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Pepchem

Gao lab @ UIC

Chemistry + Biology + Informatics

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about me

About Us

Gao lab @ UIC focuses on the development of novel chemical and informatics tools to investigate the proteome and complex biological system. By combining chemical screening, mass spectroscopy-based proteomics/metabolomics, and informatics, our research aims to interrogate the proteome and to elucidate protein interactions. List of publication ->> HERE.
  1. Gao Lab


    Gao, Yu (Tom)  yugao@uic.edu
     Assistant Professor, CV
    Department of Pharmaceutical Science
    University of Illinois Cancer Center

    B.S. (2008) Peking University, School of Pharmaceutical Sciences
    Ph.D. (2014) The Scripps Research Institute (Dr. Thomas Kodadek)
    Post-doc (2018) The Scripps Resaerch Institute (Dr. John Yates III)

  2. Gao Lab


    Shao, Xinhao  xshao8@uic.edu
     Graduate student, CV
    Department of Pharmaceutical Science

    B. Eng (2016) Heilongjiang University, pharmaceutical engineering
    M.S. (2018) Bioengineering, Illinois Institute of Technology
    Never limits challenges, challenge limits.

  3. Gao Lab


    Zhang, Ziwei  zzhan60@uic.edu
     Graduate student, CV
    Department of Pharmaceutical Science

    B.S. (2015) Peking University, Schoool of Pharmaceutical Sciences
    M.S. (2017) Peking University, Schoool of Pharmaceutical Sciences (Dr. Demin Zhou)
    May the force be with you

  4. Gao Lab


    Hollas, Michael  mhollas@uic.edu
     Post-doc, CV
    Department of Pharmaceutical Science

    MChem (2011) St. Johns College, University of Oxford
    Ph.D. (2017) University of Manchester
    i'm struggling with the funny description...

  5. Gao Lab


    Ma, Xiuyuan  mxyuan126@gmail.com
     Post-doc, CV
    Department of Pharmaceutical Science

    B.S. (2013) Nanjing University, Department of Chemistry and Chemical Engineering
    Ph.D. (2019) Rutgers University (Dr. Elena Galoppini)
    A lover of life.

  6. Gao Lab


    Abdeljaber, Ameer  aabdel38@uic.edu
     Undergraduate Student, CV
    Department of Pharmaceutical Science

    Undergraduate at University of Illinois at Chicago (2017-)
    @Gao lab since 2019.7

research interest

research interest

Chemistry + Biology + Informatics

Our 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.

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. Our research interests focuses on single-cell proteomics and highly sensitive protein detection method.

Chemical Biology

Our main interest in Chemical Biology is to create chemical tools to investigate and manipulate protein-protein interaction. Particularly, we are interested in developing activity-based probes and chemical crosslinkers to elucidate protein-protein interactions.

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. We collaborate with UICentre to create methods to identify bioactive compounds efficiently.

Bioinformatics

Bioinformatics is the key to process the massive data generated by modern mass spectrometers. Our interest in bioinformatics is to develop powerful tools to convert Big Data to Knowledge. We have been working on multi-omics data analysis, deep proteomics data analysis and metabolomics data quantitation.

  • 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

Our 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 us

Are you interested in collaborating? Have any suggestions?

Drop us an e-mail or visit our lab at University of Illinois at Chicago

Also, if you find any bug from our tools, please let us know!



Available position

1. Post-doc level researchers in the field of (a) organic chemistry (b) chemical biology (c) proteomics (d) bioinformatics (e) other related areas. Details

2. Graduate students with B.S. or B.A. in STEM.

3. Technicians, both hourly paid and long-term position. Will be in charge of mass spectrometry and other common lab duty.

4. Visiting Scholars, must be from related field, willing to learn new things.

5. Talented part-time graduate/undergraduate students

To apply, submit your CV here.

 

Our lab

Feel free to stop by:
833 S Wood St. 5th Floor, 552
Chicago, Illinois, 60612
United States

location