Alexis Black-Pyrkosz

Alexis Black-Pyrkosz

BioInformatics Coordinator, Department of Computational Mathematics, Science and Engineering;
Room 2507K, Engineering Building
  428 S. Shaw Ln.
 (517) 432-0634 
 ablackpz@msu.edu

    About Me

    Education:

    B.S., 2004, Chemistry Major Computer Science Minor, Lawrence Technological University

    Ph.D. 2010, Chemistry, University of Illinois, Urbana-Champaign

     

    Bio:

    Alexis Black Pyrkosz is a Curriculum Specialist in the Department of Computational Mathematics, Science, and Engineering at Michigan State University, where she has been a faculty member since 2017.

    Black Pyrkosz coordinates the CMSE Bioinformatics Program, which educates graduate students and post-docs in genomics, programming, statistics, and visualization of large research data sets. This program consists of 4-wk modules that focus on training students in specific, modern technologies and skills. Students are encouraged to use these modules to create unique educational flowcharts that fit their research goals.

    Before arriving at Michigan State, Black Pyrkosz held a post-doctoral appointment at the United States Department of Agriculture, Agricultural Research Service, Avian Disease and Oncology Laboratory, as part of Hans Cheng's laboratory. She eventually became a bioinformatics consultant for all of the Avian Disease and Oncology Laboratory, working on various lab's datasets on Marek's Disease Virus, spontaneous tumors, and avian hosts. She also directed an Intro to Computation workshop as part of MSU's 2013 SROP program.

    Research Interests

    •    RNA-Seq

    •    Genome Assembly

    •    Phylogeography

    •    Evolution of Structure

    •    Drug Docking

    Selected Publications
    [1]
    Comparative Transcriptomics of Genetically Divergent Lines of Chickens in Response to Marek’s Disease Virus Challenge at Cytolytic PhaseKunzhe Dong, Shuang Chang, Qingmei Xie, Alexis Black-Pyrkosz, Huanmin Zhang, Plos One (2017) doi.org/10.1371/journal.pone.0178923
     
    [2]
    A New Chicken Genome Assembly Provides Insight into Avian Genome StructureWesley C. Warren, LaDeana W. Hillier, Chad Tomlinson, Patrick Minx, Milinn Kremitzki, Tina Graves, Chris Markovic, Nathan Bouk, Kim D. Pruitt, Francoise Thibaud-Nissen, Valerie Schneider, Tamer A. Mansour, C. Titus Brown, Aleksey Zimin, Rachel Hawken, Mitch Abrahamsen, Alexis B. Pyrkosz, Mireille Morisson, Valerie Fillon, Alain Vignal, William Chow, Kerstin Howe, Janet E. Fulton, Marcia M. Miller, Peter Lovell, Claudio V. Mello, Morgan Wirthlin, Andrew S. Mason, Richard Kuo, David W. Burt, Jerry B. Dodgson and Hans H. Cheng, G3: GENES, GENOMES, GENETICS, January 1, 2017 vol. 7 no. 1 109-117

    ...

    Teaching

    FS-17/SS-18: CMSE 890, Sec 301 Programming for Bioinformatics

    FS-17/SS-18: CMSE 890, Sec 302 Statistical Analysis and Visualization

    FS-17/SS-18: CMSE 890, Sec 303 Transcriptomic Data Analysis

    Click "Teaching" link to see past courses.