Opto™ Assure Cld Assays - Berkeley Lights
Berkeley Lights
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Jonathan Cheng Email & Phone Number
Opto™ Assure CLD Assays - Berkeley Lights
at
Berkeley Lights
1 work email found
@bms.com
1 phone found area 510
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✓ Verified Jun 2026
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Current company
Role
Opto™ Assure CLD Assays - Berkeley Lights
Location
San Francisco Bay Area, United States, United States
Who is Jonathan Cheng? Overview
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Quick answer
Jonathan Cheng is listed as Opto™ Assure CLD Assays - Berkeley Lights at Berkeley Lights, based in San Francisco Bay Area, United States, United States. AeroLeads shows a work email signal at bms.com, phone signal with area code 510, and a matched LinkedIn profile for Jonathan Cheng.
Jonathan Cheng previously worked as Principal Data Scientist at Bristol Myers Squibb and Bioinformatics Scientist at Berkeley Lights. Jonathan Cheng holds Doctor Of Philosophy (Ph.D.), Bioengineering And Biomedical Engineering from University Of Washington.
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{first}.{last}@bms.com
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Profile bio
About Jonathan Cheng
I am a data scientist passionate about building tools for the life sciences. I am experienced in extracting insights from biology datasets of many types. My PhD training was in bioengineering with a focus in microfluidics for high-throughput cell biology applications. Since then, I have gained valuable experience in the biotechnology tools industry, having worked in technology development of several NGS platforms: Berkeley Lights Beacon, 10x Genomics Spatial Transcriptomics (Visium), NanoString Hyb&Seq and CosMx Spatial Molecular Imager. I'm proud to have been an inventor on several patents at each of these companies. Most of all, I have become enamored with making sense of big datasets from high-throughput technologies. To this end, I have pivoted from hybrid experimentalist / computational roles to a dedicated computational career path, as a Data Scientist. I believe that my domain knowledge at the intersection of DNA sequencing, biophysics, statistics and data science, and new technology development gives me unique value in the life sciences tools space. I am always curious and driven to learn new things in this ever-changing field.Skills:• Data analysis, both ad hoc and pipeline development, using Python, R, and MATLAB, most fluent in Python data science stack: numpy, pandas, scipy, scikit-learn, matplotlib, seaborn, plotly; shell scripting• Comfortable with software engineering best practices: Git, PyCharm, VS Code, Azure DevOps ecosystem, object-oriented programming• Well-versed in modern molecular biology methods, especially in NGS workflows: inventor of NGS methods, as demonstrated in multiple patents • Strong background in fluorescence microscopy, optics and image processing using MATLAB, ImageJ, opencv• Effective science communicator adept at tailoring clear communications to audiences of all backgrounds as demonstrated in leading projects, training sessions, customer engagements, and science museum volunteer activity
Listed skills include Microscopy, Cell, Fluorescence Microscopy, Matlab, and 39 others.
Current workplace
Jonathan Cheng's current company
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11 roles · 24 years
Jonathan Cheng work experience
A career timeline built from the work history available for this profile.
Principal Data Scientist
- Data scientist in Informatics & Predictive Sciences group supporting large molecule drug discovery
Bioinformatics Scientist
- Bioinformatics data scientist within software team, extracting insights from Berkeley Lights multi-omics datasets; data inputs include sequencing, imaging, and BLI platform-specific data
- Thought leader in driving novel computational experiments: collaborate with R&D scientists to design and optimize experiments; insights have led to innovative technical recommendations
- Built several command line-interface Python packages for single cell analysis, contributing to improved accuracy and insights in R&D projects
- Built algorithms for linking single cell genomic to phenomic data collected on Berkeley Lights Beacon platform
- Applied statistics and machine learning concepts in single cell analysis, including use of signal processing, time series analysis, dimensionality reduction, classification, survival analysis
Apr 2022 - Mar 2023
Senior Applications Development Engineer
- Integration engineer / scientist developing microfluidic cell-based assays on the Berkeley Lights Beacon platform: early stage technology development integrating cell biology / biochemistry with complex instrumentation.
- Prototype data analysis / data science pipelines handling large datasets from the Beacon instrument using Python and Tableau
- Contributor to Applications Engineering code base: develop automated workflows within the Berkeley Lights Cell Analysis Suite software using a Python API and software engineering best practices including Object.
- Collaborate with multi-disciplinary teams in Applications Engineering, Biology, Consumables, Hardware and Software Engineering to develop new products following the Product Development Process
- Technical lead and co-inventor on a patent "Methods of Assaying Biomolecules within a Microfluidic Device" pertaining to a released product: Opto Assure Cell Line Development Assay (see Patents section)
Jan 2021 - Apr 2022
Scientist Ii
- R&D scientist, Chemistry Technology Development group: worked on a high-resolution array-based spatial transcriptomics product: NGS workflow optimization, microscopy, surface chemistry, product development, and.
- Co-inventor on seven invention disclosures on spatial transcriptomics
- Left to pursue a more computationally-focused role at Berkeley Lights
May 2020 - Jan 2021
Scientist
- R&D integration scientist leading research on Hyb&Seq, an amplification and library-free hybridization-based single molecule sequencing platform
- Developed novel DNA barcoding schemes and workflows: oligonucleotide sequence design, including extensive use of DNA modifications to build molecular workflows
- Developed flow cell surface chemistries and methods for oligonucleotide surface conjugation which resulted in 60% increase in performance efficiencies
- Built several custom bioinformatics pipeline modules using Python-based libraries, e.g. correlations between instrumentation and sequencing metrics; metrics for assessing hybridization chemistry performance which.
- Co-inventor on patent on spatial transcriptomics (see Patents section)
- Collaborated with instrumentation team to develop fluidic / optical instrument prototypes, enabling automation of new workflows
Jun 2018 - Mar 2020
Research Scientist / Engineer
- Develop methods and instrumentation for high-throughput protein-protein interaction analysis
- Develop methods for image acquisition, analysis, and base-calling of protein barcoding data, a powerful extension of next-generation DNA sequencing technologies
- Application in measuring multimeric protein-protein interactions of engineered proteins
- Develop automated data analysis pipelines, including image processing workflows using MATLAB and Python
- Develop instrumentation for measuring protein-protein interactions consisting of a combination of microfluidics and fluorescence microscopy
- Present high-throughput interactome data using a combination of statistical tools using MATLAB and Python
Nov 2015 - May 2018
Graduate Research Assistant
- Designed and built micro-fabricated and microfluidic platforms for control of cell culture microenvironments for study of developmental neurobiology (neuromuscular synaptogenesis)
- Characterized microfluidic device performance using brightfield and fluorescence microscopy; surface characterization using contact angle, ToF-SIMS, AFM, SEM; correlated performance with mathematical modeling of.
- Acquired and analyzed high-throughput live cell fluorescence microscopy data
- Investigated the application of cell-based therapy using osteoclasts to treat ectopic calcification
- Tested the efficacy of a microporous fibrin scaffold loaded with growth factors for bone tissue engineering using microCT
- Presented work at four international conferences, two journal articles
Sep 2008 - Sep 2014
Teaching Assistant - Cellular Bioengineering Graduate Level Course
- Coordinated course in cellular bioengineering
- Delivered lecture on bone tissue engineering
- Graded homework and exams, kept attendance records
- Webmaster for course website
Jan 2010 - Mar 2010
Staff Research Associate Ii - Musculoskeletal Quantitative Imaging Research Group
- Assessed quantitative MRI techniques as a diagnostic tool for measuring cartilage biochemical composition in early stage osteoarthritis
- Investigated feasibility of quantitative MRI imaging in predicting clinical arthroscopic scoring of cartilage focal lesions
- Presented work at three international conferences, co-author on four papers
Nov 2006 - Jul 2008
2002 - 2004
~2 yrs
4 education records
Jonathan Cheng education
Doctor Of Philosophy (Ph.D.), Bioengineering And Biomedical Engineering
University Of Washington
Master Of Science (M.S.), Bioengineering And Biomedical Engineering
Uc Irvine
Bachelor Of Science (B.S.), Bioengineering And Biomedical Engineering
University Of California, Berkeley
Education record
Maria Carrillo High School
FAQ
Frequently asked questions about Jonathan Cheng
Quick answers generated from the profile data available on this page.
What company does Jonathan Cheng work for?
Jonathan Cheng works for Berkeley Lights.
What is Jonathan Cheng's role at Berkeley Lights?
Jonathan Cheng is listed as Opto™ Assure CLD Assays - Berkeley Lights at Berkeley Lights.
What is Jonathan Cheng's email address?
AeroLeads has found 1 work email signal at @bms.com for Jonathan Cheng at Berkeley Lights.
What is Jonathan Cheng's phone number?
AeroLeads has found 1 phone signal(s) with area code 510 for Jonathan Cheng at Berkeley Lights.
Where is Jonathan Cheng based?
Jonathan Cheng is based in San Francisco Bay Area, United States, United States while working with Berkeley Lights.
What companies has Jonathan Cheng worked for?
Jonathan Cheng has worked for Berkeley Lights, Bristol Myers Squibb, 10X Genomics, Nanostring Technologies, Inc., and Institute For Protein Design, University Of Washington.
How can I contact Jonathan Cheng?
You can use AeroLeads to view verified contact signals for Jonathan Cheng at Berkeley Lights, including work email, phone, and LinkedIn data when available.
What schools did Jonathan Cheng attend?
Jonathan Cheng holds Doctor Of Philosophy (Ph.D.), Bioengineering And Biomedical Engineering from University Of Washington.
What skills is Jonathan Cheng known for?
Jonathan Cheng is listed with skills including Microscopy, Cell, Fluorescence Microscopy, Matlab, Drug Delivery, Biomaterials, Cell Biology, and R&D.
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