Laboratory of Genomic Data Science and Epigenome Biology
Department of Microbiology, Immunology, and Cell Biology
School of Medicine
West Virginia University
Dr. Hu’s laboratory combines computational methods and experimental techniques to understand epigenetic regulation of gene expression of immune cells under physiologic conditions and in disease such as cancers. It is a “moisture” lab with both dry and wet components.
The epigenome of an eukaryotic cell consists of chemical changes to DNA sequence and histone proteins wrapped by the DNA sequence. Chromatin modifying enzymes, transcription factors, and transcription machinery collectively modulate the epigenome to instruct gene expression program. The overarching goal of the lab is to understand the impact of environmental stimuli on the epigenetic regulation of transcription program of immune cells and explore the dysregulation leading to disease and drug resistance. We are particularly interested in how epigenome senses environmental stimuli and then transforms to modulate transcription program in response, taking multiple myeloma in the bone-marrow microenvironment as a model system.
We combine computational methods with experimental sequencing data produced in public and generated in-house for hypothesis generation and testing. We measure the epigenome using established genome-wide profiling techniques to determine the genome-wide landscapes of different epigenetic components, such as histone modifications and transcription factors with ChIP-Seq, chromatin accessibility with ATAC-Seq, 3D chromatin with Hi-C, and gene expression with RNA-Seq. We utilize existing and develop new computational tools to explore the complexities of epigenetic regulation related to disease, in cell populations and at single cell level.
As systems immunologists, we are thrilled to embrace the era of data-rich cancer and immunology research driven by deep sequencing. Trainees in the lab will have ample opportunities to develop both computational skills and experimental skills to generate/process sequencing data and to formulate/test hypotheses. We encourage trainees with biology background to learn basics in data analysis with programming and building pipelines, and mentor trainees with computation/mathematics/physics background to formulate biology questions through interaction with biologists. The lab also commits to offer trainees opportunities to acquire essential skills for team-science through collaborations with on-campus and/or off-campus laboratories from distinctive but relevant research fields.
- The lab welcome new members Weijun Yi and Garrett Perkin.
- The lab received an one-year WV-INBRE Supplement grant from NIGMS for a collaborative project with Dr. Tamer Fandy from University of Charleston.
- After two years, our second paper co-authored with Dr Edwin Wan's lab now submitted. Drake contributed to the analysis. Fingers crossed.
- Second manuscript on microbiome submitted, this time co-authored with Dr. Cole Vonder Haar's lab. Jasleen contributed to part of the analysis. Fingers crossed.
- Nikki Cannon received WVU's 2021 Gilman Scholars. Nikki has been an undergraduate student worker in the lab since Aug 2020 for nine months before joining NIH as a summer intern. During the time, she has contributed actively to several research projects, with one co-author publication in PNAS. Congratulations!
- Emily Lecea won a runners-up award in the Health Sciences Category at the 2021 Summer Undergraduate Research Symposium for her summer work in the lab. Congratulation to Emily and thanks Sebastian for his guidance.
- We got ATAC-Seq work with a kit from Illumina. That kit does not come with a manual. It could be that the assay is so simple that a manual is not needed. It turned out not to be the case. But we got it work anyway.
- With strong supports from the WVU Genomics Core, the lab got its first set of RNA-Seq libraries using only thousands of cells. The quality looks impressive after visualizing the sequencing data with IGV.
- The lab welcome Mr. Olamide Adegbamigbe from Shepherd University join as a summer intern.
- Co-authored manuscript submitted with Dr. Stacey Anderson's lab from NIOSH. Jasleen from the team contributed to data analysis. update, in press with Toxicological Sciences
- Co-authored manuscript submitted with Dr Ivan Martinez's lab and Dr. John Barnett's lab. Sebastian from the lab contributed to part of the data analysis. Fingers crossed.
- Another co-authored manuscript submitted with Dr. Jeff Zhu's lab from NIAID. Fingers crossed.
- Happy to share that three undergraduates in the lab received internships this summer: Emily with the departmental IMMB internship, Lev with the WVU Cancer Institute Summer Undergraduate Research Program, and Nikki with NIH Summer Internship Program. What a busy summer we will have.
- Co-authored manuscript submitted with Dr Lori Hazlehurst's lab. Update published with Cells.
- Co-authored manuscript submitted with Dr. Jeff Zhu's lab from NIAID. Nikki from the team contributed to data analysis. Update, published with PNAS
- Got invitation from Cells to join editorial board. Yes, happily accepted.
- Co-authored manuscript submitted with Dr. Lan Guo's lab. Update, published with IJMS
- Got invited to serve as Associate Editor for Frontiers in Immunology - T Cell Biology. Yes, happily accepted.
- Halima from Bangladesh safely boarded Morgantown. Welcome to the lab.
- Three students in the lab got a GPA of 4 in the last semester. Impressive.
- Finally, excited to learn that the single cell DNase now in high-throughput is accepted for publication. Thank you Keji for having had me in the team!!!
- Co-authored manuscript submitted with Dr. Elena Pugacheva's lab. Jasleen from the team contributed to data analysis. Update in press with Oncogene.
- The lab welcome new member Rachel.
- The Lab welcome new member Evan.
- The lab welcome Dr Muhammad Shahid joining the lab as a senior Post-Doc from Cedars-Sinai Medical Center, Los Angele.
- The lab received an one-year Biostart grant from WVCTSI to use patient samples from WVU Tissue Bank.
- The lab welcome new members Jasleen, Lev, Drake, Halima, Nikki, Jacob, and Emily.
- Co-authored manuscript submitted with Dr Slawomir Lukomski's lab. Update, published with PLoS One.
- The lab received an one-year Pilot award from the Tumor Microenvironment Center of Biomedical Research Excellence (TME CoBRE).
- Jasleen Gandhi, the first undergraduate student-worker in the lab, was admitted to a master program of Bioinformatics in the Department of Computational and Systems Biology, University of Pittsburgh. Congratulations! Update: Jasleen also got admitted to the master program of Biomedical Sciences in Health Science Center, WVU. Guess what? Jasleen chose to stay with us!!!
- Co-authored manuscript submitted with Dr Ming Pei's lab. Update 09/14/2020, in press with Biomaterials
- Co-authored manuscript submitted with Dr Lori Hazlehurst's lab. Update: published with Current Opinion in Pharmacology on 09/06/2020.
- Sebastian Dziadowicz joined the lab as my first graduate student. Welcome again.
- The lab welcomes Sebastian Dziadowicz to join for rotation.
- Manuscript with Dr Jeff Zhu's lab at NIAID published in Immunity on Christmas Eve, a Santa's gift.
- Co-authored manuscript submitted with Dr Wei Du's lab. Update, published with Stem cells on 03/04/2020.
- Co-authored manuscript submitted with Dr Ming Pei's lab. Update, published by Frontiers in Cell and Developmental Biology on 04/15/2020.
- Dr Lei Wang from Institute of Biophysics, CAS, committed to join the lab as a bioinformatics post-doc. Dr Wang has numerous major author publications in respected journals. He also has several now under-review with top journals. Congratulations! Lei.
- Co-authored manuscript submitted with Dr Ivan Martinez's lab. Update Published with Cancer Research on 07/03/2020.
- Guess what? Later of today (09/20/2019), we had our first WVU-branded co-corresponding paper submitted with Dr Edwin Wan's lab. From data analysis to paper submission, it was less than two months. Yes, that's the speed of mountaineers. Fingers crossed. Update, published with Frontiers in Immunology on 11/26/2019.
- Manuscript submitted for iHiC, a set of C++ utilities for data pre/post-procession to facilitate Hi-C data analysis. Update, published as a book chapter with Methods in Molecular Biology: Stem Cell Transcriptional Networks on 01/21/2020.
- ACT-Seq for single-cell ChIP-Seq of histone modification accepted by Nature Communications (Dr Hu as a co-author).
- Aniello Infante joined the lab/core as a lead bioinformatician. Welcome Niel!