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Paolo Amedeo, PhD is a staff scientist at the J. Craig Venter Institute leading the Viral Bioinformatics Group, providing informatics support for viral sequencing, genomic assembly, annotation and submission to public repository, and helping both JCVI Faculty and external collaborators with custom analysis of viral genomics datasets. Prior to joining the Viral Bioinformatics group, Dr. Amedeo led the Eukaryotic Bioinformatics group.

Before joining TIGR/JCVI in 2003, Dr. Amedeo worked as Bioinformatics Specialist at the Torrey Mesa Research Institute of Syngenta, in the Fungal Group, Plant Health division. He received his PhD in Botany and Molecular Biology from the University of Basel (CH) and his Master in Molecular Biology from the University of Pavia (IT).

Research Priorities

Improve annotation tools for viral genomes.

  • Rewriting JCVI Viral Genome ORF Reader (VIGOR) to improve its strength and flexibility.
  • Improving JCVI Deep Sequencing Analysis pipeline to detect and possibly phase statistically significant sequence variations in the sample.
  • Creating tools to automate the selection of representative sequences from multi-sequence alignments.

Streamlining the high-throughput processing of viral samples.

  • Improving tools to demultiplex raw sequences and automating reference-bases assemblies.
  • Increasing the degree of automation in the annotation and GenBank submission pipelines.

Developing tools to help improving the ability of isolating viral sequences from complex biological samples.

  • Creating a tool for aiding on the design of viral sequences pull-down probes.
  • Improving JCVI primer creation pipeline.


Select Publications

Identification of Dezidougou Virus in a DAK AR 41524 Zika Virus Stock.
Genome announcements. 2017-07-27; 5.30:
PMID: 28751385
New assembly, reannotation and analysis of the Entamoeba histolytica genome reveal new genomic features and protein content information.
PLoS neglected tropical diseases. 2010-06-15; 4.6: e716.
PMID: 20559563
Activation of an AP1-like transcription factor of the maize pathogen Cochliobolus heterostrophus in response to oxidative stress and plant signals.
Eukaryotic cell. 2005-02-01; 4.2: 443-54.
PMID: 15701806
Endogenous targets of transcriptional gene silencing in Arabidopsis.
The Plant cell. 2000-07-01; 12.7: 1165-78.
PMID: 10899982
Disruption of the plant gene MOM releases transcriptional silencing of methylated genes.
Nature. 2000-05-11; 405.6783: 203-6.
PMID: 10821279
High-efficiency transformation of Arabidopsis thaliana with a selectable marker gene regulated by the T-DNA 1' promoter.
The Plant journal : for cell and molecular biology. 1997-10-01; 12.4: 945-8.
PMID: 9375405