Publications by authors named "Mark Ebbert"

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A bioinformatic survey of RNA isoform diversity and expression across 9 GTEx tissues using long-read sequencing data.
Madeline L Page, Bernardo Aguzzoli Heberle, J Anthony Brandon, Mark E Wadsworth, Lacey A Gordon, Mark T W Ebbert

BMC Genomics· December 2025

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Genome annotations matter: characterizing Ensembl hg38 annotations from 2014 to 2023.
Madeline L Page, Mark E Wadsworth, Bernardo Aguzzoli Heberle, David W Fardo, Mark T W Ebbert

BMC Genomics· December 2025

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Decoding the human PBMC isonome: Isoform-level resolution with single-cell long-read transcriptomics.
Patricia Hayes Doyle, Madeline L Page, J Anthony Brandon, Bernardo Aguzzoli-Heberle, Brendan J White, Mark T W Ebbert

bioRxiv· October 2025

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Author Correction: GWAS of multiple neuropathology endophenotypes identifies new risk loci and provides insights into the genetic risk of dementia.
Lincoln M P Shade, Yuriko Katsumata, Erin L Abner, Khine Zin Aung, Steven A Claas, Mark T W Ebbert

Nat Genet· July 2025

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Publisher Correction: GWAS of multiple neuropathology endophenotypes identifies new risk loci and provides insights into the genetic risk of dementia.
Lincoln M P Shade, Yuriko Katsumata, Erin L Abner, Khine Zin Aung, Steven A Claas, Mark T W Ebbert

Nat Genet· July 2025

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Sequencing the gaps: dark genomic regions persist in CHM13 despite long-read advances.
Mark E Wadsworth, Madeline L Page, Bernardo Aguzzoli Heberle, Justin B Miller, Cody Steely, Mark T W Ebbert

bioRxiv· May 2025

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Mapping medically relevant RNA isoform diversity in the aged human frontal cortex with deep long-read RNA-seq.
Bernardo Aguzzoli Heberle, J Anthony Brandon, Madeline L Page, Kayla A Nations, Ketsile I Dikobe, Mark T W Ebbert

Nat Biotechnol· April 2025

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Systematic review and meta-analysis of bulk RNAseq studies in human Alzheimer's disease brain tissue.
Bernardo Aguzzoli Heberle, Kristin L Fox, Lucas Lobraico Libermann, Sophia Ronchetti Martins Xavier, Guilherme Tarnowski Dallarosa, Mark T W Ebbert

Alzheimers Dement· March 2025

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Ramp Sequence May Explain Synonymous Variant Association with Alzheimer's Disease in the Paired Immunoglobulin-like Type 2 Receptor Alpha (PILRA).
Justin B Miller, J Anthony Brandon, Lauren M Harmon, Hady W Sabra, Chloe C Lucido, Mark T W Ebbert

Biomedicines· March 2025

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RNApysoforms: fast rendering interactive visualization of RNA isoform structure and expression in Python.
Bernardo Aguzzoli Heberle, Madeline L Page, Emil K Gustavsson, Mina Ryten, Mark T W Ebbert

Bioinform Adv· March 2025

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Ramp sequence may explain synonymous variant association with Alzheimer's disease in the Paired Immunoglobulin-like Type 2 Receptor Alpha ().
Justin B Miller, J Anthony Brandon, Lauren M McKinnon, Hady W Sabra, Chloe C Lucido, Mark T W Ebbert

bioRxiv· January 2025

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Targeted long-read sequencing to quantify methylation of the C9orf72 repeat expansion.
Evan Udine, NiCole A Finch, Mariely DeJesus-Hernandez, Jazmyne L Jackson, Matthew C Baker, Mark T W Ebbert

Mol Neurodegener· December 2024

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GWAS of multiple neuropathology endophenotypes identifies new risk loci and provides insights into the genetic risk of dementia.
Lincoln M P Shade, Yuriko Katsumata, Erin L Abner, Khine Zin Aung, Steven A Claas, Mark T W Ebbert

Nat Genet· November 2024

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Systematic review and meta-analysis of bulk RNAseq studies in human Alzheimer's disease brain tissue.
Bernardo Aguzzoli Heberle, Kristin L Fox, Lucas Lobraico Libermann, Sophia Ronchetti Martins Xavier, Guilherme Tarnowski Dallarosa, Mark T W Ebbert

bioRxiv· November 2024

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RNApysoforms: Fast rendering interactive visualization of RNA isoform structure and expression in Python.
Bernardo Aguzzoli Heberle, Madeline L Page, Emil K Gustavsson, Mina Ryten, Mark T W Ebbert

bioRxiv· November 2024

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Surveying the landscape of RNA isoform diversity and expression across 9 GTEx tissues using long-read sequencing data.
Madeline L Page, Bernardo Aguzzoli Heberle, J Anthony Brandon, Mark E Wadsworth, Lacey A Gordon, Mark T W Ebbert

bioRxiv· June 2024

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Using deep long-read RNAseq in Alzheimer's disease brain to assess medical relevance of RNA isoform diversity.
Bernardo Aguzzoli Heberle, J Anthony Brandon, Madeline L Page, Kayla A Nations, Ketsile I Dikobe, Mark T W Ebbert

bioRxiv· December 2023

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The Polygenic Risk Score Knowledge Base offers a centralized online repository for calculating and contextualizing polygenic risk scores.
Madeline L Page, Elizabeth L Vance, Matthew E Cloward, Ed Ringger, Louisa Dayton, Mark T W Ebbert

Commun Biol· September 2022

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Transcriptional response to VZV infection is modulated by RNA polymerase III in lung epithelial cell lines.
Brianna M Doratt, Elizabeth Vance, Delphine C Malherbe, Mark T W Ebbert, Ilhem Messaoudi

Front Cell Infect Microbiol· August 2022

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Web-Based Protein Interactions Calculator Identifies Likely Proteome Coevolution with Alzheimer's Disease-Associated Proteins.
Katrisa M Ward, Brandon D Pickett, Mark T W Ebbert, John S K Kauwe, Justin B Miller

Genes (Basel)· July 2022

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The Ramp Atlas: facilitating tissue and cell-specific ramp sequence analyses through an intuitive web interface.
Justin B Miller, Taylor E Meurs, Matthew W Hodgman, Benjamin Song, Kyle N Miller, Mark T W Ebbert

NAR Genom Bioinform· June 2022

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Curated variation benchmarks for challenging medically relevant autosomal genes.
Justin Wagner, Nathan D Olson, Lindsay Harris, Jennifer McDaniel, Haoyu Cheng, Mark T W Ebbert

Nat Biotechnol· May 2022

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Culture shock: microglial heterogeneity, activation, and disrupted single-cell microglial networks in vitro.
Mika P Cadiz, Tanner D Jensen, Jonathon P Sens, Kuixi Zhu, Won-Min Song, Mark Ebbert

Mol Neurodegener· March 2022

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Pairwise Correlation Analysis of the Alzheimer's Disease Neuroimaging Initiative (ADNI) Dataset Reveals Significant Feature Correlation.
Erik D Huckvale, Matthew W Hodgman, Brianna B Greenwood, Devorah O Stucki, Katrisa M Ward, Mark T W Ebbert

Genes (Basel)· October 2021

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Long-read targeted sequencing uncovers clinicopathological associations for C9orf72-linked diseases.
Mariely DeJesus-Hernandez, Ross A Aleff, Jazmyne L Jackson, NiCole A Finch, Matthew C Baker, Mark T W Ebbert

Brain· May 2021

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