Cecilia ArighiCecilia Arighi, Ph.D.


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: 205A Delaware Biotechnology Institute

Mailing address:
Delaware Biotechnology Institute
15 Innovation Way, Room 205
University of Delaware
Newark, DE 19711

Phone: (302) 831-3444
FAX: (302) 831-4841
E-Mail: arighi@dbi.udel.edu
Web Site:Protein Information Resource

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)

Honors (in US)

2001-2003 PEW  Trust Latin American Fellowship for the Biomedical Sciences
2003-2005 National Institutes of Health Visiting Fellowship
2008 Fellowship for Computational and Comparative Genomic Course at Cold Spring Harbor Laboratory

Service (in US)

2004- Reviewer for BMC Bioinformatics, BMC genomics, and ISMB conference papers.
2007-Present Organizer of the Protein Ontology Workshops and the Protein Ontology Annotation Jamboree.
2008 Thesis committee member for Linshan Yuan, M.S. in Biostatistics (GUMC)
2009-Present Member of the International Society for Biocurators.
2010 Member of the PIR executive committee
2010 Organizer of the BioCreative III workshop.
2010 Organizer of the PIR workshop at the Plant and Animal Genome meeting
2010 Organizer of the Skate Genome Annotation workshop

Teaching (in US)

2005-2009 Lecturer in graduate level bioinformatic-related courses at GUMC: TBIO-530 and BCHB521
2006-Present Proteomics Workshop, FAES, NIH. Instructor.
2008-Present Bioinformatics Workshop. FAES, NIH. Instructor.

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. My activities include (i) database manual curation (UniProtKB/Swiss-Prot), (ii) protein family classification based on evolution (PIRSF), (iii) the development (in collaboration with text mining group) and evaluation of natural language processing tools to assist the biologists in retrieving information about proteins, (iv) the development and head of curation team of the protein ontology (PRO).

Selected Publications

* Co-first authorship

  1. Cecilia Arighi, Amy Siu, Catalina O Tudor, Jules Nchoutmboube, Cathy H Wu, and K Vijay-Shanker, eFIP: A Tool for Mining Functional Impact of Phosphorylation from Literature, Bioinformatics for Comparative Proteomics. A volume in Series Methods in Molecular Biology. Humana Press. (in press).
  2. Cecilia Arighi. A Tutorial on Protein Ontology Resources for Proteomic Studies. Bioinformatics for Comparative Proteomics. A volume in Series Methods in Molecular Biology. Humana Press. (in press).
  3. Anastasia N. Nikolskaya, Arighi C., Hongzhan Huang, Winona C. Barker and Cathy H. Wu PIRSF Family Classification System for Protein Functional and Evolutionary Analysis. Evolutionary Bioinformatics Online 2, 209-221 (2006).
  4. Natale DA, Arighi CN, Barker W, Blake J, Chang T, Hu ZZ, Liu H, Smith B, Wu CH. Framework for a Protein Ontology. Proceedings of ACM First International Workshop on Text Mining in Bioinformatics, TMBIO 2006.
  5. Natale DA, Arighi CN*, Barker W, Blake J, Chang T, Hu ZZ, Liu H, Smith B, Wu CH. Framework for a Protein Ontology. BMC Bioinformatics 8(Suppl 9):S1, 2007.
  6. Huang H, Hu ZZ, Arighi C, Wu CH. Integration of Bioinformatics Resources for Functional Analysis of Gene Expression and Proteomic Data. Frontiers in Biosciences 12, 5071-5088, 2007.
  7. UniProt Consortium*. The Universal Protein Resource (UniProt). Nucleic Acids Res. 36(Database issue):D190-195 (2008).
  8. Drabkin, H.J., Arighi, C.N., Wu, C. H., Blake, J.A. Functional Annotation of Protein Isoforms and Modified Forms. BioComp2008.
  9. Cecilia Arighi, Hongfang Liu, Darren Natale, Winona Barker, Harold Drabkin, Zhangzhi Hu, Judith Blake, Barry Smith and Cathy Wu, "TGF-beta Signaling Proteins and the Protein Ontology", Bio-Ontologies 2008, Special Interest Groups meeting at ISMB 2008, Booklet pg.25-29.
  10. UniProt Consortium*. The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res. 37(Database issue):D169-174.
  11. Anna M. Masci, Cecilia N. Arighi, Alexander D. Diehl, Anne E. Lieberman, Chris Mungall, Richard H. Scheuermann, Barry Smith, and Lindsay G. Cowell, “An improved ontological representation of dendritic cells as a paradigm for all cell types”, 2009 BMC Bioinformatics 10:70.
  12. Cecilia Arighi, Hongfang Liu, Darren Natale, Winona Barker, Harold Drabkin, Zhangzhi Hu, Judith Blake, Barry Smith and Cathy Wu, "TGF-beta Signaling Proteins and the Protein Ontology", 2009 BMC Bioinformatics 10 Suppl 5:S3.

 


 

Center for Bioinformatics & Computational Biology • 15 Innovation Way • Newark, DE 19711 • USA
Phone: 302-831-0161 • E-mail: bioinformatics@udel.edu

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