Clinical PathoScope: rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data. - Allyson L. Byrd; Joseph F. Perez-Rogers; Solaiappan Manimaran; Eduardo Castro-Nallar; Ian Toma; Tim McCaffrey; Marc Siegel; Gary Benson; Keith A. Crandall; William Johnson (BMC Bioinform., 2014)

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)