Publications by authors named "Scott Ness"

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Gene-Expression Programs in Salivary Gland Adenoid Cystic Carcinoma Analyzed Using Single-Cell and Spatial Transcriptomics.
Ifeoma Ebinumoliseh, Gopikrishnan Bijukumar, Kendall Hoff, Kathryn J Brayer, Elaine L Bearer, Scott A Ness

bioRxiv· September 2025

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Identification of host lncRNAs that impact Venezuelan equine encephalitis virus replication.
Mahgol Behnia, Chunyan Ye, Kim Somfleth, Olufunmilola M Oyebamiji, Kathryn J Brayer, Scott A Ness

bioRxiv· May 2025

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The inflammatory response of human pancreatic cancer samples compared to normal controls.
Kathryn J Brayer, Joshua A Hanson, Shashank Cingam, Cathleen Martinez, Scott A Ness

PLoS One· November 2023

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Deep neural network based tissue deconvolution of circulating tumor cell RNA.
Fengyao Yan, Limin Jiang, Fei Ye, Jie Ping, Tetiana Y Bowley, Scott A Ness

J Transl Med· November 2023

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Somatic mutation effects diffused over microRNA dysregulation.
Hui Yu, Limin Jiang, Chung-I Li, Scott Ness, Sara G M Piccirillo

Bioinformatics· September 2023

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Humanized Patient-derived Xenograft Models of Disseminated Ovarian Cancer Recapitulate Key Aspects of the Tumor Immune Environment within the Peritoneal Cavity.
Mara P Steinkamp, Irina Lagutina, Kathryn J Brayer, Fred Schultz, Danielle Burke, Scott A Ness, Angela Wandinger-Ness

Cancer Res Commun· February 2023

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Dominant Gene Expression Profiles Define Adenoid Cystic Carcinoma (ACC) from Different Tissues: Validation of a Gene Signature Classifier for Poor Survival in Salivary Gland ACC.
Kathryn J Brayer, Huining Kang, Adel K El-Naggar, Simon Andreasen, Preben Homøe, Scott A Ness

Cancers (Basel)· February 2023

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Surveying mutation density patterns around specific genomic features.
Hui Yu, Scott Ness, Chung-I Li, Yongsheng Bai, Peng Mao

Genome Res· October 2022

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Genomic landscape of lymphatic malformations: a case series and response to the PI3Kα inhibitor alpelisib in an -of-1 clinical trial.
Montaser F Shaheen, Julie Y Tse, Ethan S Sokol, Margaret Masterson, Pranshu Bansal, Scott A Ness

Elife· July 2022

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SBSA: an online service for somatic binding sequence annotation.
Limin Jiang, Fei Guo, Jijun Tang, Hui Yu, Scott Ness

Nucleic Acids Res· January 2022

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Comprehensive Analysis of Co-Mutations Identifies Cooperating Mechanisms of Tumorigenesis.
Limin Jiang, Hui Yu, Scott Ness, Peng Mao, Fei Guo

Cancers (Basel)· January 2022

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EditPredict: Prediction of RNA editable sites with convolutional neural network.
Jiandong Wang, Scott Ness, Roger Brown, Hui Yu, Olufunmilola Oyebamiji

Genomics· November 2021

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MetaGSCA: A tool for meta-analysis of gene set differential coexpression.
Yan Guo, Hui Yu, Haocan Song, Jiapeng He, Olufunmilola Oyebamiji, Scott Ness

PLoS Comput Biol· May 2021

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A streamlined solution for processing, elucidating and quality control of cyclobutane pyrimidine dimer sequencing data.
Quanhu Sheng, Hui Yu, Mingrui Duan, Scott Ness, Jiapeng He

Nat Protoc· April 2021

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SMDB: pivotal somatic sequence alterations reprogramming regulatory cascades.
Limin Jiang, Mingrui Duan, Fei Guo, Jijun Tang, Olufunmilola Oybamiji, Scott Ness

NAR Cancer· December 2020

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Global Autozygosity Is Associated with Cancer Risk, Mutational Signature and Prognosis.
Limin Jiang, Fei Guo, Jijun Tang, Shuguan Leng, Scott Ness

Cancers (Basel)· December 2020

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Advancing Pan-cancer Gene Expression Survial Analysis by Inclusion of Non-coding RNA.
Bo Ye, Jianxin Shi, Huining Kang, Olufunmilola Oyebamiji, Deirdre Hill, Scott Ness

RNA Biol· November 2020

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Alternative Applications of Genotyping Array Data Using Multivariant Methods.
David C Samuels, Jennifer E Below, Scott Ness, Hui Yu, Shuguang Leng

Trends Genet· November 2020

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Two-step mixed model approach to analyzing differential alternative RNA splicing.
Li Luo, Huining Kang, Xichen Li, Scott A Ness, Christine A Stidley

PLoS One· November 2020

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Oncogenic Orphan Nuclear Receptor NR4A3 Interacts and Cooperates with MYB in Acinic Cell Carcinoma.
David Y Lee, Kathryn J Brayer, Yoshitsugu Mitani, Eric A Burns, Pulivarthi H Rao, Scott A Ness

Cancers (Basel)· August 2020

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MutEx: a multifaceted gateway for exploring integrative pan-cancer genomic data.
Jie Ping, Olufunmilola Oyebamiji, Hui Yu, Scott Ness, Jeremy Chien

Brief Bioinform· July 2020

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Non-canonical RNA-DNA differences and other human genomic features are enriched within very short tandem repeats.
Hui Yu, Shilin Zhao, Scott Ness, Huining Kang, Quanhu Sheng

PLoS Comput Biol· June 2020

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AnnoGen: annotating genome-wide pragmatic features.
Quanhu Sheng, Hui Yu, Olufunmilola Oyebamiji, Jiandong Wang, Danqian Chen, Scott Ness

Bioinformatics· May 2020

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Corrigendum: Genomic Positional Dissection of RNA Editomes in Tumor and Normal Samples.
Michael Chigaev, Hui Yu, David C Samuels, Quanhu Sheng, Olufunmilola Oyebamiji, Scott Ness

Front Genet· February 2020

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N-Terminal Truncated Myb with New Transcriptional Activity Produced Through Use of an Alternative MYB Promoter in Salivary Gland Adenoid Cystic Carcinoma.
Candace A Frerich, Hailey N Sedam, Huining Kang, Yoshitsugu Mitani, Adel K El-Naggar, Scott A Ness

Cancers (Basel)· December 2019

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