Blake Hummer
Scientist | Bioinformatician | Programmer
Cell and Molecular Biology Ph.D. with over 8 years of research experience in neuroscience, genetics, cell biology, and biochemistry. Skilled in assay development, cell line and protein engineering, synthetic biology, and Next Generation Sequencing. Highly passionate about many fields in science and currently developing and honing skills related to computer and data science, bioinformatics, and programming.
I currently work at Bio-Rad Laboratories with a focus on digital biology platforms and applications, primarily droplet digital PCR. Additionally, I provide support in oncology diagnostics and generating programs to automate the design process.
Featured Projects
View selected projects below. More information can be found at my Github page.
Soma Aptamer Analysis Package
An R software package to streamline Somalogic aptamer proteomic analysis. Still a very much ongoing effort.
View project
Primer Designer
A shell program to automate primer design for use in NGS, ddPCR, or RT-PCR. It is predicated on Primer3 and Bedtools.
View project
WaterPlotR
R package to create waterfall plots to visualize target basepair coverage of an NGS sequencing panel.
View projectWork Experience
Scientist - Digital Biology
Bio-Rad Laboratories, Inc.
September 2022 - Present
Scientist with a focus on support of the ddPCR platform and associated applications.
- Design of Minimal Residual Disease oncology diagnostics.
- Develop programs and software to automate diagnostic assay design.
- Create technical documentation for support of ddPCR instruments, optics systems, and assay multiplexing.
- Perform ddPCR assays for assay validation or application testing for customers.
Chief Data Scientist
Dupuytren's Research Group
September 2022 - Present
Data scientist with a focus on database creation and management, technical research expertise, and proteomic and genomic analyses with the goal of identification of disease biomarkers.
- Analyze proteomic data sets for detection and identification of novel biomarkers of Dupuytren's disease.
- Analyze protein fingerprint biomarker data to identify biomarkers of Dupuytren's disease.
- Creation and management of databases of patient data, literature, and curated SNP and SNV data.
- Assist in preparation of peer-reviewed manuscripts.
Assay Development Scientist
Invitae
January 2021 - September 2022
R&D scientist with extensive experience in cancer diagnostic development using Next Generation Sequencing.
- Design cancer diagnostics using bioinformatic tools and databases.
- Test oncology diagnostic panels and perform NGS genomic analysis.
- Lead a team of analysts to perform quality control testing of our diagnostic products.
- Worked with multidisciplinary departments (e.g., Tech Transfer, IVD R&D, Software, QA) to develop and redesign assay protocols, determine acceptance criteria and test metrics, implement bioinformatic pipelines, reassess methods of data analysis, and perform CAPAs (Corrective and Preventative Action).
PhD Candidate/Postdoctoral Research Associate
University of Denver
July 2015 - January 2021
PhD candidate and Postdoc in the DU Neuroendocrinology lab studing membrane trafficking and cell line engineering.
- Engineered dozens of cell lines either expressing or knocking down genes of interest using CRISPR/Cas9 or through viral strategies.
- Skilled in scientific discussion, experimental design, and manuscript writing and preparation.
- Demonstrated teamwork by collaborating with multiple labs to publish peer-reviewed manuscripts.
- Mentored and trained the next generation of lab technicians, graduate and undergraduate students on laboratory techniques, equipment, and general lab safety.
- Assisted in pioneering a new lab alongside a young principal investigator which included training and mentoring incoming personnel, establishing lab protocols, and securing vendors for lab supplies.
Research Assistant
University of Wisconsin - Milwaukee
May 2014 - July 2015
Research assistant in the UWM Neurophysiology lab studying gene expression related to aging.
- Trained in animal handling and behavioral analysis, surgery, and tissue harvesting and processing for further analysis.
- Processing tissue through immunohistochemistry and immunofluorescence, and acquiring images of processed tissues using light microscopy and immunofluorescence microscopy.
- Performed extensive microscopy-based data collection, analysis, organization, and presentation in the form of scientific posters.
Education
University of Denver - Denver, CO
Ph.D. in Cell and Molecular Biology
2016-2020
Advisor: Cedric Asensio, Ph.D.
Thesis: Sorting of Cargo Proteins Within the Regulated Secretory Pathway: The Peripheral Membrane Protein HID-1 as a Sorting and Vesicle Biogenesis Factor
Primary focus on cell biology, molecular and synthetic biology, genetics, and biochemistry.
University of Wisconsin - Milwaukee, WI
B.S. in Psychology
2012-2015
Primary focus on neurophysiology, neurobiology, neuropharmacology, and cognitive neuroscience.