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Latest revision as of 12:53, 22 September 2024

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

Fieldwork Gallery

Oct 2023, Long Island, NY
June 2022, MA
June 2021, MA

Lab publications

Lyme Genomics, Evolution, & Ecology

Akther et al. 2024. "Natural selection and recombination at host-interacting lipoprotein loci drive genome diversification of Lyme disease and related bacteria" mBio 0:e01749-24. Press coverage: CUNY Graduate Center News Story; Hunter press

Akther et al. 2024. "Natural selection and recombination at host-interacting lipoprotein loci drive genome diversification of Lyme disease and related bacteria" mBio 0:e01749-24. Press coverage: CUNY Graduate Center News Story; Hunter press

Di, Chong, Brian Sulkow, Weigang Qiu, and Shipeng Sun. 2023. "Effects of Micro-Scale Environmental Factors on the Quantity of Questing Black-Legged Ticks in Suburban New York" Applied Sciences 13, no. 20: 11587.

Di, Chong, Brian Sulkow, Weigang Qiu, and Shipeng Sun. 2023. "Effects of Micro-Scale Environmental Factors on the Quantity of Questing Black-Legged Ticks in Suburban New York" Applied Sciences 13, no. 20: 11587.

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) Blog Post

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) Blog Post

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.

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.

Di L, Wan Z, Akther S, Ying CX, Larracuente A, Li L, Di C, Nunez R, Cucura DM, Goddard NL, Krampis K, Qiu WG. (2018). Genotyping and Quantifying Lyme Pathogen Strains by Deep Sequencing of the Outer Surface Protein C (ospC) Locus. Journal of Clinical Microbiology. 56(11):e00940-18.

Di L, Wan Z, Akther S, Ying CX, Larracuente A, Li L, Di C, Nunez R, Cucura DM, Goddard NL, Krampis K, Qiu WG. (2018). Genotyping and Quantifying Lyme Pathogen Strains by Deep Sequencing of the Outer Surface Protein C (ospC) Locus. Journal of Clinical Microbiology. 56(11):e00940-18.

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)	Brandon Ely: CUNY Grad Center, Biology/MCD doctoral program Dr Yozen Hernandez: System administrator (part-time), Ph.D. from Boston University	Tasmina Hassan: Hunter Bio/CS Mathew DiCicco: Hunter Math/CS Tara Doma Lama: Hunter Bio/Bioinformatics Hagar Abuzaid: Hunter Bio
Alumni (Since Fall 2002)	Li Li (Lily, 2023): CUNY Grad Center, Biology/EEB doctoral program Dr Lia Di: Ph.D. Postdoctoral Research Associate, 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) Dr Oliver Attie: Postdoctoral Research Associate, Ph.D. from NYU	(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 (or from published papers)

Borrelia diagnostic antigens (App developed by Liann Aris-Henry; Data from Arumugam et al (2019))

Borrelia diagnostic antigens (App developed by Liann Aris-Henry; Data from Arumugam et al (2019))

Borrelia growth transcriptome (App developed by Laziz Asamov; Data from Arnold et al (2016))

Borrelia growth transcriptome (App developed by Laziz Asamov; Data from Arnold et al (2016))

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

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

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)

S. pombe transcriptomes (with Zhong Lab @Hunter)

S. pombe transcriptomes (with Zhong 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)

Curricular Development & Bioinformatics/QuBi Advising

QuBi advisors: Weigang Qiu, Ntino Krampis, Rabindra Mandal (Biology); Saad Mneimeih, Lei Xie (CS); Akira Kawamura (Chem); Dana Sylvan (Math & Stats)
- Permission for non-Biology majors to take BIOL203 & BIOL425, every Spring
- Collect names, major, and IDs to send to course coordinator to grant permission. Waive BIOL10200 pre-reqs for taking BIOL203.
Curricular resources:
QuBi advising:
- Declaration of Bioinformatics concentration: In-person advising to work out the semester-by-semester courses
- Approve on department spreadsheet (or send email to "Samantha Sheppard-Lahiji" and "HTR Bio" <biology@hunter.cuny.edu>)
- Students should take Bioinformatics-specific electives (8 cred; see Hunter Catalog below), not general electives
  - Examples: Anthrop302 (3 cr); Chem333 (3 cr); BIOL47119 & BIOL47120 (3cr); BIOL48002 (2 cr)
- Students need to take BIOL48002 (2 cr), which counts towards as research credit, to graduate as honors
General advising:
- ~40 students every semester. Send out emails to students. Go through student courses by Email or by appointment
- Recommend new math courses: MATH15200 & STAT21350
Hosting QuBi students in lab
- This is to enhance the informatics and coding skills of our students
- Students should register and get BIOL48002 credits, which counts towards their elective credits & eligibility for honors
- 3-5 students per semester
Outside research opportunities
- MIT Quantitative Workshop (first week of January, in Boston). Coordination with CS (Saad & Susan Epstein) in Fall
- Simons Foundation/Flatiron Institute Center for Computational Biology (CCB) Internship program. Open House in Spring

Course/Lecture syllabi

Computational Genomics (KIZ, Fall 2024)
NYRaMP Workshop (August 2024)
BIOL47120 BioMedical Genomics (Spring 2024). Tutorials: R Markdown Cluster analysis single-cell RNA-seq
BIOL425 Computational Molecular Biology (Spring, 2023). Lecture material on github
BIOL714 Cell Biology: R Demo (Spring 2024) R Demo (Spring 2023)
QuBi module: BIOL20300 Molecular Genetics, Lab 12 (2023)
QuBi module: BIOL20300 Molecular Genetics, Lab 13 (2022)
QuBi module: BIOL30300 Cell Biology, Bioinformatics Lab (transcriptome analysis)
Big Data (Summer, 2020)
BIOL47120 Biomedical Genomics II (Spring, 2020)
BIOL425 Computational Molecular Biology (Spring, 2020)
BIOL37500, Molecular Evolution (Fall, 2019)
Southwest University R course (Summer, 2019)
Analysis of Biological Data (Spring, 2017)
Bioinformatics Workshop (Summer, 2014)

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

Monte Carlo Club
NY-RaMP Mentoring
Borreliella genome sequencing consortium: Weekly meetings (Tu @11): Since Jan 2023
Borreliella diagnostic antigens (Fall 2023-Fall 2027):
- Zoom call (Jan 23, 2024)
- Next meeting: March 23, 2024
Qiu lab network first-time user guide
Qiu lab Github repositories: https://github.com/weigangq/?tab=repositories
Mini-Protocols (frequently used computer codes and pipelines)
Tick handling protocols
Hunter HPC Usage
R for Data Science (2e), (2024) by Wickham, Grolemund & Çetinkaya-Rundel (Bookdown version)

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