The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing. - Nathan L. Clement; Quinn Snell; Mark J. Clement; Peter C. Hollenhorst; Jahnvi Purwar; Barbara J. Graves; Bradley R. Cairns; W. Evan Johnson (Bioinform., 2010)

Parallel Mapping Approaches for GNUMAP. - Nathan L. Clement; Mark J. Clement; Quinn Snell; W. Evan Johnson (IPDPS Workshops, 2011)

Parallel Pair-HMM SNP Detection. - Nathan L. Clement; Brent A. Shepherd; Paul M. Bodily; Sukhbat Tumur-Ochir; Younghoon Gim; Quinn Snell; Mark J. Clement; W. Evan Johnson (IPDPS Workshops, 2012)

The sva package for removing batch effects and other unwanted variation in high-throughput experiments. - Jeffrey T. Leek; W. Evan Johnson; Hilary S. Parker; Andrew E. Jaffe; John D. Storey (Bioinform., 2012)

Probabilistic alignment leads to improved accuracy and read coverage for bisulfite sequencing data. - Changjin Hong; Nathan L. Clement; Spencer Clement; Saher Sue Hammoud; Douglas T. Carrell; Bradley R. Cairns; Quinn Snell; Mark J. Clement; William Evan Johnson (BMC Bioinform., 2013)

Alternative preprocessing of RNA-Sequencing data in The Cancer Genome Atlas leads to improved analysis results. - Mumtahena Rahman; Laurie K. Jackson; W. Evan Johnson; Dean Y. Li; Andrea H. Bild; Stephen R. Piccolo (Bioinform., 2015)

ASSIGN: context-specific genomic profiling of multiple heterogeneous biological pathways. - Ying Shen; Mumtahena Rahman; Stephen R. Piccolo; Daniel Gusenleitner; Nader N. El-Chaar; Luis Cheng; Stefano Monti; Andrea H. Bild; W. Evan Johnson (Bioinform., 2015)

BatchQC: interactive software for evaluating sample and batch effects in genomic data. - Solaiappan Manimaran; Heather Marie Selby; Kwame Okrah; Claire Ruberman; Jeffrey T. Leek; John Quackenbush; Benjamin Haibe-Kains; Héctor Corrada Bravo; W. Evan Johnson (Bioinform., 2016)

Alternative empirical Bayes models for adjusting for batch effects in genomic studies. - Yuqing Zhang; David F. Jenkins; Solaiappan Manimaran; W. Evan Johnson (BMC Bioinform., 2018)

scruff: an R/Bioconductor package for preprocessing single-cell RNA-sequencing data. - Zhe Wang 028; Junming Hu; W. Evan Johnson; Joshua D. Campbell (BMC Bioinform., 2019)

Robustifying genomic classifiers to batch effects via ensemble learning. - Yuqing Zhang; Prasad Patil; W. Evan Johnson; Giovanni Parmigiani (Bioinform., 2021)

ICAT: a novel algorithm to robustly identify cell states following perturbations in single-cell transcriptomes. - Dakota Y. Hawkins; Daniel T. Zuch; James Huth; Nahomie Rodriguez-Sastre; Kelley R. McCutcheon; Abigail Glick; Alexandra T. Lion; Christopher F. Thomas; Abigail E. Descoteaux; William Evan Johnson; Cynthia A Bradham (Bioinform., 2023)

Interactive analysis of single-cell data using flexible workflows with SCTK2. - Yichen Wang; Irzam Sarfraz; Nida Pervaiz; Rui Hong; Yusuke Koga; Vidya Akavoor; Xinyun Cao; Salam Alabdullatif; Syed Ali Zaib; Zhe Wang 028; Frederick Jansen; Masanao Yajima; et al. (Patterns, 2023)