Tumor microenvironment deconvolution identifies cell-type-independent aberrant DNA methylation and gene expression in prostate cancer

by Samuel R. Reynolds, Ze Zhang, Lucas A. Salas, Brock C. Christensen
Published 2024-01-01

Down Syndrome Altered Cell Composition in Blood, Brain, and Buccal Swab Samples Profiled by DNA-Methylation-Based Cell-Type Deconvolution

by Ze Zhang, Hannah G. Stolrow, Brock C. Christensen, Lucas A. Salas
Published 2023-04-01

A Novel Framework for the Identification of Reference DNA Methylation Libraries for Reference-Based Deconvolution of Cellular Mixtures

by Shelby Bell-Glenn, Jeffrey A. Thompson, Lucas A. Salas, Devin C. Koestler
Published 2022-03-01

Detailed immune profiling in pediatric Crohn’s disease using methylation cytometry

by Samuel R. Reynolds, Lucas A. Salas, Ji-Qing Chen, Brock C. Christensen
Published 2024-12-01

Immunological shifts during early-stage Parkinson’s disease identified with DNA methylation data on longitudinally collected blood samples

by Steven C. Pike, Matthew Havrda, Francesca Gilli, Ze Zhang, Lucas A. Salas
Published 2024-01-01

A cluster-randomized controlled trial of handrubs for prevention of infectious diseases among children in Colombia Ensayo controlado aleatorizado por conglomerados sobre el uso de...

by Juan C. Correa, Diana Pinto, Lucas A. Salas, Juan C. Camacho, Martín Rondón, Juliana Quintero
Published 2012-06-01

Absence of an embryonic stem cell DNA methylation signature in human cancer

by Ze Zhang, John K. Wiencke, Devin C. Koestler, Lucas A. Salas, Brock C. Christensen, Karl T. Kelsey
Published 2019-07-01

HiTIMED: hierarchical tumor immune microenvironment epigenetic deconvolution for accurate cell type resolution in the tumor microenvironment using tumor-type-specific DNA methylati...

by Ze Zhang, John K. Wiencke, Karl T. Kelsey, Devin C. Koestler, Brock C. Christensen, Lucas A. Salas
Published 2022-11-01

Integrative epigenetic and genetic pan-cancer somatic alteration portraits

by Lucas A. Salas, Kevin C. Johnson, Devin C. Koestler, Dylan E. O'Sullivan, Brock C. Christensen
Published 2017-07-01

MethylNet: an automated and modular deep learning approach for DNA methylation analysis

by Joshua J. Levy, Alexander J. Titus, Curtis L. Petersen, Youdinghuan Chen, Lucas A. Salas, Brock C. Christensen
Published 2020-03-01

Maternal swimming pool exposure during pregnancy in relation to birth outcomes and cord blood DNA methylation among private well users

by Lucas A. Salas, Emily R. Baker, Mark J. Nieuwenhuijsen, Carmen J. Marsit, Brock C. Christensen, Margaret R. Karagas
Published 2019-02-01

Identification of a foetal epigenetic compartment in adult human kidney

by John K. Wiencke, Ze Zhang, Devin C. Koestler, Lucas A. Salas, Annette M. Molinaro, Brock C. Christensen, Karl T. Kelsey
Published 2022-03-01

An optimized library for reference-based deconvolution of whole-blood biospecimens assayed using the Illumina HumanMethylationEPIC BeadArray

by Lucas A. Salas, Devin C. Koestler, Rondi A. Butler, Helen M. Hansen, John K. Wiencke, Karl T. Kelsey, Brock C. Christensen
Published 2018-05-01

Assessment of emerging pretraining strategies in interpretable multimodal deep learning for cancer prognostication

by Zarif L. Azher, Anish Suvarna, Ji-Qing Chen, Ze Zhang, Brock C. Christensen, Lucas A. Salas, Louis J. Vaickus, Joshua J. Levy
Published 2023-07-01

MethylMasteR: A Comparison and Customization of Methylation-Based Copy Number Variation Calling Software in Cancers Harboring Large Scale Chromosomal Deletions

by Michael P. Mariani, Michael P. Mariani, Jennifer A. Chen, Ze Zhang, Ze Zhang, Steven C. Pike, Steven C. Pike, Lucas A. Salas
Published 2022-04-01

Molecular and epigenetic profiles of BRCA1-like hormone-receptor-positive breast tumors identified with development and application of a copy-number-based classifier

by Youdinghuan Chen, Yue Wang, Lucas A. Salas, Todd W. Miller, Kenneth Mark, Jonathan D. Marotti, Arminja N. Kettenbach, Chao Cheng, Brock C. Christensen
Published 2019-01-01

Associations in cell type-specific hydroxymethylation and transcriptional alterations of pediatric central nervous system tumors

by Min Kyung Lee, Nasim Azizgolshani, Ze Zhang, Laurent Perreard, Fred W. Kolling, Lananh N. Nguyen, George J. Zanazzi, Lucas A. Salas, Brock C. Christensen
Published 2024-04-01

Enhanced cell deconvolution of peripheral blood using DNA methylation for high-resolution immune profiling

by Lucas A. Salas, Ze Zhang, Devin C. Koestler, Rondi A. Butler, Helen M. Hansen, Annette M. Molinaro, John K. Wiencke, Karl T. Kelsey, Brock C. Christensen
Published 2022-02-01

MethylSPWNet and MethylCapsNet: Biologically Motivated Organization of DNAm Neural Networks, Inspired by Capsule Networks

by Joshua J. Levy, Youdinghuan Chen, Nasim Azizgolshani, Curtis L. Petersen, Alexander J. Titus, Erika L. Moen, Louis J. Vaickus, Lucas A. Salas, Brock C. Christensen
Published 2021-08-01

Assessment of immune cell profiles among post-menopausal women in the Women’s Health Initiative using DNA methylation-based methods

by Emily Nissen, Alexander Reiner, Simin Liu, Robert B. Wallace, Annette M. Molinaro, Lucas A. Salas, Brock C. Christensen, John K. Wiencke, Devin C. Koestler, Karl T. Kelsey
Published 2023-04-01