Biography

Chenghao Zhu is a postdoctoral scholar in the Cancer Data Science Center of the Jonsson Comprehensive Cancer Center at UCLA, working with Dr. Paul Boutros. He’s research interests include developing algorithms and softwares for proteogenomic analysis, and utilizing proteogenomics in diagnosis, prognosis, and understanding the clinico-epidemiologic differences in cancer.

Interests

  • Proteogenomics
  • Cancer Genomics
  • Bioinformatics and Computational Biology
  • Neoantigen

Education

  • PhD in Nutritional Biology, 2019

    University of California, Davis

  • MS in Food Sciencei and Technology, 2013

    University of California, Davis

  • BS in Applied Biological Science, 2012

    Zhejiang University, China

Recent Publications

moPepGen: Rapid and Comprehensive Proteoform Identification

Gene expression is a multi-step transformation of biological information from its storage form (DNA) into functional forms (protein and …
Code DOI

Human gut microbiome composition and tryptophan metabolites were changed differently by fast food and Mediterranean diet in four days: A pilot study

Diets rich in animal source foods vs. plant-based diets have different macronutrient composition, and they have been shown to have …
DOI

Site-Specific Glycoprofiles of HDL-Associated ApoE are Correlated with HDL Functional Capacity and Unaffected by Short-Term Diet

Since high-density lipoprotein (HDL) glycoprofiles are associated with HDL functional capacity, we set out to determine whether diet …
DOI

The HDL lipidome is widely remodeled by fast food versus Mediterranean diet in 4 days.

INTRODUCTION: HDL is associated with increased longevity and protection from multiple chronic diseases. The major HDL protein ApoA-I …
DOI

Github Projects

  1. moPepGen A graph-based algorithm to generate custom protein sequence databases for non-canonical peptide discovery from proteomics data.

  2. NFTest Command line tool for automated testing of Nextflow pipelines and scripts. The tool allows for automated assertions on output files and customizable output directory settings.

  3. exceRNApipeline A data processing pipeline for extracellular RNA-seq from extracellular vesicles and exosomes. The pipeline is built with the python pipeline framework snakemake

  4. HTSet R package for storing, handling, anlyzing, and visualizing high though-put experiment data, such as metabolomics and proteomics.

  5. ShinyMetabase R package with a shiny app wrapped up. ShinyMetabase shiny app allows user to perform normalization, linear model analysis, visualization, multivariant analysis, and network analysis by importing their own data.

Teaching

I was a teaching assistant for the following courses at the University of California, Davis:

  • BIS 2A: Introduction to Biology, Department of Microbiology
  • BIS 102: Structure and Function of Biomolecules, Department of Molecular and Cellular Biology
  • EXB 110: Exercise Metabolism, Department of Neurobiology, Physiology, and Behavior
  • NUT 10: Discoveries and Concepts in Nutrition, Department of Nutrition
  • NUT 11: Current Topics and Controversies in Nutrition, Department of Nutrition
  • NUT 117: Experimental Nutrition, Department of Nutrition
  • CHE 2B: general chemistry, Department of Chemistry

Skills

python R C++ javascript nextflow flask react shiny vue snakemake mysql docker

Contact