John

About John

I am an experienced computational biologist with more than 10 years’ of experience developing methods that link next-generation sequencing data with medicine.With a background in biochemistry and genetics, I developed and implemented molecular and computational methods with primary investigators and different types of collaborators to mine the clinical significance of genomics data. A known problem solver, I have been able to identify details and patterns among data of different scales to identify risk factors of Type II diabetes, lymphoma, myeloma, and leukemia.As part of my work, I have developed extensive written and oral communication skills through monthly presentations of data and algorithms to a wide range of audiences, and through regular authorship which explains my methods in detail. Furthermore, I developed leadership skills through the mentorship of undergraduate interns and summer students in the laboratory.My experience in a startup laboratory and volunteering experience in start-up biotech companies also fostered me the importance of cost reduction and workflow optimization, and a lifelong interest in law provided a strong sense of rights and obligations that need to be used to the fullest.I am seeking to build my professional network. Let’s connect!Technical skills: Computational biology, Next-generation sequencing data analysis, transcriptome analysis, neoantigen identification, gene coexpression network analysis, machine learning, data clustering, eQTL, gene expression analysis, neoantigen, epitope, single-cell sequencing, ATAC-seq, survival analysis, Single-cell sequencing, CITE-seqSoftware: R, Perl, Python, Bioconductor, bioPerl, scikit-Learn, GATK, STAR, bwa, SQL, NextFlow, pyTorch

Experience

1. Bioinformatics Scientist

   BioLegend

   May 2020 — Present · San Diego, US

   Involved in six product and protocol development projects for BioLegend’s single-cell proteogenomics analysis platform, in collaboration with internal and external molecular scientists and academic stakeholders.• Analyzed more than a dozen in-house R&D and external single-cell multi-omics Next-generation sequencing experiments using a combination of off-the-shelf and in-house tools. • Created more than 20 Python and R scripts that have been integrated into in-house data processing pipelines for different types of CITE-seq applications.• Created two customer-facing application notes for newly-developed CITE-seq applications and existing third-party tools, in collaboration with the internal marketing team and published to the public.• Built four machine-learning models to perform cell-type prediction from single-cell expression data.

Education

• The Hong Kong University of Science and Technology

  Master of Science (MSc), Bioengineering and Biomedical Engineering

  2005 — 2007

• Udacity

  Data Analyst Nanodegree

  2015 — 2016

• The Hong Kong University of Science and Technology

  Bachelor of Science (BSc), Biochemistry

  2002 — 2005

• University of Iowa

  Doctor of Philosophy - PhD, Genetics

Skills

• Bowtie
• Microsoft Office
• Cardiovascular Biology
• Python
• Data Analysis
• Molecular Biology
• C
• Quantitative Genetics
• Bioconductor
• Rnaseq
• Dna Sequencing
• Ngs
• Computational Genomics
• Variation Analysis
• Dna
• Metabolic Syndrome
• Snp Genotyping
• Statistics
• Gene Expression Profiling
• Cluster
• Next Gen
• Rna Isolation
• Perl
• Shell Scripting
• Computational Biology
• Genetics
• Bioinformatics
• Life Sciences
• Science
• Genomics
• Data Modeling
• Problem Solving
• Hdf5
• Intellectual Property
• Dimensionality Reduction
• Exome Sequencing
• Rna Sequencing
• Sql
• Linux
• R