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Hire Dr. Andrea C.

Italy

USD 50 /hr

Bioinformatics & Software Engineering Consultant | RNA & Cancer Genomics | NGS Pipelines | Structural Biology & AI Drug

Profile Summary

I provide advanced bioinformatics and software engineering solutions in RNA and protein structure modeling, cancer genomics, and next-generation sequencing (NGS) pipelines. My expertise covers structural bioinformatics, molecular docking, conformational ensembles, Cryo-EM map refinement, and AI-driven drug discovery. I have developed and published widely used resources such as MODOMICS and NACDDB in Nucleic Acids Research, and contributed to studies on RNA modifications, tumor driver genes, and extracellular vesicles in cancer biology. Alongside data analysis, I design and implement robust software systems: reproducible pipelines (Nextflow, Snakemake), database and web application development, and custom tools tailored for biotech and pharma applications. My technical expertise includes Python, C++, Rust, R, JavaScript (Vanilla and React), Bash, and workflow automation, combined with experience in HPC and cloud environments for large-scale datasets. Selected ongoing projects include: Development of a new RNA folding and structure prediction software integrating physics-based models with deep learning potentials for accurate and scalable simulations. Computational classification of orphan proteins to assign putative families, functions, and annotations using sequence- and structure-derived features. Analysis of RNA modifications via circular dichroism (NACDDB), linking spectral profiles to conformational states. Nanopore-based NGS pipelines for RNA modification detection. Freelance consulting projects covering bioinformatics analyses, software development, and cloud-based solutions. With a PhD in Bioinformatics (expected defense October 2025, IIMCB Warsaw) and a strong publication record, I deliver reproducible analyses, publication-ready reports, and scalable software tools for industry and academic partners.

Subject Matter Expertise

• ☆ Chemoinformatics
• ☆ Computational Biology
• ☆ Evolutionary Biology
• ☆ Biostatistics
• ☆ Biochemistry
• ☆ Biochemical Assays
• ☆ Structural Biology
• ☆ Binding Assays
• ☆ Molecular Biology
• ☆ Genetics
• ☆ Next Generation Sequencing (NGS)
• ☆ ATAC-Seq
• ☆ Gene Expression Analysis
• ☆ RNA Synthesis
• ☆ RNA Sequencing
• ☆ ChIP-Seq
• ☆ Cell Biology
• ☆ Cell Signaling Pathways
• ☆ Gene Regulation
• ☆ Stem Cell Research
• ☆ Computer Science
• ☆ Parallel Computing
• ☆ Software Engineering
• ☆ Internet of Things
• ☆ Software Architecture
• ☆ Data Analysis
• ☆ Biomarker Discovery
• ☆ Phylogenetics
• ☆ Python
• ☆ Matlab
• ☆ SQL
• ☆ Excel
• ☆ Tensorflow
• ☆ LaTex
• ☆ R
• ☆ Scikit-learn
• ☆ Markup Languages
• ☆ Drug Discovery
• ☆ Drug Design
• ☆ Cancer Research
• ☆ Cancer Biology

Services

• Writing
• Research
• Consulting
• Data & AI

Writing Medical Writing, Technical Writing, General Proofreading & Editing, Translation

Research Meta-Research, Feasibility Study, Technology Scouting, Fact Checking, Gap Analysis, Scientific and Technical Research, Systematic Literature Review, Secondary Data Collection

Consulting Scientific and Technical Consulting

Data & AI Predictive Modeling, Statistical Analysis, Algorithm Design-ML, Data Visualization, Big Data Analytics

Work Experience

Bioinformatician/Computational Biologist and Software Engineer

Freelancer

October 2024 - Present

PhD student

International Institute of Molecular and Cell Biology

August 2021 - September 2024

BIoinformatician

Superior Institute of Health

January 2021 - August 2021

Education

Master's degree

University of Padua

- Present

Master's

Università degli Studi di Roma La Sapienza Facoltà di Ingegneria Civile e Industriale

- Present

Certifications

• Certification details not provided.

Publications

JOURNAL ARTICLE

Etienne Boileau, Harald Wilhelmi, Anne Busch, Andrea Cappannini, Andreas Hildebrand, Janusz M Bujnicki, Christoph Dieterich, Sci-ModoM: a quantitative database of transcriptome-wide high-throughput RNA modification sites, Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D310–D317, https://doi.org/10.1093/nar/gkae972 .

Andrea Cappannini, Eliana Destefanis, Denise Sighel, Davide Dalfovo, Riccardo Gilmozzi, Francesca Broso, Janusz M Bujnicki, Alessandro Romanel, Erik Dassi, Alessandro Quattrone (2024). The three YTHDF paralogs and VIRMA are strong cross-histotype tumor driver candidates among m6A core genes . NAR Cancer.

Natalia A Szulc, Filip Stefaniak, Małgorzata Piechota, Anna Soszyńska, Gabriela Piórkowska, Andrea Cappannini, Janusz M Bujnicki, Chiara Maniaci, Wojciech Pokrzywa, DEGRONOPEDIA: a web server for proteome-wide inspection of degrons, Nucleic Acids Research, Volume 52, Issue W1, 5 July 2024, Pages W221–W232, https://doi.org/10.1093/nar/gkae238 .

Andrea Cappannini, Giorgia Castellani, Mariachiara Buccarelli, Quintino Giorgio D’Alessandris, Ramona Ilari, Francesca Pedini, Alessandra Boe, Valentina Lulli, Isabella Parolini, Stefano Giannetti, et al. (2024). Extracellular vesicles produced by irradiated endothelial or Glioblastoma stem cells promote tumor growth and vascularization modulating tumor microenvironment . Cancer Cell International.

Andrea Cappannini, Angana Ray, Elżbieta Purta, Sunandan Mukherjee, Pietro Boccaletto, S Naeim Moafinejad, Antony Lechner, Charles Barchet, Bruno P Klaholz, Filip Stefaniak, et al. (2024). MODOMICS: a database of RNA modifications and related information. 2023 update . Nucleic Acids Research.

Andrea Cappannini, Kevin Mosca, Sunandan Mukherjee, S Naeim Moafinejad, Richard R Sinden, Veronique Arluison, Janusz Bujnicki, Frank Wien (2023). NACDDB: Nucleic Acid Circular Dichroism Database . Nucleic Acids Research.

Pietro Boccaletto, Filip Stefaniak, Angana Ray, Andrea Cappannini, Sunandan Mukherjee, Elżbieta Purta, Małgorzata Kurkowska, Niloofar Shirvanizadeh, Eliana Destefanis, Paula Groza, Gülben Avşar, Antonia Romitelli, Pınar Pir, Erik Dassi, Silvestro G Conticello, Francesca Aguilo, Janusz M Bujnicki, MODOMICS: a database of RNA modification pathways. 2021 update, Nucleic Acids Research, Volume 50, Issue D1, 7 January 2022, Pages D231–D235, https://doi.org/10.1093/nar/gkab1083 .

Andrea Cappannini, Sergio Forcelloni, Andrea Giansanti(2021). Evolutionary pressures and codon bias in low complexity regions of plasmodia . Genetica. 149. (4). p. 217--237. Springer Science and Business Media {LLC}

(2021). Elesclomol-induced increase of mitochondrial reactive oxygen species impairs glioblastoma stem-like cell survival and tumor growth . Journal of experimental & clinical cancer research : CR.