Jonathan Cheng

Jonathan Cheng Email and Phone Number

Data Scientist / Bioinformatics Scientist @ Bristol Myers Squibb
Jonathan Cheng's Location
San Francisco Bay Area, United States, United States
Jonathan Cheng's Contact Details
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

Jonathan Cheng's Current Company Details
Bristol Myers Squibb

Bristol Myers Squibb

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Data Scientist / Bioinformatics Scientist
Jonathan Cheng Work Experience Details
  • Bristol Myers Squibb
    Principal Data Scientist
    Bristol Myers Squibb May 2023 - Present
    Lawrence Township, Nj, Us
    • Data scientist in Informatics & Predictive Sciences group supporting large molecule drug discovery
  • Berkeley Lights
    Bioinformatics Scientist
    Berkeley Lights Apr 2022 - Mar 2023
    Emeryville, Ca, Us
    • 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
  • Berkeley Lights
    Senior Applications Development Engineer
    Berkeley Lights Jan 2021 - Apr 2022
    Emeryville, Ca, Us
    • 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 and automation• 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 Oriented Programming, Git, and Microsoft Azure DevOps• 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)
  • 10X Genomics
    Scientist Ii
    10X Genomics May 2020 - Jan 2021
    Pleasanton, California, Us
    • 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 collaborations with microfluidics, instrumentation, product integration, and manufacturing groups• Co-inventor on seven invention disclosures on spatial transcriptomics• Left to pursue a more computationally-focused role at Berkeley Lights
  • Nanostring Technologies, Inc.
    Scientist
    Nanostring Technologies, Inc. Jun 2018 - Mar 2020
    Seattle, Wa, Us
    • 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 informed project decision-making• 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• Mentored and supervised a group of research associates, enabling streamlined QC workflows
  • Institute For Protein Design, University Of Washington
    Research Scientist / Engineer
    Institute For Protein Design, University Of Washington Nov 2015 - May 2018
    Seattle, Washington, Us
    • 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
  • University Of Washington
    Graduate Research Assistant
    University Of Washington Sep 2008 - Sep 2014
    Seattle, Wa, Us
    • 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 molecular transport• 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• Mentored two undergraduate students on research projects
  • University Of Washington
    Teaching Assistant - Cellular Bioengineering Graduate Level Course
    University Of Washington Jan 2010 - Mar 2010
    Seattle, Wa, Us
    • Coordinated course in cellular bioengineering• Delivered lecture on bone tissue engineering• Graded homework and exams, kept attendance records• Webmaster for course website
  • Ucsf
    Staff Research Associate Ii - Musculoskeletal Quantitative Imaging Research Group
    Ucsf Nov 2006 - Jul 2008
    San Francisco, California, Us
    • 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
  • Medtronic Vascular
    R&D Intern (Summers)
    Medtronic Vascular 2002 - 2004
    Minneapolis, Mn, Us
    - R&D in vascular biology and polymer groups

Jonathan Cheng Skills

Microscopy Cell Fluorescence Microscopy Matlab Drug Delivery Biomaterials Cell Biology R&d Cell Culture Image Analysis Biomedical Engineering Microfabrication Mammalian Cell Culture Laboratory Skills Neuroscience Public Speaking Mems Confocal Microscopy Molecular Biology Grant Writing Science Communication Autocad Adobe Illustrator Photolithography Pcr Fluid Mechanics Live Cell Imaging Neuromuscular Laboratory Automation Mentoring Of Staff University Teaching Design Of Experiments Adobe Photoshop Mri Photography Super Resolution Image Processing Digital Image Processing Surface Chemistry Optics Research And Development Python Pandas

Jonathan Cheng Education Details

  • University Of Washington
    University Of Washington
    Bioengineering And Biomedical Engineering
  • Uc Irvine
    Uc Irvine
    Bioengineering And Biomedical Engineering
  • University Of California, Berkeley
    University Of California, Berkeley
    Bioengineering And Biomedical Engineering
  • Maria Carrillo High School
    Maria Carrillo High School

Frequently Asked Questions about Jonathan Cheng

What company does Jonathan Cheng work for?

Jonathan Cheng works for Bristol Myers Squibb

What is Jonathan Cheng's role at the current company?

Jonathan Cheng's current role is Data Scientist / Bioinformatics Scientist.

What is Jonathan Cheng's email address?

Jonathan Cheng's email address is jo****@****ics.com

What is Jonathan Cheng's direct phone number?

Jonathan Cheng's direct phone number is +151054*****

What schools did Jonathan Cheng attend?

Jonathan Cheng attended University Of Washington, Uc Irvine, University Of California, Berkeley, Maria Carrillo High School.

What are some of Jonathan Cheng's interests?

Jonathan Cheng has interest in The Simpsons, Golden State Warriors, Culinary Arts, Ultimate Frisbee, Beck, Health, Education, Seattle, Photography, Science And Technology.

What skills is Jonathan Cheng known for?

Jonathan Cheng has skills like Microscopy, Cell, Fluorescence Microscopy, Matlab, Drug Delivery, Biomaterials, Cell Biology, R&d, Cell Culture, Image Analysis, Biomedical Engineering, Microfabrication.

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