Research Associate Professor
Department of Computer & Information Sciences
University of Delaware (UD)
Adjunct Assistant Professor
Department of Biochemistry and Molecular & Cell Biology
Georgetown University Medical Center (GUMC)
Contact
Office: 147 Ammon-Pinizzotto Biopharmaceutical Innovation Center
Mailing address:
Delaware Biotechnology Institute
590 Avenue 1743, Suite 147
Newark, DE 19713
Phone: (302) 831-3444
E-Mail: arighi@udel.edu
Education
B.S.: University of Buenos Aires, Argentina
Ph.D.: University of Buenos Aires, Argentina
Postdoctoral: National Institutes of Health, USA
Previous Positions
Research Assistant, Department of Biological Chemistry, School of Pharmacy and Biochemistry, University of Buenos Aires, Argentina (1992-1996)
Postdoctoral Fellow. Laboratory of Dr. Juan S. Bonifacino, Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, NIH, MD (2001-2005)
Research Assistant Professor, Department of Biochemistry and Molecular & Cell Biology, GUMC (2005-2009)
Research Assistant Professor. Center for Bioinformatics and Computational Biology, Department of Computer and Information Sciences, UD (2009-2012)
Honors, Professional Appointments and Activities
Honors
| 2001-2003 | PEW Trust Latin American Fellowship for the Biomedical Sciences | |
| 2003-2005 | National Institutes of Health Visiting Fellowship | |
| 2008 | Fellowship to attend Computational and Comparative Genomic Course, Cold Spring Harbor Lab | |
| 2010-2011 | Travel expenses to chair the PIR workshop at Plant and Animal Genome XVIII meeting |
Other Experience and Professional Memberships
| 2004-present | Ad hoc reviewer, scientific journals such as BMC Bioinformatics, BMC genomics, PeerJ, Proteomics, J Proteomics Bioinformatics, PloS, Nucleic Acids Research, Immunology, Faculty1000 | |
| 2010-present | Member, PIR Executive Board | |
| 2010-present | Member, Scientific and organizing committee of BioCreative series BioCreative III to VII, and organizer of text mining session at ISB 2010, 2012 and ISB 2015 | |
| 2013 | External grant reviewer, Swiss Science Foundation | |
| 2013-2014 | Course Director of BCHB521 Bioinformatics at GUMC. | |
| 2014-present | Member, Editorial Board of Database: The Journal of Biological Databases and Curation | |
| 2015-2018 | Member, Executive Board of the International Society for Biocuration (Chair in 2018) | |
| 2016 | External grant reviewer, Swiss Institute of Bioinformatics | |
| 2017-2021 | Member (Chair 2019-2021), Faculty Library Senate Committee at University of Delaware | |
| 2017 | Co-Editor, Book Protein Bioinformatics: From Protein Modifications and Networks to Proteomics. Methods in Molecular Biology 1558 (2017). | |
| 2017-present | Director of e-learning course BIOINF644 Introduction to Bioinformatics at UD | |
| 2018 | External reviewer ELIXIR French node | |
| 2018-present | Co-Chair, Text mining session (2018-2019) and text mining COSI (2020- ) at ISMB | |
| 2019-present | Member, Advisory Board for Europe PubMed Central | |
| 2019-2021 | Member, Coordinating Committee on Education at University of Delaware | |
| 2021-present | Member, Instructional Computing and Research Support Committee | |
| 2021-present | Member, Open and Affordable Teaching Materials working group | |
| 2021-present | Member, Advisory Board for HGNC |
Research interest
My general interest is in the accurate representation of protein information (e.g sequence, evolution, function, post-translational modifications, and pathways), that can be reasoned both by humans and computers, to provide the basis for hypothesis generation. I work within the framework of many international and interdisciplinary Consortia, such as UniProt (lead of curation group and text mining efforts at PIR), Protein Ontology (lead of curation team, and workshop organizer), and BioCreative (current PI of the NIH BioCreative Conference grant, and since 2009 workshop organizer, organizer of the User Interactive Text Mining track, user advisory group chair). Activities in my group include (i) database curation and bibliography mapping (UniProtKB), (ii) curation of proteoforms for the Protein Ontology, (iii) the development (in collaboration with text mining group) and evaluation of natural language processing tools to assist the researcher in retrieving information about genes, proteins and miRNAsin collaboration with Dr. Vijay Shanker, iV) bioinformatics/text mining support for other research groups
Publications
Full list of publications available here.
Current Projects
- UniProt: https://www.uniprot.org/
- BioCreative: https://biocreative.bioinformatics.udel.edu/
- iTextMine: https://research.bioinformatics.udel.edu/itextmine/integrate
- iPTMnet: https://research.bioinformatics.udel.edu/iptmnet/
- emiRIT: https://research.bioinformatics.udel.edu/emirit/
- Incorporating image-based features into biomedical document classification