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Erik Amézquita
Topological Data Analysis (TDA) and shape quantification meet plant biology
Career and Education
Preparing Future Faculty for Inclusive Excellence Postdoctoral Fellow
University of Missouri
Columbia, MO
present - 2023
- Division of Plant Science & Technology (80%)
- Department of Mathematics (20%)
PhD, Computational Mathematics, Science & Engineering
Michigan State University
East Lansing, MI
2023 - 2018
- Advisors: Elizabeth Munch and Dan Chitwood
- Defended: March 2023
- Dissertation: Exploring the Mathematical Shape of Plants
Lic. Mathematics (B.S.)
Universidad de Guanajuato
Guanajuato, Gto.
2018 - 2013
- Advisor: Antonio Rieser (CONACYT-CIMAT)
- Defended: May 2018
- Thesis: Efficient Object Classification using the Euler Characteristic
Peer-reviewed work
Decoding the coiling patterns of Cuscuta campestris with automated image processing
M. Bentelspacher, E.J. Amézquita, S. Adhikari, J. Barros, S.Y. Park
N/A
2024
- Plant Cell Reports 24(282). DOI: 10.1007/s00299-024-03337-1
Allometry and volumes in a nutshell: Analyzing walnut morphology using three-dimensional X-ray computed tomography
E.J. Amézquita, M.Y. Quigley, P.J. Brown, E. Munch, D.H. Chitwood
N/A
2024
- The Plant Phenome Journal 7: e20095. DOI: 10.1002/ppj2.20095
Genomics data analysis via spectral shape and topology
E.J. Amézquita, F. Nasrin, K.M. Storey, M. Yoshizawa
N/A
2023
- PLoS ONE 18(4): 30284820. DOI: 10.1371/journal.pone.0284820
A critical analysis of plant science literature reveals ongoing inequities
R.A. Marks, E.J. Amézquita, S. Percival, A. Rougon-Cardoso, C. Chibici-Revneanu, S.M. Tebele, J.M. Farrant, R. VanBuren, D.H. Chitwood
N/A
2023
- PNAS 120(10): e2217564120. DOI: 10.1073/pnas.2217564120
The shape of aroma: measuring and modeling citrus oil gland distribution
E.J. Amézquita, M.Y. Quigley, T. Ophelders, D. Seymour, E. Munch, D. H. Chitwood
N/A
2023
- Plants, People, Planet 5(5): 698-711. DOI: 10.1002/ppp3.10333
Teaching Tools in Plant Biology. Plants and Python, Coding from Scratch in the Plant Sciences
R. VanBuren, A. Rougon-Cardoso, E.J. Amézquita, E. Coss-Navarrete, A. Espinosa-Jaime, O. Gonzalez-Iturbe, A. Luckie-Duque, E. Mendoza-Galindo, J. Pardo, G. Rodríguez-Guerrero, P. Rosiles-Loeza, M. Vásquez-Cruz, S. Fernandez-Valverde, T. Hernandez-Hernandez, S. Palande, and D.H. Chitwood
N/A
2022
- The Plant Cell 34(7): e1. DOI: 10.1093/plcell/koac187
The shape of things to come: Topological data analysis and biology, from molecules to organisms
E.J. Amézquita, M.Y. Quigley, T. Ophelders, E. Munch, D.H. Chitwood
N/A
2020
- Developmental Dynamics 249(7): 816-833. DOI: 10.1002/dvdy.175
Work under review
Tabula Glycine: The whole-soybean single-cell resolution transcriptome atlas
S.A. Cervantes-Pérez, S. Thibivilliers, S. Amini, J.M. Pelletier, I. Meyer, H. Xu, S. Tennant, P. Ma, C. Sprueil, A.D. Farmer, J.E. Coate, H. Nelissen, Q. Yao, O. Martin, E.J. Amézquita, R.B. Goldberg, J.J. Harada, M. Libault
N/A
2024
From hand measurements to high throughput phenotyping: understanding maize canopy structure and predicting yield
Z. Ji, E.J. Amézquita, L. Newton, D.H. Chitwood, A.M. Thompson
N/A
2024
Students Mentored
Searcy Thomas and Jake Parmentier (Undergraduate)
TDA to model spatial cell distributions. Dept. of Mathematics. Univ. of Missouri
N/A
present - 2024
Ethan Lenhardt (Undergraduate)
Mathematical network analysis of academic collaboration. Dept. of Mathematics. Univ. of Missouri.
N/A
present - 2024
Teaching Experience
At Michigan State University
TA for CMSE 201: Computational Modelling and Data Analysis I. Fall 2019
N/A
2019
At CIMAT/Universidad de Guanajuato
TA for Precalculus and analytic geometry. Spring 2018
TA for Topology I (Intro to point-set topology). Fall 2017
TA for 14th Calculus Problem-solving Workshop. Summer 2017
TA for Introduction to C++ and data structures (Online). Summer 2017
TA for Introduction to probability. Fall 2016
N/A
2016 - 2018
Invited talks
Characterizing spatial patterns and distributions with Topological Data Analysis (TDA)
NAPPN AI/ML Affinity Group. North American Plant Phenotyping Network. Virtual
N/A
2024
Mapper and the topological shape of genomic analysis
MU-GNU International Symposium in Plant Biotechnology. Bond LSC. Columbia, MO
N/A
2023
A primer on Topological Data Analysis
Geometry and Topology Seminar. Department of Mathematics. University of Missouri. Columbia, MO
N/A
2023
Exploring the mathematical shape of plants
CS Colloquium. Department of Computer Science. Saint Louis University. St. Louis, MO
N/A
2023
When topology meets plant morphology
USTARS 2023. Underrepresented Students in Topology and Algebra Research Symposium, Seattle
N/A
2023
The mathematical shape of plants
Plant Sciences Seminar. Department of Botany and Plant Sciences. University of California, Riverside
N/A
2023
Directional statistics to describe the distribution of citrus oil glands
JMM 2023. Joint Mathematics Meeting. American Mathematical Society. Boston, MA.
N/A
2023
The mathematical shape of plants
Plant Science Seminar. Division of Plant Science and Technology. University of Missouri, Columbia
N/A
2022
Using applied topology in plant science
Stochastic Topology seminar. Max Planck Institute for Mathematics in the Sciences (MiS). Virtual.
N/A
2022
TDA to harness plant morphology
Multicellular dynamics seminar. Max Planck Institute for Plant Breeding Research (MPIPZ). Virtual
N/A
2022
Using the Euler characteristic to quantify the shape of barley seeds
OU Topology and Data Science Seminar. Department of Math. University of Oklahoma. Virtual
N/A
2022
Bridging applied topology and plant biology
JMM 2022. Joint Mathematics Meeting. American Mathematical Society
N/A
2022
Measuring the shape of plants with the Euler Characteristic Transform
UFTDA 2022. University of Florida Topological Data Analysis Conference. Gainesville, FL
N/A
2022
Analyzing maize leaf angles and modeling leaf curvature
2021 NAPPN. North American Plant Phenotyping Network. Virtual
N/A
2021
TDA to bridge mathematics and archaeology
16th School on Probability and Statistics. CIMAT. Guanajuato. Gto.
N/A
2018
Efficient object classification using the Euler characteristic
II Coloquio de Desarrollo Tecnológico al Servicio del Patrimonio Cultural. Guanajuato. Gto.
N/A
2017
Recent contributed talks
Topological Data Analysis to model spatial data
MMBS. Midwest Mathematical Biology Seminar. Virtual.
N/A
2024
Topological Data Analysis to characterize transcriptomic spatial distributions
SIAM-CSS24. SIAM Central States Section. Kansas City, MO
N/A
2024
The wal(nut)zing nutcracker: linking morphological and commercial traits in walnuts
IPG Plant Talks. Interdisciplinary Plant Group. University of Missouri. Columbia, MO
N/A
2023
Workshops lead
The shape of things: Measuring the shape of plants with Topological Data Analysis
2022 NAPPN. North American Plant Phenotyping Network. Athens, GA. Check material.
N/A
2022
Using the Euler characteristic to quantify the shape in biology
2021 AATRN Tutorial-a-thon. Applied Algebraic Topology Research Network. Watch video.
N/A
2021
Measuring the shape of plants with Topological Data Analysis
2021 NAPPN. North American Plant Phenotyping Network. Check material.
N/A
2021
Select Flash Talks (with posters)
Topological Data Analysis to characterize transcriptomic spatial distributions
CAFNR Research Symposium. College of Ag., Food, and Nat. Resources. University of Missouri
N/A
2024
The shape and size of shells, kernels, and cracks, in a nutshell
NAPPN 2024. North American Plant Phenotyping Network. West Lafayette, IN
N/A
2024
Modeling the shape of citrus and their oil gland distribution
NAPPN 2023. North American Plant Phenotyping Network. St. Louis, MO
N/A
2023
Using topology to analyze the shape of plants
IPPS2022. International Plant Phenotyping Symposium. Wageningen, The Netherlands
N/A
2022
Using Euler Characteristic Curves to model barley shape
YRF@SoCG. Young Researcher Forum @ CG Week, Symposium on Computational Geometry. Virtual
N/A
2020
Select workshops and hackathons attended
Graduate Wellness and Mental Health Ambassador Program.
The Graduate School. Michigan State University, East Lansing, MI
N/A
2023
NatSci Cultural Competency. Workshop Semester Series
DEI Office. College of Natural Science. Michigan State University. East Lansing, MI
N/A
2022
Beyond Abstract Measures: geometry and computation
Organized by the Lorentz Center, Leiden, The Netherlands
N/A
2022
Datathon4Justice
D4J@QSIDE. Institute for Quantitative Study of Inclusion, Diversity, and Equity. Virtual
N/A
2021
Immersive Visualization Institute
IVI2021. Abrams Planetarium, MSU Libraries, and MSU Museum. East Lansing. MI
N/A
2021
MSU Dialogues: Race. Semester I
Office for Institutional Diversity and Inclusion. Michigan State University. Virtual
N/A
2021
Applied Mathematical Modeling with Topological Techniques.
ICERM. Institute for Computational and Experimental Research in Mathematics. Providence, RI
N/A
2019
Outreach
If life gives you lemons, analyze the shape of their aroma
Science on Tap. International Tap House. Columbia, MO
N/A
2023
Un matemático y un botánico van por una limonada
¡Science on Wheels en Español! SACNAS Mizzou. Columbia, MO
N/A
2023
Mental Health in Mathematics and Computer Science
Panel organizer and moderator. SGI23. Massachussets Institute of Technology. Virtual
N/A
2023
Webinar de Solicitudes al Doctorado en Estados Unidos
Panelist. Organized by the Coloquio de Exestudiantes CIMAT/DEMAT. Virtual
N/A
2022
Mental Health in Mathematics and Computer Science
Panel organizer and moderator. SGI22. Massachussets Institute of Technology. Virtual
N/A
2022
A topologist and a plant biologist go for a newly shaped beer
Hispanics in STEM celebration. WaMPS. Michigan State University. East Lansing, MI
N/A
2021
Demeter y Euler van por una cerveza
Seminario Junior de Estudiantes. Departamento de Matemáticas. Universidad de Guanajuato. Virtual.
N/A
2021
Cuantificando la forma de la cebada con ATD
Seminario de Matemáticas y Estadística. Instituto Politécnico Nacional. Virtual
N/A
2020
Using topology to quantify the shape of barley
Summer Math Academy. Math Department. University of Toronto. Virtual
N/A
2020
Wrangling and Presenting Data with Pandas and Seaborn in Python
Social Science Data Analytics Initiative. Michigan State University. Virtual
N/A
2020
Narrating our data with RMarkdown
Social Science Data Analytics Initiative. Michigan State University. Virtual
N/A
2020
La maldición de la dimensión y aprendizaje de máquina
Ciencia es Cultura. Dirección de Extensión Cultural. UGto. San Luis, Gto.
N/A
2018
Un matemático y un psicólogo se hallan en Hanoi
Ciencia es Cultura. Dirección de Extensión Cultural. UGto. Guanajuato, Gto.
N/A
2017
Infinitos grandes e infinitos pequeños
Ciencia es Cultura. Dirección de Extensión Cultural. UGto. San Miguel Allende, Gto.
N/A
2016
Select Service
In-house data scientist
Division of Plant Science and Technology. University of Missouri
N/A
present - 2024
- Management and rearrangement of various databases concerning several projects carried out by DPST.
Faculty Search Committee (Data Science Instructor)
Division of Plant Science and Technology. University of Missouri
N/A
present - 2024
Mentor for BIPS: Bioinformatics in Plant Science
Division of Plant Science and Technology. University of Missouri
N/A
2023
- Lead weekly workshops on good coding practices. Geared toward plant science undergraduate students.
Mentor for SGI REU: Summer Geometry Initiative
Geometric Data Processing Group. Massachussets Institute of Technology. Remote
N/A
2023 - 2021
- General technical support. Organized panels on Mental Health for the 2022 and 2023 editions.
CMSE Chair Search Committee
Department of Computational Mathematics, Science, and Engineering. Michigan State University.
N/A
2023 - 2022
Mentor for the ACRES REU: Advanced Computational Research Experience
Institute for Cyber-enabled Research. Michigan State University.
N/A
2022
- Conducted weekly professional development workshops, such as CV and academic poster design.
President of the CMSE Graduate Student Organization
Council of Graduate Students. Michigan State University
N/A
2022 - 2021
- Lead department-wide events, committees, and inquiries to attend graduate students’ needs
Student Representative
College of Natural and Exact Sciences Council. Universidad de Guanajuato.
N/A
2017 - 2016
- Logged each session minutes, such as budget or policy, and shared them with the math students.
High School Mathematics Seminar Co-Organizer
Escuela de Nivel Medio Superior, Guanajuato. Guanajuato.
N/A
2016 - 2015
- Organized lectures on college-level math topics, such as combinatorics or group theory.
Select and Recent Awards
Travel Grant (US$650)
SIAM-MDS24. Early Career Award. SIAM-Mathematics of Data Science. Atlanta, GA
N/A
2024
Best Flash Talk (1st place out of 52 talks)
2024 NAPPN. North American Plant Phenotyping Network. West Lafayette, IN
N/A
2024
Distinguished Graduate Student. Travel Grant (US$700)
USTARS 2023. Underrepresented Students in Topology and Algebra Research Symposium.
N/A
2023
Best Poster Award. 3rd place out of 173 posters.
IPPS2022. International Plant Phenotyping Symposium. Wageningen, The Netherlands
N/A
2022
Travel Grant (EUR 2000)
IPPS2022. International Plant Phenotyping Symposium. Wageningen, The Netherlands
N/A
2022
Fitch H. Beach Award (2nd place)
College of Engineering. Michigan State University. Most outstanding graduate research.
N/A
2022
Travel Grant (US$800)
Applied Mathematical Modeling with Topological Techniques. ICERM. Providence, RI
N/A
2019
IMPACTS Fellowship
Awarded jointly by Michigan State University and the NRT-NSF program (NSF DGE-1828149).
N/A
2019
Sotero Prieto Medal
Sociedad Mexicana de Matemáticas. Best undergrad math thesis produced in Mexico
N/A
2018
Francisco Aranda Ordaz Award (3rd place)
Asociación Mexicana de Estadística. Best undergrad statistics thesis produced in Mexico.
N/A
2018
Raymond P. and Marie M. Ginther Graduate Fellowship
Awarded by CMSE to outstanding incoming graduate students.
N/A
2018
CIMAT Academic Excellence Scholarship
Merit-based scholarship for math undergraduates.
N/A
2018 - 2013
Best Undergraduate Mathematics, Physics and Earth Sciences Research Project (3rd place).
4to Congreso Interinstitucional de Jóvenes Investigadores.
N/A
2017
Best Undergraduate Engineering Research Project (1st place)
5to Encuentro de Jóvenes Investigadores. Universidad de Guanajuato.
N/A
2017