Integrated single cell data analysis reveals cell specific networks and novel coactivation markers. - Shila Ghazanfar; Adam J. Bisogni; John T. Ormerod; David M. Lin; Jean Yee Hwa Yang (BMC Syst. Biol., 2016)

Characterizing mutation-expression network relationships in multiple cancers. - Shila Ghazanfar; Jean Yee Hwa Yang (Comput. Biol. Chem., 2016)

Statistical approaches to harness high throughput sequencing data in diverse biological systems. - Shila Ghazanfar (2017)

DCARS: differential correlation across ranked samples. - Shila Ghazanfar; Dario Strbenac; John T. Ormerod; Jean Yee Hwa Yang; Ellis Patrick (Bioinform., 2019)

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. - Michael P. Snyder; Shin Lin; Amanda Posgai; Mark Atkinson; Aviv Regev; Jennifer Rood; Orit Rozenblatt-Rosen; Leslie Gaffney; Anna Hupalowska; Rahul Satija; Nils Gehlenborg; Jay Shendure; et al. (Nat., 2019)

SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor. - Dario Righelli; Lukas M. Weber; Helena L. Crowell; Brenda Pardo; Leonardo Collado-Torres; Shila Ghazanfar; Aaron T. L. Lun; Stephanie C. Hicks; Davide Risso (Bioinform., 2022)

Benchmarking of analytical combinations for COVID-19 outcome prediction using single-cell RNA sequencing data. - Yue Cao; Shila Ghazanfar; Pengyi Yang; Jean Y. H. Yang (Briefings Bioinform., 2023)

MoleculeExperiment enables consistent infrastructure for molecule-resolved spatial omics data in bioconductor. - Bárbara Zita Peters Couto; Nicholas Robertson; Ellis Patrick; Shila Ghazanfar (Bioinform., 2023)