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| <center> <strong>Welcome to Qiu Lab Wiki @ Hunter</strong><br>Weigang Qiu, Ph.D., Professor<br> [http://biology.hunter.cuny.edu Department of Biological Sciences]<br>
| <center> <strong>Welcome to Qiu Lab Wiki @ Hunter</strong><br>Weigang Qiu, Ph.D., Professor<br> [http://biology.hunter.cuny.edu Department of Biological Sciences]<br>
[https://hunter.cuny.edu Hunter College] of [https://www.cuny.edu City University of New York]<br> Belfer Research Building, Room 402<br>413 East  69th Street, New York, NY 10021<br>Office: 1-212-896-0445; Email: wqiu-at-(hunter.cuny.edu)<br>[https://goo.gl/maps/xv1KmaW3XEnxaY1V7 Directions by Google Map] </center>
[https://hunter.cuny.edu Hunter College] of<br> [https://www.cuny.edu City University of New York]<br> Belfer Research Building, Room 402<br>413 East  69th Street, New York, NY 10021<br>Office: 1-212-896-0445<br>Email: wqiu-at-(hunter.cuny.edu)<br> </center>
| <center> __TOC__ </center>
| [[File:Belfer_building.jpg | x300px | thumb | [https://goo.gl/maps/xv1KmaW3XEnxaY1V7 Directions by Google Map]]]
|__TOC__
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== Lab publications (last update: March 20, 2023) ==
==Fieldwork Gallery==
<gallery widths="250" perrow="4" caption="Lyme Genomics">
<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:Tick-trip-2023.jpg|thumb|Oct 2023, Long Island, NY
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:Tick-trip-2022.jpg|thumb|June 2022, MA
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:Tick-trip-2021.jpg|thumb|June 2021, MA
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
</gallery>
</gallery>
<youtube width="200" height="150">Jb4ACK-GjM0</youtube>


<gallery widths="250" perrow="3" caption="Evolution & Learning Algorithms">
==Lab publications==
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
===Lyme Genomics, Evolution, & Ecology===
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
<gallery mode="packed" heights="200px" perrow="4" style="text-align:left">
File:Pcbi.1005677.g001.png|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. DOI: https://doi.org/10.1371/journal.pcbi.1005677
 
File:Screenshot_2024-08-15_094908.png | link=https://journals.asm.org/doi/10.1128/mbio.01749-24 | 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: [https://www.gc.cuny.edu/news/cuny-graduate-center-biologists-map-dna-lyme-disease-bacteria CUNY Graduate Center News Story]; [https://hunter.cuny.edu/news/hunter-researcher-maps-dna-of-lyme-disease-bacteria/ Hunter press]
 
File:Applsci-13-11587-g004.png | link=https://doi.org/10.3390/app132011587 | 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.
 
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 | 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) [https://microbiologycommunity.nature.com/posts/how-to-win-the-evolutionary-arms-race-against-pathogens Blog Post]
 
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 | 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.
 
File:Zjm9990961420002.jpeg | link=https://doi.org/10.1128/jcm.00940-18 | 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.  
</gallery>
</gallery>


<gallery widths="250" perrow="2" caption="Informatics Tools">
===Evolution & Learning Algorithms===
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]]
<gallery mode="packed" heights="200px" perrow="3" style="text-align:left">
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:Pathogens-12-00388-g003.png | link=https://doi.org/10.3390/pathogens12030388 | Ely, Koh, Ho, Hassan, Pham, Qiu (2023). Novelty Search Promotes Antigenic Diversity in Microbial Pathogens. '''''Pathogens''''' 12:388.
File:Pone.0224552.g005.png | link=https://doi.org/10.1371/journal.pone.0224552 | Attie, Sulkow, Di, Qiu (2019). Genetic codes optimized as a traveling salesman problem. '''''PLoS ONE''''' 14(10): e0224552.
File:Pcbi.1005677.g001.png | link=https://doi.org/10.1371/journal.pcbi.1005677 | 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.
</gallery>
 
===Informatics Tool Development===
<gallery mode="packed" heights="200px" style="text-align:left">
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 | link=https://pubmed.ncbi.nlm.nih.gov/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>
</gallery>


* [http://scholar.google.com/citations?hl=en&user=Ds6u39QAAAAJ) Full list by Google Scholar]
* [http://scholar.google.com/citations?hl=en&user=Ds6u39QAAAAJ) Full list by Google Scholar]
* [http://www.ncbi.nlm.nih.gov/sites/myncbi/weigang.qiu.1/bibliography/42770924/public/ Full list by NCBI Bibliography]
* [http://www.ncbi.nlm.nih.gov/sites/myncbi/weigang.qiu.1/bibliography/42770924/public/ Full list by NCBI Bibliography]
last update: March 20, 2023
==Lab members and trainees==
{| class="wikitable"
|-
! 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)<br>
* 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)===
<gallery mode="packed" heights="200px" perrow="4" style="text-align:left">
File:Screenshot_2024-06-19_205621.png | link=https://cov.genometracker.org/finalelisa-app/ | Borrelia diagnostic antigens (App developed by Liann Aris-Henry; Data from [https://journals.asm.org/doi/10.1128/jcm.01142-19 Arumugam et al (2019)])
File:Screenshot_2024-06-18_144931.png | link=https://cov.genometracker.org/borrelia-app/ | Borrelia growth transcriptome (App developed by Laziz Asamov; Data from [https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0164165 Arnold et al (2016)])
File: Silac.png | link=http://borreliabase.org/~wgqiu/Polotskaia_etal_2014/supp-fig-s1/ | Data & [http://borreliabase.org/~wgqiu/Polotskaia_etal_2014/supp-table-s1/ GSEA] associated with Polotskaia_etal_2014 (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:Spombe.png | link=Spombe | S. pombe transcriptomes (with Zhong 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 122245.png | link=http://borreliabase.org/~wgqiu/oneKGenome/ | 1K genome (with Ogunwobi Lab @Hunter)
File:Screenshot 2023-03-24 122450.png | link=http://borreliabase.org/~wgqiu/E_faecalis/ | E faecalis genome browser (with Morales Lab @WCMC)
File:Screenshot 2023-03-24 122145.png | link=http://borreliabase.org/~wgqiu/carmen-proteomics/ | Proteomics GSEA results (with Melendez Lab @Hunter)
File:Screenshot 2023-03-24 122051.png | link=http://borreliabase.org/~wgqiu/Tcell-pHis-ACS/ | pHis Protein Browser (with Skolnik lab @NYU)
</gallery>
===Qiu Lab Apps===
<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 133320.png | link=http://borreliabase.org/~wgqiu/pf-trees/ | Lyme pathogen plasmid partitioning gene trees
File:Screenshot 2023-03-24 133636.png | link=http://borreliabase.org/vls-finder/ | vls Finder in Lyme pathogen genomes
File:Screenshot 2023-03-24 122359.png | link=http://borreliabase.org/~wgqiu/code-wheel | Codon Wheel
File:PhyloView.png | link=http://borreliabase.org/~wgqiu/PhyloView | Co-visualization of a tree with an alignment and character matrix
File:Screenshot 2023-03-24 122521.png | link=http://borreliabase.org/~wgqiu/ospC-sequencing | OspC amplicon sequencing from ticks
File:Screenshot 2023-03-24 122340.png | link=http://borreliabase.org/~wgqiu/asm-challenge | Genomic epidemiology of a Salmonella outbreak (ASM Challenge)
</gallery>
==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:
** [http://biology.hunter.cuny.edu/index.php?option=com_content&view=article&id=66&Itemid=73 Biology courses and pre-reqs]
** [https://hunter-undergraduate.catalog.cuny.edu/programs/BIO1-BA Hunter Biology Major 1 (including the Bioinformatics Option)]
** [https://hunter-undergraduate.catalog.cuny.edu/programs/CHEM2-BA Hunter Chemistry Major 2 (including the Bioinformatics Option)]
** [https://hunter-undergraduate.catalog.cuny.edu/programs/COMPSCI-BA Hunter Computer Science (including Bioinformatics Concentration)]
** [https://hunter-undergraduate.catalog.cuny.edu/programs/MATH-BA Hunter Mathematics (including the Quantitative Biology Concentration)]
** [https://hunter-undergraduate.catalog.cuny.edu/programs/STATS-BA Hunter Statistics (including the Quantitative Biology Concentration)]
* 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-Informatics-2024|NYRaMP Workshop (August 2024)]]
* BIOL47120 BioMedical Genomics (Spring 2024). Tutorials: [https://borreliabase.org/~wgqiu/tutorial-markdown.html R Markdown] [https://borreliabase.org/~wgqiu/cluster-analysis.html Cluster analysis] [https://borreliabase.org/~wgqiu/scRNA-analysis.html single-cell RNA-seq]
* BIOL425 Computational Molecular Biology (Spring, 2023). [https://github.com/weigangq/CSB-BIOL425/tree/master/lecture-materials Lecture material on github]
* BIOL714 Cell Biology: [http://borreliabase.org/~wgqiu/r-demo-2024.html R Demo (Spring 2024)] [http://borreliabase.org/~wgqiu/r-demo-2023.html R Demo (Spring 2023)]
* QuBi module: [[QuBi/module/bio203-lab12—2022|BIOL20300 Molecular Genetics, Lab 12 (2023)]]
* QuBi module: [[QuBi/modules/biol203-geno-pheno-association-2022|BIOL20300 Molecular Genetics, Lab 13 (2022)]]
* QuBi module: [[QuBi/modules/biol303|BIOL30300 Cell Biology, Bioinformatics Lab (transcriptome analysis)]]
* [[BigData 2020|Big Data (Summer, 2020)]]
* [[BioMed-R-2020|BIOL47120 Biomedical Genomics II (Spring, 2020)]]
** [http://borreliabase.org/~wgqiu/tutorial-markdown.html Tutorial: R Markdown (Spring 2024)]
** [http://borreliabase.org/~wgqiu/cluster-analysis.html Tutorial: Cluster analysis (Spring 2024)]
** [http://borreliabase.org/~wgqiu/scRNA-analysis.html Tutorial: single-cel transcriptome analysis (Spring 2024)]
* [[Biol425 2020|BIOL425 Computational Molecular Biology (Spring, 2020)]]
* [[Biol375 2019|BIOL37500, Molecular Evolution (Fall, 2019)]]
* [[Southwest-University|Southwest University R course (Summer, 2019)]]
* [[Biol20N02 2017|Analysis of Biological Data (Spring, 2017)]]
* [[Bioinformatics_Workshop_2014|Bioinformatics Workshop (Summer, 2014)]]
==SARS-CoV-2 genome evolution==
<gallery mode="packed" heights="200px" perrow="3" style="text-align:left">
File:Cov-fig1.jpg | Akther, Bezrucenkovas, Sulkow, Panlasigui, Qiu, Di (April, 2020). "CoV Genome Tracker: tracing genomic footprints of Covid-19 pandemic". '''''[https://www.biorxiv.org/content/biorxiv/early/2020/04/14/2020.04.10.036343.full.pdf BioRxiv]'''''; [https://cov.genometracker.org/ Web app: SARS-CoV-2 Genome Tracker]; Github: https://github.com/weigangq/cov-browser
File:Rec-fig2.png | 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).
File:Cov-fig3-trace.png | 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". '''''[https://www.biorxiv.org/content/biorxiv/early/2021/05/10/2021.05.07.443114.full.pdf BioRxiv link]''''': . Github:  https://github.com/weigangq/cov-db
</gallery>


== Lab Resources ==
==Lab Resources & Protocols==
* Github repositories: https://github.com/weigangq/?tab=repositories
* [[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 Guide|first-time user guide]]
* Qiu lab Github repositories: https://github.com/weigangq/?tab=repositories
* [[Mini-Tutorals|Mini-Protocols]] (frequently used computer codes and pipelines)
* [[Mini-Tutorals|Mini-Protocols]] (frequently used computer codes and pipelines)
* [[Monte Carlo Club]] (summer projects)
* T[[Tick protocol|ick handling protocols]]
* T[[Tick protocol|ick handling protocols]]
* [[A Primer on the Cluster System at Hunter|Hunter HPC Usage]]
* [[A Primer on the Cluster System at Hunter|Hunter HPC Usage]]
* [https://r4ds.hadley.nz/ R for Data Science (2e)], (2024) by Wickham, Grolemund & Çetinkaya-Rundel ([https://bookdown.org/ Bookdown version])


== Wiki Help ==
== Wiki Help ==

Latest revision as of 12:53, 22 September 2024

Protrait-July-2024-Qiu.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

Fieldwork Gallery

  • Oct 2023, Long Island, NY

    Oct 2023, Long Island, NY

  • June 2022, MA

    June 2022, MA

  • June 2021, 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)
  • 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)

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

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

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