Shareef Dabdoub
Assistant Professor at University of Iowa
Iowa City, Iowa, United States
Summary
🤩
Rockstar🎓
Top SchoolShareef Dabdoub is an Assistant Professor in Biostatistics and Computational Biology at the University of Iowa with 16 years of experience at the intersection of microbial ecology, multi-omics, and data visualization. He combines deep wet-lab and sequencing expertise with software engineering skills, developing widely used open-source tools such as PhyloToAST, kraken-biom, PyMGRAST, FIND, and ProkaryMetrics to advance species-level and phylogenetic analyses. His research uniquely links human oral and peri-implant microbiomes to environmental exposures like vaping, and he was the first to show that peri-implant communities are distinct from adjacent periodontal microbiota. Trained as a computational biophysicist (PhD) and experienced in building interactive 3D visualization and robust analysis pipelines, he bridges computational method development with practical clinical microbiology questions. Colleagues value his ability to translate complex multi-dimensional datasets into reproducible, user-friendly tools that enable new biological insights.
16 years of coding experience
16 years of employment as a software developer
Master of Science (M.S.) a.b.t., Computer Science, Master of Science (M.S.) a.b.t., Computer Science at University of CincinnatiDoctor of Philosophy (PhD), Biophysics (spec. Computational Biology), Doctor of Philosophy (PhD), Biophysics (spec. Computational Biology) at The Ohio State University
Github Skills (125)
nmf10
genomes10
kraken10
microbiome10
refined10
rna-seq10
biodiversity10
metagenomics10
bioinformatics10
population-genetics10
comparative-genomics10
science9
taxonomy9
seq9
kallisto9
Programming languages (9)
Github contributions (5)
smdabdoub/kraken-biom
Apr 2016 - Mar 2022
Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
Contributions:3 releases, 1 review, 49 commits in 6 years
biom-formatjhukrakenedu
smdabdoub/ProkaryMetrics
Jul 2011 - Apr 2012
Contributions:56 commits in 8 months
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