An analytical pipeline for genomic representations used for cytosine methylation studies. - Reid F. Thompson; Mark Reimers; Batbayar Khulan; Mathieu Gissot; Todd A. Richmond; Quan Chen; Xin Zheng; Kami Kim; John M. Greally (Bioinform., 2008)

A pipeline for the quantitative analysis of CG dinucleotide methylation using mass spectrometry. - Reid F. Thompson; Masako Suzuki; Kevin W. Lau; John M. Greally (Bioinform., 2009)

The Einstein Genome Gateway using WASP - A High Throughput Multi-Layered Life Sciences Portal for XSEDE. - Aaron Golden; Andrew S. McLellan; Robert A. Dubin; Qiang Jing; Pilib Ó Broin; David Moskowitz; Zhengdong Zhang; Masako Suzuki; Joseph Hargitai; R. Brent Calder; John M. Greally (HealthGrid, 2012)

SMITE: an R/Bioconductor package that identifies network modules by integrating genomic and epigenomic information. - N. Ari Wijetunga; Andrew D. Johnston; Ryo Maekawa; Fabien Delahaye; Netha Ulahannan; Kami Kim; John M. Greally (BMC Bioinform., 2017)

Aneuvis: web-based exploration of numerical chromosomal variation in single cells. - Daniel G. Piqué; Grasiella A. Andriani; Elaine Maggi; Samuel E. Zimmerman; John M. Greally; Cristina Montagna; Jessica Cara Mar (BMC Bioinform., 2019)

AptCompare: optimized de novo motif discovery of RNA aptamers via HTS-SELEX. - Kevin R. Shieh; Christina Kratschmer; Keith E. Maier; John M. Greally; Matthew Levy; Aaron Golden (Bioinform., 2020)

The shape of gene expression distributions matter: how incorporating distribution shape improves the interpretation of cancer transcriptomic data. - Laurence de Torrenté; Samuel E. Zimmerman; Masako Suzuki; Maximilian Christopeit; John M. Greally; Jessica Cara Mar (BMC Bioinform., 2020)

Regulatory landscape enrichment analysis (RLEA): a computational toolkit for non-coding variant enrichment and cell type prioritization. - Samuel Rosean; Eric A. Sosa; Donal F. O'Shea; Srilakshmi M. Raj; Cathal Seoighe; John M. Greally (BMC Bioinform., 2024)