Paul Cantalupo
Systems Programmer at University of Pittsburgh
Greater Pittsburgh Region United States
Summary
👤
Senior🎓
Top SchoolPaul Cantalupo is a systems programmer and computational virology researcher with over two decades at the University of Pittsburgh, where he built the Pickaxe pipeline to detect and assemble known and novel viruses from NGS data. His work has led to key discoveries—including linking HPV to bladder cancer and identifying HeLa contamination artifacts—and contributed complete viral genomes from environmental samples like sewage. Combining deep wet-lab experience in microbiology with strong bioinformatics and Perl/R skills, he routinely performs RNA-Seq analyses and develops robust, tested tools (notably contributing bug fixes and Infernal 1.1 support to BioPerl). Paul’s research focuses on mining the vast “dark matter” of metagenomes to reveal novel viral genomes and their impact on host regulation in cancer.
13 years of coding experience
Masters, Information Science, QPA 3.9, Masters, Information Science, QPA 3.9 at University of Pittsburgh
English
Stackoverflow
2,218reputation
123kreached
98answers
12questions
Github Skills (13)
bioinformatics10
bioperl10
debug10
perl10
testing10
git6
http-header6
macos6
alias6
wget6
github6
r6
user-agent6
Programming languages (16)
Github contributions (5)
bioperl/bioperl-live
Oct 2012 - Dec 2017
Core BioPerl 1.x code
Role in this project:
Back-end Developer
Back-end DeveloperContributions:31 commits, 2 PRs, 9 pushes in 5 years 2 months
Contributions summary:Paul primarily contributed to bug fixes and enhancements within the BioPerl code base, focusing on improving the accuracy of calculations, addressing parsing issues, and adding unit tests. Their work involved modifications to various Perl modules, including those related to sequence searching (hmmer2 and infernal) and sequence manipulation (Bio::SeqUtils). They also implemented support for Infernal version 1.1 and addressed multiple issues reported by the community.
bioperlpdb-filesbiologytoolkitbioinformatics
pcantalupo/examples
Jul 2015 - Aug 2020
Contributions:47 pushes, 3 branches in 5 years 1 month
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