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00 / PROFILE

Joanne Y. Chan

Analytical Scientist · Proteomics, Multi-Omics & Scientific Software

Quantitative proteomics, liquid chromatography-tandem mass spectrometry (LC-MS/MS), multi-omics research, and laboratory operations form the scientific foundation of a career that has expanded into technical training, data systems, and scientific software.

Scientific software extends the same evidence-driven practice into structured data, reproducible workflows, testing, traceability, and tools designed for technical review.

01Analytical ScienceProteomics · LC-MS/MS · Method Development
02Scientific DataData Quality · Reproducibility · Traceability
03Software EngineeringPython · Testing · Release Engineering
04Teaching & CommunicationSTEM Education · Instructional Design · Training

02 / EXPERIENCE

Experience

GRADUATE STUDY

Master of Science in Information Technology

Software Engineering · Data & Machine Learning · Human-Centered Systems · Project Operations

University of the People · June 2025 – August 2026

Graduate study covered software engineering, algorithms, databases, operating systems, machine learning, human-computer interaction, cybersecurity, programming languages, and project/program management.

The program extended scientific practice into software engineering and information systems, with recurring emphasis on reproducibility, system behavior, user needs, security, and technical decision-making.

Selected Graduate Work

Software & Algorithms

Python, Java, and Racket; data structures, graph algorithms, heaps, interpreter design, abstract syntax trees, desugaring, SOLID, interfaces/adapters, UML, idempotency, and transaction/concurrency reasoning.

Data, Machine Learning & Systems

Relational design, normalization, indexes, views, constraints, access control, transaction logs, recovery reasoning, operating-system concurrency and resource management, plus hands-on implementations of linear regression, Gaussian Naive Bayes, K-Means, and multilayer perceptrons with attention to evaluation limits.

Human-Centered & Secure Systems

Personas, task analysis, usability, accessibility/WCAG, NASA-TLX, authorized network scanning, Nessus, Zero Trust, incident response, digital evidence, and chain-of-custody reasoning.

Project & Research Operations

Risk ownership, stakeholder communication, budget controls, quality planning, service downtime and queue-backlog analysis, vendor handoffs, go/no-go decisions, accessibility planning, and project/program management.

INDEPENDENT STUDY / PROFESSIONAL DEVELOPMENT

Intellectual Property & Technology Transfer

Biotechnology · Patents · Research Agreements · Commercialization

March 2023 – June 2025

Mentored, self-directed study covered biotechnology patents and university technology transfer, including sponsored-research, collaboration, material-transfer, and confidentiality agreements, university intellectual-property management, commercialization, and technology evaluation.

Senior Analytical Scientist / Laboratory Manager

Quantitative Proteomics · LC-MS/MS · Multi-Omics · Laboratory Operations

Stanford Medicine · Department of Genetics · March 2016 – April 2022

Developed and optimized high-throughput LC-MS/MS workflows for protein and peptide identification and quantitative proteomics, often carrying collaborator samples from biological material through sample preparation and mass spectrometry acquisition across tissues, cells, biofluids, and stool. Methods included Tandem Mass Tag (TMT) workflows, phosphopeptide enrichment, and protein/PTM profiling.

Operated, maintained, and troubleshot Thermo Scientific Q Exactive, Q Exactive Plus, Orbitrap Fusion, and Orbitrap Fusion Lumos mass spectrometers alongside Waters ACQUITY UPLC H-Class and M-Class systems, including 2D-LC configurations, and Waters 1D-UPLC systems. Used a dedicated Agilent 1260 Infinity HPLC for serum-depletion workflows, developing automated fraction-collection methods and sample sequences and monitoring run quality when collections required troubleshooting. Used Xcalibur and MassLynx for instrument control and data acquisition, Proteome Discoverer for proteomics processing, and Python, R, and Ingenuity Pathway Analysis for downstream analysis. Performed routine preventive maintenance and worked with field-service engineers on instrument issues and service needs.

Trained and advised students, postdoctoral researchers, and staff in experimental design, LC-MS workflows, and data analysis while managing laboratory safety, purchasing, budgets, instrument and service coordination, and vendor relationships.

Laboratory Manager / Researcher

Pathology · Molecular Biology · Behavioral Research · Laboratory Operations

UC Davis Health · Pathology · May 2015 – March 2016

Managed wet-laboratory and Long-Evans behavioral research involving behavioral data analysis, Western blotting, immunohistochemistry, flow cytometry, ELISA, human and animal tissue handling, tissue processing and sectioning, microscopy, and laboratory operations. Responsibilities also included laboratory safety, inventory, research coordination, and staff and intern training.

UNDERGRADUATE RESEARCH, INTERNSHIPS, TEACHING & LEADERSHIP

Undergraduate Research & Technical Foundations

Research Science · Human & Veterinary Health · Education & Policy · Technical Systems · Leadership & Service

University of California, Davis · September 2010 – June 2014

Undergraduate experience at UC Davis spanned research science, human and veterinary health, education and policy, technical systems, and organizational leadership. Those overlapping roles established an early pattern of moving between scientific evidence, real-world workflows, teaching, and responsibility for people and systems.

Selected Undergraduate Roles & Research

Research Science

UC Davis · Department of Evolution & Ecology
Undergraduate Research Assistant / Research Intern · June 2011 – January 2012. Analyzed sage-grouse mate-selection behavior datasets and presented data to postdoctoral and graduate researchers.

UC Davis · Department of Molecular & Cellular Biology
Undergraduate Research Assistant · January – April 2012. Supported molecular-biology research using PCR, cloning, gel/blotting workflows, and MATLAB/Python with graduate researchers.

UC Davis · School of Veterinary Medicine
Paid Research Assistant · October 2012 – April 2013. Supported feline research in the School of Veterinary Medicine and provided technical assistance for a resulting peer-reviewed veterinary study.

MARBLES · UC Davis MIND Institute / Public Health Sciences
Research Intern · January – April 2013. Supported participant recruitment and screening, study communication, data transcription, journal-club work, and family engagement for longitudinal environmental-health and autism-risk research.

Human & Veterinary Health

Sutter Health
Clinical internship sequence · April 2011 – January 2013. Worked across health-information, oncology, surgery, and cardiac-rehabilitation settings, supporting staff, patient transport, specimen movement, stocking, and patient/family needs across placements.

UC Davis Medical Center
Cardiology Intern · Winter 2012.

UC Davis Veterinary Medical Teaching Hospital
Veterinary Cardiology Intern · Fall 2012.

The Willow Clinic / Joan Viteri Memorial Clinic
Undergraduate Liaison · April 2012 – June 2014. Supported patient intake, vitals, rooming, case-presentation workflows, and undergraduate-intern training in a medical-student-run community clinic.

Education & Policy

UC Davis CalTeach/Mathematics and Science Teaching Program (CalTeach/MAST)
September 2010 – June 2014. Taught and tutored high-school Algebra I/II, trigonometry, and AP Calculus and elementary English and mathematics through school placements, including Leonardo da Vinci High School and Fred T. Korematsu Elementary; designed activity-based lessons and instructional materials.

RAND Corporation / UC Davis School of Education
Research Assistant · April – August 2011. Supported statewide education-finance and public-policy research, including surveys and outreach with California school districts and district finance leaders.

UC Davis Ecological Garden / School Gardening
Program Field Learning Demonstration Intern · March – June 2014. Supported school-gardening, environmental education, and experiential-learning activities.

Technical Systems

Early research included MATLAB and Python use with graduate researchers. Molecular & Cellular Biology Club responsibilities later included website, listserv, and social-media coordination as Vice President / Web Coordinator in 2012–2013. Prytanean technical service included website maintenance, presentation materials, and troubleshooting during 2013–2014.

Leadership & Service

Molecular & Cellular Biology Club
Active Member · 2010–2011; Treasurer · 2011–2012; Vice President / Web Coordinator · 2012–2013; President · 2013–2014.

Phi Sigma Pi · Zeta Upsilon Chapter
Founding Class; Fundraising Chair · 2012–2013; Parliamentarian · 2013–2014.

Prytanean Women’s Honor Society
Member · December 2012 – June 2014; Technical and Web Developer · 2013–2014.

Veterinary Aide Club
Member · September 2012 – June 2014.

03 / RESEARCH

Selected Research

Research spans human tissue proteomics and multi-omics, quantitative proteomics and protein regulation, metaproteomics, functional genomics, and pathology and disease biology, with contributions ranging from mass-spectrometry data generation and proteomic analysis to experimental-method design, pathology review, and reproducible methods documentation.

Human Tissue Proteomics & Multi-Omics

Human tissue studies connecting proteomics with broader molecular, genetic, and disease context.

Quantitative Proteomics & Protein Regulation

Quantitative LC-MS/MS, labeled proteomics, protein/PTM profiling, normalization research, and protein-regulation studies.

Metaproteomics & Microbiome

High-throughput LC-MS workflows for human stool metaproteomics, including reproducibility-focused preparation and microbial peptide/protein identification.

Functional Genomics & Disease Biology

Proteomics contributions to genome-scale functional studies and a disease-biology thread extending from pathology research into later colorectal studies.

Publications & Research Outputs

Peer-reviewed articles, consortium-associated research, preprints, protocols, and conference presentations are listed separately by output type.

Peer-Reviewed Articles

Consortium Research & Program Outputs

Preprints

Protocols & Reproducible Methods

Conference Posters & Presentations

Proteomic Variation in Human Heart Tissues

Stanford University Mass Spectrometry Research Applications Symposium (SUMS-RAS), 2019 · co-author poster

SUMS-RAS

Integrated Omics Analysis Across 32 Human Tissues

SUMS-RAS, 2019 · co-author poster

SUMS-RAS

04 / ABOUT

About

Identify the question
Inspect the evidence
Test the explanation
Document the result
Revisit with new information

Experimental science established the foundation for responsibilities spanning analytical instrumentation, quantitative data, laboratory operations, technical training, and collaborative research. Scientific software applies those evidence-driven habits to structured data, versioned rules, testing, traceability, and technical review.

I tend to approach technical problems through a repeatable sequence: identify the question, inspect the evidence, test the explanation, document the result, and revisit it when new information appears.

Years in proteomics and laboratory operations established QA/QC, reproducibility, troubleshooting, and documentation as everyday practices. Teaching and scientific training reinforced precise explanations of complex mechanisms, while graduate computing provided additional ways to translate those habits into testable systems and usable software.

Capabilities

Analytical Science

LC-MS/MS · MS3 · HPLC · UPLC · Quantitative Proteomics · TMT 16-plex · Metaproteomics · Protein/PTM Profiling · Phosphopeptide Enrichment · Ubiquitination Workflows · Method Development · Instrument Troubleshooting

Scientific Data and Software

Python · FastAPI · SQLite · R · MATLAB · SQL · HTML · CSS · JavaScript · CSV · JSON · Git · GitHub · pytest · GitHub Actions · Data Validation · Software Testing · Proteome Discoverer · Skyline · Xcalibur · MassLynx · GraphPad Prism · Ingenuity Pathway Analysis

Quality and Operations

QA/QC · SOPs · Method Validation · Root-Cause Analysis · Data Integrity · Laboratory Operations · Preventive Maintenance · Procurement · Vendor Coordination

Teaching & Communication

Community Mentoring · Researcher and Staff Training · STEM Education · Instructional Design · Assessment Design · Scientific Writing · Technical Writing · Technical Documentation

Teaching, Training & Technical Communication

  • Community Teaching

    Adventure Christian Church of North Natomas · June 2023–Present

    Volunteer mentoring and small-group leadership with elementary-age students.

  • Curriculum, Classroom & Experiential Learning

    UC Davis CalTeach/MAST · September 2010–June 2014

    Taught and tutored mathematics and elementary English and mathematics through school placements; designed science and mathematics lessons, experiential-learning activities, and assessment materials.

  • Scientific Training

    Stanford Medicine · Department of Genetics · March 2016–April 2022

    Trained and advised students, postdoctoral researchers, and staff in experimental design, LC-MS workflows, and data analysis.

Education

Master of Science in Information Technology

University of the People
GPA 4.00
June 2025–August 2026

Executive Ph.D. Program in Biochemistry and Molecular Biology

University of Miami Miller School of Medicine
Doctoral Coursework Completed · All But Dissertation (ABD) · GPA 3.80
2017–2021

Bachelor of Science in Biochemistry and Molecular Biology

University of California, Davis
Minor in Education
September 2010–June 2014

05 / CONTACT

Contact