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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)

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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.
  

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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. (*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.
  

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  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

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  Ely, Koh, Ho, Hassan, Pham, Qiu (2023). Novelty Search Promotes Antigenic Diversity in Microbial Pathogens. Pathogens 12:388.
  

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  Attie, Sulkow, Di, Qiu (2019). Genetic codes optimized as a traveling salesman problem. PLoS ONE 14(10): e0224552.
  

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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.
  

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.
  

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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.
  

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

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

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  Data & GSEA associated with Polotskaia_etal_2014 (with Bargonetti Lab @Hunter)
  

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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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  S. pombe transcriptomes (with Zhong 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)
  

Teaching & Curricular Development

• 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 (2020)
• Southwest University R course (2019)
• BIOL425 Computational Molecular Biology (2020)
• Analysis of Biological Data (2017)
• BIOL37500, Molecular Evolution (2019)
• Bioinformatics Workshop (2014)
• BIOL47120 Biomedical Genomics II (2020)
• BIOL471 R Demo (2023)

SARS-CoV-2 genome evolution

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  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

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  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).

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  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

• 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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