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IMG CNR

Filippo Biscarini

Researcher: bioinformatics, biostatistics, genetics, plant & animal breeding

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Education

2006–2010 PhD in Animal Breeding & Genomics, Wageningen University, The Netherlands.
1996–2002 MSc in Veterinary Medicine, University of Perugia, Italy.
1999 Erasmus Programme, University of Utrecht, The Netherlands.

Work Experience

Research and teaching

2016–present Tenured Researcher, CNR: National Council for Research: Institute of Biology and Biotechnology in Agriculture, Milan, Italy.
Research in biostatistics, bioinformatics, plant and animal breeding. Recent research areas include: i) the effect of data errors on the efficiency of genomic predictions, ii) alternative strategies to genome-wide association studies, iii) the analysis of metagenomics and metabarcoding data, iv) the development of R packages for the detection of runs (homozygosity/heterozygosity) in diploid genomes, and v) and the development of bioinformatic pipelines for the functional analysis of genes and for the functional profiling of microbial communities.
2016–present Scientific Collaborator, Università degli Studi di Teramo - Faculty of Bioscience and Agro-Food and Environmental Technology, Teramo, Italy.
Research in Animal Breeding & Genetics, Biostatistics and Bioinformatics. Teaching animal breeding & genetics.
2014–present Principal Investigator, PTP Science Park, Lodi, Italy. Biostatistics and bioinformatics for the analysis of NGS (Next Generation Sequencing) data in animal, plant and human projects. Scientific coordination of national and international research projects. Coordinating a research group of 2/3 persons. Supervision of PhD and Master students.
2017 IAEA Expert Mission, Département de recherches zootechniques et vétérinaires; Centre national de la recherche appliquée au développement rural, Antananarivo, Madagascar. UN-IAEA mission to carry out a 5-days training course for local researchers and technicians (in French) on “Animal Identification, Recording Phenotypes and Performance Data to Enhance Cattle Breeding in Madagascar”
2016 COST Short Term Scientific Mission, IRTA —Institut de Recerca i Tec- nologia Agroalimentàries, Caldes de Montbui, Spain. COST Methagene Short-Term Scientific Mission to work on Bayesian statistical analysis of rumen methane emissions data in cattle.
2011–2014 Marie-Curie post-doctoral researcher, PTP Science Park, Lodi, Italy. Research on plant (sugar beet, rice, peach) and animal (sheep, cattle, goats, buffalo) statistical genetics, genomics and bioinformatics. Teaching statistics, programming and genetics courses. Supervision of PhD students.
2013 ESF Visiting Scientist, Cardiff University —School of Biosciences, Cardiff, UK. ESF (European Science Foundation) Grant to work on the genetic adaptation of animals to the environment.
2010–2011 Post-doctoral researcher, Georg-August Universität, Göttingen, Germany. Research on genomic predictions and selection in cattle. Teaching statistics. Supervision of PhD students.
2006–2010 Marie-Curie Phd fellow, Wageningen University, Wageningen, The Netherlands. Research on quantitative genetics and statistical genomics in laying hens. Assistant teacher in the master course “Animal breeding and genetics”. Supervision of master students.
2009–2010 Secondary school trainee teacher, Vwo - Havo school ’t Hooghe Landt, Amersfoort, The Netherlands. Project “Becoming a teacher”: training in teaching in secondary schools and classes given under the supervision of a regular teacher. The subject of teaching was biology and the language dutch.
2003–2006 Quantitative Geneticist, Italian Holstein Association, Cremona, Italy. Routine genetic evaluation of dairy cattle. Research on dairy cattle quantitative genetics.
2005 Visiting scientist, University of Guelph, Guelph, Canada. Research project on selection index theory and breeding schemes in dairy cattle.
2002 Web-programmer, ICBF (Irish Cattle Breeders Federation), Cork, Ireland. Web-programmer, database analyst and trainee in quantitative genetics.

Miscellaneous

2016–2017 "Big data" statistical analyst, smartStat - www.smartstat.it/, Milan, Italy. Statistical consultant for the analysis of large commercial datasets
2016 Scientific Consultant, Legramanti Breeding and Selection, Italy. Consultancy on data management and analysis, quantitative genetics, design of breeding programmes and strategies in meat chickens —broilers— and laying hens
2001–2017 Web-programmer, Perugia in Internet, Italy.
Founder, programmer and book-keeper of the association “Perugia in Internet”, active in the realisation of web-sites (e.g. www.studiolegalespinelli, www.largebearenclosures.com, www.ambulatorio-veterinario.com, www.colleinceralto.com) and related services.
2014/2015 Simultaneous translations.

  • “Centenary Celebration of the Sugar Beet Research Station (October 2014: Rovigo, Italy):
    Scientific congress and field excursion. English to Italian, Italian to English
  • “The future of dairy farming: calves and heifers” (July 2015: PTP Science Park, Lodi, Italy):
    Scientific congress: English to Italian, Italian to English.

2009–2010 Guitar teacher, Wageningen, The Netherlands.
2008 Translations.

  • "Landscape ecology of Monte di Portofino" (Book, English to Italian, Wageningen University, The Netherlands)
  • "Basic income sustainability and productivity growth in cognitive capitalism: a first theoretical framework" (Paper, Italian to English, University of Bergamo, Italy) 2003–2005 Veterinary practitioner, Cremona, Italy.
    Part-time dairy cows and pets veterinary practice
    2001–2002 Swimming instructor, Perugia, Italy.
    2001–2002 Theatre and cabaret actor, Perugia, Italy.
    2001 Summer camp tutor, Perugia, Italy.

Computer skills

Web: PHP, HTML/HTML5, CSS, Javascript, XML, JQuery, Ajax, Markdown

Programming: Python, Ruby, Fortran 77/90, C \C++, SQL

Statistics: R, SAS,Weka

Mathematics: Octave, Matlab

OS: Linux (Ubuntu, Centos), MS Windows (XP, Vista, 7, 8), MAC OsX

Software: Asreml, SamTools, GATK, VcfTools, Plink, Structure, Tassel, Admixture, Haploview, GS3, MS Office, Libre Office, GIMP, etc ...

Programming frameworks; YAML (data serialization), Apache-Spark (cloud computing), Django (web programming), development of R packages, development of bioinformatics pipelines

Database: MySql, SQLite, MS Access, Graph databases -Neo4j

Miscellaneous: LATEX, AWK, Git/GitHub, Bioinformatics pipelines, development of R packages

Publications

35 peer-reviewed papers (all in English); 40 conference papers (2 in Spanish, 1 in German, 1 in Italian; the remainder in English). See my page on Research Gate

Languages

Italian: native speaker

Spanish: fluent

English: fluent

French: good

German: good

Dutch: good

Portuguese: basic

Additional qualifications

- PADI Scuba Diving Licence (Las Herraduras, Spain, 2004)

- Sommelier licence (basic level, Todi, Italy, 2000)

- Swimming instructor licence (Perugia, Italy, 1994)

Research projects and funding

2016-2020 EU H2020: Image “Innovative Management of Genetic Resources”: Task leader
2016-2020 EU H2020: Saphir “Strengthening Animal Production and Health through the Immune Response”: WP leader
2016-2017 LegPipe “Legumes GBS Pipeline Exploration”: approved project to use remote computation and storage resources at CINECA (www.cineca.it)
2015-2018 FACCE JPI/ERA-NET: Climgen “Climate genomics for animal adaptation”: WPleader
2014-2018 EU FP7: Indigo “Investigation of Novel biomarkers and Definition of the role of the microbiome In Graves’ Orbitopathy”: WP leader
2013-2017 EU FP7: Fecund (Grant agreement n. 312097) “Optimisation of early reproductive success in dairy cattle through the definition of new trait and improved reproductive biotechnology”: Project coordinator
2013-2017 COST Action: Methagene “Large-scale methane measurements on individual ruminants for genetic evaluations”: WG leader. Organizer of the 2016 annual meeting in Padova, Italy, 12-14 October
2013-2015 Italian national project: MiRCO: “Micro-Rna in Clinical Oncology”. WP leader, statistical advisor
2013-2015 Italian national project: Diamond: “Epstein-Barr viral miRNA profiles in tumor patients”. Statistical advisor
2013 ESF Exchange Grant “Detection of selection signatures of domestication in ancestral and domestic goats”; University of Cardiff
2012-2015 EU FP7: Gene2Farm: “Next generation European system for cattle improvement and management”: Task leader
2012-2015 EU FP7: RuminOmics: “Connecting the animal genome, gastrointestinal microbiomes and nutrition to improve digestion efficiency and the environmental impacts of ruminant livestock production”: Task leader
2011–2014 EU FP7: Nextgen: “Next generation methods to preserve farm animal biodiversity by optimizing present and future breeding options”: Task leader
2011-2014 EU MC-ERG: Neutradapt: Marie-Curie ERG on the estimation of neutral and adaptive genetic variation in cattle, sheep and goats
2010–2011 EU FP7: 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”: Task leader.
2006–2009 Robustness in laying hens: national dutch project for the genetic improvement of laying hens better able to cope with changing farming environment.

Seminars (given)

2016 "The use of genotypes and phenotypes in plant & animal breeding: a few applications and perspectives", IRTA (Institut de Recerca i Tecnologia Agroalimentaries), Caldes de Montbui (Spain)
2016 "Genome-enabled predictions for classification problems and their application to animal breeding", University of Pisa (Italy)
2015 "The Nextgen EU project: domestication of small ruminants and conservation of genetic resources”, University of Pisa (Italy)
2015 "Using SNP genotypes to predict mutation carriers in cattle populations", University of Perugia (Italy)
2014 "The role of the SLITRK5 gene in the pathogenesis of displacement of the abomasum", University of Perugia (Italy) 2012 "Selección genómica para caracteres productivos y funcionales en vacuno lechero de raza Brown Swiss", INIA, Madrid (Spain)
2012 "Detection of signatures of selection in plant and animal species", University of Perugia (Italy)
2011 "Genomic selection for production and functional traits in dairy cattle", University of Perugia (Italy)
2010 "Genetic analysis of production, immunity and behaviour in laying hens", University of Perugia (Italy)

 
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