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Weigang Qiu, Ph.D., Professor Department of Biological Sciences Hunter College of City University of New York Belfer Research Building, Room 402 413 East 69th Street, New York, NY 10021 Office: 1-212-896-0445 Email: wqiu-at-(hunter.cuny.edu) |
Fieldwork Gallery
Lab publications
Lyme Genomics, Evolution, & Ecology
Akther et al. 2024. "Natural selection and recombination at host-interacting lipoprotein loci drive genome diversification of Lyme disease and related bacteria" mBio 0:e01749-24. Press coverage: CUNY Graduate Center News Story; Hunter press
Di*, Akther*, Bezrucenkovas, Ivanova, Sulkow, Wu, Mneimneh, Gomes-Solecki, Qiu (2021). "Maximum antigen diversification in a lyme bacterial population and evolutionary strategies to overcome pathogen diversity". The ISME Journal. 16, 447-464. (*co-first authors) Blog Post
Evolution & Learning Algorithms
Informatics Tool Development
last update: March 20, 2023
Lab members and trainees
Year/Period | Doctoral members & trainees | Other members & trainees |
---|---|---|
Current Academic Year
(Fall 2022, Spring 2023 & Summer 2023) |
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Alumni (Since Fall 2002) |
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(published coauthors)
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Web Apps
Apps with Collaborators (or from published papers)
Borrelia diagnostic antigens (App developed by Liann Aris-Henry; Data from Arumugam et al (2019))
Borrelia growth transcriptome (App developed by Laziz Asamov; Data from Arnold et al (2016))
Data & GSEA associated with Polotskaia_etal_2014 (with Bargonetti Lab @Hunter)
Qiu Lab Apps
Curricular Development & Bioinformatics/QuBi Advising
- QuBi advisors: Weigang Qiu, Ntino Krampis, Rabindra Mandal (Biology); Saad Mneimeih, Lei Xie (CS); Akira Kawamura (Chem); Dana Sylvan (Math & Stats)
- Permission for non-Biology majors to take BIOL203 & BIOL425, every Spring
- Collect names, major, and IDs to send to course coordinator to grant permission. Waive BIOL10200 pre-reqs for taking BIOL203.
- Curricular resources:
- Biology courses and pre-reqs
- Hunter Biology Major 1 (including the Bioinformatics Option)
- Hunter Chemistry Major 2 (including the Bioinformatics Option)
- Hunter Computer Science (including Bioinformatics Concentration)
- Hunter Mathematics (including the Quantitative Biology Concentration)
- Hunter Statistics (including the Quantitative Biology Concentration)
- QuBi advising:
- Declaration of Bioinformatics concentration: In-person advising to work out the semester-by-semester courses
- Approve on department spreadsheet (or send email to "Samantha Sheppard-Lahiji" and "HTR Bio" <biology@hunter.cuny.edu>)
- Students should take Bioinformatics-specific electives (8 cred; see Hunter Catalog below), not general electives
- Examples: Anthrop302 (3 cr); Chem333 (3 cr); BIOL47119 & BIOL47120 (3cr); BIOL48002 (2 cr)
- Students need to take BIOL48002 (2 cr), which counts towards as research credit, to graduate as honors
- General advising:
- ~40 students every semester. Send out emails to students. Go through student courses by Email or by appointment
- Recommend new math courses: MATH15200 & STAT21350
- Hosting QuBi students in lab
- This is to enhance the informatics and coding skills of our students
- Students should register and get BIOL48002 credits, which counts towards their elective credits & eligibility for honors
- 3-5 students per semester
- Outside research opportunities
- MIT Quantitative Workshop (first week of January, in Boston). Coordination with CS (Saad & Susan Epstein) in Fall
- Simons Foundation/Flatiron Institute Center for Computational Biology (CCB) Internship program. Open House in Spring
Course/Lecture syllabi
- Computational Genomics (KIZ, Fall 2024)
- NYRaMP Workshop (August 2024)
- BIOL47120 BioMedical Genomics (Spring 2024). Tutorials: R Markdown Cluster analysis single-cell RNA-seq
- BIOL425 Computational Molecular Biology (Spring, 2023). Lecture material on github
- BIOL714 Cell Biology: R Demo (Spring 2024) R Demo (Spring 2023)
- QuBi module: BIOL20300 Molecular Genetics, Lab 12 (2023)
- QuBi module: BIOL20300 Molecular Genetics, Lab 13 (2022)
- QuBi module: BIOL30300 Cell Biology, Bioinformatics Lab (transcriptome analysis)
- Big Data (Summer, 2020)
- BIOL47120 Biomedical Genomics II (Spring, 2020)
- BIOL425 Computational Molecular Biology (Spring, 2020)
- BIOL37500, Molecular Evolution (Fall, 2019)
- Southwest University R course (Summer, 2019)
- Analysis of Biological Data (Spring, 2017)
- Bioinformatics Workshop (Summer, 2014)
SARS-CoV-2 genome evolution
Akther, Bezrucenkovas, Sulkow, Panlasigui, Qiu, Di (April, 2020). "CoV Genome Tracker: tracing genomic footprints of Covid-19 pandemic". BioRxiv; Web app: SARS-CoV-2 Genome Tracker; Github: https://github.com/weigangq/cov-browser
Akther, Bezrucenlovas, Li, Sulkow, Di, Pante, Martin, Luft, Qiu (Sep, 2021). "Following the Trail of One Million Genomes: Footprints of SARS-CoV-2 Adaptation to Humans". BioRxiv link: . Github: https://github.com/weigangq/cov-db
Lab Resources & Protocols
- Monte Carlo Club
- NY-RaMP Mentoring
- Borreliella genome sequencing consortium: Weekly meetings (Tu @11): Since Jan 2023
- Borreliella diagnostic antigens (Fall 2023-Fall 2027):
- Zoom call (Jan 23, 2024)
- Next meeting: March 23, 2024
- Qiu lab network first-time user guide
- Qiu lab Github repositories: https://github.com/weigangq/?tab=repositories
- Mini-Protocols (frequently used computer codes and pipelines)
- Tick handling protocols
- Hunter HPC Usage
- R for Data Science (2e), (2024) by Wickham, Grolemund & Çetinkaya-Rundel (Bookdown version)
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