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.
[2019-01] Bo’s paper PepQuery enables fast, accurate, and convenient proteomic validation of novel genomic alterations has been published in Genome Research. Congratulations, Bo! PepQuery is a peptide-centric search engine that allows quick and easy proteomic validation of genomic alterations without customized database construction. Next generation sequencing-based genomic studies continuously identify new genomic alterations that may lead to novel protein sequences, which are attractive candidates for disease biomarkers and therapeutic targets after proteomic validation. The popular approach for proteomic validation requires customized database construction and a full evaluation of all possible spectrum-peptide pairs, which is time-consuming. We implemented PepQuery as both stand-alone and web-based applications. The stand-alone version supports batch analysis and user-provided MS/MS data. The web version provides access to more than half a billion MS/MS spectra from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) and other cancer proteomic studies, making MS/MS data directly available and useful to scientists outside the proteomics community. PepQuery can be accessed at http://www.pepquery.org.
[2019-01] Jonathan Lei joined the lab as a postdoctoral research fellow. Welcome, Jonathan!
[2019-01] Ahmed Gad from TBMM interdisciplinary program joined the lab for a research rotation. Welcome, Ahmed!
[2019-01] Jiasheng Wang from the QCB program joined the group for a research rotation. Welcome, Jiasheng!
[2018-12] Kai Li joined the lab as a bioinformatics programmer. Welcome, Kai!
[2018-10] Wen Jiang (Faye) from the QCB program joined the group for a research rotation. Welcome, Faye!
[2018-09] Bo’s paper PDV: an integrative proteomics data viewer has been published in Bioinformatics. Congratulations, Bo! PDV is a lightweight visualization tool that enables intuitive and fast exploration of diverse, large-scale proteomics datasets on standard desktop computers in both graphical user interface and command line modes.The software and the user manual are freely available at http://pdv.zhang-lab.org . The source code is available at https://github.com/wenbostar/PDV.
[2018-07] Congratulations to Sara on successfully defending her Master’s thesis!
[2018-05] Four students joined the group for summer research experience. Damilola Omotajo is an incoming graduate student in the MHG program; she has a B.S. degree in Mathematics with Minor in Biology and an M.S. degree in Biology with Minor in Statistical Methods from the Sam Houston State University.Paul Jiang, a rising junior at the Rice University pursuing a degree in Computer Science, joined the group as a Research Observer. Both Aaron Westbrook and Kailey Ferger are supported by the SMART program. Aaron just graduated from the University of St. Thomas with a B.S. degree in Bioinformatics, and this is his second summer in our group. Kailey is a rising senior at the University of Rochester pursuing a degree in Computational Biology. Welcome our new members!
[2018-02] Mr. Ram Srinivasan joined the group as a Senior Bioinformatics Programmer. Ram received his B.S. degree in Bioinformatics from the SASTRA University in India and M.S. degree in Bioinformatics from the NYU Polytechnic School of Engineering. He worked at the Icahn School of Medicine at Mount Sinai for three years before joining our lab. Welcome, Ram!
[2018-02] Dr. Yuxing Liao joined the group as a Programmer/Analyst II. Yuxing received his B.S. degree in Biological Science from the University of Science and Technology in China and just completed his Ph.D. study on Molecular Biophysics with Computational and Systems Biology specialty at the University of Texas Southwestern Medical Center. Welcome, Yuxing!
[2018-02] Mr. Noel Namai joined the group as a Programmer/Analyst I. Noel received his M.S. degree in Bioinformatics from the Northeastern University and B.S. degree in Mathematics from the Maseno University in Kenya. He worked at the Seven Bridges Genomics for two years before joining us. Welcome, Noel!
[2018-01] Mr. Leo Zhang joined the group as a Research Technician. Leo received his B.S. degree in Biological Science from the Colorado State University with a Minor in Mathematics. Welcome, Leo!
[2017-12] Xiaojing’s paper Detection of proteome diversity resulted from alternative splicing is limited by trypsin cleavage specificity. has been published in Molecular & Cellular Proteomics. Congratulations, Xiao Jing! Alternative splicing dramatically increases transcriptome complexity but its contribution to proteome diversity remains controversial. Exon-exon junction spanning peptides provide direct evidence for the translation of specific splice isoforms and are critical for delineating protein isoform complexity. In this paper, we studied the proteomic coverage of exon-exon junctions in three publicly available proteomics data sets and found that trypsin preferentially cleaves exon-exon junctions and thus hinders the detection of junction-spanning peptides. This phenomenon was explained by evolutionarily conserved preferential nucleotide usage at exon boundaries according to nucleotide sequence analysis of five eukaryotic genomes. Our in silico and experimental analyses showed that complementary digestion schemes are essential to study the translation of alternative mRNA splicing to proteome diversity.
[2017-11] Dr. Eric Jaehnig joined the group as a Research Associate. Eric received his Ph.D. degree in Biology from the University of California, San Francisco, followed by postdoctoral training in systems biology at the Ludwig Institute for Cancer Research. To enhance his quantitative skills, Eric recently completed a Master’s degree in Bioengineering from the Rice University. Welcome, Eric!
[2017-11] Suhas’ paper LinkedOmics: analyzing multi-omics data within and across 32 cancer types has been published in Nucleic Acids Research. LinkedOmics is a new and unique resource for disseminating and analyzing The Cancer Genome Atlas (TCGA) data. It is also the first multi-omics database that integrates mass spectrometry (MS)-based global proteomics data generated by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) on selected TCGA tumor samples. LinkedOmics has three analysis modules. The LinkFinder module allows flexible exploration of associations between a molecular or clinical attribute of interest and all other attributes, providing the opportunity to analyze and visualize associations between billions of attribute pairs for each cancer cohort. The LinkCompare module enables easy comparison of the associations identified by LinkFinder, which is particularly useful in multi-omics and pan-cancer analyses. The LinkInterpreter module transforms identified associations into biological understanding through pathway and network analysis. In this paper, we used five case studies to demonstrate that LinkedOmics provides a unique platform for biologists and clinicians to access, analyze and compare cancer multi-omics data within and across tumor types. Although the current version of LinkedOmics includes only TCGA and CPTAC data, it can be easily extended to support other cohort-based multi-omics studies.
[2017-10] Dr. Hyokyeong Lee joined the group as a Research Associate. Hyokyeong received her Ph.D. degree in Computer Science from the University of Southern California and was a Postdoctoral Associate in the Department of Computational and Systems Biology at University of Pittsburgh. Welcome to the lab, HyoKyeong!
[2017-10] Chaohao Gu from the SCBMB program joined the group for a research rotation. Welcome, Chaohao!
[2017-08] PepQuery, a peptide-centric search engine for novel peptide identification and validation, is now online.
[2017-08] Jingyuan Hu from the SCBMB program joined the group for a research rotation. Welcome, Jingyuan!
[2017-07] Charindu Ranmuthu, a rising junior from the Queens’ College, Cambridge joined the group for a summer internship. Welcome, Cha!
[2017-06] Our collaborative study with Drs. Sieber, Liebler, Burgess, Chen and their group members on the integrative proteogenomic analysis of colorectal cancer cell lines and human tumors has been published in Gastroenterology in a paper entitled Colorectal cancer cell line proteomes are representative of primary tumors and predict drug sensitivity.
[2017-05] Aaron Westbrook, a rising senior at the University of St. Thomas in Houston joined the group for a summer internship through the SMART program. Welcome, Aaron!
[2017-05] Jing’s paper WebGestalt 2017: a more comprehensive, powerful, flexible and interactive gene set enrichment analysis toolkit has been published in Nucleic Acids Research. The WebGestalt 2017 knowledge base supports 12 organisms, 324 gene identifiers from various databases and technology platforms, and 150,937 functional categories from public databases and computational analyses. Importantly, omics data with gene identifiers not supported by WebGestalt and functional categories not included in the WebGestalt database can also be uploaded for enrichment analysis. The analysis module supports Over-Representation Analysis, Gene Set Enrichment Analysis, and Network Topology-based Analysis. The input interface is simplified, the output interface allows interactive and efficient exploration, and the complete set of results can be easily downloaded. The new GOView tool makes it easy to compare multiple sets of GO enrichment results in the context of the GO directed acyclic graph (DAG).
[2017-02] Dr. Chen Huang joined the group as a Postdoctoral Research Fellow. Chen just received his Ph.D. degree in Biomedical Science from the Vanderbilt University earlier this month. Welcome to the lab, Chen!
[2017-02] Mr. Bo Wen joined the group as a Bioinformatics Programmer. Bo received his Bachelor’s degree in Bioinformation Technology from the Huazhong University of Science and Technology in China in 2010. After graduation, he has been working in the Proteomics Research Group at the BGI-Shenzhen, where he has developed and published multiple bioinformatics tools for proteomics and proteogenomics. Welcome, Bo!