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== Lab publications ==
== Lab publications ==
===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 |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: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|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)
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===Evolution & Learning Algorithms===
===Evolution & Learning Algorithms===
<gallery mode=packed heights=200px perrow="3" style="text-align:left">
<gallery mode="packed" heights="200px" perrow="3" style="text-align:left">
File:Pathogens-12-00388-g003.png|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
File:Pathogens-12-00388-g003.png|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
File:Pone.0224552.g005.png|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
File:Pone.0224552.g005.png|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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===Informatics Tool Development===
===Informatics Tool Development===
<gallery mode=packed heights=200px style="text-align:left">
<gallery mode="packed" heights="200px" style="text-align:left">
File: 12859 2018 2074 Fig1 HTML.png | 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. [[https://pubmed.ncbi.nlm.nih.gov/29499649/ PMID 29499649]]
File: 12859 2018 2074 Fig1 HTML.png | 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. [[https://pubmed.ncbi.nlm.nih.gov/29499649/ PMID 29499649]]
File: 12859 2014 Article 6488 Fig3 HTML.png | 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. [[https://pubmed.ncbi.nlm.nih.gov/24994456/ PMID 24994456]]
File: 12859 2014 Article 6488 Fig3 HTML.png | 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. [[https://pubmed.ncbi.nlm.nih.gov/24994456/ PMID 24994456]]
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==Web Apps==
==Web Apps==
===Collaborative works===
===Collaborative works===
<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)
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===Qiu Lab Apps===
===Qiu Lab Apps===
<gallery mode=packed heights=200px perrow="3" style="text-align:left">
<gallery mode="packed" heights="200px" perrow="3" style="text-align:left">
File:Screenshot 2023-03-24 122558.png | link=http://borreliabase.org | Lyme genome browser
File:Screenshot 2023-03-24 122558.png | link=http://borreliabase.org | Lyme genome browser
File:Screenshot 2023-03-24 133320.png | link=http://borreliabase.org/~wgqiu/pf-trees/ | Lyme pathogen plasmid partitioning gene trees
File:Screenshot 2023-03-24 133320.png | link=http://borreliabase.org/~wgqiu/pf-trees/ | Lyme pathogen plasmid partitioning gene trees
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==Lab members and trainees==
==Lab members and trainees==
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Revision as of 14:57, 25 March 2023

2023-01-03 20.02.54.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. DOI: 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. DOI: https://doi.org/10.1128/spectrum.01743-22

  • 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)

    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)

  • 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

    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

  • 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

    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

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

Web Apps

Collaborative works

  • 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)

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

Lab Resources

Wiki Help

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