Hi, I’m
Clinton Cario
Yonkers,NY
Summary
Experienced bioinformatics professional with strong background in data analysis, automation, and team leadership. Proficient in managing advanced data analysis initiatives, solving complex problems through technology solutions, and creating scalable workflows using Docker, Nextflow, and Git.
Overview
17
years of professional experience
Work History
Stanford UniversityPalo Alto, CA
Senior Research Engineer
05.2023 - Current
Job overview
Enhanced lab data analysis by developing scalable and reproducible workflows for statistical genetics and genetic epidemiology.
- Led major cloud-based screening project focused on repeat expansion disorders that identified evidence of under-diagnosis within a cohort of 250K participants from the 'All of Us' research program.
- Provided bioinformatics consultation for high-impact publications, including contributions to Nature Genetics, by playing key role in groundbreaking research and facilitating interdisciplinary collaboration.
- Instructed graduate-level course on functional variant analysis, leveraging deep expertise and commitment to mentoring and developing future talent.
Avail BioSan Francisco, CA
CTO | Cofounder | Board Member
11.2018 - Current
Job overview
Played integral role in accelerating growth and fostering innovation within immunotherapy sector through co-founding, managing, and directing venture-backed company.
- Lead technical team of 5 within collaborative work environment to drive team toward achieving key project milestones.
- Designed and executed assay and analysis protocols for human research study involving 500+ patients.
- Utilized NGS technology to create tailored assay for high-throughput screening of over 500K antibody targets at once, optimizing sequencing efficiency and maximizing throughput on NovaSeq platform.
- Developed automation scripts utilizing OpenTrons robotic liquid handling technology to optimize lab productivity, resulting in weekly saving of 15 hours in technician time.
- Streamlined AWS cloud infrastructure to ensure effective delivery of high-performance computing resources for data analyses and applications.
- Authored grants and collaborated with academic partners to co-author research publications.
Independent Consulting
Consultant
09.2017 - Current
Job overview
Utilized bioinformatics expertise to evaluate existing systems and processes for efficiency improvements based on industry best practices.
- Optimized cloud infrastructure to enhance performance and security of digital platforms.
- Created user-friendly application as a Full Stack Developer for Y combinator demo day.
- Implemented PRS statistical genetics algorithms to enhance precision of genetic data analysis.
University of CaliforniaSan Francisco, CA
PhD Graduate Student
09.2013 - 10.2018
Job overview
Managed all aspects of comprehensive cfDNA study, from patient sample collection to NGS library preparation and variant detection.
- Initiated modular workflows using Nextflow for NGS data analysis in HPC environment, with focus on variant detection.
- Engineered 10-node MemSQL cluster database to optimize data storage, simplify retrieval processes, and maintain data integrity.
- Developed innovative machine-learning framework 'orchid' to advance cancer mutation analysis and contribute to novel research in tissue-of-origin prediction, handling hundreds of millions of datapoints.
- Designed precision-enhancing prostate cancer panels for ultra-sensitive variant detection in cfDNA, achieving detection limit of 0.1% VAF.
University of PittsburghPittsburgh, PA
System Programmer III
09.2011 - 08.2013
Job overview
- Built and maintained hardware for Apache web server.
- Developed web application that facilitated phenotype ontology selection and automated genome-wide association studies (GWAS) for murine models.
University of PittsburghPittsburgh, PA
Research Technician III
01.2008 - 01.2011
Job overview
- Modified zebrafish proteins by introducing new mutations to investigate functional changes and gain insights into protein behavior.
- Established and managed MySQL database for efficient and organized management of zebrafish colony.
- Developed LSRtrack and LSRanalyze, innovative software tools designed for advanced zebrafish image analysis, which improved data accuracy and research efficiency, resulting in multiple publications.
Education
University of CaliforniaSan Francisco, CA
Ph.D. from Bioinformatics
09-2018
Johns Hopkins UniversityBaltimore, MD
Master of Science from Bioinformatics
Pennsylvania State UniversityState College, PA
Bachelor of Science from Biochemistry And Molecular Biology
Pennsylvania State UniversityState College, PA
Bachelor of Science from Computer Science
Skills
- Scalable Workflow Development
- Cloud Infrastructure Optimization
- Bioinformatics Consultation
- Team Leadership
- NGS-Based Assay Development
- Data Quality Control
- Analytical Workflows
- Automation & Efficiency Improvements
- Full Stack Development
- Statistical Genetics Algorithms
- Machine Learning Frameworks
- Database Engineering
- Research Study Design
- Grant Writing & Publication
- Data Integration
- Software Development Lifecycle (SDLC)
Timeline
Senior Research Engineer
Stanford University
05.2023 - Current
CTO | Cofounder | Board Member
Avail Bio
11.2018 - Current
Consultant
Independent Consulting
09.2017 - Current
PhD Graduate Student
University of California
09.2013 - 10.2018
System Programmer III
University of Pittsburgh
09.2011 - 08.2013
Research Technician III
University of Pittsburgh
01.2008 - 01.2011
University of California
Ph.D. from Bioinformatics
Johns Hopkins University
Master of Science from Bioinformatics
Pennsylvania State University
Bachelor of Science from Biochemistry And Molecular Biology
Pennsylvania State University
Bachelor of Science from Computer Science
Coreproficiencies
- Scalable Workflow Development
- Cloud Infrastructure Optimization
- Bioinformatics Consultation
- Team Leadership
- NGS-Based Assay Development
- Data Quality Control
- Analytical Workflows
- Automation & Efficiency Improvements
- Full Stack Development
- Statistical Genetics Algorithms
- Machine Learning Frameworks
- Database Engineering
- Research Study Design
- Grant Writing & Publication
- Data Integration
- Software Development Lifecycle (SDLC)
Presentations
- UCSF Prostate Cancer Tissue Board, 2017
- Liquid Biopsy Summit, 2016
- NIH Transforming Epidemiology through Advanced Methods, 2015
- American Association for Cancer Research, 2018
- UCSF iPQB Program Retreat, 2017
- UCSF Prostate Cancer Symposium, 2017
- UCSF Quantitative Biosciences Consortium Retreat, 2016
- American Society for Human Genetics, 2016
- UCSF Institute of Human Genetics Symposium, 2015
- BioIT Cloud Computing Conference, 2012
- Pittsburgh International Lung Conference, 2012
- Northeast Ecology and Evolution Conference (NEEC), 2005
Awards
- Amazon AWS for Research Awardee 2016
- Microsoft Azure Cloud Compute for Research Awardee 2016
- Best TA Award 2015
- Research Experiences for Undergraduates (REU) Fellowship 2006
- Bausch and Lomb Science Award 2001
- Pennsylvania Governor’s School for Information Technology 2000
Publications
- Cell-Free DNA Detection of Tumor Mutations in Heterogeneous, Localized Prostate Cancer via Targeted, Multiregion Sequencing, Chen E, Cario CL, Leong L, et al., JCO Precis Oncol, 2021-04-27, 10.1200/PO.20.00428, 34250416, PMC8232833
- Cell-free DNA concentration and fragment size as a biomarker for prostate cancer, Chen E, Cario CL, Leong L, et al., Sci Rep, 2021-03-03, 10.1038/s41598-021-84507-z, 33658587, PMC7930042
- A Large-Scale Association Study Detects Novel Rare Variants, Risk Genes, Functional Elements, and Polygenic Architecture of Prostate Cancer Susceptibility, Emami NC, Cavazos TB, Rashkin SR, et al., Cancer Res, 2021-04-01, 10.1158/0008-5472.CAN-20-2635, 33293427, PMC8137514
- A machine learning approach to optimizing cell-free DNA sequencing panels: with an application to prostate cancer, Cario CL, Chen E, Leong L, et al., BMC Cancer, 2020-08-28, 10.1186/s12885-020-07318-x, 32859160, PMC7456018
- Samasy: an automated system for sample selection and robotic transfer, Cario CL, Witte JS, Biotechniques, 2018-12-01, 10.2144/btn-2018-0090, 30477330
- Orchid: A machine learning framework for cancer mutations, Cario CL, Witte JS, Bioinformatics, 2017-11-02, 10.1093/bioinformatics/btx709
- An open-source technique to analyze optokinetic reflex responses in larval zebrafish: validation for developmental and chemical biology applications, Scheetz SD, Shao E, Zhou Y, et al., J Neurosci Methods, 2017-10-14, 10.1016/j.jneumeth.2017.10.012
- Mouse genome-wide association study identifies polymorphisms on chromosomes 4, 11, and 15 for age-related cardiac fibrosis, Li Q, Berndt A, Sundberg BA, et al., Mamm Genome, 2016-06-01, 10.1007/s00335-016-9634-y, 27126641
- Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting, Mavor D, Barlow K, Thompson S, et al., Elife, 2016-04-25, 10.7554/eLife.15802, 27111525
- A large multiethnic genome-wide association study of prostate cancer identifies novel risk variants and substantial ethnic differences, Hoffmann TJ, Van Den Eeden SK, Sakoda LC, et al., Cancer Discov, 2015-08-01, 10.1158/2159-8290.CD-15-0315, 26034056
- Quantification of larval zebrafish motor function in multiwell plates using open-source MATLAB applications, Zhou Y, Cattley RT, Cario CL, et al., Nat Protoc, 2014-07-01, 10.1038/nprot.2014.094, 24901738
- Early gene expression differences in inbred mouse strains with susceptibility to pulmonary adenomas, Stearns TM, Cario CL, Savage HS, et al., Exp Mol Pathol, 2012-09-28, 10.1016/j.yexmp.2012.09.015, 23026400
- A major X-linked locus affects kidney function in mice, Leduc MS, Savage HS, Stearns TM, et al., Mol Genet Genomics, 2012-09-26, 10.1007/s00335-016-9634-y, 23011808
- Identification of fat4 and tsc22d1 as novel candidate genes for pulmonary adenomas, Berndt A, Cario CL, Silva KA, et al., Cancer Res, 2011-09-01, 10.1158/0008-5472.CAN-11-1411, 21764761, PMC3165088
- Evaluation of spontaneous propulsive movement as a screening tool to detect rescue of Parkinsonism phenotypes in zebrafish models, Farrell TC, Cario CL, Milanese C, et al., Neurobiol Dis, 2011-10-01, 10.1016/j.nbd.2011.06.006, 21669287, PMC3153634
- Automated measurement of zebrafish larval movement, Cario CL, Farrell TC, Milanese C, et al., J Physiol, 2011-08-01, 10.1113/jphysiol.2011.214155, 21646414, PMC3171879
Coreproficiencies
- Scalable Workflow Development
- Cloud Infrastructure Optimization
- Bioinformatics Consultation
- Team Leadership
- NGS-Based Assay Development
- Data Quality Control
- Analytical Workflows
- Automation & Efficiency Improvements
- Full Stack Development
- Statistical Genetics Algorithms
- Machine Learning Frameworks
- Database Engineering
- Research Study Design
- Grant Writing & Publication
- Data Integration
- Software Development Lifecycle (SDLC)
Presentations
- UCSF Prostate Cancer Tissue Board, 2017
- Liquid Biopsy Summit, 2016
- NIH Transforming Epidemiology through Advanced Methods, 2015
- American Association for Cancer Research, 2018
- UCSF iPQB Program Retreat, 2017
- UCSF Prostate Cancer Symposium, 2017
- UCSF Quantitative Biosciences Consortium Retreat, 2016
- American Society for Human Genetics, 2016
- UCSF Institute of Human Genetics Symposium, 2015
- BioIT Cloud Computing Conference, 2012
- Pittsburgh International Lung Conference, 2012
- Northeast Ecology and Evolution Conference (NEEC), 2005
Awards
- Amazon AWS for Research Awardee 2016
- Microsoft Azure Cloud Compute for Research Awardee 2016
- Best TA Award 2015
- Research Experiences for Undergraduates (REU) Fellowship 2006
- Bausch and Lomb Science Award 2001
- Pennsylvania Governor’s School for Information Technology 2000
Publications
- Cell-Free DNA Detection of Tumor Mutations in Heterogeneous, Localized Prostate Cancer via Targeted, Multiregion Sequencing, Chen E, Cario CL, Leong L, et al., JCO Precis Oncol, 2021-04-27, 10.1200/PO.20.00428, 34250416, PMC8232833
- Cell-free DNA concentration and fragment size as a biomarker for prostate cancer, Chen E, Cario CL, Leong L, et al., Sci Rep, 2021-03-03, 10.1038/s41598-021-84507-z, 33658587, PMC7930042
- A Large-Scale Association Study Detects Novel Rare Variants, Risk Genes, Functional Elements, and Polygenic Architecture of Prostate Cancer Susceptibility, Emami NC, Cavazos TB, Rashkin SR, et al., Cancer Res, 2021-04-01, 10.1158/0008-5472.CAN-20-2635, 33293427, PMC8137514
- A machine learning approach to optimizing cell-free DNA sequencing panels: with an application to prostate cancer, Cario CL, Chen E, Leong L, et al., BMC Cancer, 2020-08-28, 10.1186/s12885-020-07318-x, 32859160, PMC7456018
- Samasy: an automated system for sample selection and robotic transfer, Cario CL, Witte JS, Biotechniques, 2018-12-01, 10.2144/btn-2018-0090, 30477330
- Orchid: A machine learning framework for cancer mutations, Cario CL, Witte JS, Bioinformatics, 2017-11-02, 10.1093/bioinformatics/btx709
- An open-source technique to analyze optokinetic reflex responses in larval zebrafish: validation for developmental and chemical biology applications, Scheetz SD, Shao E, Zhou Y, et al., J Neurosci Methods, 2017-10-14, 10.1016/j.jneumeth.2017.10.012
- Mouse genome-wide association study identifies polymorphisms on chromosomes 4, 11, and 15 for age-related cardiac fibrosis, Li Q, Berndt A, Sundberg BA, et al., Mamm Genome, 2016-06-01, 10.1007/s00335-016-9634-y, 27126641
- Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting, Mavor D, Barlow K, Thompson S, et al., Elife, 2016-04-25, 10.7554/eLife.15802, 27111525
- A large multiethnic genome-wide association study of prostate cancer identifies novel risk variants and substantial ethnic differences, Hoffmann TJ, Van Den Eeden SK, Sakoda LC, et al., Cancer Discov, 2015-08-01, 10.1158/2159-8290.CD-15-0315, 26034056
- Quantification of larval zebrafish motor function in multiwell plates using open-source MATLAB applications, Zhou Y, Cattley RT, Cario CL, et al., Nat Protoc, 2014-07-01, 10.1038/nprot.2014.094, 24901738
- Early gene expression differences in inbred mouse strains with susceptibility to pulmonary adenomas, Stearns TM, Cario CL, Savage HS, et al., Exp Mol Pathol, 2012-09-28, 10.1016/j.yexmp.2012.09.015, 23026400
- A major X-linked locus affects kidney function in mice, Leduc MS, Savage HS, Stearns TM, et al., Mol Genet Genomics, 2012-09-26, 10.1007/s00335-016-9634-y, 23011808
- Identification of fat4 and tsc22d1 as novel candidate genes for pulmonary adenomas, Berndt A, Cario CL, Silva KA, et al., Cancer Res, 2011-09-01, 10.1158/0008-5472.CAN-11-1411, 21764761, PMC3165088
- Evaluation of spontaneous propulsive movement as a screening tool to detect rescue of Parkinsonism phenotypes in zebrafish models, Farrell TC, Cario CL, Milanese C, et al., Neurobiol Dis, 2011-10-01, 10.1016/j.nbd.2011.06.006, 21669287, PMC3153634
- Automated measurement of zebrafish larval movement, Cario CL, Farrell TC, Milanese C, et al., J Physiol, 2011-08-01, 10.1113/jphysiol.2011.214155, 21646414, PMC3171879
Publications
- Genome-wide association study of prostate-specific antigen levels in 392,522 men identifies new loci and improves cross-ancestry prediction. Hoffmann TJ, Graff RE, Madduri RK, et al. Preprint. medRxiv. 2023;2023.10.27.23297676. Published 2023 Oct 30. doi:10.1101/2023.10.27.23297676
- Cell-Free DNA Detection of Tumor Mutations in Heterogeneous, Localized Prostate Cancer via Targeted, Multiregion Sequencing, Chen E, Cario CL, Leong L, et al., JCO Precis Oncol, 2021-04-27, 10.1200/PO.20.00428, 34250416, PMC8232833
- Cell-free DNA concentration and fragment size as a biomarker for prostate cancer, Chen E, Cario CL, Leong L, et al., Sci Rep, 2021-03-03, 10.1038/s41598-021-84507-z, 33658587, PMC7930042
- A Large-Scale Association Study Detects Novel Rare Variants, Risk Genes, Functional Elements, and Polygenic Architecture of Prostate Cancer Susceptibility, Emami NC, Cavazos TB, Rashkin SR, et al., Cancer Res, 2021-04-01, 10.1158/0008-5472.CAN-20-2635, 33293427, PMC8137514
- A machine learning approach to optimizing cell-free DNA sequencing panels: with an application to prostate cancer, Cario CL, Chen E, Leong L, et al., BMC Cancer, 2020-08-28, 10.1186/s12885-020-07318-x, 32859160, PMC7456018
- Samasy: an automated system for sample selection and robotic transfer, Cario CL, Witte JS, Biotechniques, 2018-12-01, 10.2144/btn-2018-0090, 30477330
- Orchid: A machine learning framework for cancer mutations, Cario CL, Witte JS, Bioinformatics, 2017-11-02, 10.1093/bioinformatics/btx709
- An open-source technique to analyze optokinetic reflex responses in larval zebrafish: validation for developmental and chemical biology applications, Scheetz SD, Shao E, Zhou Y, et al., J Neurosci Methods, 2017-10-14, 10.1016/j.jneumeth.2017.10.012
- Mouse genome-wide association study identifies polymorphisms on chromosomes 4, 11, and 15 for age-related cardiac fibrosis, Li Q, Berndt A, Sundberg BA, et al., Mamm Genome, 2016-06-01, 10.1007/s00335-016-9634-y, 27126641
- Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting, Mavor D, Barlow K, Thompson S, et al., Elife, 2016-04-25, 10.7554/eLife.15802, 27111525
- A large multiethnic genome-wide association study of prostate cancer identifies novel risk variants and substantial ethnic differences, Hoffmann TJ, Van Den Eeden SK, Sakoda LC, et al., Cancer Discov, 2015-08-01, 10.1158/2159-8290.CD-15-0315, 26034056
- Quantification of larval zebrafish motor function in multiwell plates using open-source MATLAB applications, Zhou Y, Cattley RT, Cario CL, et al., Nat Protoc, 2014-07-01, 10.1038/nprot.2014.094, 24901738
- Early gene expression differences in inbred mouse strains with susceptibility to pulmonary adenomas, Stearns TM, Cario CL, Savage HS, et al., Exp Mol Pathol, 2012-09-28, 10.1016/j.yexmp.2012.09.015, 23026400
- A major X-linked locus affects kidney function in mice, Leduc MS, Savage HS, Stearns TM, et al., Mol Genet Genomics, 2012-09-26, 10.1007/s00335-016-9634-y, 23011808
- Identification of fat4 and tsc22d1 as novel candidate genes for pulmonary adenomas, Berndt A, Cario CL, Silva KA, et al., Cancer Res, 2011-09-01, 10.1158/0008-5472.CAN-11-1411, 21764761, PMC3165088
- Evaluation of spontaneous propulsive movement as a screening tool to detect rescue of Parkinsonism phenotypes in zebrafish models, Farrell TC, Cario CL, Milanese C, et al., Neurobiol Dis, 2011-10-01, 10.1016/j.nbd.2011.06.006, 21669287, PMC3153634
- Automated measurement of zebrafish larval movement, Cario CL, Farrell TC, Milanese C, et al., J Physiol, 2011-08-01, 10.1113/jphysiol.2011.214155, 21646414, PMC3171879
Awards
- Amazon AWS for Research Awardee 2016
- Microsoft Azure Cloud Compute for Research Awardee 2016
- Best TA Award 2015
- Research Experiences for Undergraduates (REU) Fellowship 2006
- Bausch and Lomb Science Award 2001
- Pennsylvania Governor’s School for Information Technology 2000
Presentations
- UCSF Prostate Cancer Tissue Board, 2017
- Liquid Biopsy Summit, 2016
- NIH Transforming Epidemiology through Advanced Methods, 2015
- American Association for Cancer Research, 2018
- UCSF iPQB Program Retreat, 2017
- UCSF Prostate Cancer Symposium, 2017
- UCSF Quantitative Biosciences Consortium Retreat, 2016
- American Society for Human Genetics, 2016
- UCSF Institute of Human Genetics Symposium, 2015
- BioIT Cloud Computing Conference, 2012
- Pittsburgh International Lung Conference, 2012
- Northeast Ecology and Evolution Conference (NEEC), 2005
Computer Language Experience
- Python
- Nextflow
- R
- Bash
- Julia
- Ruby
- C++
- Matlab
- Perl
- Ruby on Rails
- HTML/CSS/JS
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