Jim
Havrilla
I am the Senior Director of Informatics at Pathnostics. Before that, I was a Product Manager at the Bioinformatics R&D division of Sema4, and before that, a Bioinformatics Scientist in Kai Wang's lab at the Children's Hospital of Philadelphia. I have a PhD in Human Genetics by way of Aaron Quinlan's lab at the University of Utah. My PhD work focused primarily on discovering constraint in human genomes and clinical variant prioritization. I have written tools for phenotypic and genomic data analysis, investigate clinical and population-scale variant data, and assist in the interpretation and standardization of electronic health record data.
Social Footprint
My professional accounts. I use my Twitter for general news and science, but my LinkedIn is more active and professionally focused. GitHub is where most of my older work is stored, though most is private. My Stack Overflow account shows questions I've answered or posted in the programming community. My Google Scholar profile is simply a place to search for my papers. Finally, I have created a blog on this website, but it is pretty sparse at the moment.
Talks
- Identifying highly constrained protein-coding regions using population-scale genetic variation. ASHG 2016
- Identifying highly constrained protein-coding regions using population-scale genetic variation. Genome Informatics 2016
- Meta-analysis of Protein Structural Alignment. Bioinformatics and Biomedicine (BIBM) 2012 (Part of the 2012 Computational Structural Bioinformatics Workshop)
Publications
Here are my publications. To my knowledge all the papers I am officially listed in are in here. Bit of a self-promotion but my first first author paper of my PhD got the cover of Nature Genetics which you can see in the next panel.
- Zhao, M.*, Havrilla, J.M.*, Fang L.*, Chen Y., Peng J., Liu C., Wu C., Sarmady M., Botas P., Isla J., Lyon G., Weng C., Wang K. Phen2Gene: rapid phenotype-driven gene prioritization for rare diseases. NAR Genomics and Bioinformatics (2020). doi:10.1093/nargab/lqaa032
- Boukas, L., Havrilla, J.M., Hickey, P.F., Quinlan, A.R., Bjornsson, H.T., Hansen, K.D. Co-expression patterns define epigenetic regulators associated with neurological dysfunction. Genome Research (2019). doi:10.1101/gr.239442.118
- Havrilla, J.M., Pedersen, B.S., Layer, R.M. & Quinlan, A.R. A map of constrained coding regions in the human genome. Nature Genetics (2018). doi:10.1038/s41588-018-0294-6
- Belyeu, J.R., Nicholas, T.J., Pedersen, B.S., Sasani, T.A., Havrilla, J.M., Kravitz, S.N., Conway, M.E., Lohman, B.K., Quinlan, A.R., Layer, R.M. SV-plaudit: A cloud-based framework for manually curating thousands of structural variants. GigaScience, giy064 (2018). doi:10.1093/gigascience/giy064
- Havrilla, J. & Saçan, A. Meta-analysis of protein structural alignment. 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops (2012). doi:10.1109/bibmw.2012.6470218
Posters
- Pathoscore: a tool for unbiased evaluation of variant pathogenicity metrics. ASHG 2018
- Pathoscore: a tool for unbiased evaluation of variant pathogenicity metrics. Genome Informatics 2018
- A map of constrained coding regions in the human genome. Biology of Genomes 2018
- A map of highly constrained coding regions in the human genome. ASHG 2017 (Reviewers Choice, Top 10%, Included in press poster walk on Big Data)
- Using the landscape of genetic variation in protein domains to improve functional consequence predictions. Biology of Genomes 2016
- Using the landscape of genetic variation in protein domains to improve functional consequence predictions. Genome Informatics 2015
- Using the landscape of genetic variation in protein domains to improve functional consequence predictions. Biology of Genomes 2015
Documentation and Data Visualization
For an example of my work in visualizing data look at the CCR Browser which I created myself.
To see an example of my code documentation visit the CCR documentation or the Phen2Gene documentation.
For a further example of data visualization I performed to compare different variant prioritization tools look at pathoscore run on ClinVar.
Curriculum Vitae
My CV can be found here.
You can contact me via my LinkedIn or through my Twitter account.Miscellaneous
Side notes about me, or fizzbuzz
Motto
Memory, comprehension, communication, motivation
Fizzbuzz (Python)
from __future__ import print_function # so it works in 2.7 and 3.5
print('\n'.join("Fizz"*(i%3==0)+"Buzz"*(i%5==0) or str(i) for i in range(1,101)))