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Pepchem

Welcome !

Yu (Tom) Gao's personal web page about my research in chemistry, chemical biology and proteomics/bioinformatics. My CV (click here).
If you are interested in my research or potential collaboration, contact me!
If you are looking for research tools developed by me, go to Downloads

Learn more about me
about me

about me

My name is Yu (Tom) Gao. I was born in Changchun, a beautiful city in the northeast of China, near the Great Siberia, a really cold and beautiful city. It is also where Ei-ichi Negishi, 2010 Nobel Laureate in Chemistry and Liu Xiaobo, 2010 Nobel Peace Prize, were born. I grew up on the campus of Jilin University, where my father works. When I was 6, my family did a little trip in Europe while my dad was pursuing his Ph.D. in Polymer Chemistry. We spent 2 years in Darmstadt, Germany and 3 years in Genova, Italy. I went school there, and I can still speak a little Italiano.



My journey in science

I got my B.S. from Peking University, then came to the US in 2008 for the graduate school. I joined Dr. Kodadek's lab at University of Texas Southwestern Medical Center at Dallas and then moved with him to The Scripps Research Institute, Florida in early 2009. I graduated from The Scripps Research Institute in 2014 with a Ph.D. in Chemistry and moved to San Diego to join Dr. Yates lab as a research associate.

research interest

my research interest

Chemistry + Biology + Informatics

My research goal is to combine Chemical, Analytical and Informatics tools to systematically investigate protein-protein interactions. How small molecules interact with proteins? How protein interact with each other? These are the central questions in both Chemistry and Biology. During my thesis research with Dr. Thomas Kodadek at The Scripps Research Institute, Florida, I worked on the synthesis, characterization, and screening of large-scale peptidomimetic libraries against various proteins. We tried to answer a fundamental question: if rigid structure binds better to protein targets? (to see my answers, see my CV, publication 7-14) My current research in Dr. John Yates' lab at The Scripps Research Institute, La Jolla, focused on both chemical proteomics and metabolomics. Here is my CV if you are interested.

Chemical Biology

My main interest in Chemical Biology is to create chemical tools to investigate and manipulate protein-protein interaction. Particularly, I am interested in developing activity-based probes and chemical crosslinkers.

Proteomics/Metabolomics

Mass spectrometry-based Proteomics and Metabolomics are power tools to survey the biological system. When combined with chemical enrichment and chemical labeling, these tools are even more powerful. My research interests include single-cell proteomics, chemical enrichment and crosslinking.

High-throughput screening

Combinatorial Chemistry allows us to synthesize millions of compounds in days. Within these millions of compounds, many of them are potent binders and inhibitors. My research focuses on how to identify these bioactive compounds efficiently.

Bioinformatics

Bioinformatics is the key to process the massive data generated by modern mass spectrometers. My interest in bioinformatics is to develop powerful tools to convert Big Data to Knowledge (BD2K). I have been working on multi-omics data analysis, metabolomics data quantitation and metaproteomics data analysis.

  • Chemistry

    1. Combinatorial compound library synthesis
    2. High-throughput Screening
    3. Chemical probe synthesis

  • Mass spectrometry

    1. Glycoproteomics
    2. Phosphoproteomics
    3. Quantitative analysis

  • Bioinformatics

    1. Multi-omics data integration
    2. Statistical analysis
    3. Software development

downloads

my tools for research

All the software provided here are developed by me and free to use for research purposes. If you used my tools for you publication, please include proper citations.
For any other use, please contact bathyg(at)gmail.com

PATS

Post-acquisition targeted search (PATS) is a powerful tool to search novel peptide sequence (or protein), with or without PTMs, in large interactome data sets. PATS identifies all potential protein interactors of your target peptide sequence and generate protein correlation matrix based on known protein interactions. This allows you to predict putative functions of your target peptide sequence (or protein) by the "guilt by association" concept.

Go to PATS website

Dilu

Dilu is a new end-to-end platform for metabolomics data analysis. Dilu is written by me in C and Python. Dilu uses MS2 and MS1 to align and group features in each cohort. Dilu is developed in collaboration with the Saghatelian lab at Salk.

Go to Download

t2d2mzxml and raw2ms

These are two software that designed for converting ABI 4700/4800 .t2d files to mzxml and converting Thermofisher/Finnigan .raw data file to ms1/ms2 (mzxml support is coming)). The best part of these two are: THEY DO NOT NEED VENDOR LIBRARY!!!

Go to Download

Peptoid Chemdraw Generator

This is a software that designed to meet the need of drawing peptoid/peptide in various ways. It complies with the standard naming system of peptoid and I am adding the spectrum sequencing ability to it as well. Please take a look.

Go to Download

ProLuCID GUI

This is the graphic user interface of Prolucid database search engine. This tool allows quick and easy protein/peptide identification from bottom-up proteomics data for all researchers.

Go to Download
contact me

contact me

Are you interested in collaborating? Tell me about your project:
drop me an e-mail or visit my lab at The Scripps Research Institute
Also, if you find any bug from my software, please let me know!

 

Our lab

Feel free to stop by:
10550 North Torrey Pines Road, SR-302
San Diego, California, 92037
United States

location