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Welcome to Dr. Bing Zhang’s Lab at the Baylor College of Medicine. We develop and use integrative bioinformatics approaches to extract biological meanings from experimental data and generate hypotheses for experimental validation. Please explore our website to learn more about our people and our research.

Lab News

[2023-12] Dr. Seunghyuk Choi joined the lab as a postdoctoral research associate. Welcome, Seunghyuk!

[2023-11] Dr. Wenrong Chen joined the lab as a postdoctoral research associate. Welcome, Wenrong!

[2023-11] Sara’s paper IDPpub: Illuminating the Dark Phosphoproteome Through PubMed Mining has been published in Molecular & Cellular Proteomics. Phosphorylation is an essential component of cellular signaling, and phosphoproteomics enables global identification and quantification of phosphosites from biological samples. However, interpretation of phosphoproteomic findings is hindered by our limited knowledge on functions, phenotype associations, and regulating enzymes of the phosphosites. We developed a computational pipeline that uses BioBERT to extract phosphorylation sites from biomedical abstracts. The pipeline further aligns the sites to human and mouse reference sequences to facilitate computational applications and intersection with mass spectrometry experiments. The extracted evidence sentences can be used to identify regulating enzymes and biological functions. We made all data available in the IDPpub web portal for easy exploration.

[2023-10] The review article Current perspectives on mass spectrometry-based immunopeptidomics: the computational angle to tumor antigen discovery co-authored by Drs. Zhang and Bassani-Sternberg has been published in The Journal for ImmunoTherapy of Cancer.

[2023-10] The paper ClinicalOmicsDB: exploring molecular associations of oncology drug responses in clinical trials led by James and John has been published in Nucleic Acids Research. Congratulations! This paper describes ClinicalOmicsDB, a web application for exploring molecular associations of oncology drug responses in clinical trials. This database encompasses data from 40 clinical trial studies and a total of 5913 patients, including 1224 patients treated with immunotherapy. Three case studies were presented to demonstrate the utility of this resource in human cancer research.

[2023-10] QCB student Minhang Xu joined the group for a research rotation. Welcome, Minhang!

[2023-09] Yongchao’s paper SEPepQuant enhances the detection of possible isoform regulations in shotgun proteomics has been published in Nature Communications. Shotgun proteomics is crucial for identifying and quantifying proteins in biomedical research. However, characterizing protein isoforms is challenging due to shared peptides among proteins. We introduce SEPepQuant, a graph theory-based method to tackle this challenge. SEPepQuant addresses limitations of existing methods, enhancing isoform characterization, identifying isoform-level regulation events, and facilitating cross-study comparisons. Our results support a significant role of protein isoform regulation in normal and disease processes, making SEPepQuant valuable for biological and translational research. Source code is available in the Zhang Lab GitHub.

[2023-09] Jonathan attended the HUPO Conference held in Busan, Korea, where he delivered an oral presentation titled “Pan-cancer proteogenomics expands the landscape of therapeutic targets”. He was honored with a travel award in recognition of this work. Congratulations! HUPO2023Busan

[2023-08] Our paper A proteogenomics data-driven knowledge base of human cancer has been published in Cell Systems. Congratulations to Yuxing, Sara, and all co-authors! This paper describes LinkedOmicsKB, a knowledge base built upon consistently processed and systematically precomputed CPTAC pan-cancer proteogenomics data. With approximately 40,000 gene-, protein-, mutation-, and phenotype-centric web pages, it enables anyone with internet access to conduct meaningful inquiries into CPTAC data, facilitating data-driven scientific discoveries. The paper uses three case studies to illustrate the practical utility of LinkedOmicsKB in providing new insights into genes, phosphorylation sites, somatic mutations, and cancer phenotypes.

[2023-08] The CPTAC perspective article Proteogenomic data and resources for pan-cancer analysis has been published in Cancer Cell. Congratulations to Yongchao and all co-authors! This article describes efforts by the CPTAC pan-cancer working group in data harmonization, data dissemination, and the provision of computational resources to facilitate biological discoveries. All processed data tables can be accessed at the Proteome Data Commons.

[2023-08] The CPTAC study Proteogenomic insights suggest druggable pathways in endometrial carcinoma has been published in Cancer Cell. Congratulations to Yongchao and all co-authors! Some of the key findings include identifying two peptides that can predict antigen processing and presentation machinery activity, revealing a potential role for metformin treatment in non-diabetic patients with elevated MYC activity, discoverying PIK3R1 in-frame indels as a primary driver of elevated AKT phosphorylation and increased sensitivity to AKT inhibitors, and connecting CTNNB1 hotspot mutations to pS45 phosphorylation-induced degradation of β-catenin.

[2023-08] QCB student Juliana Yue joined the group for a research rotation. Welcome, Juliana!

[2023-06] Most of our lab members participated in the ASMS Conference held in Houston, where we showcased our recent work. One notable highlight was Yongchao delivering an oral presentation titled “SEPepQuant Enhances the Detection of Possible Isoform Regulations in Shotgun Proteomics”. ASMS2023Houston

[2023-05] QCB student Tobie Lee joined the group for a research rotation. Welcome, Tobie!

[2023-05] Faye successfully defended her PhD thesis, congratulations, Dr. Jiang! She will be joining AstraZeneca as a Senior Computational Biologist next month. Best wishes for a bright future!
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[2023-04] Faye, James, Jonathan, Sara and Dr. Zhang attended the AACR Conference in Orlando, FL. James received a 2023 AACR-Sanofi Scholar-in-Training Award for his work on “Bridging the gap between clinical-omics and machine learning to improve cancer treatment”, and Jonathan received the same award for the work on “Pan-cancer proteogenomics expands the landscape of therapeutic targets”. Congratulations! Both works were also selected for oral presentations. Faye did a poster presentation on CoPheeMap, and Sara did a poster presentation on LinkedOmicsKB.
AACR2023

[2023-04] Bo’s paper PepQuery2 democratizes public MS proteomics data for rapid peptide searching has been published in Nature Communications. One of the most important milestones in proteomics is the Amsterdam Principles, which require mandatory raw MS/MS data deposition to promote broad reuse of the data. However, because of the challenges involved in understanding, downloading, analyzing, and interpreting MS/MS data, investigation and reuse of these public data are largely restricted to computational proteomics researchers. By enabling rapid identification of any known or novel peptide sequences of interest in any local or publicly available MS-based proteomics datasets in a targeted manner, PepQuery2 provides a practical solution that makes public MS/MS data easily useful to the general research community. Both the command line version and the web version of PepQuery2 are available at http://www.pepquery.org. The source code of PepQuery2 is available at https://github.com/bzhanglab/PepQuery.

[2023-03] Congratulations to Lindsey for passing the CCB PhD Qualifying Exam!

[2023-03] Faye, Lindsey and Dr. Zhang attended the US HUPO Conference in Chicago. Faye received a Travel Award for her work on “Illuminating the Dark Cancer Phosphoproteome Through a Machine Learned Co-Regulation Map of 30,000 Phosphosites”, which was also selected for an oral presentation. Dr. Zhang received the Gilbert S. Omenn Computational Proteomics Award and gave an award talk entitled “Embracing Complexity, Seeking Simplicity”. Congratulations!
USHUPO

[2023-01] Lunch party to celebrate the new year and welcome new lab members!
2023_NewYear

[2023-01] Duy Pham and John Elizarraras joined the group as Bioinformatics Programmers. Welcome, Duy and John!

[2023-01] CCB student Evelyn de Groot joined the group for a research rotation. Welcome, Evelyn!

[2022-12] Lindsey Lindsey_HUPO2022 gave an oral presentation on “Tripartite graph modeling enables comprehensive protein isoform characterization in shotgun proteomics” at the HUPO 2022 conference in Cancun.

[2022-11] Faye, James, and Lindsey were selected for oral presentation at the 17th Annual Breast Center Retreat, and James won the 2nd place prize for his presentation entitled “ClinicalOmicsDB – Bridging the gap between clinical omics data and machine learning”. Congratulations!

[2022-10] Bo’s paper OmicsEV: a tool for comprehensive quality evaluation of omics data tables has been published in Bioinformatics. This paper describes an R package for quality evaluation of omics data tables. For each data table, OmicsEV uses a series of methods to evaluate data depth, data normalization, batch effect, biological signal, platform reproducibility, and multi-omics concordance, producing comprehensive visual and quantitative evaluation results that help assess data quality of individual data tables and facilitate the identification of the optimal data processing method and parameters for the omics study under investigation. OmicsEV and documentation can be downloaded at https://github.com/bzhanglab/OmicsEV.

[2022-10] QCB students Jiaye Chen and Daniel Palacios joined the group for a research rotation. Welcome, Jiaye and Daniel!

[2022-08] Dr. Chenwei Wang joined the lab as a postdoctoral research associate. Welcome, Chenwei!

[2022-08] QCB student Xuqian Tan joined the group for a research rotation. Welcome, Xuqian!

[2022-07] Our U01 application entitled “Illuminating understudied druggable proteins using pan-cancer proteogenomics data” has been selected for funding by the Illuminating the Druggable Genome (IDG) consortium.

[2022-07] James was offered a position in the CTR Certificate of Added Qualification program and the program’s T32 grant. The CAQ training is designed to develop leaders in translational research who are well equipped to translate discoveries from the laboratory to the clinic to the benefit of human health. Congratulations!

[2022-06] The Office of Cancer Clinical Proteomics Research at the National Cancer Institute (NCI) has reaffirmed its commitment to furthering proteogenomics research by announcing the next round of Clinical Proteomic Tumor Analysis Consortium (CPTAC) centers. As part of this new phase, our lab will continue to serve as a Proteogenomic Data Analysis Center (PGDAC) over the next five years.

[2022-06] Xinpei and Sara gave oral presentations about their computational tools DeepRescore2 and IDPpub, respectively, at the 70th ASMS Conference on Mass Spectrometry and Allied Topics (ASMS 2022) took place 5-9 June 2022 in Minneapolis, MN, USA. DeepRescore2 leverages deep learning to improve phosphopeptide identification and site localization in phosphoproteomics, whereas IDPpub aims to illuminate the dark phosphoproteome through PubMed mining.

[2022-06] Byron Jia, a rising senior at Carleton College joined the group for a summer internship through the SMART program. Welcome, Byron!

[2022-05] CCB student Lindsey Olsen joined the group as a graduate student. Welcome, Lindsey!

[2022-03] Faye has been awarded funding on the CPRIT BCM Comprehensive Cancer Training Program to support her research on “Leveraging Artificial Intelligence to Illuminate the Cancer Phosphoproteome”. Congratulations!

[2022-02] Dr. Zhang is a recipient of a CPRIT Individual Investigator Research Award for Computational Systems Biology.

[2022-01] Congratulations to James for passing the QCB PhD Qualifying Exam!

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