Author

Simona Panni

University of CalabriaORCID 0000-0002-7500-4028Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Research Focus:database / resource· 3 Approach:statistical model· 3 Organism:human· 2 Assay:protein sequence· 2 Approach:benchmark study· 1 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Research Focus:differential expression· 1

Frequent Co-Authors

Henning HermjakobiD· 4 shared Luana LicataiD· 4 shared Sandra E. OrchardiD· 4 shared Kalpana PanneerselvamiD· 3 shared Livia PerfettoiD· 3 shared Margaret DuesburyiD· 3 shared Marta IannuccelliiD· 3 shared Pablo PorrasiD· 3 shared

Activity by Year

2018-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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4 shared papersBioinformatics

Henning HermjakobORCID

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Author profile →

5 papers

Recent·Most cited

Capturing domain-level detail of molecular interactions in the IMEx Consortium binding domain data set

Alessia Pinto, Prisca Lo Surdo, Juan Jose Medina Reyes, Lou Bergogne, Carla Luciana Padilla Franzotti, Marta Iannuccelli, Simona Panni, Kalpana Panneerselvam, Sylvie Ricard‐Blum, Eliot Ragueneau, Sandra E. Orchard, Henning Hermjakob, Andreas Zanzoni, Luana Licata

The paper presents a manually curated dataset of protein binding domains, linking them to molecular interactions and genomic variations for benchmarking and disease mechanism studies.

bioRxiv · Oct 16, 2026 · PreprintBioinformatics

GOFlowLLM - Curating miRNA literature with Large Language Models and flowcharts

Andrew Green, Nancy Ontiveros‐Palacios, Isaac Jandalala, Simona Panni, Valerie Wood, Giulia Antonazzo, Helen L. Attrill, Alex G. Bateman, Blake Sweeney

GOFlowLLM automates miRNA literature curation using LLMs and flowcharts, achieving high accuracy and efficiency in annotating gene silencing data.

Bioinformatics · Jan 1, 2026Peer-reviewedBioinformatics

The landscape of microRNA interactions annotation: analysis of three rare disorders as case study

Simona Panni, Kalpana Panneerselvam, Pablo Porras, Margaret Duesbury, Livia Perfetto, Luana Licata, Henning Hermjakob, Sandra E. Orchard

The paper analyzes microRNA interactions in three rare disorders to assess data availability and annotation consistency across databases.

bioRxiv · Jun 20, 2023 · PreprintBioinformatics

The IMEx Coronavirus interactome: an evolving map of Coronaviridae-Host molecular interactions

Livia Perfetto, Chiara Pastrello, Noemí del‐Toro, Margaret Duesbury, Marta Iannuccelli, Max Kotlyar, Luana Licata, Birgit Meldal, Kalpana Panneerselvam, Simona Panni, Negin Rahimzadeh, Sylvie Ricard‐Blum, Łukasz Salwiński, Anjali Shrivastava, Gianni Cesareni, , Pablo Porras

The paper curates a dataset of physical molecular interactions between SARS-CoV-2, SARS-CoV-1, and other Coronaviridae proteins, providing a resource for studying virus-host interactions.

Database · Jan 1, 2020Peer-reviewedBioinformatics

Capturing variation impact on molecular interactions: the IMEx Consortium mutations data set

J. Khadake, Birgit Meldal, Simona Panni, David Thorneycroft, K. Van Roey, Sara Abbani, Łukasz Salwiński, Matteo A. Pellegrini, Marta Iannuccelli, Luana Licata, G. Cesareni, Bernd Roechert, Alan James Bridge, Mais G. Ammari, Fiona McCarthy, , Pablo Porras

The paper presents a dataset of 28,000 annotations describing how amino acid mutations affect protein interactions, available through the IntAct website.

Nature Communications · Dec 27, 2018Peer-reviewedBioinformatics