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** [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://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.
** [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"]
** 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)]
** 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]]
** [[A_Primer_on_the_Cluster_System_at_Hunter|An introduction and tutorial for using Hunter's new cluster system]]

Revision as of 13:28, 2 April 2022

Welcome to the Wiki for Dr. Qiu's Evolutionary Bioinformatics Lab at Hunter College!

Lab Gallery

{{#ev:youtube|Jb4ACK-GjM0|400|right|Tick Expedition, Fire Island, New York, 2019}}

  • Massachusetts, Summer 2021

    Massachusetts, Summer 2021

  • Jan 31, 2014, Participants: Daniel, Girish, Pedro, Rayees, Raymond, Regina, Saymon, Weigang

    Jan 31, 2014, Participants: Daniel, Girish, Pedro, Rayees, Raymond, Regina, Saymon, Weigang

  • Collecting ticks

    Collecting ticks

  • A host-seeking female adult Lyme tick (Ixodes scapularis)

    A host-seeking female adult Lyme tick (Ixodes scapularis)

  • The same tick moving

    The same tick moving

  • Nymphs are small (and ~25% carry Lyme)

    Nymphs are small (and ~25% carry Lyme)

  • Summer 2021 collection

    Summer 2021 collection

video link: Fire Island, Summer 2018

Lab Resources

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.

Courses & Curricular Development

Bioinformatics career & Summer programs

Software Development

Research and other Publications (since 2008)

  • Jenner's Dilemma and how to win evolutionary arms race against microbial pathogens
  • Xia & Qiu (2021). "Twin Guardians of Civilizations". DailyClout
  • 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. 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. 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. 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. 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. 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.
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