Leonardo Varuzza's Site

About Me

I'm a bioinformatician working in bioinformatics support for NGS sequencers of Life Technologies. I have a graduation in Physics and a PhD on Bioinformatics, both from USP.

This page is my humble site. Instead of using some platform or hosted solution, I just decided to go in the hard way and create an ec2 instance to host this page. Actually, you can't find much stuff in this site, only a bunch of links for my presence in the web.

Bioinformatics Lecture Notes

I have been working in lectures notes for NGS analysis, specially for Ion Torrent PGM sequencer. The PDF file is available here: apostila.pdf (sorry, only in portuguese).

Other projects

During my PhD I developed the kempbasu program for testing differencial expression in Digital Gene expression Experiments like SAGE. The software is available here: KempBasu Page. I also created the simcluster program to cluster samples based on their gene expression profiles. The software is availabe at USP and at The Institute for Systems Biology.

Publications

A comparative transcriptome analysis reveals expression profiles conserved across three Eimeria spp. of domestic fowl and associated with multiple developmental stages.
Int J Parasitol. 2012 Jan;42(1):39-48. doi: 10.1016/j.ijpara.2011.10.008. Epub 2011 Nov 22. PubMed PMID: 22142560.
Novaes J, Rangel LT, Ferro M, Abe RY, Manha AP, de Mello JC, Varuzza L, Durham AM, Madeira AM, Gruber A.
Ultra-deep sequencing reveals the microRNA expression pattern of the human stomach.
PLoS One. 2010 Oct 8;5(10):e13205. doi: 10.1371/journal.pone.0013205. PubMed PMID: 20949028; PubMed Central PMCID: PMC2951895.
Ribeiro-dos-Santos Â, Khayat AS, Silva A, Alencar DO, Lobato J, Luz L, Pinheiro DG, Varuzza L, Assumpção M, Assumpção P, Santos S, Zanette DL, Silva WA Jr, Burbano R, Darnet S.
Searching for molecular markers in head and neck squamous cell carcinomas (HNSCC) by statistical and bioinformatic analysis of larynx-derived SAGE libraries.
BMC Med Genomics. 2008 Nov 11;1:56. doi: 10.1186/1755-8794-1-56. PubMed PMID: 19014460; PubMed Central PMCID: PMC2629771.
Silveira NJ, Varuzza L, Machado-Lima A, Lauretto MS, Pinheiro DG, Rodrigues RV, Severino P, Nobrega FG; Head and Neck Genome Project GENCAPO, Silva WA Jr, de B Pereira CA, Tajara EH.
Simcluster: clustering enumeration gene expression data on the simplex space.
BMC Bioinformatics. 2007 Jul 11;8:246. PubMed PMID: 17625017; PubMed Central PMCID: PMC2147035.
Vêncio RZ, Varuzza L, de B Pereira CA, Brentani H, Shmulevich I.
EGene: a configurable pipeline generation system for automated sequence analysis.
Bioinformatics. 2005 Jun 15;21(12):2812-3. Epub 2005 Apr 6. PubMed PMID: 15814554.
Durham AM, Kashiwabara AY, Matsunaga FT, Ahagon PH, Rainone F, Varuzza L, Gruber A.