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===Lyme Genomics===
===Lyme Genomics===
<gallery mode="packed" heights="200px" perrow="4" style="text-align:left">
<gallery mode="packed" heights="200px" perrow="4" style="text-align:left">
File:Spectrum.01743-22-f003.gif | 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
File:Spectrum.01743-22-f003.gif | link=https://doi.org/10.1128/spectrum.01743-22  | 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.  
File:Fig7-small.png | 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. [[https://pubmed.ncbi.nlm.nih.gov/34413477/ PMID 34413477]] (*co-first authors)
File:Fig7-small.png | link= https://pubmed.ncbi.nlm.nih.gov/34413477 | 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)
File:Ira-fig2.png | 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
File:Ira-fig2.png | link=https://doi.org/10.21775/9781913652616 | Schwartz, Margos, Casjens, Qiu, Eggers (2020). "Multipartite Genome of Lyme Disease ''Borrelia'': Structure, Variation and Prophages". '''''Current Issues in Molecular Biology'''''. 42:409-454.  
File:Fig6-1-Barbour.png | 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
File:Fig6-1-Barbour.png | link=https://doi.org/10.1002/9781118960608.gbm01525 | 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:  
</gallery>
</gallery>


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===Apps with Collaborators===
===Apps with Collaborators===
<gallery mode="packed" heights="200px" perrow="4" style="text-align:left">
<gallery mode="packed" heights="200px" perrow="4" style="text-align:left">
File:Screenshot_2023-03-24_122016.png| link=http://borreliabase.org/~wgqiu/clickme-khalikuz/temp-Points.html | Phosphoproteome MDM2KD data set (with Bargonetti Lab @Hunter)
File:Screenshot_2023-03-24_122016.png | link=http://borreliabase.org/~wgqiu/clickme-khalikuz/temp-Points.html | Phosphoproteome MDM2KD data set (with Bargonetti Lab @Hunter)
File:Screenshot_2023-03-24_122312.png| link=http://borreliabase.org/~wgqiu/mpai-v3/ | Genes & Pathways Associated with mTP53 (with Bargonetti Lab @Hunter)
File:Screenshot_2023-03-24_122312.png | link=http://borreliabase.org/~wgqiu/mpai-v3/ | Genes & Pathways Associated with mTP53 (with Bargonetti Lab @Hunter)
File:Screenshot 2023-03-24 122223.png | link=http://borreliabase.org/~wgqiu/gbs-browser-v3/ | Group B Streptococcus (GBS) genome browser (with Wu Lab @Shenzhen)
File:Screenshot 2023-03-24 122223.png | link=http://borreliabase.org/~wgqiu/gbs-browser-v3/ | Group B Streptococcus (GBS) genome browser (with Wu Lab @Shenzhen)
File:Screenshot 2023-03-24 122245.png | link=http://borreliabase.org/~wgqiu/oneKGenome/ | 1K genome (with Ogunwobi Lab @Hunter)
File:Screenshot 2023-03-24 122245.png | link=http://borreliabase.org/~wgqiu/oneKGenome/ | 1K genome (with Ogunwobi Lab @Hunter)

Revision as of 20:02, 25 March 2023

Portrait-2022-blur.jpg
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
Belfer building.jpg

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.
    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)
    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.
    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:
    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

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. [PMID 29499649]

    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]

  • 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]

    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]

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)

  • 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), Ph.D. from Boston University
  • Dr Oliver Attie: Research associate (volunteer), Ph.D. from NYU
  • Tasmina Hassan: Hunter Bio/CS
  • Mathew DiCicco: Hunter Math/CS
  • Tara Doma Lama: Hunter Bio/Bioinformatics
  • Hagar Abuzaid: Hunter Bio
Alumni (Since Fall 2002)
  • Dr Lia Di: Ph.D. from Nanjing Agricultural University & Wisconsin Blood Institute
  • Dr Saymon Akther (2022): CUNY Grad Center, Biology/EEB
  • Dr Rayees Rahman: Hunter Bio/Bioinformatics, Ph.D. from Mt Sinai Medical School
  • Dr Che Martin (2013): CUNY Grad Center, Biology/MCD
  • Dr James Haven (2011): CUNY Grad Center, Biology/MCD
  • Dr Tika Sukarna (2009): CUNY Grad Center, Biology/MCD
  • Dr Juan Coronado (2008): CUNY Grad Center, Biology/MCD (Dr Peter Lipke)
  • Dr William McCaig: CUNY BA, Ph.D. from Stony Brook University
  • Dr Vincent Xue: CUNY CS/Bioinformatics, Ph.D. from MIT
  • Dr Fubin Li: CUNY Grad Center, Biology/MCD (Dr Laurel Eckhardt)

(published coauthors)

  • Brian Sulkow: CUNY Grad Center, Mathematics
  • Winston Koh: Hunter Bio/CS
  • Eamen Ho: Hunter Bio/Bioinformatics
  • Ahn Pham: Hunter Bio/Bioinformatics
  • Chris Panlasigui: Hunter Bio/Bioinformatics
  • Amanda Amanda Larracuente: CUNY Grad Center, Biology/MCD
  • Pedro Pagan: Hunter Bio/Bioinformatics
  • Edgaras Bezrucenkovas: Hunter Chem/Bioinformatics
  • Girish Ramrattan: Hunter Bio/Bioinformatics
  • Levy Vargas: Hunter Bio/Bioinformatics
  • Chong Di: Hunter Geography
  • Roy Nunez: Hunter Bio
  • Mei Wu: CUNY City Tech
  • Desiree Pante: Hunter Bio
  • Saimtun Shipa: Hunter Stat (MA)
  • Bing Wu: Hunter Bio/Biotechnology
  • Svidatoslav Kendall (Slav): Hunter Biology
  • Philip Romov: Hunter CS

Web Apps

Apps with Collaborators

  • Phosphoproteome MDM2KD data set (with Bargonetti Lab @Hunter)
    Phosphoproteome MDM2KD data set (with Bargonetti Lab @Hunter)
  • Genes & Pathways Associated with mTP53 (with Bargonetti Lab @Hunter)
    Genes & Pathways Associated with mTP53 (with Bargonetti Lab @Hunter)
  • Group B Streptococcus (GBS) genome browser (with Wu Lab @Shenzhen)
    Group B Streptococcus (GBS) genome browser (with Wu Lab @Shenzhen)
  • 1K genome (with Ogunwobi Lab @Hunter)
    1K genome (with Ogunwobi Lab @Hunter)
  • E faecalis genome browser (with Morales Lab @WCMC)
    E faecalis genome browser (with Morales Lab @WCMC)
  • Proteomics GSEA results (with Melendez Lab @Hunter)
    Proteomics GSEA results (with Melendez Lab @Hunter)
  • pHis Protein Browser (with Skolnik lab @NYU)
    pHis Protein Browser (with Skolnik lab @NYU)

Qiu Lab Apps

  • Lyme genome browser
    Lyme genome browser
  • Lyme pathogen plasmid partitioning gene trees
    Lyme pathogen plasmid partitioning gene trees
  • vls Finder in Lyme pathogen genomes
    vls Finder in Lyme pathogen genomes
  • Codon Wheel
    Codon Wheel
  • Co-visualization of a tree with an alignment and character matrix
    Co-visualization of a tree with an alignment and character matrix
  • OspC amplicon sequencing from ticks
    OspC amplicon sequencing from ticks
  • Genomic epidemiology of a Salmonella outbreak (ASM Challenge)
    Genomic epidemiology of a Salmonella outbreak (ASM Challenge)

Teaching & Curricular Development

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, 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, 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

    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

Wiki Help

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