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Revision as of 20:07, 25 March 2023

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

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

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

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.

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.

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.

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.

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)	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)

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1K genome (with Ogunwobi Lab @Hunter)
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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

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Lyme genome browser
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Lyme pathogen plasmid partitioning gene trees

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

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)

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, 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

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.

@@ Line 27: / Line 27: @@
 ===Informatics Tool Development===
 <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 | link=https://pubmed.ncbi.nlm.nih.gov/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.
-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 | link=https://pubmed.ncbi.nlm.nih.gov/24994456/ 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.
 </gallery>