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===Bioinformatics/QuBi Advising=== | ===Bioinformatics/QuBi Advising=== | ||
* QuBi advisors: Weigang Qiu, Ntino Krampis, Rabindra Mandal (Biology); Saad Mneimeih, Lei Xie (CS); Akira Kawamura (Chem); Dana Sylvan (Math & Stats) | * QuBi advisors: Weigang Qiu, Ntino Krampis, Rabindra Mandal (Biology); Saad Mneimeih, Lei Xie (CS); Akira Kawamura (Chem); Dana Sylvan (Math & Stats) | ||
* | * Curricular resources: | ||
** [http://biology.hunter.cuny.edu/index.php?option=com_content&view=article&id=66&Itemid=73 Biology courses and pre-reqs] | |||
** [https://hunter-undergraduate.catalog.cuny.edu/programs/CHEM2-BA Hunter Chemistry Major 2 (including the Bioinformatics Option)] | ** [https://hunter-undergraduate.catalog.cuny.edu/programs/CHEM2-BA Hunter Chemistry Major 2 (including the Bioinformatics Option)] | ||
** [https://hunter-undergraduate.catalog.cuny.edu/programs/COMPSCI-BA Hunter Computer Science (including Bioinformatics Concentration)] | ** [https://hunter-undergraduate.catalog.cuny.edu/programs/COMPSCI-BA Hunter Computer Science (including Bioinformatics Concentration)] | ||
| Line 141: | Line 142: | ||
** Students should take Bioinformatics-specific electives (8 cred; see Hunter Catalog below), not general electives | ** Students should take Bioinformatics-specific electives (8 cred; see Hunter Catalog below), not general electives | ||
** Students need to take BIOL48002 (2 cr), which counts towards as research credit, to graduate as honors | ** 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 | * 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 | |||
* Outside research opportunities | * Outside research opportunities | ||
** MIT Quantitative Workshop (first week of January, in Boston). Coordination with CS (Saad & Susan Epstein) in Fall | ** MIT Quantitative Workshop (first week of January, in Boston). Coordination with CS (Saad & Susan Epstein) in Fall | ||
Revision as of 14:58, 14 February 2024
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
Oct 2023, Long Island, NY
June 2022, MA
June 2021, MA
Lab publications
Lyme Genomics, Evolution, & Ecology
Di, Chong, Brian Sulkow, Weigang Qiu, and Shipeng Sun. 2023. "Effects of Micro-Scale Environmental Factors on the Quantity of Questing Black-Legged Ticks in Suburban New York" Applied Sciences 13, no. 20: 11587.
Li, Di, Zeglis, Qiu (2022). “Evolution of the vls antigenic variability locus of the Lyme Disease pathogen and development of recombinant monoclonal antibodies targeting conserved VlsE epitopes”. Microbial Spectrum 10 (5):1-15.
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
Schwartz, Margos, Casjens, Qiu, Eggers (2020). "Multipartite Genome of Lyme Disease Borrelia: Structure, Variation and Prophages". Current Issues in Molecular Biology. 42:409-454.
Barbour & Qiu (2019). Borreliella. In Bergey's Manual of Systematics of Archaea and Bacteria. John Wiley & Sons, Inc., in association with Bergey's Manual Trust.
Di L, Wan Z, Akther S, Ying CX, Larracuente A, Li L, Di C, Nunez R, Cucura DM, Goddard NL, Krampis K, Qiu WG. (2018). Genotyping and Quantifying Lyme Pathogen Strains by Deep Sequencing of the Outer Surface Protein C (ospC) Locus. Journal of Clinical Microbiology. 56(11):e00940-18.
Evolution & Learning Algorithms
Ely, Koh, Ho, Hassan, Pham, Qiu (2023). Novelty Search Promotes Antigenic Diversity in Microbial Pathogens. Pathogens 12:388.
Attie, Sulkow, Di, Qiu (2019). Genetic codes optimized as a traveling salesman problem. PLoS ONE 14(10): e0224552.
Yan, Deforet, Boyle, Rahman, Liang, Okegbe, Dietrich, Qiu, Xavier (2017). Bow-tie signaling in c-di-GMP: Machine learning in a simple biochemical network. PLoS Comput Biol 13(8): e1005677.
Informatics Tool Development
Hernandez, Bernstein, Pagan, Vargas, McCaig, Ramrattan, Akther, Larracuente, Di, Vieira, Qiu. (2018). BbWrapper: BioPerl-based sequence and tree utilities for rapid prototyping of bioinformatics pipelines. BMC Bioinformatics 19(1):76.
Di, Pagan, Packer, Martin, Akther, Ramrattan, Mongodin, Fraser, Schutzer, Luft, Casjens and Qiu. (2014). BorreliaBase: a phylogeny-centered browser of Borrelia genomes. BMC Bioinformatics 15:233.
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) |
|
|
| Alumni (Since Fall 2002) |
|
(published coauthors)
|
Web Apps
Apps with Collaborators
Data & GSEA associated with Polotskaia_etal_2014 (with Bargonetti Lab @Hunter)
Phosphoproteome MDM2KD data set (with Bargonetti Lab @Hunter)
Genes & Pathways Associated with mTP53 (with Bargonetti Lab @Hunter)
S. pombe transcriptomes (with Zhong Lab @Hunter)
Group B Streptococcus (GBS) genome browser (with Wu Lab @Shenzhen)
1K genome (with Ogunwobi Lab @Hunter)
E faecalis genome browser (with Morales Lab @WCMC)
Proteomics GSEA results (with Melendez Lab @Hunter)
pHis Protein Browser (with Skolnik lab @NYU)
Qiu Lab Apps
Lyme genome browser
Lyme pathogen plasmid partitioning gene trees
vls Finder in Lyme pathogen genomes
Codon Wheel
Co-visualization of a tree with an alignment and character matrix
OspC amplicon sequencing from ticks
Genomic epidemiology of a Salmonella outbreak (ASM Challenge)
Teaching & 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)
- Curricular resources:
- 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
- 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
- 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 syllabus
- BIOL425 Computational Molecular Biology (Spring, 2023). Lecture material on github
- BIOL714 Cell Biology, 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, Li, Martin, Di, Sulkow, Pante, Bezrucenlovas, Luft, Qiu (May, 2020). "Origin, recombination, and missed opprotunities: a genomic perspective of the first 100 days of COVID-19 pandemic". (Unpublished).
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
- 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)
- Monte Carlo Club (summer projects)
- Tick handling protocols
- Hunter HPC Usage
- R for Data Science (2e), (2024) by Wickham, Grolemund & Çetinkaya-Rundel (Bookdown version)
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