Publications by authors named "Matthew Bootsma"

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Analysis of cfDNA fragmentomics metrics and commercial targeted sequencing panels.
Kyle T Helzer, Marina N Sharifi, Jamie M Sperger, Matthew R Chrostek, Matthew L Bootsma

Nat Commun· October 2025

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Transcriptomic Signatures of Monocyte-Derived Macrophages Associate With Androgen Receptor Pathway Inhibitor Progression in Prostate Cancer.
Marina Nasrin Sharifi, Erika Heninger, Matthew Leeson Bootsma, Emma Elizabeth Recchia, Matthew Thomas Breneman

Prostate· September 2025

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Adverse prognosis gene expression patterns in metastatic castration-resistant prostate cancer.
Marina N Sharifi, Eric Feng, Nicholas R Rydzewski, Amy K Taylor, Jamie M Sperger, Matthew L Bootsma

Mol Oncol· August 2025

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Genetic and Epigenetic Reprogramming of Transposable Elements Drives ecDNA-Mediated Metastatic Prostate Cancer.
Lisanne Mout, Thaidy Moreno-Rodriguez, Giacomo Grillo, Ankita Nand, Tina Keshavarzian, Matthew Bootsma

bioRxiv· August 2025

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High-purity CTC RNA sequencing identifies prostate cancer lineage phenotypes prognostic for clinical outcomes.
Marina N Sharifi, Jamie M Sperger, Amy K Taylor, Katharine E Tippins, Shannon R Reese, Matthew L Bootsma

Cancer Discov· May 2025

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Live Cell Sorting of Differentiated Primary Human Osteoclasts Allows Generation of Transcriptomic Signature Matrix.
Joshua Lang, Adeline Ding, Erika Henninger, Shannon Reese, Kyle Helzer, Matthew Bootsma

Res Sq· April 2025

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A phenocopy signature of TP53 loss predicts response to chemotherapy.
Hamza Bakhtiar, Marina N Sharifi, Kyle T Helzer, Yue Shi, Matthew L Bootsma

NPJ Precis Oncol· October 2024

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Clinical cell-surface targets in metastatic and primary solid cancers.
Marina N Sharifi, Yue Shi, Matthew R Chrostek, S Carson Callahan, Tianfu Shang, Matthew L Bootsma

JCI Insight· September 2024

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Integrated analyses highlight interactions between the three-dimensional genome and DNA, RNA and epigenomic alterations in metastatic prostate cancer.
Shuang G Zhao, Matthew Bootsma, Stanley Zhou, Raunak Shrestha, Thaidy Moreno-Rodriguez

Nat Genet· August 2024

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A platform-independent AI tumor lineage and site (ATLAS) classifier.
Nicholas R Rydzewski, Yue Shi, Chenxuan Li, Matthew R Chrostek, Hamza Bakhtiar, Matthew L Bootsma

Commun Biol· March 2024

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Machine Learning & Molecular Radiation Tumor Biomarkers.
Nicholas R Rydzewski, Kyle T Helzer, Matthew Bootsma, Yue Shi, Hamza Bakhtiar

Semin Radiat Oncol· July 2023

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Intrinsic Molecular Subtypes of Metastatic Castration-Resistant Prostate Cancer.
Eric Feng, Nicholas R Rydzewski, Meng Zhang, Arian Lundberg, Matthew Bootsma

Clin Cancer Res· December 2022

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A new GTSeq resource to facilitate multijurisdictional research and management of walleye .
Peter T Euclide, Wesley A Larson, Matthew Bootsma, Loren M Miller, Kim T Scribner

Ecol Evol· December 2022

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Longitudinal Molecular Profiling of Circulating Tumor Cells in Metastatic Renal Cell Carcinoma.
Matthew Bootsma, Rana R McKay, Hamid Emamekhoo, Rory M Bade, Jennifer L Schehr

J Clin Oncol· November 2022

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Identification of phenocopies improves prediction of targeted therapy response over DNA mutations alone.
Hamza Bakhtiar, Kyle T Helzer, Yeonhee Park, Yi Chen, Nicholas R Rydzewski, Matthew L Bootsma

NPJ Genom Med· October 2022

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Predicting cancer drug TARGETS - TreAtment Response Generalized Elastic-neT Signatures.
Nicholas R Rydzewski, Erik Peterson, Joshua M Lang, Menggang Yu, S Laura Chang, Matthew L Bootsma

NPJ Genom Med· September 2021

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The ghosts of propagation past: haplotype information clarifies the relative influence of stocking history and phylogeographic processes on contemporary population structure of walleye ().
Matthew L Bootsma, Loren Miller, Greg G Sass, Peter T Euclide, Wesley A Larson

Evol Appl· April 2021

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A GT-seq panel for walleye (Sander vitreus) provides important insights for efficient development and implementation of amplicon panels in non-model organisms.
Matthew L Bootsma, Kristen M Gruenthal, Garrett J McKinney, Levi Simmons, Loren Miller

Mol Ecol Resour· November 2020

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Attack of the PCR clones: Rates of clonality have little effect on RAD-seq genotype calls.
Peter T Euclide, Garrett J McKinney, Matthew Bootsma, Charlene Tarsa, Mariah H Meek

Mol Ecol Resour· January 2020

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