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Erik Amézquita
Topological Data Analysis meets Plant Biology
Career and Education
PFFIE Postdoctoral Future Faculty Fellow
University of Missouri
Columbia, MO
present - 2023
- Division of Plant Sciences & 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
Lic. Mathematics (B.S.)
Universidad de Guanajuato
Guanajuato, Gto.
2018 - 2013
- Advisor: Antonio Rieser (CONACYT-CIMAT)
- Defended: May 2018
Peer-reviewed work
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
- Submitted
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
- Submitted
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
- Submitted. Preprint available. DOI: 10.1101/10.1101/2024.02.29.582789
Teaching and Mentoring Experience
At University of Missouri
- Undegraduate Research mentor for Ethan Lenhardt. Mathematical network analysis of academic collaboration. Department of Mathematics. Spring 2024 - present.
- Undegraduate Research mentor for Gibson Tschappler. Topological Data Analysis of spatial data. Division of Plant Science & Technology. Summer 2024 - present.
- Mentor for BIPS. Conducted weekly workshops on good coding practices. Fall 2023.
N/A
Leading projects at the intersection of mathematics, computer science, and plant biology
2023 - present
At Michigan State University
- Mentor for the ACRES REU. Conducted weekly professional development workshops. Summer 2022.
- TA for CMSE 201: Intro to Computational Modelling and Data Analysis. Fall 2019
N/A
Audience was mainly undergraduate students with no prior coding experience
2022 - 2019
At other institutions
- Mentor for SGI 2023. Summer Geometry Initiative REU. Massachusetts Institute of Technology.
- Mentor for SGI 2022. Summer Geometry Initiative REU. Massachusetts Institute of Technology.
- Mentor for SGI 2021. Summer Geometry Institute REU. Massachusetts Institute of Technology.
- TA fo Code In Place. Stanford University.
N/A
Conducted virtually
2023 - 2021
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
Some courses involved leading tutorials on C++ or R
2018 - 2016
Invited and recent talks
The wal(nut)zing nutcracker: linking morphological and commercial traits in walnuts
IPG Plant Talks. University of Missouri. Columbia, MO
N/A
2023
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
Measuring the shape of plants and nuts using topological data analysis
JMM 2023. Joint Mathematics Meeting. American Mathematical Society. Boston, MA.
N/A
2023
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
Efficient object classification using the Euler characteristic
II Coloquio de Desarrollo Tecnológico al Servicio del Patrimonio Cultural. Guanajuato. Gto.
N/A
2018
Selected 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
Selected posters presented
Genomics data analysis via spectral shape and topology
EFCCRD 2024. University of Missouri. Columbia, MO
N/A
2024
The shape and size of shells, kernels, and cracks, in a nutshell
CAFNR Research Symposium. University of Missouri. Columbia, MO
N/A
2023
Using topology to analyze the shape of plants
IPPS2022. International Plant Phenotyping Symposium. Wageningen, The Netherlands
N/A
2022
Modeling the shape of citrus and their oil gland distribution
OSU PSS. The Ohio State University Plant Sciences Symposium. Virtual
N/A
2022
Archaeological object classification using the Euler characteristic
Barrett Memorial Lectures. Math Department. University of Tennessee. Knoxville, TN
N/A
2017
Selected workshops and hackathons attended
Beyond Abstract Measures: geometry and computation
Organized by the Lorentz Center, Leiden, The Netherlands
N/A
2022
Datathon4Justice
D4J. Organized by 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
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
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
President of the CMSE Graduate Student Organization
CMSE and the Council of Graduate Students
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
- Delivered lectures on math topics usually not covered at high school levels, such as combinatorics or group theory.
Tutor of the Guatemalan Math Olympiad Team
Math Olympiad National Team. Guatemala.
N/A
2013 - 2012
- Successfully lobbied the Guatemalan Department of Education to obtain funding for 3 students to participate in the 15th Central American and Caribbean Math Olympiad.
Awards
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
College of Engineering. Michigan State University
N/A
2022
- 2nd place. Most outstanding graduate research within the College of Engineering.
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
N/A
2018
- Best undergrad math thesis produced in Mexico during the 2017-18 academic year.
Francisco Aranda Ordaz Award
Asociación Mexicana de Estadística
N/A
2018
- 3rd place. Best undergrad statistics theses produced in Mexico during the 2016-18 academic years.
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 Innovation Research Project.
4to Congreso Interinstitucional de Jóvenes Investigadores. 3rd Place. Nationwide event.
N/A
2017
Best Undergraduate Engineering Research Project
5to Encuentro de Jóvenes Investigadores. 1st Place. Statewide event
N/A
2017