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Welcome to Qiu Lab Wiki @ Hunter 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) Directions by Google Map

Lab publications

Lyme Genomics

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  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. DOI: https://doi.org/10.1128/spectrum.01743-22

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  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. [PMID 34413477] (*co-first authors)

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  Schwartz, Margos, Casjens, Qiu, Eggers (2020). "Multipartite Genome of Lyme Disease Borrelia: Structure, Variation and Prophages". Current Issues in Molecular Biology. 42:409-454. DOI: https://doi.org/10.21775/9781913652616

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  Barbour & Qiu (2019). Borreliella. In Bergey's Manual of Systematics of Archaea and Bacteria (eds W. B. Whitman, F. Rainey, P. Kämpfer, M. Trujillo, J. Chun, P. DeVos, B. Hedlund and S. Dedysh). John Wiley & Sons, Inc., in association with Bergey's Manual Trust. DOI: https://doi.org/10.1002/9781118960608.gbm01525

Evolution & Learning Algorithms

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  Ely, Koh, Ho, Hassan, Pham, Qiu (2023). Novelty Search Promotes Antigenic Diversity in Microbial Pathogens. Pathogens 12:388. DOI: https://doi.org/10.3390/pathogens12030388

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  Attie, Sulkow, Di, Qiu (2019). Genetic codes optimized as a traveling salesman problem. PLoS ONE 14(10): e0224552. DOI: https://doi.org/10.1371/journal.pone.0224552

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  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. DOI: https://doi.org/10.1371/journal.pcbi.1005677

Informatics Tool Development

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  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. [PMID 29499649]

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  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. [PMID 24994456]

• Full list by Google Scholar
• Full list by NCBI Bibliography

last update: March 20, 2023

Web Apps

Collaborative works

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  Phosphoproteome MDM2KD data set (with Bargonetti Lab @Hunter)
  

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  Genes & Pathways Associated with mTP53 (with Bargonetti Lab @Hunter)
  

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  Group B Streptococcus (GBS) genome browser (with Wu Lab @Shenzhen)
  

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  1K genome (with Ogunwobi Lab @Hunter)
  

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  E faecalis genome browser (with Morales Lab @WCMC)
  

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  Proteomics GSEA results (with Melendez Lab @Hunter)
  

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  pHis Protein Browser (with Skolnik lab @NYU)
  

Qiu Lab Apps

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  Lyme genome browser
  

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  Lyme pathogen plasmid partitioning gene trees
  

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  vls Finder in Lyme pathogen genomes
  

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  Codon Wheel
  

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  Co-visualization of a tree with an alignment and character matrix
  

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  OspC amplicon sequencing from ticks
  

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  Genomic epidemiology of a Salmonella outbreak (ASM Challenge)
  

Lab members and trainees

Year/Period	Doctoral	Others
Current (Fall 2022, Spring 2023, Summer 2023 )	Li Li (Lily): CUNY Grad Center, Biology/EEB doctoral program Brandon Ely: CUNY Grad Center, Biology/MCD doctoral program Dr Yozen Hernandez: System administrator (part-time) Dr Oliver Attie: Research associate (volunteer) || Tasmina Hassan: Hunter Bio/CS Mathew Tara Hagar
Alumni	Saymon Akther (2022): CUNY Grad Center, Biology/EEB doctoral program Che Martin (2013): CUNY Grad Center, Biology/MCD doctoral program James Haven (2011): CUNY Grad Center, Biology/MCD doctoral program Tika Sukarna (2009): CUNY Grad Center, Biology/MCD doctoral program || Winston Koh Eamen Ho

Teaching & Training

• BIOL20300 Molecular Genetics, Lab 4
• BIOL20300 Molecular Genetics, Lab 7
• BIOL30300 Cell Biology, Bioinformatics Lab (transcriptome analysis)
• Big Data (2020)
• Southwest University R course (2019
• BIOL425 Computational Molecular Biology (2020)
• Analysis of Biological Data (2017)
• BIOL37500, Molecular Evolution (2019)

Lab Resources

• 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

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