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==Teaching & Curricular Development== | ==Teaching & Curricular Development== | ||
* BIOL425 Computational Molecular Biology (Spring 2023). [https://github.com/weigangq/CSB-BIOL425/tree/master/lecture-materials Lecture material on github] | * BIOL425 Computational Molecular Biology (Spring, 2023). [https://github.com/weigangq/CSB-BIOL425/tree/master/lecture-materials Lecture material on github] | ||
* [http://borreliabase.org/~wgqiu/r-demo-2023.html BIOL714 Cell Biology, R Demo (Spring 2023)] | |||
* The Quantitative Biology (QuBi) Program at Hunter | * The Quantitative Biology (QuBi) Program at Hunter | ||
** [https://hunter-undergraduate.catalog.cuny.edu/programs/BIO1-BA Hunter Biology Major I (including the Bioinformatics Conentration)] | ** [https://hunter-undergraduate.catalog.cuny.edu/programs/BIO1-BA Hunter Biology Major I (including the Bioinformatics Conentration)] | ||
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** QuBi module: [[QuBi/modules/biol203-geno-pheno-association-2022|BIOL20300 Molecular Genetics, Lab 13 (2022)]] | ** QuBi module: [[QuBi/modules/biol203-geno-pheno-association-2022|BIOL20300 Molecular Genetics, Lab 13 (2022)]] | ||
** QuBi module: [[QuBi/modules/biol303|BIOL30300 Cell Biology, Bioinformatics Lab (transcriptome analysis)]] | ** QuBi module: [[QuBi/modules/biol303|BIOL30300 Cell Biology, Bioinformatics Lab (transcriptome analysis)]] | ||
* [[BigData 2020|Big Data (2020)]] | * [[BigData 2020|Big Data (Summer, 2020)]] | ||
* [[Southwest-University|Southwest University R course (2019)]] | * [[Southwest-University|Southwest University R course (Summer, 2019)]] | ||
* [[Biol425 2020|BIOL425 Computational Molecular Biology (2020)]] | * [[Biol425 2020|BIOL425 Computational Molecular Biology (Spring, 2020)]] | ||
* [[Biol20N02 2017|Analysis of Biological Data (2017)]] | * [[Biol20N02 2017|Analysis of Biological Data (2017)]] | ||
* [[Biol375 2019|BIOL37500, Molecular Evolution (2019)]] | * [[Biol375 2019|BIOL37500, Molecular Evolution (Fall, 2019)]] | ||
* [[Bioinformatics_Workshop_2014|Bioinformatics Workshop (2014)]] | * [[Bioinformatics_Workshop_2014|Bioinformatics Workshop (2014)]] | ||
* [[BioMed-R-2020|BIOL47120 Biomedical Genomics II (2020)] | * [[BioMed-R-2020|BIOL47120 Biomedical Genomics II (Spring, 2020)]] | ||
==SARS-CoV-2 genome evolution== | ==SARS-CoV-2 genome evolution== | ||
Revision as of 11:05, 10 September 2023
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) |
Lab publications
Lyme Genomics
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)
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. DOI:
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
- BIOL425 Computational Molecular Biology (Spring, 2023). Lecture material on github
- BIOL714 Cell Biology, R Demo (Spring 2023)
- The Quantitative Biology (QuBi) Program at Hunter
- Hunter Biology Major I (including the Bioinformatics Conentration)
- 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 module: BIOL20300 Molecular Genetics, Lab 12 (2022)
- QuBi module: BIOL20300 Molecular Genetics, Lab 13 (2022)
- QuBi module: BIOL30300 Cell Biology, Bioinformatics Lab (transcriptome analysis)
- Big Data (Summer, 2020)
- Southwest University R course (Summer, 2019)
- BIOL425 Computational Molecular Biology (Spring, 2020)
- Analysis of Biological Data (2017)
- BIOL37500, Molecular Evolution (Fall, 2019)
- Bioinformatics Workshop (2014)
- BIOL47120 Biomedical Genomics II (Spring, 2020)
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
- Qiu lab network first-time user guide
- 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
Wiki Help
- Configuration settings list
- MediaWiki FAQ
- MediaWiki release mailing list
- Localise MediaWiki for your language
- Learn how to combat spam on your wiki
- Consult the User's Guide for information on using the wiki software.