Publications by authors named "Michelle Stitzer"

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Widespread turnover of a conserved cis-regulatory code across 589 grass species.
Charles O Hale, Sheng-Kai Hsu, Jingjing Zhai, Aimee J Schulz, Taylor Aubuchon-Elder, Michelle Stitzer

Mol Biol Evol· December 2025

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GeneCAD: Plant Genome Annotation with a DNA Foundation Model.
Zong-Yan Liu, Ana Berthel, Eric Czech, Michelle Stitzer, Sheng-Kai Hsu

bioRxiv· November 2025

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Fishing for a reelGene: evaluating gene models with evolution and machine learning.
Aimee J Schulz, Jingjing Zhai, Taylor AuBuchon-Elder, Carson M Andorf, Mohamed Z El-Walid, Michelle C Stitzer

Plant J· September 2025

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Cross-species modeling of plant genomes at single-nucleotide resolution using a pretrained DNA language model.
Jingjing Zhai, Aaron Gokaslan, Yair Schiff, Ana Berthel, Zong-Yan Liu, Michelle C Stitzer

Proc Natl Acad Sci U S A· June 2025

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Evolutionary signatures of the erosion of sexual reproduction genes in domesticated cassava (Manihot esculenta).
Evan M Long, Michelle C Stitzer, Brandon Monier, Aimee J Schulz, Maria Cinta Romay

G3 (Bethesda)· February 2025

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Extensive genome evolution distinguishes maize within a stable tribe of grasses.
Michelle C Stitzer, Arun S Seetharam, Armin Scheben, Sheng-Kai Hsu, Aimee J Schulz

bioRxiv· January 2025

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Correction: Double triage to identify poorly annotated genes in maize: The missing link in community curation.
Marcela K Tello-Ruiz, Cristina F Marco, Fei-Man Hsu, Rajdeep S Khangura, Pengfei Qiao, Michelle C Stitzer

PLoS One· November 2024

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Cross-species modeling of plant genomes at single nucleotide resolution using a pre-trained DNA language model.
Jingjing Zhai, Aaron Gokaslan, Yair Schiff, Ana Berthel, Zong-Yan Liu, Michelle C Stitzer

bioRxiv· August 2024

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New whole-genome alignment tools are needed for tapping into plant diversity.
Baoxing Song, Edward S Buckler, Michelle C Stitzer

Trends Plant Sci· March 2024

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Two teosintes made modern maize.
Ning Yang, Yuebin Wang, Xiangguo Liu, Minliang Jin, Miguel Vallebueno-Estrada, Michelle C Stitzer

Science· December 2023

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Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion.
Manisha Munasinghe, Andrew Read, Michelle C Stitzer, Baoxing Song, Claire C Menard

PLoS Genet· December 2023

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A multiple alignment workflow shows the effect of repeat masking and parameter tuning on alignment in plants.
Yaoyao Wu, Lynn Johnson, Baoxing Song, Cinta Romay, Michelle Stitzer

Plant Genome· June 2022

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Adaptive significance of flowering time variation across natural seasonal environments in Arabidopsis thaliana.
Alexandre Fournier-Level, Mark A Taylor, Jefferson F Paril, Alejandra Martínez-Berdeja, Michelle C Stitzer

New Phytol· April 2022

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Controlling for Variable Transposition Rate with an Age-Adjusted Site Frequency Spectrum.
Robert Horvath, Mitra Menon, Michelle Stitzer, Jeffrey Ross-Ibarra

Genome Biol Evol· February 2022

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AnchorWave: Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism, and whole-genome duplication.
Baoxing Song, Santiago Marco-Sola, Miquel Moreto, Lynn Johnson, Edward S Buckler, Michelle C Stitzer

Proc Natl Acad Sci U S A· January 2022

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The genomic ecosystem of transposable elements in maize.
Michelle C Stitzer, Sarah N Anderson, Nathan M Springer, Jeffrey Ross-Ibarra

PLoS Genet· October 2021

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Using high-throughput multiple optical phenotyping to decipher the genetic architecture of maize drought tolerance.
Xi Wu, Hui Feng, Di Wu, Shijuan Yan, Pei Zhang, Michelle Stitzer

Genome Biol· June 2021

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Double triage to identify poorly annotated genes in maize: The missing link in community curation.
Marcela K Tello-Ruiz, Cristina F Marco, Fei-Man Hsu, Rajdeep S Khangura, Pengfei Qiao, Michelle C Stitzer

PLoS One· March 2020

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Functional variants of control seed chilling responses and variation in seasonal life-history strategies in .
Alejandra Martínez-Berdeja, Michelle C Stitzer, Mark A Taylor, Miki Okada, Exequiel Ezcurra

Proc Natl Acad Sci U S A· February 2020

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Transposable elements contribute to dynamic genome content in maize.
Sarah N Anderson, Michelle C Stitzer, Alex B Brohammer, Peng Zhou, Jaclyn M Noshay

Plant J· December 2019

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Dynamic Patterns of Transcript Abundance of Transposable Element Families in Maize.
Sarah N Anderson, Michelle C Stitzer, Peng Zhou, Jeffrey Ross-Ibarra, Cory D Hirsch

G3 (Bethesda)· November 2019

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Hybrid Decay: A Transgenerational Epigenetic Decline in Vigor and Viability Triggered in Backcross Populations of Teosinte with Maize.
Wei Xue, Sarah N Anderson, Xufeng Wang, Liyan Yang, Peter A Crisp, Michelle C Stitzer

Genetics· September 2019

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The genome-wide dynamics of purging during selfing in maize.
Kyria Roessler, Aline Muyle, Concepcion M Diez, Garren R J Gaut, Alexandros Bousios, Michelle C Stitzer

Nat Plants· September 2019

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Monitoring the interplay between transposable element families and DNA methylation in maize.
Jaclyn M Noshay, Sarah N Anderson, Peng Zhou, Lexiang Ji, William Ricci, Michelle C Stitzer

PLoS Genet· September 2019

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Digest: Hybrid incompatibilities and introgression in wild monkeyflowers.
Michelle C Stitzer, Philipp Brand

Evolution· November 2018

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