Going between math, data science, plant biology, and education

.title[
# Going between math, data science, plant biology, and education
]
.subtitle[
## My interdisciplinary journey
]
.author[
### Erik Amézquita<br>—<br>Division of Plant Science & Technology<br>Department of Mathematics<br>University of Missouri<br>—
]
.date[
### 2025-08-18
]

---

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# About me: From MX to MI to MO at MU

## I work across multiple disciplines and countries

.right-column[
- 2013 - 2018 : Licenciatura (Bachelor): Mathematics @ Universidad de Guanajuato and CIMAT. Thesis focused on Topological Data Analysis applied to archaeology.

- 2018 - 2023 : PhD: CMSE @ MSU. Dissertation: Exploring the mathematical shape of plants. 
- 2023 - 2025 : ~~PFFFD~~ ~~PFFIE~~ PFF Postdoctoral Fellow: Plant Science (80%) / Mathematics (20%) @ University of Missouri (MU).

- 2025 - present: Assistant Professor: Plant Science (100%) / Math (0%) @ MU. 
]

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# Roadmap for today

1. My research before CMSE 
   - Mixing TDA (Topological Data Analysis) with archaeology

1. My research while at CMSE
   - Mixing TDA with plant biology

1. My research right after CMSE
   - Jack of all trades, master of none

1. Current projects that excite me
   - Taking a leaf from CMSE 201

---

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# A mathematician by training, a data scientist by trade, and a plant biologist by ~~collaboration~~ osmosis

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# 2017: Pre-CMSE &rarr; TDA &oplus; Archaeology

Topological Data Analysis for pre-Columbian mask classification

<img src="../../demat/figs/barrett_poster-1.jpg" width="310" style="display: block; margin: auto;" />
]

``` r
*- Lessons learned for better 
* future interdisciplinary 
* collaborations
  
*- Always include the other
* discipline experts at
* every stage of the analysis
```
]

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# 2018: CMSE &rarr; TDA &oplus; Plant Biology

Mathematically quantify the shape of plants with Liz Munch and Dan Chitwood

.pull-left[
![](../../barley/figs/x3000_setup.jpg)
<img src="../../arabidopsis/figs/DSCN0077.jpg" width="500" style="display: block; margin: auto;" />
]

.pull-right[
![](../../arabidopsis/figs/Screen Shot 2021-08-02 at 12.17.43 PM.png)
![](../../arabidopsis/figs/ecc_axis_X.gif)
]

---

# Come for the math, stay for the plants

<div class="row" style="font-family: 'Yanone Kaffeesatz'; font-size:22px;">
  <div class="column" style="max-width:33%">
    <p style="line-height:0;text-align: center; font-size:28px">The shape of adaptability</p>
    <img style="padding: 0 70px;" src="../../barley/figs/S017_L3_1.gif"></img>
    <img style="padding: 0 55px;" src="../../barley/figs/ecc_X.gif"></img>
    <p style="text-align: center;">Topological Data Analysis</p>
    <p style="text-align: center;">Euler Characteristic Transform</p>
  </div>
  <div class="column" style="max-width:33%">
    <p style="line-height:0;font-size:28px;text-align: center;">The shape of development</p>
    <img style="padding: 0 60px;" src="../../citrus/figs/SR01_L01_black_exocarp.gif"></img>
    <img style="padding: 0 27px;" src="../../citrus/figs/SW03_CRC1241-B_12B-4-3_L00_lambproj_v.jpg"></img>
    <p style="text-align: center;">Ellipsoidal modeling</p>
    <p style="text-align: center;">Directional statistics</p>
  </div>
  <div class="column" style="max-width:33%">
    <p style="line-height:0;font-size:28px;text-align: center;">The shape of domestication</p>
    <img style="padding: 0 35px;" src="../../walnuts/figs/2014SBa_R5_T81_meat_2.gif"></img>
    <img style="padding: 0 10px;" src="../../walnuts/figs/kernel_volume_vs_nut_volume.png"></img>
    <p style="text-align: center;">Allometry of multiple tissues</p>
    <p style="text-align: center;">Convexity indices</p>
  </div>
</div>

---

# 2023: Post-CMSE &rarr; Math &oplus; Plants

## It is far easier to switch countries than to switch disciplines

## But CMSE trained me for the cultural shock

<p style="font-size: 10px; text-align: center; color: Grey;">Credits: <a href="http://dx.doi.org/10.2140/agt.2005.5.237">Kaufmann (2005)</a></p>

---

# Tracking how a vegetarian plant wiggles

- *Cuscuta campestris* inoculated at different times of the day for 24h
- In collaboration with Soyon Park

---

## Phenotyping movement: how *wiggly* is a wiggle?
  
<video width="900" controls>
  <source src="../../cuscuta/video/4pm_rep7_plant_01.mp4" type="video/mp4">
</video>

- Mathematically model how *Cuscuta* moves under various environmental conditions to ultimately stop it from attaching to crops in the first place.

---

## Phenotyping patterns: How *patterny* is a pattern?

![](../../mcarto/figs/cell_sample.jpg)

- Beyond gene expression counts: Spatial segregation and asymmetrical distribution of mRNA across the cytosol in the soybean nodule.
- Molecular Cartography&trade; data provided by the Libault Lab

---

## Topological Data Analysis to quantify our intuition

![](../../mcarto/figs/GLYMA_05G092200_TDA_c00541_transp.gif)

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## Define a morphospace of transcriptomic patterns

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## More data, more shapes, more phenotyping

Academic social network analysis of the IPG (Interdisciplinary Plant Group)

Similar work to be done with gene coexpression and biota interaction networks.

]

Use TDA to analyze geographical patterns across the state.

<p style="font-size: 10px; text-align: center; color: Grey;">Credits: <a href="https://doi.org/10.1137/19M1241519">Feng and Porter (2021)</a></p>

A voting district looks like a plant cell.

]

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# Shaping the next generation of interdisciplinary scientists

## Large amounts of data require large amounts of people

## PLNT_SCI 2500: Data Science for Life Sciences I

![](../../tutorials/figs/myzou_plnt_sci_2500.png)

---

## Taking a leaf from CMSE 201

---

## PLNT_SCI 2500: With data from Missouri faculty!

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# The shape of things to come

![](../../mcarto/figs/Infected_Cells_05G216000_red_05G092200_green.jpg)

]

- Make the teaching of data science in life sciences a scientific endeavor in itself.

- More **translations** of Topological Data Analysis and other mathematical techniques to quantify plant biology-inspired data

- Explore more applications of complex network theory to biology and meta-biology contexts.

**Adverstisement**

- I will be looking for PhD students to start next year working with me at the intersection of math, data science, and plant science
]

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## Thank you!

**Research while at CMSE**

- Liz Munch
- Dan Chitwood
- Michelle Quigley
- Tim Ophelders
- Jacob Landis
- Dan Koenig
- Danelle Seymour
- Pat Brown

**Cuscuta rhythm and locomotion**

- Max Bentelspacher
- Supral Adhikari
- Jaime Barros-Rios
- Joseph Lynch
- So-Yon Park

**mRNA sub-cellular localization**

- Sutton Tennant
- Sandra Thibivillers
- Sai Subhash
- Benjamin Smith
- Samik Bhattacharya
- Jasper Kläver
- Marc Libault

]

**Collaboration of the IPG network**

- Ethan Lenhardt
- Sophia Knehans
- Roberto Herrera
- David Braun

**Data Science for Life Sciences I**

- Kent Shannon
- Andrew Scaboo
- Jianfeng Zhou
- Debbie Finke

**Other ongoing projects**

- Leyre Urmeneta
- Laura Martins
- Mather Khan
- David Mendoza-Cozatl
- Jie Zhu

**More details**

<p style="font-size: 20px; text-align: center; color: Blue;">ejamezquita.github.io/</p>
<p style="font-size: 20px; text-align: center; color: Blue;">eah4d@missouri.edu</p>

]