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<big>'''Welcome to the Wiki for Dr. Qiu's Evolutionary Bioinformatics Lab at [http://hunter.cuny.edu Hunter College]!'''</big>
{|
* Site under construction
|-
* Current official website: http://qiu.bioweb.hunter.cuny.edu.  
|
[[File:Portrait-2022-blur.jpg| x250 px | thumb]]
| <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<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>
| [[File:Belfer_building.jpg | x300px | thumb | [https://goo.gl/maps/xv1KmaW3XEnxaY1V7 Directions by Google Map]]]
|__TOC__
|}


===Lab Gallery===
==Fieldwork Gallery==
<gallery>
<gallery mode="packed" heights="200px" perrow="4" style="text-align:left">
Image:Tick-hunting-2010-07-212.jpg|Collecting ticks
File:Tick-trip-2023.jpg|thumb|Oct 2023, Long Island, NY
Image:tick2-small.jpg|A host-seeking female adult Lyme tick (''Ixodes scapularis'')
File:Tick-trip-2022.jpg|thumb|June 2022, MA
Image:tick1-small.jpg|The same tick moving
File:Tick-trip-2021.jpg|thumb|June 2021, MA
</gallery>
</gallery>
<youtube width="200" height="150">Jb4ACK-GjM0</youtube>


===Research Interests===
==Lab publications==
* '''Evolution, microbial diversity, and pathogen genomics.''' I am interested in the population genomics of microbial species. The main focus of my lab is the comparative analysis of multiple genomes of the Lyme disease pathogen. The goals of my research include reconstructing the history of worldwide diversification of the Lyme disease bacteria, an understanding of the mechanisms of their genome evolution (e.g., the roles of recombination and natural selection), and inference of gene and genome functions.
===Lyme Genomics, Evolution, & Ecology===
<gallery mode="packed" heights="200px" perrow="4" style="text-align:left">
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.


* '''Bioinformatics & fieldwork.''' I use computational and statistical approaches to test evolutionary and functional hypotheses. Students learn and use modern computational tools such as relational database/SQL, Perl/BioPerl, and statistical computing with R.
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.  


===Courses & Curricular Development===
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]
* '''BIOL 425/790.49''' Computational Molecular Biology [[Biol425_2011|(Spring 2011 Syllabus)]]
* '''BIOL 375/790.64''' Molecular Evolution [http://diverge.hunter.cuny.edu/~weigang/lab-website/BIOL375-Fall-2012.html]
* The '''QuBi''' Curricular Improvement Project in Quantitative Biology [http://www.hunter.cuny.edu/qubi]


===Software Development===
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.  
* '''Borrelia Ortholog Retriever.''' Obtain ortholog alignments from 23 Borrelia spp genomes. Search by gene names and IDs.[http://borreliagenome.org/orth_get/]
* '''SimBac.''' A package for simulating bacterial genome evolution [http://sourceforge.net/projects/bacsim/files/]
* '''DNATweezer.''' A Perl wrapper of some BioPerl modules [https://sourceforge.net/p/dnatwizzer/home/Home/]


===Research Publications (since 2008)===
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.
* Casjens SR, Mongodin EF, Qiu W-G, Luft BJ, Schutzer SE, Eddie B. Gilcrease, Wai Mun Huang, Marija Vujadinovic, John K. Aron, Levy C. Vargas, Sam Freeman, Diana Radune, Janice F. Weidman, George I. Dimitrov, Hoda M. Khouri, Julia E. Sosa, Rebecca A. Halpin, John J. Dunn, Claire M. Fraser. (2012) Genome Stability of Lyme Disease Spirochetes: Comparative Genomics of Borrelia burgdorferi Plasmids. PLoS ONE 7(3): e33280. doi:10.1371/journal.pone.0033280
 
* Schutzer SE, Fraser-Liggett CM, Qiu WG, Kraiczy P, Mongodin EF, Dunn JJ, Luft BJ, Casjens SR (2012). Whole-Genome Sequences of Borrelia bissettii, Borrelia valaisiana, and Borrelia spielmanii. Journal of Bacteriology 194: 545-546.
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.
* Haven J, Vargas LC, Mongodin EF, Xue V, Hernandez Y, Pagan P, Fraser-Liggett CM, Schutzer SE, Luft BJ, Casjens SR, Qiu WG. (2011). Pervasive Recombination and Sympatric Genome Diversification Driven by Frequency-Dependent Selection in Borrelia burgdorferi, the Lyme disease Bacterium. Genetics. 189:951-966.
</gallery>
* Chavadi SS, Stirrett KL, Edupuganti UR, Vergnolle O, Sadhanandan G, Marchiano E, Martin C, Qiu WG, Soll CE, Quadri LE. (2011). Mutational and phylogenetic analyses of the mycobacterial mbt gene cluster. J Bacteriol. 2011 Aug 26.  
 
* Weigang Qiu. (2011). A Review of Lyme Disease: The Ecology of a Complex System by Richard S. Ostfeld. The Quarterly Review of Biology 86 (3): 241.
===Evolution & Learning Algorithms===
* Xie XF, WG Qiu, PN Liple. 2011. Accelerated and adaptive evolution of yeast sexual adhesins. Mol. Biol. Evol. 28 (11): 3127-37.  
<gallery mode="packed" heights="200px" perrow="3" style="text-align:left">
* Sherwood R. Casjens, Claire M. Fraser-Liggett, Emmanuel F. Mongodin, Wei-Gang Qiu,John J. Dunn, Benjamin J. Luft, and Steven E. Schutzer. (2011). Whole Genome Sequence of an Unusual Borrelia burgdorferi Sensu Lato Isolate. J. Bacteriology. 193:1489-1490.
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.
* Schutzer, SE; Fraser-Liggett, CM; Casjens, SR; Qiu, WG; Dunn, JJ; Mongodin EF; Luft, BJ. (2011). Whole-Genome Sequences of Thirteen Isolates of Borrelia burgdorferi. J. Bacteriology. 193:1018-1020.
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.
* Wywial E, Haven J, Casjens SR, Hernandez YA, Singh S, Mongodin EF, Fraser-Liggett CM, Luft BJ, Schutzer SE, Qiu WG. (2009). Fast, adaptive evolution at a bacterial host-resistance locus: The PFam54 gene array in Borrelia burgdorferi. Gene. 445:26-37.
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.
* Tran D, Haven J, Qiu WG, Polle JE. (2009). An update on carotenoid biosynthesis in algae: phylogenetic evidence for the existence of two classes of phytoene synthase. Planta. 229(3):723-9.
</gallery>
* Arva NC, Talbott KE, Okoro DR, Brekman A, Qiu WG, Bargonetti J. (2008). Disruption of the p53-Mdm2 complex by Nutlin-3 reveals different cancer cell phenotypes. Ethnicity and Disease. 18(S2):1-8.
 
* Qiu, WG; Bruno, JF; McCaig, WD; Xu, Y.; Livey, I.; Schriefer, ME; Luft, BJ. 2008. Wide distribution of a high-virulence borrelia burgdorferi clone in Europe and North America. Emerging Infectious Diseases. 14(7):1097-1104. [Open Access]
===Informatics Tool Development===
* Qiu, WG; Bruno, JF; McCaig, WD; Xu, Y.; Livey, I.; Schriefer, ME; Luft, BJ. (2008). Wide distribution of a high-virulence Borrelia burgdorferi clone in Europe and North America. Emerging Infectious Diseases. 14(7):1097-1104. [Open Access]
<gallery mode="packed" heights="200px" style="text-align:left">
* Otoo HN; Lee KG; Qiu WG; Lipke PN. (2008). Candia albicans Als adhesins have conserved amyloid-forming sequences. Eukaryotic Cell. 7 (5):776-82.
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>
 
* [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]
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)
||
* 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)<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===
<gallery mode="packed" heights="200px" perrow="4" style="text-align:left">
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>
 
==Teaching & 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 syllabus===
* BIOL425 Computational Molecular Biology (Spring, 2023). [https://github.com/weigangq/CSB-BIOL425/tree/master/lecture-materials Lecture material on github]
* [http://borreliabase.org/~wgqiu/r-demo-2023.html BIOL714 Cell Biology, 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)]]
* [[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]'''''; 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 & Protocols==
* 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)
* [[Monte Carlo Club]] (summer projects)
* T[[Tick protocol|ick handling protocols]]
* [[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 ==
* [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:Configuration_settings Configuration settings list]
* [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/postorius/lists/mediawiki-announce.lists.wikimedia.org/ MediaWiki release mailing list]
* [https://www.mediawiki.org/wiki/Special:MyLanguage/Localisation#Translation_resources Localise MediaWiki for your language]
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* Consult the [[mediawikiwiki:Special:MyLanguage/Help:Contents|User's Guide]] for information on using the wiki software.

Revision as of 18:55, 16 February 2024

Portrait-2022-blur.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

  • 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)

  • 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

  • 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)

Teaching & 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 syllabus

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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