David A. Ostrov, Marco Salemi, Simone Marini, Brittany Rife Magalis, Andrea S. Ramirez-Mata

Scalable de novo classification of antibiotic resistance of Mycobacterium tuberculosis

Bioinformatics(2024)10.1093/bioinformatics/btae243

N/A

0DataRank · unranked

17 citations

Simone Marini, Jarno Alanko, Noelle Noyes, Mattia Prosperi, Christina Boucher +1 more

Forecasting dominance of SARS-CoV-2 lineages by anomaly detection using deep AutoEncoders

Briefings in Bioinformatics(2024)10.1093/bib/bbae535

N/A

0DataRank · unranked

14 citations

Giovanna Nicora, Mattia Prosperi, Riccardo Bellazzi, Marco Salemi, Simone Marini +1 more

OCTOPUS: Disk-based, Multiplatform, Mobile-friendly Metagenomics Classifier

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.03.15.585215

N/A

0DataRank · unranked

4 citations

Alexander Barquero, Anisha Ashok Wadhwani, Jiang Bian, Jaime Ruiz, Christina Boucher +2 more

Leveraging large language models to predict antibiotic resistance in Mycobacterium tuberculosis

Bioinformatics(2025)10.1093/bioinformatics/btaf232

N/A

0DataRank · unranked

3 citations

Sakshi Pandey, Mohammadali Serajian, Simone Marini, Mattia Prosperi, Christina Boucher +1 more

Endogenous CCN family member WISP1 inhibits trauma-induced heterotopic ossification

JCI Insight(2020)10.1172/jci.insight.135432

N/A

0DataRank · unranked

23 citations

Simone Marini, Stefano Negri, Yiyun Wang, Jiajia Xu, Chase A. Pagani +9 more

Differing impacts of global and regional responses on SARS-CoV-2 transmission cluster dynamics

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.06.370999

N/A

0DataRank · unranked

7 citations

Andrea S. Ramirez-Mata, Anna Zhukova, Carla Mavian, Simone Marini, Frédéric Lemoine +4 more

Brain tissue transcriptomic analysis of SIV-infected macaques identifies Poly (ADP-ribose) polymerases (PARPs) as potential biomarkers for neuropathogenesis.

(2020)10.21203/rs.3.rs-30629/v1

N/A

0DataRank · unranked

0 citations

Andrea S. Ramirez-Mata, James J. Dollar, David J. Nolan, Shannan N. Rich, Kevin White +9 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.05.21.109140

N/A

0DataRank · unranked

0 citations

Andrea S. Ramirez-Mata, James J. Dollar, David J. Nolan, Kevin White, Shannan N. Rich +9 more

NGF-TrkA signaling dictates neural ingrowth and aberrant osteochondral differentiation after soft tissue trauma

Nature Communications(2021)10.1038/s41467-021-25143-z

N/A

0DataRank · unranked

87 citations

Charles Hwang, Simone Marini, Robert J. Tower, Qizhi Qin, Stefano Negri +19 more

Optimizing viral genome subsampling by genetic diversity and temporal distribution (TARDiS) for phylogenetics

Bioinformatics(2021)10.1093/bioinformatics/btab725

N/A

0DataRank · unranked

17 citations

Carla Mavian, Alberto Riva, Mattia Prosperi, Marco Salemi, Brittany Rife Magalis +1 more

Fast and exact quantification of motif occurrences in biological sequences

BMC Bioinformatics(2021)10.1186/s12859-021-04355-6

N/A

0DataRank · unranked

5 citations

Simone Marini, Christina Boucher, Mattia Prosperi

Exploring Prediction of Antimicrobial Resistance Based on Protein Solvent Accessibility Variation

Frontiers in Genetics(2021)10.3389/fgene.2021.564186

N/A

0DataRank · unranked

5 citations

Marco Antônio Oliva, Ilya B. Slizovskiy, Noelle Noyes, Christina Boucher, Mattia Prosperi +1 more

Towards routine employment of computational tools for antimicrobial resistance determination via high-throughput sequencing

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.11.03.467126

N/A

0DataRank · unranked

1 citations

Rodrígo Mora, Christina Boucher, Noelle Noyes, Mattia Prosperi, Simone Marini

Macrophage TGF-β signaling is critical for wound healing with heterotopic ossification after trauma

JCI Insight(2022)10.1172/jci.insight.144925

N/A

0DataRank · unranked

51 citations

Johanna Nunez, Michael Sorkin, Simone Marini, Chase A. Pagani, Amy L. Strong +13 more

Towards routine employment of computational tools for antimicrobial resistance determination via high-throughput sequencing

Briefings in Bioinformatics(2022)10.1093/bib/bbac020

N/A

0DataRank · unranked

16 citations

Rodrígo Mora, Christina Boucher, Noelle Noyes, Mattia Prosperi, Simone Marini

Predicting emerging SARS-CoV-2 variants of concern through a One Class dynamic anomaly detection algorithm

BMJ Health & Care Informatics(2022)10.1136/bmjhci-2022-100643

N/A

0DataRank · unranked

17 citations

Marco Salemi, Simone Marini, Riccardo Bellazzi, Giovanna Nicora

Simone Marini

Indexed papers

Top data-sharing exemplar

Papers