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Hire Dr. Davide C.

Germany

USD 100 /hr

I am a passionate data scientist with extensive experience in computational biology, bioinformatics and biostatistics

Profile Summary

I have been working for more than 15 years as a computational biologist, bioinformatician and biostatistician in prestigious research institutions as the Max Planck Institutes and the University of Cambridge. My expertise ranges across the following topics: - NGS data analysis and integration: expert-level knowledge in the analysis and integration of -omics data (genomics, transcriptomics, metabolomics and proteomics), in data visualisation and automated reporting (e.g. Shiny, KnitR); professional knowledge of the software and tools for bioinformatics data analysis; expert level proficiency in the design and implementation of (automated) software pipelines and SOPs for the analysis of -omics data; extensive expertise in the methods, software and pipelines for the processing and analysis of genomics data, from the raw data to the variant calling , to the ‘’downstream analysis’’ (e.g. GWAS, mendelian randomization, colocalization, post GWAS analysis) to identify candidate biomarkers/drug targets or to infer possible genotype(s)/phenotype relation- ships; substantial working knowledge of large genomics databanks (UK-biobank, Genomics England)expert level knowledge of the methods and for pre-processing and analysis of transcriptomics data, e.g. bulk RNA-seq, scRNA- seq, ChIP-seq, ATAC-seq, spatial transcriptomics, RNA-seq time series. - Statistical data analysis and modelling: experience in multivariate data analysis, factor analysis and clustering meth- ods, modelling and simulation of (bio)chemical processes, experimental design, theory of stochastic processes, Monte Carlo Methods, machine learning (current focus on recurrent neural networks), data visualization; proven experience in the design, implementation and validation of algorithms for the modelling simulation of (bio)chemical systems; - Biostatistics: expertise in clinical trials design (non-adaptive and adaptive designs, e.g., multi-arm multi-stage (MAMS), umbrella studies, adaptive randomisation) and in the design and analysis of precision medicine trials, e.g. basket, umbrella, adaptive signature and adaptive enrichment designs, bayesian hierarchical modelling, instrumen- tal variable methods; substantial experience in the methods for the analysis of clinical data, including benefit-risk assessment (e.g. via the Clinical Utility Index). - Scripting and software development: extensive expertise in R, Matlab and Python scripting for statistical computing and bioinformatics and in Linux/bash scripting; expertise in GNU/Linux, Mac OS and Microsoft Windows Operating Systems; familiarity with C++ and Linux kernel programming; professional (Agile) software developer: versioning (github), module testing. - Scientific computing/data management: substantial experience in setting up and running computational biology- oriented facilities, from the design of the computational infrastructure to the recruitment and supervision of the scientific staff; experience in the installation and maintenance of scientific software and in data management and (automated) workflow organization with a particular attention to scalable and reproducible scientific workflows (e.g. usage of software for workflow management – Snakemake, Nextflow, software containers and version control) that can implement the FAIR data principles; active member of the Data Champion community of the University of Cambridge; basic IT system management. I hold a Master Degree in molecular biology (with a focus on mathematics and statistics) and a PhD in computer science. Relying on my multidisciplinary education it is natural for me to act as an interface between researchers coming from different scientific areas. As a consequence, I have developed peculiar communication skills that allow me to effectively cooperate, report and teach to audiences with diversified backgrounds.

Subject Matter Expertise

• ★ Computational Biology
• ☆ Biostatistics
• ☆ Molecular Biology
• ☆ Omics
• ☆ Transcriptomics
• ☆ Genomics
• ☆ Neuroscience
• ☆ Computational Neuroscience
• ☆ Data Analysis
• ☆ Computer Simulation/Computational Modeling
• ☆ Statistics
• ☆ Health Data Analysis
• ☆ Bioinformatics
• ☆ Gene & Protein Expression Analysis
• ☆ Systems Biology
• ☆ Applied Mathematics
• ☆ Mathematical Models
• ☆ Clinical Trials Data Analysis

Services

• Writing
• Research
• Data & AI

Writing Technical Writing, Newswriting

Research Meta-Research, Fact Checking, Gap Analysis, Systematic Literature Review, Secondary Data Collection

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

Work Experience

Line Manager

Bioinformatics and Biostatistics Core Facility - Institute of Metabolic Science, University of Cam

April 2018 - Present

Seinior Post Doctoral Scientis

Max Planck Institute for Infection Biology - MPU for the Science of Pathogens (Charpenier)t)

October 2016 - March 2018

Post Doctoral Research Associate

Max Planck Institute For Colloids and Interfaces

April 2016 - October 2016

Post-doctoral Fellow

Max Planck Institute For Colloids and Interfaces

April 2014 - March 2016

Senior Post-doctoral Fellow

Italian Istitute of Technology (IIT)

December 2012 - March 2014

Associate Research Fellow

University of Siena

October 2008 - November 2012

Education

PhD Computer Science

University of Siena (Italy)

February 2006 - April 2009

Master Degree (Faculty of Mathematics, Physics and natural Sciences)

University of Pisa

November 2002 - January 2005

MSc. Molecular Biology

University of Pisa (Italy)

October 2002 - January 2005

Certifications

• Certification details not provided.

Publications

JOURNAL ARTICLE

Davide Chiarugi, Samuel Furse, Samuel Virtue, Stuart G. Snowden, Antonio Vidal-Puig, Philip C. Stevenson, Albert Koulman (2022). Dietary PUFA drives diverse systems-level changes in lipid metabolism . Molecular Metabolism.

Davide Chiarugi, Samuel Furse, Adam J. Watkins, Huw E. L. Williams, Stuart G. Snowden, Albert Koulman(2022). Paternal nutritional programming of lipid metabolism is propagated through sperm and seminal plasma . Metabolomics. 18. (2). Springer Science and Business Media {LLC}

Davide Chiarugi, Samuel Furse, Adam J. Watkins, Nima Hojat, James Smith, Huw E. L. Williams, Albert Koulman (2021). Lipid Traffic Analysis reveals the impact of high paternal carbohydrate intake on offsprings’ lipid metabolism . Communications Biology.

Lu, Y., Basatemur, G., Scott, I.C., Chiarugi, D., Clement, M., Harrison, J., Jugdaohsingh, R., Yu, X., Newland, S.A., Jolin, H.E., et al.(2020). Interleukin-33 Signaling Controls the Development of Iron-Recycling Macrophages . Immunity. 52. (5). p. 782-793.e5.

Roberts, G.P., Larraufie, P., Richards, P., Kay, R.G., Galvin, S.G., Miedzybrodzka, E.L., Leiter, A., Li, H.J., Glass, L.L., Ma, M.K.L., et al.(2019). Comparison of human and murine enteroendocrine cells by transcriptomic and peptidomic profiling . Diabetes. 68. (5). p. 1062-1072.

Adriaenssens, A.E., Biggs, E.K., Darwish, T., Tadross, J., Sukthankar, T., Girish, M., Polex-Wolf, J., Lam, B.Y., Zvetkova, I., Pan, W., et al.(2019). Glucose-Dependent Insulinotropic Polypeptide Receptor-Expressing Cells in the Hypothalamus Regulate Food Intake . Cell Metabolism. 30. (5). p. 987-996.e6.

Sin, C., Chiarugi, D., Valleriani, A.(2016). Degradation parameters from pulse-chase experiments . PLoS ONE. 11. (5).

Sin, C., Chiarugi, D., Valleriani, A.(2016). Quantitative assessment of ribosome drop-off in E. coli . Nucleic Acids Research. 44. (6). p. 2528-2537.

Paradisi, P., Allegrini, P., Chiarugi, D.(2015). A renewal model for the emergence of anomalous solute crowding in liposomes . BMC Systems Biology. 9. (3).

Chiarugi, D., Falaschi, M., Hermith, D., Olarte, C., Torella, L.(2015). Modelling non-Markovian dynamics in biochemical reactions . BMC Systems Biology. 9. (3).

Sin, C., Chiarugi, D., Valleriani, A.(2015). Single-molecule modeling of mRNA degradation by miRNA: Lessons from data . BMC Systems Biology. 9. (3).

Rading, M.M., Sandmann, M., Steup, M., Chiarugi, D., Valleriani, A.(2015). Weak correlation of starch and volume in synchronized photosynthetic cells . Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 91. (1).

Chiarugi, D., Falaschi, M., Hermith, D., Olarte, C.(2015). Verification of Spatial and Temporal Modalities in Biochemical Systems . Electronic Notes in Theoretical Computer Science. 316. p. 29-44.

Olarte, C., Chiarugi, D., Falaschi, M., Hermith, D.(2015). A proof theoretic view of spatial and temporal dependencies in biochemical systems . Theoretical Computer Science. 641. p. 25-42.

Bodei, C., Bortolussi, L., Chiarugi, D., Guerriero, M.L., Policriti, A., Romanel, A.(2015). On the impact of discreteness and abstractions on modelling noise in gene regulatory networks . Computational Biology and Chemistry. 56. p. 98-108.

Bodei, C., Brodo, L., Bruni, R., Chiarugi, D.(2014). A flat process calculus for nested membrane interactions . Scientific Annals of Computer Science. 24. (1). p. 91-136.

Chiarugi, D., Falaschi, M., Hermith, D., Guzman, M., Olarte, C.(2013). Simulating signalling pathways with BioWayS . Electronic Notes in Theoretical Computer Science. 293. p. 17-34.

Bodei, C., Brodo, L., Chiarugi, D.(2012). Control flow analysis of Generalised Boolean Networks . Electronic Notes in Theoretical Computer Science. 284. p. 3-22.

Bodei, C., Bracciali, A., Chiarugi, D.(2009). Control Flow Analysis for Brane Calculi . Electronic Notes in Theoretical Computer Science. 227. (C). p. 59-75.

Bodei, C., Bracciali, A., Chiarugi, D.(2008). On deducing causality in metabolic networks . BMC Bioinformatics. 9. (SUPPL. 4).

Chiarugi, D., Degano, P., Marangoni, R.(2007). A computational approach to the functional screening of genomes . PLoS Computational Biology. 3. (9). p. 1801-1806.

Chiarugi, D., Bartolini, G.(1968). Occupational evaluation methods in mental retardation,Metodi di valutazione professionale degli insufficienti mentali . Rivista di Neurobiologia. 14. (1). p. 142-147.

OTHER

Davide Chiarugi, Samuel Furse, Adam J. Watkins, Nima Hojat, James Smith, Huw E. L. Williams, Albert Koulman(2020). Revealing grand-paternal programming of lipid metabolism using a novel computational tool . Cold Spring Harbor Laboratory

BOOK

Chiarugi, D., Falaschi, M., Olarte, C., Palamidessi, C.(2015). A declarative view of signaling pathways . Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9465. p. 183-201.

Chiarugi, D., Degano, P., Van Klinken, J.B., Marangoni, R.(2008). Cells in silico: A holistic approach . Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5016 LNCS. p. 366-386.

Chiarugi, D., Chinellato, M., Degano, P., Lo Brutto, G., Marangoni, R.(2006). Feedbacks and oscillations in the virtual cell VICE . Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4210 LNBI. p. 93-107.

CONFERENCE PAPER

Chiarugi, D., Falaschi, M., Olarte, C., Palamidessi, C.(2010). Compositional modelling of signalling pathways in timed concurrent constraint programming . 2010 ACM International Conference on Bioinformatics and Computational Biology, ACM-BCB 2010. p. 414-417.

Bodei, C., Bracciali, A., Chiarugi, D., Gori, R.(2010). A taxonomy of causality-based biological properties . Electronic Proceedings in Theoretical Computer Science, EPTCS. 19. p. 116-133.

Chiarugi, D., Curti, M., Degano, P., Marangoni, R.(2005). VICE: A vIrtual CEll . Lecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science). 3082. p. 207-220.