Main Page: Difference between revisions

From QiuLab
Jump to navigation Jump to search
imported>Weigang
No edit summary
 
(257 intermediate revisions by 3 users not shown)
Line 1: Line 1:
<div id="mf-home">
{|
<big>'''Welcome to the Wiki for Dr. Qiu's Evolutionary Bioinformatics Lab at [http://hunter.cuny.edu Hunter College]!'''</big>
|-
* Address: Belfer Research Building, 413 East 69th Street (between York and 1st Avenue), New York, NY 10021. Direction: [https://www.google.com/maps/place/413+E+69th+St,+New+York,+NY+10021/@40.7655886,-73.9561743,17z/data=!3m1!4b1!4m2!3m1!1s0x89c258c3d235f76f:0x4f3d0d5d8a78fe6?hl=en Google Map]
|
* Office phone: 1-212-896-0445.
[[File:Protrait-July-2024-Qiu.jpg| x250 px | thumb]]
* [http://biology.hunter.cuny.edu Biology Department Website]
| <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>
* [http://www.hunter.cuny.edu/belfer/faculty Belfer Hunter faculty]
[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>
* [http://www.hunter.cuny.edu/qubi Quantitative Biology (QuBi) Programs] at Hunter:[http://catalog.hunter.cuny.edu/preview_program.php?catoid=37&poid=7732 Curriculum map for Biology/Bioinformatics]
| [[File:Belfer_building.jpg | x300px | thumb | [https://goo.gl/maps/xv1KmaW3XEnxaY1V7 Directions by Google Map]]]
----
|__TOC__
===Lab Gallery===
|}
{{#ev:youtube|Jb4ACK-GjM0|400|right|Tick Expedition, Fire Island, New York, 2019}}
 
<gallery>
==Fieldwork Gallery==
Image: Beaver-lake.jpg|Massachusetts, Summer 2021
<gallery mode="packed" heights="200px" perrow="4" style="text-align:left">
Image: Hackaton.png|Jan 31, 2014, Participants: Daniel, Girish, Pedro, Rayees, Raymond, Regina, Saymon, Weigang
File:Tick-trip-2023.jpg|thumb|Oct 2023, Long Island, NY
Image:Tick-hunting-2010-07-212.jpg|Collecting ticks
File:Tick-trip-2022.jpg|thumb|June 2022, MA
Image:tick2-small.jpg|A host-seeking female adult Lyme tick (''Ixodes scapularis'')
File:Tick-trip-2021.jpg|thumb|June 2021, MA
Image:tick1-small.jpg|The same tick moving
</gallery>
Image:nymph-1.jpg|Nymphs are small (and ~25% carry Lyme)
<youtube width="200" height="150">Jb4ACK-GjM0</youtube>
Image:nymph-3.jpg|Summer 2021 collection
 
==Lab publications==
===Lyme Genomics, Evolution, & Ecology===
<gallery mode="packed" heights="200px" perrow="4" style="text-align:left">
 
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>
video link: [https://youtu.be/Jb4ACK-GjM0 Fire Island, Summer 2018]


----
===Evolution & Learning Algorithms===
<gallery mode="packed" heights="200px" perrow="3" style="text-align:left">
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>


===Lab Resources===
===Informatics Tool Development===
* [[Monte_Carlo_Club | Monte Carlo Club]] (Spring 17; Summer 17; Summer 18; Spring 2022): Probability by simulation
<gallery mode="packed" heights="200px" style="text-align:left">
* [[Mini-Tutorals | Mini-tutorials/Protocols for most commonly used software tools, pipelines, and databases]]
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.
* [[Tick_protocol | Tick handling protocol]]
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.
* Data Science Tool Tutorials
</gallery>
** [https://rstudio.cloud/learn/primers An RStudio Tutorial]
** [http://korflab.ucdavis.edu/Unix_and_Perl/current.html Linux/Unix tutorials]
** [http://diverge.hunter.cuny.edu/~weigang/Intro_to_Python.html A python tutorial (by Edgar)] [https://pandas.pydata.org/pandas-docs/stable/user_guide/visualization.html pandas visualization]
** [https://stats.libretexts.org/Bookshelves/Applied_Statistics/Book%3A_Learning_Statistics_with_R_-_A_tutorial_for_Psychology_Students_and_other_Beginners_(Navarro)/17%3A_Bayesian_Statistics Bayesian alternatives for conventional statistics]. Use the BayesFactor package. BUGS and STAN packages should be more powerful.
** Problem of p-hacking: [https://www.nature.com/articles/506150a Nuzzo (2014). Nature. "Scientific method: statistical errors"]
** ASA Statement on p-value. [[file:///C:/Users/weiga/Dropbox/PDFs/ASA-statement-on-p-value.pdf|Ronald L. Wasserstein & Nicole A. Lazar (2016)]] The ASA Statement on
p-Values: Context, Process, and Purpose, The American Statistician
** [[A_Primer_on_the_Cluster_System_at_Hunter|An introduction and tutorial for using Hunter's new cluster system]]
** [http://www.huber.embl.de/msmb/index.html A Free (advanced, probability & simulated based) Biostatistics TextBook in R]
** [https://www.rstudio.com/wp-content/uploads/2015/03/ggplot2-cheatsheet.pdf Ggplot2 cheat sheet (from RStudio)]
** [https://rkabacoff.github.io/datavis/index.html Data Visualization with R (by Rob Kabacoff)]
** [https://cgi.duke.edu/web/sciwriting/ A Duke university course for scientific writing (highly recommended)]
* [[Summer_2021|Summer Research (2021)]]
* [[Undergrad_Research_Experience|Undergraduate Research (Fall 2020, Spring 2021)]]
* [[Hackathon_2020 | 2nd Hackathon of QiuLab (Feb 8, 2020): Phylogeography of Coronavirus outbreaks]]
* [[Summer_2019 | Summer 2019 Research Wiki Page]]
* [[Year_2019|Spring-Summer 2019 Research Wiki]]
* [[Summer_2018 | Summer 2018 Research Wiki Page]]
* [[Qiu_Lab_Meetings| Past Lab Meetings]] (2013; 2014; 2015; 2016)
* [[First_Time_Guide| First-time guide to lab computer system]]
* [[Lab_Orientation | Orientation for new lab members ]]


===Research Interests===
* [http://scholar.google.com/citations?hl=en&user=Ds6u39QAAAAJ) Full list by Google Scholar]
* '''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.
* [http://www.ncbi.nlm.nih.gov/sites/myncbi/weigang.qiu.1/bibliography/42770924/public/ Full list by NCBI Bibliography]
last update: March 20, 2023


* '''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.
==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==
===Courses & Curricular Development===
===Apps with Collaborators (or from published papers)===
* Spring 2022. BIOL47120. [[BioMed-R-2022|Biomedical Genomics II]]
<gallery mode="packed" heights="200px" perrow="4" style="text-align:left">
* BIOL48002. Independent studies
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)])
** Counts towards elective for biology major
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)])
** Counts as undergraduate-research credits, which is a requirement for graduation with honor
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)
** Follow this template for final report: [[File:BIOL48002 Final Report Template.pdf|thumbnail]]
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)
* Spring 2021. BIOL47120. [[BioMed-R-2021|Biomedical Genomics II]]
File:Screenshot_2023-03-24_122312.png | link=http://borreliabase.org/~wgqiu/mpai-v3/ | Genes & Pathways Associated with mTP53 (with Bargonetti Lab @Hunter)
* August 6, 2020. [[EEB_BootCamp_2020|EEB Bioinformatics Bootcamp: Genomic Epidemiology]]
File:Spombe.png | link=Spombe | S. pombe transcriptomes (with Zhong Lab @Hunter)
* Spring 2020. BIOL47120. [[BioMed-R-2020|Biomedical Genomics II]].
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)
* Fall 2019. BIOL 375/790.64. Molecular Evolution. [[Biol375_2019|(Fall 2019 Syllabus)]]
File:Screenshot 2023-03-24 122245.png | link=http://borreliabase.org/~wgqiu/oneKGenome/ | 1K genome (with Ogunwobi Lab @Hunter)
* Summer 2019. [[Southwest-University|Biomedical Genomics]], Southwest University, China, July 8-19
File:Screenshot 2023-03-24 122450.png | link=http://borreliabase.org/~wgqiu/E_faecalis/ | E faecalis genome browser (with Morales Lab @WCMC)
* BIOMEDICAL BIG DATA WEEK [[BigData_2019|Phylo-Genomics Syllabus (June 20, 2019, 9-12)]]; [[BigData_2020|Phylo-Genomics Syllabus (July 22, 2020)]]
File:Screenshot 2023-03-24 122145.png | link=http://borreliabase.org/~wgqiu/carmen-proteomics/ | Proteomics GSEA results (with Melendez Lab @Hunter)
* Spring 2019. BIOL47120. [[BioMed-R|Biomedical Genomics II]]. (syllabus on Blackboard)
File:Screenshot 2023-03-24 122051.png | link=http://borreliabase.org/~wgqiu/Tcell-pHis-ACS/ | pHis Protein Browser (with Skolnik lab @NYU)
* Fall 2018. BIOL 375/790.64. Molecular Evolution. [[Biol375_2018|(Fall 2018 Syllabus)]]
</gallery>
* Summer 2018. BIOMEDICAL BIG DATA WEEK 2018 (June 18-22). [[BigData_2018|Phylo-Genomics Syllabus (June 21, 2018, 9-12)]]
* Fall 2017. BIOL 375/790.64. Molecular Evolution. [[Biol375_2017|(Fall 2017 Syllabus)]]
* Spring 2017. BIOL 20N02. Analysis of Biological Data. [[Biol20N02_2017|(Spring 2017 Syllabus)]]
* Fall 2016. BIOL 375/790.64. Molecular Evolution. [[Biol375_2016|(Fall 2016 Syllabus)]]
* Spring 2016. BIOL 20N02. Analysis of Biological Data. [[Biol20N02_2016|(Spring 2016 Syllabus)]]
* Guest Lecture on R/Rstudio. [[r-tutorial|a brief tutorial on R/RStudio]]
* (Instructor: Dr Krampis) Spring 2016. BIOL 425/790.49. Computational Molecular Biology. [[Biol425_2016|(Syllabus)]]
* Fall 2015. BIOL 375/790.64. Molecular Evolution. [[Biol375_2015|(Fall 2015 Syllabus)]]
* Spring 2015. BIOL 425/790.49. Computational Molecular Biology. [[Biol425_2015|(Syllabus)]]
* Fall 2014. BIOL 375/790.64. Molecular Evolution. [[Biol375_2014|(Fall 2014 Syllabus)]]
* Summer II 2014. BIOL 470.83/790.86. Summer Bioinformatics Workshop. [[Bioinformatics_Workshop_2014|(Summer II, 2014 Syllabus)]]
* Spring 2014. BIOL 425/790.49. Computational Molecular Biology. [[Biol425_2014|(Syllabus)]]
* Fall 2013. BIOL 105. Introduction to Genome Biology. [[Intro_Genome_Bio_2013|(Fall 2013 Syllabus)]]
* Summer 2013. BIOL 470.83/790.86. Summer Bioinformatics Workshop. [[Bioinformatics_Workshop_2013|(Summer I, 2013 Syllabus)]]
* Spring 2013. BIOL 425/790.49. Computational Molecular Biology. [[Biol425_2013|(Spring 2013 Syllabus)]]
* Fall 2012. BIOL 375/790.64. Molecular Evolution. [http://diverge.hunter.cuny.edu/~weigang/lab-website/BIOL375-Fall-2012.html (Fall 2012 Syllabus)]
* '''The QuBi Project''' [http://www.hunter.cuny.edu/qubi (Quantitative Biology/Bioinformatics Curricular Options in Hunter)]
** [[QuBi/QuBi-News|QuBi Announcements]]
** Bioinformatics Modules for BIOL 203. Molecular Genetics (Spring 2020): [[QuBi/module/bio203-lab12%E2%80%942020|Lab 12]];
** Bioinformatics Modules for BIOL 203. Molecular Genetics (Spring 2018): [[QuBi/module/bio203-lab12%E2%80%942018|Lab 12]]; [[QuBi/modules/biol203-geno-pheno-association|Lab 13]]
** Bioinformatics Modules for BIOL 203. Molecular Genetics (Spring 2017): [[QuBi/module/bio203-lab12%E2%80%942017|Lab 12]]; [[QuBi/modules/biol203-geno-pheno-association|Lab 13]]; [[File:Bio203-Spring-2017-v1.png|50px]]
** Bioinformatics Modules for BIOL 203. Molecular Genetics (Spring 2016): [[QuBi/module/bio203-mdm2-lab|Lab 12]]; [[QuBi/modules/biol203-geno-pheno-association|Lab 13]]
** Bioinformatics Modules for BIOL 203. Molecular Genetics (Spring 2015): [[QuBi/modules/biol203-Lab4|Lab 4]]; [[QuBi/modules/biol203-Lab7|Lab 7]]
** [[QuBi/modules/biol303|Bioinformatics Module for BIOL 303. Cell Biology]] (Fall 2014)
** [[QuBi/bio203|Bioinformatics Module for BIOL 203. Molecular Genetics]] (Spring 2014)
** [[Qubi/biol202|Bioinformatics Module for BIOL 202. Cell Biology II]] (Fall 2013)
** [[QuBi/modules/biol302|Bioinformatics Module for BIOL 302. Molecular Genetics]] (Spring 2013)


===Bioinformatics career & Summer programs===
===Qiu Lab Apps===
* [https://www.aphl.org/fellowships/pages/bioinformatics.aspx CDC Bioinformatics Fellowship Program (Apply Nov - Feb annually)]
<gallery mode="packed" heights="200px" perrow="3" style="text-align:left">
* [https://simonsfoundation.wd1.myworkdayjobs.com/en-US/ccbcareers/job/162-Fifth-Avenue/Summer-Research-Assistant-Associate--Center-for-Computational-Biology_R0000915 Simons Foundation, Summer Research Assistant/Associate]. Deadline: Feb 15, 2022
File:Screenshot 2023-03-24 122558.png | link=http://borreliabase.org | Lyme genome browser
* [https://simonsfoundation.wd1.myworkdayjobs.com/en-US/ccbcareers/job/162-Fifth-Avenue/Flatiron-Research-Fellow--Center-for-Computational-Biology_R0000896 Simons Foundation, Post-doc program in computational biology]
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>


===Software Development===
==Lab Resources & Protocols==
* '''BorreliaBase—a Phylo-centric Browser of Borrelia Genomes'''. [http://borreliabase.org/ Obtain ortholog alignments from 23 Borrelia spp genomes. ]
* [[Monte Carlo Club]]
* '''SimBac.''' A package for simulating bacterial genome evolution [http://sourceforge.net/projects/bacsim/files/]
* [[NY-RaMP Mentoring]]
* '''BbWrapper.''' Perl wrappers of popular BioPerl modules [https://metacpan.org/pod/Bio::BPWrapper]; clone from GitHub: <code>git clone https://github.com/bioperl/p5-bpwrapper.git</code>
* Borreliella genome sequencing consortium: Weekly meetings (Tu @11): Since Jan 2023
* '''Amino Acid Mutual Information''': [http://borreliagenome.org/aavar Species-Specific AA Variations of Yeast Cell-Wall Proteins]
* Borreliella diagnostic antigens (Fall 2023-Fall 2027):
* '''Codon View''': [http://borreliagenome.org/codon-view Visualize codon alignments]
** 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)
* 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])


===Research and other Publications (since 2008)===
== Wiki Help ==
* [https://go.nature.com/3xAxOYh Jenner's Dilemma and how to win evolutionary arms race against microbial pathogens]
* [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:Configuration_settings Configuration settings list]
* [https://dailyclout.io/opinion-twin-guardians-of-civilizations/ Xia & Qiu (2021). "Twin Guardians of Civilizations". DailyClout]
* [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:FAQ MediaWiki FAQ]
* [http://scholar.google.com/citations?user=Ds6u39QAAAAJ Google Scholar Citation Indices]
* [https://lists.wikimedia.org/postorius/lists/mediawiki-announce.lists.wikimedia.org/ MediaWiki release mailing list]
* Lia Di, Pedro E Pagan, Daniel Packer, Che L Martin, Saymon Akther, Girish Ramrattan, Emmanuel F Mongodin, Claire M Fraser, Steven E Schutzer, Benjamin J Luft, Sherwood R Casjens and Wei-Gang Qiu. (2014). ''BorreliaBase'': a phylogeny-centered browser of Borrelia genomes. [http://www.biomedcentral.com/1471-2105/15/233 ''BMC Bioinformatics'' 2014, 15:233].
* [https://www.mediawiki.org/wiki/Special:MyLanguage/Localisation#Translation_resources Localise MediaWiki for your language]
* Matthew McKnight Croken, Weigang Qiu, Michael W White and Kami Kim (2014). Gene Set Enrichment Analysis (GSEA) of Toxoplasma gondii expression datasets links cell cycle progression and the bradyzoite developmental program. [http://www.biomedcentral.com/1471-2164/15/515 ''BMC Genomics'' 2014, 15:515.]
* [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:Combating_spam Learn how to combat spam on your wiki]
* Qiu WG, Martin CL. (2014) Evolutionary genomics of ''Borrelia burgdorferi'' sensu lato: Findings, hypotheses, and the rise of hybrids. ''Infection Genetics & Evolution''. [http://www.ncbi.nlm.nih.gov/pubmed/24704760 PubMed Link]
* Consult the [[mediawikiwiki:Special:MyLanguage/Help:Contents|User's Guide]] for information on using the wiki software.
* Mongodin EF, Casjens SR, Bruno JF, Xu Y, Drabek EF, Riley DR, Cantarel BL, Pagan PE, Hernandez YA, Vargas LC, Dunn JJ, Schutzer SE, Fraser CM, Qiu WG, Luft BJ. (2013). Inter- and intra-specific pan-genomes of ''Borrelia burgdorferi'' sensu lato: genome stability and adaptive radiation. [http://www.biomedcentral.com/1471-2164/14/693 ''BMC Genomics'' 2013, 14(1):693].
* 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. [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0033280 PLoS ONE 7(3): e33280].
* 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.
* 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.
* 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.
* Xie XF, WG Qiu, PN Liple. 2011. Accelerated and adaptive evolution of yeast sexual adhesins. Mol. Biol. Evol. 28 (11): 3127-37.
* 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.
* 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.
* 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.
* 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.
* 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]
* 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]
* Otoo HN; Lee KG; Qiu WG; Lipke PN. (2008). Candia albicans Als adhesins have conserved amyloid-forming sequences. Eukaryotic Cell. 7 (5):776-82.
</div>

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

Wiki Help

Retrieved from "https://wiki.genometracker.org/index.php?title=Main_Page&oldid=6491"