Hu

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Dr. Hu's laboratory exemplifies the effortless merger of Large Language Models (LLMs), such as ChatGPT, with bioinformatics education and research. This commitment has birthed 'Prompt Bioinformatics', an innovative concept to harness the profound potential of natural language in guiding the complex processes of bioinformatics data analysis. In addition, our investigative efforts extend into the innovative use of LLMs across a vast spectrum of clinical settings.

Simultaneously, we deeply immerse ourselves in another cornerstone of our research - decoding the cryptic epigenetic mechanisms that breed drug resistance in hematological malignancies. Equipped with a comprehensive collection of epigenetic assays such as RNA-Seq, ChIP-Seq, ATAC-Seq, and single-cell Multiome, our mission is to dissect intricate epigenetic processes leading to drug resistance, consequently setting the stage for the identification of new drug targets.

Recent news:
Feb 2024

  • We have three manuscripts accepted in a row within two weeks: 1) the Co-corresponding manuscript submitted with Dr Boone's lab; 2) our story on GPT-4V in reading scientific figures; and 3) the co-author manuscript with Dr Franko's lab.
  • Co-authored manuscript submitted with Dr. Jeff Zhu's lab from NIAID.

Jan 2024

  • Co-authored manuscript submitted with Dr Busada's lab.

Nov 2023

  • Co-authored manuscript submitted with Dr Adjeroh's lab.

Oct 2023

  • A manuscript on GPT-4V(ision) from the lab was submitted.
  • Co-authored manuscript submitted with Dr Franko's lab. Jasleen (now at NIH) contributed to data analysis.
  • Co-corresponding manuscript submitted with Dr Boone's lab. Li from the lab contributed to data analysis.

Sep 2023

  • Co-authored manuscript submitted with Dr Linsey's lab. Sebastian and Halima contributed to data analysis. Update: in press.

Aug 2023

  • Co-corresponding manuscript submitted with Dr Frisch's lab. Halima and Leo contributed to data analysis.

Jul 2023

  • A manuscript on chatbots in sports rehab from the lab was submitted.
  • A manuscript on Code Interpreter in ChatGPT from the lab was submitted. update: published. Highlighted in WVUToday, TechTimes, Cryptopolitan, knowridge, the daily science, etc.
  • A manuscript on Inflammatory Bone Marrow Mesenchymal Stem Cells in Multiple Myeloma from the lab was submitted. Update: Published.

Jun 2023

  • The lab welcomes Evelyn Shue's revisiting this summer (virtual), student volunteers April Chen and Tina Cheng, and cancer institute summer intern Joseph McBee, all working on the innovative use of ChatGPT in research.
  • A manuscript on the responsible use of chatbots in bioinformatics submitted. Update: published in GPB.
  • Our ChatGPT-aided bioinformatics learning is highlighted in WVUToday, the State Journal, and Tech Feature in Nature.

May 2023

  • Co-author Manuscript submitted with Dr. Tim Eubank's lab. Fingers crossed. Update: Published.

Mar, 2023

  • Congratulations to Evelyn for getting multiple offers from prestigious universities including two Ivy League!
  • Congratulations to Emily for getting into Dartmouth College!
  • A co-authored manuscript on ChatGPT in Finance and Economics submitted.
  • Another co-authored manuscript submitted with Dr. Jeff Zhu's lab from NIAID. Fingers crossed. Update: Published.
  • Congratulations to Rachel for getting into Vanderbilt. Enjoy the music scene, particularly country music, in Nashville!

Feb, 2023

  • A manuscript about ChatGPT-assisted education on data analysis submitted. Now published with Quantitative Biology.
  • Co-authored manuscript submitted with Dr. Ekaterina Weil's lab here at WVU. Fingers crossed. update: published.

Jan, 2023

  • Co-authored manuscript submitted with Salik lab. Jasleen and Leo contributed to data analysis. update: published.

Dec, 2022:

  • Two manuscripts submitted this month. One with Dr. Rio Rita's lab and the other with Dr. Cory Robinson's lab (in press). Fingers crossed. update: both published.

Aug, 2022:

  • The lab congratulates Jasleen for her new job as a bioinformatics scientist working for NIH from this Sep!!!
  • Third co-authored manuscript with Dr Ming Pei's lab submitted. Halima and Leo from the team contributed to data analysis. Now in press with Bioactive Materials.

Jul, 2022:

  • Rachel Mangano won a runners-up award in the Health Sciences Category at the 2022 Summer Undergraduate Research Symposium for her summer work in the lab. Congratulation to Rachel and thanks Sebastian for his guidance.
  • Co-authored manuscript submitted with Dr Edwin Wan's lab. Lei and Halima from the team contributed to data analysis.

Jun, 2022:

  • The lab welcome Dr Li Ma join as a Post-Doc Fellow.
  • Co-authored manuscript submitted with Salik lab. Drake from the team contributed to data analysis. Published in Redox Biology.
  • Sebastian received the 2022 Jennifer Gossling Fellowships. Congratulations.

May, 2022:

  • The lab welcome Alan Mizener join as a MD/PHD rotation student.

Apr, 2022:

Mar, 2022:

  • Another co-authored manuscript submitted with Dr. Jeff Zhu's lab from NIAID. Fingers crossed.
  • The lab welcomes Evelyn Shue from Richard Montgomery High School (Maryland) joining the lab as a special volunteer.

Feb, 2022:

  • We got CUT&TAG work: the second epigenetic assay successfully implemented in the lab.
  • Sebastian's abstract submitted to Experimental Biology 2022 (Phelidepiha in April) was selected as an oral presentation in the Spotlight Session. Congratulations!!!
  • The lab was recommended for funding as a Project Leader (renewable up to three years) with the Tumor Microenvironment Center of Biomedical Research Excellence (TME CoBRE).

Jan, 2022:

  • Sebastian had his first first-author manuscript submitted with equal contribution from Leo. Published with Cancers
  • The lab welcomes Zahra Pourteymourfard Tabrizi to join for rotation
  • Third co-authored manuscript submitted with Dr Lori Hazlehurst's lab. Sebastian contributed RNA-SEQ data analysis. Now in press with Cancers.

Nov, 2021:

  • Emily Lecea received an AAI Undergraduate Award and an undergraduate Poster Award at the 2021 Autumn Immunology Conference in Chicago. Congratulations.

Oct, 2021:

  • The lab welcomes Dr. Lei Wang from Fudan University and Dr. Tulika Sharma from University of Connecticut joining the lab as post-doc fellows.

Sep, 2021:

  • The lab welcomes 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.

Aug, 2021:

  • After two years, our second paper co-authored with Dr Edwin Wan's lab now submitted. Drake contributed to the analysis. now in press with PNAS.
  • Second manuscript on microbiome submitted, this time co-authored with Dr. Cole Vonder Haar's lab. Jasleen contributed to part of the analysis. Now in press with Behavioral Neuroscience.
  • 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.

Jul, 2021:

  • 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.

Jun, 2021:

  • 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. Now in press with Frontiers in Immunology

May, 2021:

  • Another co-authored manuscript submitted with Dr. Jeff Zhu's lab from NIAID. Now in press with Immunity.

Apr, 2021:

  • 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.

Mar, 2021:

  • 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.

Feb, 2021:

Jan, 2021:

  • 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.

Nov, 2020:

  • The lab welcome new member Rachel.

Oct, 2020:

  • 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.

Sep, 2020:

  • The lab received an one-year Biostart grant from WVCTSI to use patient samples from WVU Tissue Bank.

Aug, 2020:

  • The lab welcome new members Jasleen, Lev, Drake, Halima, Nikki, Jacob, and Emily.

Jul, 2020:

  • 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!!!

Jun, 2020:

May, 2020:

Mar, 2020:

Feb, 2020:

  • Sebastian Dziadowicz joined the lab as my first graduate student. Welcome again.

Jan, 2020:

  • The lab welcomes Sebastian Dziadowicz to join for rotation.

Dec, 2019:

Nov, 2019:

  • 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.

Oct, 2019:

Sep, 2019:

  • 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.

Aug, 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.

Jul, 2019:

  • 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!