ComBat-seq: batch effect adjustment for RNA-seq count data

por Zhang, Yuqing, Parmigiani, Giovanni, Johnson, W Evan
Publicado 2020

Overcoming the impacts of two-step batch effect correction on gene expression estimation and inference

por Li, Tenglong, Zhang, Yuqing, Patil, Prasad, Johnson, W Evan
Publicado 2021

Striatal transcriptome analysis of a congenic mouse line (chromosome 11: 50–60Mb) exhibiting reduced methamphetamine sensitivity

por Yazdani, Neema, Shen, Ying, Johnson, W. Evan, Bryant, Camron D.
Publicado 2016

Alternative empirical Bayes models for adjusting for batch effects in genomic studies

por Zhang, Yuqing, Jenkins, David F., Manimaran, Solaiappan, Johnson, W. Evan
Publicado 2018

scruff: an R/Bioconductor package for preprocessing single-cell RNA-sequencing data

por Wang, Zhe, Hu, Junming, Johnson, W. Evan, Campbell, Joshua D.
Publicado 2019

Systematic evaluation of transcriptomic disease risk and diagnostic biomarker overlap between COVID-19 and tuberculosis: a patient-level meta-analysis

por Sheerin, Dylan, Abhimanyu, Wang, Xutao, Johnson, W Evan, Coussens, Anna
Publicado 2020

A Field Guide to Genomics Research

por Bild, Andrea H., Chang, Jeffrey T., Johnson, W. Evan, Piccolo, Stephen R.
Publicado 2014

Effects of ADARs on small RNA processing pathways in C. elegans

por Warf, M. Bryan, Shepherd, Brent A., Johnson, W. Evan, Bass, Brenda L.
Publicado 2012

Metagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data

por Odom, Aubrey R., Faits, Tyler, Castro-Nallar, Eduardo, Crandall, Keith A., Johnson, W. Evan
Publicado 2023

animalcules: interactive microbiome analytics and visualization in R

por Zhao, Yue, Federico, Anthony, Faits, Tyler, Manimaran, Solaiappan, Segrè, Daniel, Monti, Stefano, Johnson, W. Evan
Publicado 2021

ETS-4 Is a Transcriptional Regulator of Life Span in Caenorhabditis elegans

por Thyagarajan, Bargavi, Blaszczak, Adam G., Chandler, Katherine J., Watts, Jennifer L., Johnson, W. Evan, Graves, Barbara J.
Publicado 2010

Census-based rapid and accurate metagenome taxonomic profiling

por Shamsaddini, Amirhossein, Pan, Yang, Johnson, W Evan, Krampis, Konstantinos, Shcheglovitova, Mariya, Simonyan, Vahan, Zanne, Amy, Mazumder, Raja
Publicado 2014

Decontamination of ambient RNA in single-cell RNA-seq with DecontX

por Yang, Shiyi, Corbett, Sean E., Koga, Yusuke, Wang, Zhe, Johnson, W Evan, Yajima, Masanao, Campbell, Joshua D.
Publicado 2020

DNA Specificity Determinants Associate with Distinct Transcription Factor Functions

por Hollenhorst, Peter C., Chandler, Katherine J., Poulsen, Rachel L., Johnson, W. Evan, Speck, Nancy A., Graves, Barbara J.
Publicado 2009

Genomic pathway analysis reveals that EZH2 and HDAC4 represent mutually exclusive epigenetic pathways across human cancers

por Cohen, Adam L, Piccolo, Stephen R, Cheng, Luis, Soldi, Rafaella, Han, Bing, Johnson, W Evan, Bild, Andrea H
Publicado 2013

Evaluation of computational methods for human microbiome analysis using simulated data

por Miossec, Matthieu J., Valenzuela, Sandro L., Pérez-Losada, Marcos, Johnson, W. Evan, Crandall, Keith A., Castro-Nallar, Eduardo
Publicado 2020

Immunopathogenic overlap between COVID-19 and tuberculosis identified from transcriptomic meta-analysis and human macrophage infection

por Sheerin, Dylan, Abhimanyu, Peton, Nashied, Vo, William, Allison, Cody Charles, Wang, Xutao, Johnson, W. Evan, Coussens, Anna Kathleen
Publicado 2022

Respiratory syncytial virus M2-1 protein associates non-specifically with viral messenger RNA and with specific cellular messenger RNA transcripts

por Braun, Molly R., Noton, Sarah L., Blanchard, Emmeline L., Shareef, Afzaal, Santangelo, Philip J., Johnson, W. Evan, Fearns, Rachel
Publicado 2021

Genome-wide profiling of the C. elegans dsRNAome

por Whipple, Joseph M., Youssef, Osama A., Aruscavage, P. Joseph, Nix, David A., Hong, Changjin, Johnson, W. Evan, Bass, Brenda L.
Publicado 2015

Celda: a Bayesian model to perform co-clustering of genes into modules and cells into subpopulations using single-cell RNA-seq data

por Wang, Zhe, Yang, Shiyi, Koga, Yusuke, Corbett, Sean E, Shea, Conor V, Johnson, W Evan, Yajima, Masanao, Campbell, Joshua D
Publicado 2022