Filippo Biscarini, Ph.D. Biostatistician @ CNR Bioinformatics, biostatistics, genomics, machine learning, deep learning

National Research Council (CNR)
Institute for Biology and Biotechnology Via A. Corti n. 12, 20133 Milan (Italy)

• filippo.biscarini [at] cnr.it
• my ResearchGate
• my Google Scholar
• my Scopus
• my institutional CNR page
• my Github

Research summary

My research activities span from plant and animal breeding & genetics, to bioinformatics and biostatistics applications in plant & animal science and human medicine. I worked for the breeding industry, for universities and research centres and for international organizations in many places: Italy, Ireland, Canada, The Netherlands, Germany, Spain, Madagascar, The United Kingdom, Belgium. I am now Senior Scientist at CNR. Currently, I have rejoined my research group in Milan after being seconded for two years at the Data Analysis Team of the ERC (European Research Council). Current projects include: deep neural network models for image, sound, text and tabular data in (semi)supervised and unsupervised problems; machine learning methods for the prediction of GHG (greenhouse gas) emissions from dairy farms; measuring the accuracy of imputing missing genetic variants in diploid genomes under challenging scenarios; using environmental descriptors (“enviromics”) to model GxE (genotype by environment) interactions in genomic predictions; GWAS for survival to covid-19 in a large integrated heterogeneous dataset; developing methods and tools to detect and interpret runs of homozygosity (ROH) and heterozygosity-rich regions (HRR) in diploid genomes.

Research topics

• Statistics, machine and deep learning: explore the boundaries of predictions
• GHG emissions from agriculture: tools for predictions and monitoring emissions, strategies for reduction and mitigation
• Imputation of missing data: methods, accuracy and scenarios for the imputation of any type of missing data (not only genotypes!)
• Computer vision: methods and applications in agriculture and medicine
• Biomarkers discovery and precision medicine
• The role of microbiome in animals, plants, humans, food and environments
• Antimicrobial resistance in farm animals: approaches to reduce or replace the use of antimicrobials in farm animals
• Genotype-by-environment interactions in plant and animal breeding: more accurate and robust predictions, adaptation of populations to changing climate and environments
• GWAS: methods and applications
• Genomics: structure, distribution and practical applications of homozygous and heterozygos regions in diploid genomes (ROH, HRR)
• Plant and animal breeding: increase yield, sustainability and production efficiency in farm animals and crops (any ploidy)

Dissemination

• founding member of The Bioinformateachers
• teacher at Physalia courses (freie Universität Berlin):
  • [since 2018] Introduction to GWAS
  • [since 2020] Introduction to Machine Learning
  • [since 2020] Introduction to Deep Learning
  • [since 2023] Analysis of longitudinal data
• teacher at the University of Pisa:
  • [2022-2024] Animal breeding and genetics
• teacher at the Universities of Parma, Bari:
  • [2023-2024] Introduction to Neural Netowrks for animal science
• teacher at the University of Catania:
  • [2013] Molecular microbiology and statistical epidemiology
• assistant teacher at Wageningen University:
  • [2009] Animal breeding and genetics

Research positions

• [since 2018] Senior Scientist at CNR (National Research Council, Milan, Italy)
• [2018-2020] Seconded National Expert on Data Science at ERCEA (European Research Council Ex. Agency, Bruxelles, Belgium)
• [2017-2018] Marie-Curie Senior Biostatistician, Cardiff University (School of Medicine) (Cardiff, United Kingdom)
• [2016-2018] Tenured Scientist at CNR (National Research Council, Milan, Italy)
• [Feb 2017] UN-IAEA Expert Mission, Centre national de la recherche appliquée au développement rural (Antananarivo, Madagascar)
• [2016] Researcher at the School of Biosciences, University of Teramo (Italy)
• [2014-2016] Principal Investigator at PTP Science Park (Lodi, Italy)
• [Oct 2016] COST Short-Term Scientific Mission, IRTA (Institut de Recerca i Tecnologia Agroalimentàries) (Caldes de Montbui, Spain)
• [2011-2014] Marie-Curie post-doctoral researcher at PTP Science Park (Lodi, Italy)
• [Mar 2013] ESF Visiting Scientist, Cardiff University (School of Biosciences) (Cardiff, UK)
• [2010-2011] Post-doctoral researcher (Wissenschaftlicher Mitarbeiter), Georg-August Universität (Göttingen, Germany)
• [2006-2010] Marie-Curie Phd fellow, Wageningen University (Wageningen, The Netherlands)
• [2003-2006] Quantitative Geneticist at the R\&D office of the Italian Holstein Association (ANAFIBJ) (Cremona, Italy)
• [2005] Visiting scientist at the Centre for Genetic Improvement of Livestock (CGIL), University of Guelph (Guelph, Canada)
• [2002] Data analyst and programmer at ICBF (Irish Cattle Breeders Federation) (Cork, Ireland)

Alumni

Very smart people who I had the honor of mentoring:

• Giulia Moscatelli (2024 - ongoing)
• Delower Hossain (2024 - ongoing)
• Tania Bobbo (2022 - ongoing)
• Arianna Manunza (2022 - ongoing)
• Johanna Ramírez Díaz (2022 - ongoing)
• Chiara Gini (2021 - ongoing)
• Chiara Broccanello (2013 - 2023)
• Giorgio Chessari (2022 - ongoing)
• Rafaela Martins Morasi (2023 - ongoing)
• Giulia Masetti (2015 - 2023)
• Xavier Zaoui (2020)
• Eva-Maria Pirker (2019)
• Daniel Pitt (2016 - 2020)
• Jody Leigh Edmunds (2017 - ongoing)
• Silvia Sandrini (2022 - ongoing)
• Laura Filippone Pavesi (2022 - ongoing
• Mona Hashemi (2017 - 2018)
• Sowah Addo (2009 - 2010)
• Michael Kramer (2010 - 2011)
• Farhad Vahidi (2010 - 2011)

Education

• [2018] Habilitation as Associate and Full Professor in Animal Breeding and Genetics; Habilitation as Associate Professor in Plant Breeding and Genetics
• [2006-2010] Doctor of Philosophy in Animal Breeding and Genomics (Wageningen University, The Netherlands)
• [1996-2002] Master of Science in Veterinary Medicine (University of Perugia)
• [1999] Erasmus Programme - Veterinary Epidemiology and Food Safety (Utrecht University, The Netherlands)

Projects

• 2024-2026: DeepMicroCore: Harnessing the power of artificial intelligence to identify the core microbiome - CNR-IVI bilateral agreement (artificial intelligence, neural networks, core microbiome; Principal Investigator; Project ID: 69001)
• 2024-2026: Sheep-TreeSeq: Scalable analysis of sheep genome diversity using tree sequences - Royal Society - International Exchanges (graph algorithms, animal genomics; Principal Investigator; Ref.: R3709)
• 2023-2025: MISS.GO: Microbiota and Immune SignatureS of Graves’ disease and Orbitopathy - PRIN 2022 (Graves disease, orbitopathy, gut microbiome, gut-immune system axis; Task Leader: Microbiome)
• 2023-2025: Polyploidbreeding 4.0: Expanding the toolbox for cereal breeding: high-throughput genomics, 2D-3D phenomics and artificial intelligence for breeding with increasing genome complexity, from barley to durum and bread wheat - PRIN 2022. (plant breeding: genomics, phenomics, neural networks, machine learning; Scientific coordinator; G.A.: 2022BACN8A; website)
• 2024-2029: Breast cancer and thyroid autoimmunity: Cross-reactive immune responses between breast cancer and thyroid autoimmunity: impact on prognosis and treatment - AIRC-MFAG 2023 (breast cancer, endocrinology, gut microbiome; Task Leader: Microbiome)
• 2021-2024: GENOBU: Sequencing the buffalo genome for the genetic improvement of production - PON01 00486 (buffalo, genomic predictions; Task Leader: Genomics)
• 2020-2023: Gen-COVID: Impact of Host Genome on COVID-19 clinical variability. (human genetics, clinical phenotypes; Principal Investigator; website)
• 2019-2023: Freeclimb: Fruit Crops Resilience to Climate Change in the Mediterranean Basin - EU-PRIMA 2018. (plant breeding: genomics, phenomics; Principal Investigator; G.A.: 1813-2; website)
• 2018-2023: SMARTER: SMAll RuminanTs breeding for Efficiency and Resilience - EU Horizon2020. (animal genomics and phenomics; team member; G.A.: 772787; website)
• 2018-2021: FARM-INN: FARM-level interventions supporting industry INNovation - AGER. (animal and food microbiome; Task Leader Microbiome; G.A.: 2017-1130; website)
• 2018-2021: RABOLA: Sustainable strategies to reduce the use of antibiotics in dairy cattle farming - Regione Lombardia, Call 2018 ddsn 4403. (animal and food microbiome, antimicrobial resistance; Task Leader Microbiome; G.A.: d.d.s. 19442/2018; website)
• 2018-2019: TT AgriLab: Technology Transfer for SMEs in the AgriFood industry - Assolombarda - TTAgriLab. (knowledge and technology transfer; Scientific Expert; Ref.: 2017/0001874)
• 2016-2017: LegPipe: Legumes GBS Pipeline Exploration - CINECA. (computational infrastructure, bioinformatics pipelines; team member; Ref.: HPL13D6NFZ)
• 2015-2018: Climgen: Climate genomics for animal adaptation - FACCE ERANET+. (animal genomics, climate change; WP co-leader; G.A.: ANR-14-JFAC-0002-01; website)
• 2014-2018: INDIGO: Investigation of Novel biomarkers and Definition of the role of the microbiome In Graves’ Orbitopathy - EU-FP7. (human microbiome, transcriptomics, miRNA, proteomics, metabolomics, biostatistics; Principal Investigator; G.A.: 612116; website)
• 2013-2017: Fecund: Optimisation of early reproductive success in dairy cattle through the definition of new trait and improved reproductive biotechnology - EU-FP7. (animal genetics, multiomics, biostatistics; Scientific Coordinator; G.A.: 312097; website)
• 2013-2017: Methagene: Large-scale methane measurements on individual ruminants for genetic evaluations - COST Action (climate change, animal farming, biostatistics; WG co-leader; G.A.: COST FA1302; website)
• 2013: ESF Exchange Grant: Detection of selection signatures of domestication in ancestral and domestic goats (at Cardiff University, School of Biosciences, UK) - ESF exchange grants (animal genomics, evolution; grantee; Ref.: 4103, 22/12/2012)
• 2012-2015: Gene2Farm: Next generation European system for cattle improvement and management - EU-FP7. (animal breeding: genomics, phenomics; team member; G.A.: 289592; website)
• 2012-2015: RuminOmics: Connecting the animal genome, gastrointestinal microbiomes and nutrition to improve digestion efficiency and the environmental impacts of ruminant livestock production - EU-FP7. (animal microbiome, genomics, nutrition; team member; G.A.: 289319; website)
• 2011-2014: Neutradapt: Estimating genetic variation in farm animals - Marie-Curie ERG. (animal genomics, biodiversity, biostatistics; Principal Investigator member; G.A.: 276699; website)
• 2010-2014: Nextgen: Next generation methods to preserve farm animal biodiversity by optimizing present and future breeding options - EU-FP7. (animal genomics, biodiversity, population genetics; team member; G.A.: 244356; website)
• 2010-2014: Low-input breeds: Development of integrated livestock breeding and management strategies to improve animal health, product quality and performance in European organic and ‘low input’ milk, meat and egg production - EU-FP7. (animal breeding: genetics, management, organic agriculture; team member; G.A.: 222623; website)
• 2006-2010: Robustness in laying hens - National Dutch project for the genetic improvement of laying hens better able to cope with changing farming environment (animal breeding: genetics, statistics; Task leader statistical genetics)

Invited speeches

• 22/11/2024: key note on ``Computer vision for plant phenotyping: the Polyploidbreeding 4.0 project and the AGRI-VISION initiative’’, Nordic-Baltic Plant Phenotyping Network (NBPPN) Workshop, Båstad (Sweden)
• 06/09/2018: ``Omic’ approaches to identifying biomarkers in GO’’ at the Cambridge Ophthalmological Symposium 2018, University of Cambridge (UK)
• 30/10/2016: “The application of bioinformatics and biostatistics to dairy cattle fertility” at ESDAR (European Society for Domestic Animal Reproduction) 2016 Satellite Workshop, Lisbon (Portugal)

Thesis supervision

• 27/09/2024: Member of Doctoral Thesis Defense Committee, PhD in Animal Production Science and Technology. “New insights for enhancing feed efficiency” by Mónica Mora Fenoll. Universitat Politécnica de València (Spain)

Awards

• 07/09/2023: Premio per l’originalità e la validit`{a} scientifica della ricerca - 7° Congresso AITEL 2023 (award for best presentation) - AITel (Italian Dairy Association)
• 16/12/2021: Premi per le migliori pubblicazioni DiSBA 2021: I frutti dell’eccellenza (award for best publication) – CNR (National Research Council) Award for the publication “Genetic mechanisms of critical illness in COVID-19” (Nature volume 591, pages92–98 (2021))
• 07/12/2018: Premi per le migliori pubblicazioni DiSBA 2021: I frutti dell’eccellenza (award for best publication) – CNR (National Research Council) Award for the publication “Convergent genomic signatures of domestication in sheep and goats” (Nature Communications volume 9, Article number: 813 (2018))
• 25/11/2015: Premio Lombardy Dialogues: progetto spazi espositivi per la ricerca - EXPO 2015 (award for best publication) – CNR (National Research Council) Award forthe publication “Predicting haplotype carriers from SNP genotypes in Bos taurus through linear discriminant analysis” (Genetics Selection Evolution volume 47, Article number: 4 (2015))

Hobbies

Bridge, Waterpolo, Mystery Novels