Nida Obatake

Mathematics PhD student, Texas A&M University

  • Research

    Algebraic and geometric methods for problems in mathematical biology.

  • Curriculum Vitae

    updated Nov 2019

  • Contact

    nida [at] math.tamu.edu
    For students: nobatake [at] tamu.edu

  • Nida Obatake
    • Publications

        1. "Dynamics of ERK regulation in the processive limit" with Carsten Conradi, Anne Shiu, and Xiaoxian Tang. In preparation (2019). Available from arXiv:1910.14452.

        2. "Identifiability of Linear Compartmental Models: The Effect by Moving Inputs, Outputs, and Leaks" with Seth Gerberding and Anne Shiu. In preparation (2019). Available from arXiv:1910.13549.

        3. "Modeling R-loops with Formal Grammars" with Nataša Jonoska, Svetlana Poznanovikj, Candice Price, Manda Riehl, and Mariel Vazquez. In preparation (2019).

        4. "Oscillations and bistability in a model of ERK regulation" with Anne Shiu, Xiaoxian Tang, and Angelica Torres. J. Math. Biol., 79:4, pp 1515–1549 (2019). Available from arXiv:1903.02617.

        5. "On the identification of k-inductively pierced codes using toric ideals" with Molly Hoch and Samuel Muthiah. Submitted (in revision). Available from arXiv:1807.02390.

        6. "Neural ideals and stimulus space visualization" with Elizabeth Gross and Nora Youngs. Advances in Applied Mathematics, Volume 95, Pages 65-95, ISSN 0196-8858 (2018). Available from ScienceDirect.

        7. "Drawing place field diagrams of neural codes using toric ideals." San Jose State Masters Theses (2016). Available from SJSU ScholarWorks.

        8. "Mathematical origami of a single vertex: regular K-points" with R. Alperin, R. Bommu, M. Gurdine, L. Mattick, J. Orozco, and J. Schrag. In preparation.
        • "Dynamics of ERK regulation in the processive limit" with Carsten Conradi, Anne Shiu, and Xiaoxian Tang. In preparation (2019). Available from arXiv:1910.14452.

        • "Oscillations and bistability in a model of ERK regulation" with Anne Shiu, Xiaoxian Tang, and Angelica Torres. J. Math. Biol., 79:4, pp 1515–1549 (2019). Available from arXiv:1903.02617.
        • "On the identification of k-inductively pierced codes using toric ideals" with Molly Hoch and Samuel Muthiah. Submitted (in revision). Available from arXiv:1807.02390.

        • "Neural ideals and stimulus space visualization" with Elizabeth Gross and Nora Youngs. Advances in Applied Mathematics, Volume 95, Pages 65-95, ISSN 0196-8858 (2018). Available from ScienceDirect.

        • "Drawing place field diagrams of neural codes using toric ideals." San Jose State Masters Theses (2016). Available from SJSU ScholarWorks.
        • "Identifiability of Linear Compartmental Models: The Effect by Moving Inputs, Outputs, and Leaks" with Seth Gerberding and Anne Shiu. In preparation (2019). Available from arXiv:1910.13549.

        • "Modeling R-loops with Formal Grammars" with Nataša Jonoska, Svetlana Poznanovikj, Candice Price, Manda Riehl, and Mariel Vazquez. In preparation (2019).

        • "Mathematical origami of a single vertex: regular K-points" with R. Alperin, R. Bommu, M. Gurdine, L. Mattick, J. Orozco, and J. Schrag. In preparation.
    • Research Interests

      I use methods from computational algebraic geometry to tackle questions in mathematical biology. My advisor is Dr. Anne Shiu.


      • All Publications
      • Chemical Reaction Networks
      • Neural Codes
      • Others


    Fall 2019

    • Math 140, Section 515

      Mathematics for Business and Social Sciences

      course material on eCampus
      • email nobatake [at] tamu.edu for teaching related correspondence
      • Upcoming conferences
      • Past Talks
      • Conferences Attended
      • Save the date!

        • SIAM Texas-Louisiana Sectional Meeting at Southern Methodist UniversityNov 1-3, 2019
        • I am organizing a minisymposium on "Algebraic, geometric, and combinatorial methods in mathematical biology".

        • Texas Women in Math Symposium 2020 at Texas A&M UniversityFeb 1-2, 2020
        • I am organizing TWIMS 2020 along with Prof. Laura Matusevich, Aleksandra Sobieska, Elise Walker, and Priyanga Ganesan.

































      • Past Talks

        ■ indicates invited talk

        • Sufficient conditions for 1- and 2- Inductively Pierced CodesSIAM AG 2019
        • Polyhedral Methods for Chemical Reaction NetworksTAGSS, ICTP
        • Toric ideals of Neural CodesAWM Research Symposium
        • Hopf bifurcations in the ERK networkAWM Research Symposium
        • Oscillations in the ERK networkAMS Spring Southeastern Sectional Meeting
        • Oscillations in the ERK networkGraduate Student Seminar, Texas A&M
        • Amoebas!TAMU-AMS GIGEM 2019
        • Chemical Reaction NetworksGraduate Student Seminar, Texas A&M
        • The capacity for Hopf bifurcations in the fully distributive
           dual-site phosphorylation network
          ICMS 2018

        • Place field diagrams of neural codesJMM 2018
        • Place field diagrams of neural codesAMS Fall Central Sectional Meeting
        • Toric ideals of neural codesSIAM AG 2017
        • Rat GPSGraduate Student Seminar, Texas A&M
        • Drawing place field diagrams of neural codes using toric idealsTWIMS 2016
        • Differential Forms and Manifolds, Integration, Stoke's TheoremSWAG, Texas A&M
        • Drawing place field diagrams of neural codes using toric idealsGeometry Seminar, Texas A&M
        • Algebraic methods for realizing neural codesColloquium, San Jose State University
        • Algebraic methods for realizing neural codesColloquium, Santa Clara University
        • Toric ideals of neural codesAMS Fall Western Sectional Meeting




















      • Conferences Attended

          2019:

        • Graduate Algebra Symposium, Texas A&M University - October
        • Mini Texas Algebraic Geometry Symposium - October
        • SIAM AG 2019, Bern, Switzerland - July
        • Trieste Algebraic Geometry Summer School, ICTP, Italy - July
        • Collaborative Workshop for Women in Mathematical Biology, IPAM, UCLA - June
        • AWM Research Symposium 2018, Rice University - April
        • CombinaTexas, Texas A&M University - March
        • AMS Sectional Meeting, Auburn University - March
        • GIG'EM 2019, Texas A&M University - February
        • Texas Algebraic Geometry Symposium, UT Austin - February

        • 2018:

        • Texas Women in Math Symposium (TWIMS) 2018, University of Houston - November
        • Mathematics of Reaction Networks Workshop, University of Wisconsin-Madison - August
        • SIAM Conference on the Life Sciences (SIAM-LS) 2018, Minneappolis, MN - August
        • International Congress of Mathematical Software (ICMS) 2018, Notre Dame University - July
        • CBMS Conference of Applications of Polynomial Systems, Texas Christian University - June
        • Texas Algebraic Geometry Symposium (TAGS), Texas A&M University - April
        • GIG'EM (Gathering in Graduate Expository Mathematics) 2018, Texas A&M University - March
        • Texas Geometry and Topology Conference (TGTC), University of Houston - February
        • CombinaTexas, Texas A&M University - February
        • Joint Mathematics Meeting (JMM), San Diego, CA - January

        • 2017:

        • AMS Fall Central Sectional Meeting, University of North Texas - September
        • SIAM Conference on Applied Algebraic Geometry, Georgia Tech University - August
        • Texas Algebraic Geometry Symposium (TAGS), Rice University - April

        • 2016:

        • Texas Women in Math Symposium (TWIMS), UT Austin - November
        • Texas Topology & Geometry Conference (TGTC), Texas A&M University - November
        • MAA Golden Sectional Meeting, UC Davis - February

        • 2015:

        • AMS Western Sectional Meeting, CSU Fullerton - October
        • Biology and Mathematics in the Bay Area (BaMBA), San Jose State University - October
        • Bay Area Discrete Math Day (BAD Math), San Francisco State University - October

        • 2014:

        • Biology and Mathematics in the Bay Area (BaMBA), UC Davis - October
        • Bay Area Discrete Math Day (BAD Math), Monterey, CA - October
    • Nida Obatake
    • About me

      Howdy! I am a fourth year PhD student at Texas A&M University. My research lies in the exciting field of algebraic biology. These days, I am particularly interested in the number and stability of steady states in chemical reaction networks, but I have dabbled in some other areas of mathematical biology, including neural codes and nucleic acid modeling. Other miscellaneous facts:

      • I am a mathematical software afficionado and welcome the opportunity to break beta test your programs!
      • I LOVE cold-brew coffee and an extra tangy kombucha.
      • I welcome questions from prospective math graduate students - shoot me an email!