Nida Obatake

Mathematics PhD candidate, Texas A&M University

  • Research

    Algebraic and geometric methods for problems in mathematical biology.

  • Curriculum Vitae

    updated September 2020

  • Contact

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

  • Nida Obatake
    • Publications

        1. "Mixed volume for small reaction networks" with Anne Shiu and Dilruba Sofia. Submitted to Involve (in revision) (2020). Available from arXiv:2004.14467.

        2. "Dynamics of ERK regulation in the processive limit" with Carsten Conradi, Anne Shiu, and Xiaoxian Tang. Submitted to Journal of Mathematical Biology (in revision) (2020). Available from arXiv:1910.14452.

        3. "Identifiability of Linear Compartmental Models: The Effect by Moving Inputs, Outputs, and Leaks" with Seth Gerberding and Anne Shiu. Linear and Multilinear Algebra (2020). Available from arXiv:1910.13549.

        4. "Modeling R-loops with Formal Grammars" with Nataša Jonoska, Svetlana Poznanovikj, Candice Price, Manda Riehl, and Mariel Vazquez. Springer Nature: Using Mathematics to Understand Biological Complexit (to appear) (2019).

        5. "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.

        6. "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.

        7. "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.

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

        9. "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 (2016).
        • "Mixed volume for small reaction networks" with Anne Shiu and Dilruba Sofia. Submitted to Involve (2020). Available from arXiv:2004.14467.

        • "Dynamics of ERK regulation in the processive limit" with Carsten Conradi, Anne Shiu, and Xiaoxian Tang. Submitted to Journal of Mathematical Biology (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. Submitted to Linear and Multilinear Algebra (in revision) (2019). Available from arXiv:1910.13549v2.

        • "Modeling R-loops with Formal Grammars" with Nataša Jonoska, Svetlana Poznanovikj, Candice Price, Manda Riehl, and Mariel Vazquez. Submitted to Springer special edition on Using Mathematics to Understand Biological Complexity, WIMB (in revision) (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


    Spring 2020

    • I will lead the Math 140 Week-in-Review

      Mathematics for Business and Social Sciences

      Math 140 Week-in-Review Homepage
      • 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

        • Polyhedral methods for chemical reaction networksGeometry Seminar, Texas A&M
        • Dynamics in a model of ERK regulationSIAM TX-LA Annual Meeting
        • 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 candidate 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!