Thank you to our dedicated lab members and collaborators for an inspiring year of discovery. Wishing everyone...
Updates
News
Lab announcements, paper acceptances, new funding, trainee milestones, and snapshots of what the group has been building.
2025
QCB student Abigail Beman joined the group for a research rotation. Welcome, Abby!
CCB student Hannah Engebretson joined the group for a research rotation. Welcome, Hannah!
Our collaborative project with Drs. Chonghui Cheng and Jeroen Pollet, titled “mRNA-based immunotherapy for...
Our paper DeepMVP: deep learning models trained on high-quality data accurately predict PTM sites and...
We have received funding from Pfizer for a project titled “Enhancing Proteogenomics Workflows for Drug Target...
Our collaborative project with Dr. Chonghui Cheng’s lab, titled “Targeting Cryptic Splicing-Derived...
Drs. Zhang and Dou have been awarded an MPI U01 grant from the NCI’s Informatics Technology for Cancer...
Our lab participated in the 19th Annual Breast Center Retreat, gave oral and poster presentations, and won the...
Lihong Xu from the Immunology & Microbiology Program joined the group for a research rotation. Welcome,...
Faye’s paper Deciphering the dark cancer phosphoproteome using machine-learned co-regulation of phosphosites...
Congratulations to Michael for passing the CCB PhD Qualifying Exam!
CCB student Shiyi Wu joined the group for a research rotation. Welcome, Shiyi!
QCB student Fanwei Ruan joined the group for a research rotation. Welcome, Fanwei!
2024
Holiday party at Topgolf.
The paper Mapping the functional network of human cancer through machine learning and pan-cancer...
James successfully defended his PhD thesis, congratulations, Dr. Moon! He will be joining Sage Bionetworks...
Dr. Moran Chen joined the lab as a postdoctoral research associate. Welcome, Moran!
Xinpei’s paper Tumor-associated antigen prediction using a single-sample gene expression state inference...
Congratulations to Jonathan on starting his new role as an Instructor at the Breast Center!
The paper Pan-cancer proteogenomics expands the landscape of therapeutic targets has been published in Cell !...
QCB student Siyu Wang joined the group for a research rotation. Welcome, Siyu!
Congratulations to Yongchao on the promotion to Assistant Professor at the Breast Center!
John’s paper WebGestalt 2024: faster gene set analysis and new support for metabolomics and multi-omics has...
CCB student Michael Lee joined our group and Dr. Cheng’s lab as a graduate student, co-mentored by Dr. Zhang...
Dr. Zhang received the Michael E. Debakey Excellence in Research Award . Congratulations!
Dr. Paul Shafer joined the lab as a postdoctoral research associate. Welcome, Paul!
Dr. Yanling Sun joined the lab as a postdoctoral research associate. Welcome, Yanling!
Seunghyuk, John, Lindsey, Chenwei and Bing attended the CPTAC symposium and US HUPO in Portland, OR....
Drs. Zhang and Hoyos have been awarded a CPRIT grant in Computational and Systems Biology for their project...
Breast center Spring Festival celebration.
Sara’s paper Frozen tissue coring and layered histological analysis improves cell type-specific proteogenomic...
2023
Xinpei’s paper Deep Learning Prediction Boosts Phosphoproteomics-Based Discoveries Through Improved...
Holiday bowling party.
Dr. Seunghyuk Choi joined the lab as a postdoctoral research associate. Welcome, Seunghyuk!
Dr. Wenrong Chen joined the lab as a postdoctoral research associate. Welcome, Wenrong!
Sara’s paper IDPpub: Illuminating the Dark Phosphoproteome Through PubMed Mining has been published in...
The review article Current perspectives on mass spectrometry-based immunopeptidomics: the computational angle...
The paper ClinicalOmicsDB: exploring molecular associations of oncology drug responses in clinical trials led...
QCB student Minhang Xu joined the group for a research rotation. Welcome, Minhang!
Yongchao’s paper SEPepQuant enhances the detection of possible isoform regulations in shotgun proteomics has...
Jonathan attended the HUPO Conference held in Busan, Korea, where he delivered an oral presentation titled...
Our paper A proteogenomics data-driven knowledge base of human cancer has been published in Cell Systems ....
The CPTAC perspective article Proteogenomic data and resources for pan-cancer analysis has been published in...
The CPTAC study Proteogenomic insights suggest druggable pathways in endometrial carcinoma has been published...
QCB student Juliana Yue joined the group for a research rotation. Welcome, Juliana!
Most of our lab members participated in the ASMS Conference held in Houston, where we showcased our recent...
QCB student Tobie Lee joined the group for a research rotation. Welcome, Tobie!
Faye successfully defended her PhD thesis, congratulations, Dr. Jiang! She will be joining AstraZeneca as a...
Faye, James, Jonathan, Sara and Dr. Zhang attended the AACR Conference in Orlando, FL. James received a 2023...
Bo’s paper PepQuery2 democratizes public MS proteomics data for rapid peptide searching has been published in...
Congratulations to Lindsey for passing the CCB PhD Qualifying Exam!
Faye, Lindsey and Dr. Zhang attended the US HUPO Conference in Chicago. Faye received a Travel Award for her...
Lunch party to celebrate the new year and welcome new lab members!
Duy Pham and John Elizarraras joined the group as Bioinformatics Programmers. Welcome, Duy and John!
CCB student Evelyn de Groot joined the group for a research rotation. Welcome, Evelyn!
2022
Lindsey gave an oral presentation on “Tripartite graph modeling enables comprehensive protein isoform...
Faye, James, and Lindsey were selected for oral presentation at the 17th Annual Breast Center Retreat, and...
QCB students Jiaye Chen and Daniel Palacios joined the group for a research rotation. Welcome, Jiaye and...
Our collaborative paper with Dr. Seth Lerner titled “Proteogenomic characterization unveils biomarkers...
Dr. Chenwei Wang joined the lab as a postdoctoral research associate. Welcome, Chenwei!
QCB student Xuqian Tan joined the group for a research rotation. Welcome, Xuqian!
Our U01 application entitled “Illuminating understudied druggable proteins using pan-cancer proteogenomics...
James was offered a position in the CTR Certificate of Added Qualification program and the program’s T32...
The CPTAC study “Proteogenomic analysis of the CALGB 40601 (Alliance) HER2+ breast cancer neoadjuvant trial...
The Office of Cancer Clinical Proteomics Research at the National Cancer Institute (NCI) has reaffirmed its...
Xinpei and Sara gave oral presentations about their computational tools DeepRescore2 and IDPpub, respectively,...
Byron Jia, a rising senior at Carleton College joined the group for a summer internship through the SMART...
QCB student Fanwei Ruan joined the group as a graduate student. Welcome, Fanwei!
Our collaborative paper with Dr. Julio Saez-Rodriguez’s group titled “Comprehensive evaluation of...
CCB student Lindsey Olsen joined the group as a graduate student. Welcome, Lindsey!
Faye has been awarded funding on the CPRIT BCM Comprehensive Cancer Training Program to support her research...
Dr. Zhang is a recipient of a CPRIT Individual Investigator Research Award for Computational Systems Biology .
Congratulations to James for passing the QCB PhD Qualifying Exam!
2021
We had a much needed and deserved Holiday Party at the Hermann Park. Great food and great fun! Special thanks...
Faye’s paper Deep learning-derived evaluation metrics enable effective benchmarking of computational tools for...
Congratulations to Jonathan on winning the 2nd place prize for his oral presentation at the 16th Annual Breast...
Xinpei’s paper caAtlas: An immunopeptidome atlas of human cancer has been published in iScience . This paper...
The CPTAC study Proteogenomic characterization of pancreatic ductal adenocarcinoma has been published in Cell...
The CPTAC study A proteogenomic portrait of lung squamous cell carcinoma has been published in Cell ....
Kuan Huang joined the lab as a postdoctoral research associate. Welcome, Kuan!
The paper describing the crowdsourcing precisionFDA NCI-CPTAC Multi-omics Enabled Sample Mislabeling...
Zhiao’s paper Feature selection methods for protein biomarker discovery from proteomics or multi-omics data...
Xinpei received the AACR Women in Cancer Research (WICR) Scholar Award for her work on caAtlas , which was...
QCB student Chang In Moon (James) joined the group as a graduate student. Welcome, James!
Xinpei has been selected for the trainee award by the US HUPO 2021 conference committee for her work on...
The CPTAC study Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous...
Diyahir Campos joined the lab as a bioinformatics programmer. Welcome, Diyahir!
2020
The Proteomics special issue, “ Computational Proteomics: Focus on Deep Learning “, is now online. This...
Jiayi Luo from the CCB program joined the lab for a research rotation. Welcome, Jiayi!
James Moon from the QCB program joined the lab for a research rotation. Welcome, James!
A review article led by Bo, Deep learning in proteomics , has been published in Proteomics . This paper...
Kai’s paper DeepRescore: leveraging deep learning to improve peptide identification in immunopeptidomics has...
Congratulations to Michael on successfully defending his PhD thesis!
Mariah Berner from the CCB program joined the lab for a research rotation. Welcome, Mariah!
Sara’s review article Using phosphoproteomics data to understand cellular signaling: a comprehensive guide to...
Bo’s paper Cancer neoantigen prioritization through sensitive and reliable proteogenomics analysis has been...
The CPTAC study Proteogenomic Characterization of Endometrial Carcinoma has been published in Cell ....
Our collaborative study with Drs. Ellis, Carr and other colleagues entitled Microscaled proteogenomic methods...
2019
Congratulations to Faye for passing the QCB PhD Qualifying Exam!
Chaozhong Liu from the QCB program joined the lab for a research rotation. Welcome, Chaozhong!
Zifan Zhao from the Cancer & Cell Biology program joined the lab for a research rotation. Welcome, Zifan!
Linhua Wang from the QCB program joined the group for a research rotation. Welcome, Linhua!
Sara and Zhiao’s paper Graph algorithms for condensing and consolidating gene set analysis results has been...
Yuxing’s paper WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs has been published in...
QCB student Jiasheng Wang joined the group as a graduate student. Welcome, Jiasheng!
The CPTAC study Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities has been...
QCB student Wen Jiang (Faye) joined the group as a graduate student. Welcome, Faye!
Dr. Xinpei Yi joined the lab as a postdoctoral research fellow. Xinpei just graduated from the Institute of...
Bo’s paper PepQuery enables fast, accurate, and convenient proteomic validation of novel genomic alterations...
Dr. Jonathan Lei joined the lab as a postdoctoral research fellow supported by the Breast Center T32 training...
Ahmed Gad from TBMM interdisciplinary program joined the lab for a research rotation. Welcome, Ahmed!
Jiasheng Wang from the QCB program joined the group for a research rotation. Welcome, Jiasheng!
2018
Kai Li joined the lab as a bioinformatics programmer. Welcome, Kai!
Wen Jiang (Faye) from the QCB program joined the group for a research rotation. Welcome, Faye!
Bo’s paper PDV: an integrative proteomics data viewer has been published in Bioinformatics . Congratulations,...
Congratulations to Sara on successfully defending her Master’s thesis!
Four students joined the group for summer research experience. Damilola Omotajo is an incoming graduate...
Mr. Ram Srinivasan joined the group as a Senior Bioinformatics Programmer. Ram received his B.S. degree in...
Dr. Yuxing Liao joined the group as a Programmer/Analyst II. Yuxing received his B.S. degree in Biological...
Mr. Noel Namai joined the group as a Programmer/Analyst I. Noel received his M.S. degree in Bioinformatics...
Mr. Leo Zhang joined the group as a Research Technician. Leo received his B.S. degree in Biological Science...
2017
Xiaojing’s paper Detection of proteome diversity resulted from alternative splicing is limited by trypsin...
Dr. Eric Jaehnig joined the group as a Research Associate. Eric received his Ph.D. degree in Biology from the...
Suhas’ paper LinkedOmics: analyzing multi-omics data within and across 32 cancer types has been published in...
Dr. Hyokyeong Lee joined the group as a Research Associate. Hyokyeong received her Ph.D. degree in Computer...
Chaohao Gu from the SCBMB program joined the group for a research rotation. Welcome, Chaohao!
PepQuery , a peptide-centric search engine for novel peptide identification and validation, is now online.
Jingyuan Hu from the SCBMB program joined the group for a research rotation. Welcome, Jingyuan!
Charindu Ranmuthu, a rising junior from the Queens’ College, Cambridge joined the group for a summer...
Our collaborative study with Drs. Sieber, Liebler, Burgess, Chen and their group members on the integrative...
Aaron Westbrook, a rising senior at the University of St. Thomas in Houston joined the group for a summer...
Jing’s paper WebGestalt 2017: a more comprehensive, powerful, flexible and interactive gene set enrichment...
