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 2025] Director of Research at CNR (National Research Council, Milan, Italy)
• [2018-2025] 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:

• Sachithra Yaddehige (2025 - ongoing)
• Nicol Sartori (2025 - ongoing)
• Mahsa Dehnavi (2025 - ongoing)
• Giulia Moscatelli (2024 - ongoing)
• Luiz Gustavo De Matos (2024 - 2025)
• Delower Hossain (2024 - ongoing)
• Tania Bobbo (2022 - ongoing)
• Arianna Manunza (2022 - ongoing)
• Johanna Ramírez Díaz (2022 - ongoing)
• Chiara Gini (2021 - 2024)
• Chiara Broccanello (2013 - 2023)
• Giorgio Chessari (2022 - 2025)
• Rafaela Martins Morasi (2023 - 2024)
• Giulia Masetti (2015 - 2023)
• Xavier Zaoui (2020)
• Eva-Maria Pirker (2019)
• Daniel Pitt (2016 - 2020)
• Jody Leigh Edmunds (2017 - 2022)
• Silvia Sandrini (2022 - 2024)
• Laura Filippone Pavesi (2022 - 2023)
• Mona Hashemi (2017 - 2018)
• Sowah Addo (2009 - 2010)
• Michael Kramer (2010 - 2011)
• Farhad Vahidi (2010 - 2011)

Education

• [2025] Habilitation as Full Professor in Plant Breeding and Genetics
• [2018] Habilitation as Full Professor in Animal 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

• 2025-2026: PROB-AI: Identifying novel probiotics from sequence data by means of artificial intelligence algorithms - CNR-DISBA 2024 call for projects (probiotics, machine learning, bacterial genomic sequences; Principal Investigator)
• 2023-2026: 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)
• 2025: To impute or not impute, a problem of missing data: joint project with the School of Biosciences at Cardiff University (UK) - STM (Short-term Mobility) 2025 (imputation, missing genotypes, software development; Principal Investigator)
• 2024-2025: 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)
• 2024-2025: Sheep-TreeSeq: Scalable analysis of sheep genome diversity using tree sequences - Royal Society - International Exchanges (graph algorithms, animal genomics; Principal Investigator; Ref.: R3709)
• 2023-2026: 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)
• 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

• 29/10/2025: ``Machine Learning applications in research related to agriculture and food science’’, International Research Conference of the SLTC 2025 (IRC-SLTC 2025: https://irc.sltc.ac.lk/), Padukka (Sri Lanka) (webinar)
• 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)

Latest talks

• 27/03/2026: “Microbiomes: a scientific megatrend”, CREA-GB Seminars (https://www.crea.gov.it/web/genomica-e-bioinformatica), Fiorenzuola (PC) (Italy) (in presence)
• 26/03/2026: “Genetic parameters and demography of animal populations”, 1st year Veterinary School, University of Pisa (Italy) (webinar)
• 12/03/2026: “Precision-farming applications in plants and animals”, Red de Investigación en Ganadería de Precisión y Digitalización Animal (REDIGA: https://rediga.es/es) (Spain) (webinar)
• 12/02/2026: “The Polyploidbreeding project”, PRIN plenary congress on Current Research in Durum Wheat Sustainability (https://www.cnr.it/it/evento/20363/la-ricerca-italiana-per-la-sostenibilita-della-filiera-del-frumento-duro), Auditorium “Via rieti”, Rome (Italy) (in presence)

Thesis supervision and evaluation

• 06/02/2026: Member of Doctoral Thesis Defense Committee, PhD in Veterinary Science and Food Safety. Four PhD thesis have been evaluated and discussed with the candidates (“Ciclo XXXVIII”). Università degli Studi di Padova (Italy)
• 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

• 12-13/11/2025: Best Presenter Award for the presentation ``PROB-AI: Identification of new probiotics from bacterial genomic sequences using machine learning algorithms’’ - \(5^{th}\) International Research Conference 2025 (IRC 2025), Sri Lanka Technology Campus
• 07/09/2023: Premio per l’originalità e la validità 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 2018: 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))

Editor at

• Frontiers in Genetics
• Frontiers in Endocrinology
• BMC Genomic Data
• BMC Hereditas

Hobbies

Bridge, Waterpolo, Guitar, Mystery Novels