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<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.
* [http://biology.hunter.cuny.edu Biology Department Website]
* [http://www.hunter.cuny.edu/belfer/faculty Belfer Hunter faculty]
* [http://www.hunter.cuny.edu/qubi Quantitative Biology (QuBi) Programs] at https://hunter-undergraduate.catalog.cuny.edu/programs/BIO1-BA Curriculum map for Biology/Bioinformatics] [https://adfs.hunter.cuny.edu/adfs/ls/ Online Major Declaration Form]
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===Lab Gallery===
{{#ev:youtube|Jb4ACK-GjM0|400|right|Tick Expedition, Fire Island, New York, 2019}}
<gallery>
Image: Beaver-lake.jpg|Massachusetts, Summer 2021
Image: Hackaton.png|Jan 31, 2014, Participants: Daniel, Girish, Pedro, Rayees, Raymond, Regina, Saymon, Weigang
Image:Tick-hunting-2010-07-212.jpg|Collecting ticks
Image:tick2-small.jpg|A host-seeking female adult Lyme tick (''Ixodes scapularis'')
Image:tick1-small.jpg|The same tick moving
Image:nymph-1.jpg|Nymphs are small (and ~25% carry Lyme)
Image:nymph-3.jpg|Summer 2021 collection
</gallery>
video link: [https://youtu.be/Jb4ACK-GjM0 Fire Island, Summer 2018]


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Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User's Guide] for information on using the wiki software.


===Lab Resources===
== Getting started ==
* [[Monte_Carlo_Club | Monte Carlo Club]] (Spring 17; Summer 17; Summer 18; Spring 2022): Probability by simulation
* [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:Configuration_settings Configuration settings list]
* [[Mini-Tutorals | Mini-tutorials/Protocols for most commonly used software tools, pipelines, and databases]]
* [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:FAQ MediaWiki FAQ]
* [[Tick_protocol | Tick handling protocol]]
* [https://lists.wikimedia.org/postorius/lists/mediawiki-announce.lists.wikimedia.org/ MediaWiki release mailing list]
* Data Science Tool Tutorials
* [https://www.mediawiki.org/wiki/Special:MyLanguage/Localisation#Translation_resources Localise MediaWiki for your language]
** [https://rstudio.cloud/learn/primers An RStudio Tutorial]
* [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:Combating_spam Learn how to combat spam on your wiki]
** [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]  [http://biopython.org/DIST/docs/tutorial/Tutorial.html BioPython Tutorials]
** [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.
** [https://vincentarelbundock.github.io/rethinking2/ Bayesian analysis with R/tidyverse and Stan.] Richard McElreath’s Statistical Rethinking (2nd ed.)
** [https://cran.r-project.org/web/packages/tidybayes/index.html The tidybayes package] connects rstan with tidyverse: [https://cran.r-project.org/web/packages/tidybayes/vignettes/tidybayes.html vignette, an informative walk-through example]
** Problem of p-hacking: [https://www.nature.com/articles/506150a Nuzzo (2014). Nature. "Scientific method: statistical errors"]  [[File:Ruzzo-fig.png|thumbnail]]
** ASA Statement on p-value. [https://amstat.tandfonline.com/doi/pdf/10.1080/00031305.2016.1154108 Ronald L. Wasserstein & Nicole A. Lazar (2016)]
** [[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===
* '''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.
 
* '''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.
 
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===Courses & Curricular Development===
* Spring 2022. BIOL47120. [[BioMed-R-2022|Biomedical Genomics II]]
* BIOL48002. Independent studies
** Counts towards elective for biology major
** Counts as undergraduate-research credits, which is a requirement for graduation with honor
** Follow this template for final report: [[File:BIOL48002 Final Report Template.pdf|thumbnail]]
* Spring 2021. BIOL47120. [[BioMed-R-2021|Biomedical Genomics II]]
* August 6, 2020. [[EEB_BootCamp_2020|EEB Bioinformatics Bootcamp: Genomic Epidemiology]]
* Spring 2020. BIOL47120. [[BioMed-R-2020|Biomedical Genomics II]].
* Fall 2019. BIOL 375/790.64. Molecular Evolution. [[Biol375_2019|(Fall 2019 Syllabus)]]
* Summer 2019. [[Southwest-University|Biomedical Genomics]], Southwest University, China, July 8-19
* BIOMEDICAL BIG DATA WEEK [[BigData_2019|Phylo-Genomics Syllabus (June 20, 2019, 9-12)]]; [[BigData_2020|Phylo-Genomics Syllabus (July 22, 2020)]]
* Spring 2019. BIOL47120. [[BioMed-R|Biomedical Genomics II]]. (syllabus on Blackboard)
* Fall 2018. BIOL 375/790.64. Molecular Evolution. [[Biol375_2018|(Fall 2018 Syllabus)]]
* 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===
* [https://www.aphl.org/fellowships/pages/bioinformatics.aspx CDC Bioinformatics Fellowship Program (Apply Nov - Feb annually)]
* [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
* [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]
----
 
===Software Development===
* '''BorreliaBase—a Phylo-centric Browser of Borrelia Genomes'''. [http://borreliabase.org/ Obtain ortholog alignments from 23 Borrelia spp genomes. ]
* '''SimBac.''' A package for simulating bacterial genome evolution [http://sourceforge.net/projects/bacsim/files/]
* '''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>
* '''Amino Acid Mutual Information''': [http://borreliagenome.org/aavar Species-Specific AA Variations of Yeast Cell-Wall Proteins]
* '''Codon View''': [http://borreliagenome.org/codon-view Visualize codon alignments]
----
 
===Research and other Publications (since 2008)===
* [https://go.nature.com/3xAxOYh Jenner's Dilemma and how to win evolutionary arms race against microbial pathogens]
* [https://dailyclout.io/opinion-twin-guardians-of-civilizations/ Xia & Qiu (2021). "Twin Guardians of Civilizations". DailyClout]
* [http://scholar.google.com/citations?user=Ds6u39QAAAAJ Google Scholar Citation Indices]
* 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].
* 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.]
* 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]
* 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>

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