Daniel H. Chitwood

The Euler Characteristic Transform Enables Classification of Complex Plant Shapes and Prediction of Leaf Venation from Blade Geometry

This paper introduces the Euler Characteristic Transform (ECT) for classifying plant shapes and predicting leaf venation from blade geometry using deep learning.

Procrustean pseudo-landmark methods in Python to measure massive quantities of leaf shape data

The paper introduces a Python-based method using pseudo-landmarks and Procrustes analysis to compare leaf shapes across species and development, showing shape transitions and genetic correlations.

Disentangling blade and vasculature shape in grapevine leaves

This study uses topological data analysis and deep learning to show that grapevine leaf blade and vasculature shapes are predictively linked, suggesting a one-to-one relationship between the two tissues.

Differences in apple fruit shape are independent of fruit size

The paper quantifies variation in apple fruit shape and size across diverse accessions and finds they are independent traits.

Interdisciplinarity through internationality: results from a US-Mexico graduate course bridging computational and plant science

This study evaluates how internationality affects interdisciplinary learning in a US-Mexico graduate course bridging computational and plant science, finding that cultural and linguistic diversity influences expertise distribution and skill development.

Intra-leaf modeling of Cannabis leaflet shape produces leaf models that predict genetic and developmental identities

This paper introduces a method to model Cannabis leaf shape using pseudo-landmarks, enabling accurate prediction of genetic and developmental traits.

QTL analysis of floral morphology polymorphisms between Gilia yorkii and G. capitata

The paper analyzes QTLs for floral morphology differences between Gilia yorkii and G. capitata, identifying colocalized QTL intervals on chromosomes 6 and 9.

Persistent homology: a tool to universally measure plant morphologies across organs and scales

This paper uses persistent homology to analyze plant morphology across different organs and scales, finding that genetic factors affect both shoot and root structures in tomato plants.

A Sister of PIN1 gene in tomato (Solanum lycopersicum) defines organ initiation patterns by maintaining epidermal auxin flux

This paper identifies a loss-of-function mutant in the SoPIN1 clade in tomato, showing its role in maintaining epidermal auxin flux and proper organ initiation patterns.

A new advanced backcross tomato population enables high resolution leaf QTL mapping and gene identification

The paper introduces a new tomato population for high-resolution QTL mapping and gene identification, demonstrating its utility for fine-mapping and epistatic QTL analysis.

eQTL regulating Transcript Levels Associated with Diverse Biological Processes in Tomato

This study identifies 7,200 eQTL regulating transcript levels of 5,300 genes in tomato, revealing complex genetic architecture and associations with biological processes and phenotypes.

Left-right leaf asymmetry in decussate and distichous phyllotactic systems

The paper shows that auxin asymmetry models predict mirrored leaf asymmetries in decussate and distichous phyllotactic systems, confirmed by mutant and species analyses.

Auxin signaling is a common factor underlying natural variation in tomato shade avoidance

The paper identifies auxin signaling and cell wall expansion genes as key factors in natural variation of shade avoidance in tomato, linking them to growth plasticity and QTL effects on stem elongation and developmental rate.

Light-induced indeterminacy alters shade avoiding tomato leaf morphology

This study shows that shade avoidance in tomato plants alters leaf shape through changes in gene expression related to indeterminacy, not through juvenile leaf type prolongation.