Category Archives: Featured

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

Zhe Wang, Junming Hu, W. Evan Johnson, Joshua D. Campbell Abstract Background: Single-cell RNA sequencing (scRNA-seq) enables the high-throughput quantification of transcriptional profiles in single cells. In contrast to bulk RNA-seq, additional preprocessing steps such as cell barcode identification or unique molecular identifier (UMI) deconvolution are necessary for preprocessing of data from single cell protocols. R packages that ……

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

Joshua D. Campbell, Christina Yau, Reanne Bowlby, Yuexin Liu, Kevin Brennan, Huihui Fan, Alison M. Taylor, Chen Wang, Vonn Walter, Rehan Akbani, Lauren Averett Byers, Chad J. Creighton, Cristian Coarfa, Juliann Shih, Andrew D. Cherniack, livier Gevaert, Marcos Prunello, Hui Shen, Pavana Anur, Jianhong Chen, Hui Cheng, D. Neil Hayes, Susan Bullman, Chandra Sekhar Pedamallu, ……

Alterations in Bronchial Airway miRNA Expression for Lung Cancer Detection

Ana B. Pavel, Joshua D. Campbell, Gang Liu, David Elashoff, Steven Dubinett, Kate Smith, Duncan Whitney, Marc E. Lenburg and Avrum Spira. Abstract We have previously shown that gene expression alterations in normal-appearing bronchial epithelial cells can serve as a lung cancer detection biomarker in smokers. Given that miRNAs regulate airway gene expression responses to smoking, ……

Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas

Joshua D Campbell, Anton Alexandrov, Jaegil Kim, Jeremiah Wala, Alice H Berger, Chandra Sekhar Pedamallu, Sachet A Shukla, Guangwu Guo, Angela N Brooks, Bradley A Murray, Marcin Imielinski, Xin Hu, Shiyun Ling, Rehan Akbani, Mara Rosenberg, Carrie Cibulskis, Aruna Ramachandran, Eric A Collisson, David J Kwiatkowski, Michael S Lawrence, John N Weinstein, Roel G W ……