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About

Biographies

Paolo Amedeo, Ph.D.
Lead Bioinformatics Engineer

Research Interests and Accomplishments

Paolo Amedeo, Ph.D. is a Lead Bioinformatics Engineer at the J. Craig Venter Institute (JCVI) presently involved in developing a pipeline to support the annotation and GenBank submission of viral genomes. His scientific interests span from mycology to gene silencing and virology.

Dr. Amedeo joined JCVI through one of its legacy organizations, TIGR, as a Bioinformatics Analyst working on the annotation of Cryptococcus neoformans, a basidiomycetous fungus known for being an opportunistic human pathogen responsible for severe lung infections and meningitis. It is also the first basidiomycetes to be sequenced and annotated. Additionally, he collaborated in the annotation and genomic analysis of Entamoeba histolytica. Following this work he joined the Bioinformatics Core Team as a Bioinformatics Engineer. In that position he contributed to many eukaryotic genomic sequencing projects (mostly fungi and insects) by improving the annotation pipelines, running custom analysis, and interacting with collaborators. Subsequently, he managed a team of bioinformatics engineers supporting all eukaryotic genomic projects.

He obtained a Master’s degree in Molecular Biology from the University of Pavia, IT in 1995 and a Ph.D. in Plant molecular Biology/Botany from the University of Basel, CH in 2000. From 2000 through 2003 Dr. Amedeo worked at the Torrye Mesa Research Institute (Syngenta) in San Diego, CA first as Posdoctoral Associate, then as Bioinformatics Specialist, working on the genomes of plant-pathogenic fungi.

Select Publications

Lorenzi, H. A., Puiu, D., et al.
New Assembly, Reannotation and Analysis of the Entamoeba histolytica Genome Reveal New Genomic Features and Protein Content Information

PLoS Negl Trop Dis. 2010 Jun 01; 4(6): e716.[more]

Fedorova, N. D., Khaldi, N., et al.
Genomic Islands In the Pathogenic Filamentous Fungus Aspergillus fumigatus

PLoS Genet. 2008 Apr 01; 4(4): e1000046.[more]

Nene, V., Wortman, J. R., et al.
Genome Sequence of Aedes Aegypti, a Major Arbovirus Vector

Science. 2007 May 17; 316: 1718-1723.[more]

Rokas, A., Payne, G., et al.
What Can Comparative Genomics Tell Us About Species Concepts In the Genus Aspergillus?

Stud Mycol. 2007 Jan 01; 59: 11-7.[more]

Loftus, B. J., Fung, E., et al.
The Genome of the Basidiomycetous Yeast and Human Pathogen Cryptococcus neoformans

Science. 2005 Feb 25; 307(5713): 1321-4.[more]

Loftus, B., Anderson, I., et al.
The Genome of the Protist Parasite Entamoeba histolytica

Nature. 2005 Feb 24; 433(7028): 865-8.[more]

Lev, S., Hadar, R., et al.
Activation of an AP1-like Transcription Factor of the Maize Pathogen Cochliobolus Heterostrophus In Response to Oxidative Stress and Plant Signals

Eukaryot Cell. 2005 Feb 01; 4(2): 443-54.[more]

Steimer, A., Amedeo, P., et al.
Endogenous Targets of Transcriptional Gene Silencing In Arabidopsis

Plant Cell. 2000 Jul 01; 12(7): 1165-78.[more]

Amedeo, P., Habu, Y., et al.
Disruption of the Plant Gene MOM Releases Transcriptional Silencing of Methylated Genes

Nature. 2000 May 11; 405(6783): 203-6.[more]

Mengiste, T., Amedeo, P., et al.
High-efficiency Transformation of Arabidopsis thaliana With a Selectable Marker Gene Regulated by the T-DNA 1' Promoter

Plant J. 1997 Oct 01; 12(4): 945-8.[more]