Publications

See all publications on Google Scholar or PubMed

2020

Decontamination of ambient RNA in single-cell RNA-seq with DecontX

Shiyi Yang, Sean E. Corbett, Yusuke Koga, Zhe Wang, W. Evan Johnson, Masanao Yajima, Joshua D. Campbell

2019

Characterizing smoking-induced transcriptional heterogeneity in the human bronchial epithelium at single-cell resolution

Grant E. Duclos, Vitor H. Teixeira, Patrick Autissier, Yaron B. Gesthalter, Marjan A. Reinders-Luinge, Robert Terrano, Yves M. Dumas, Gang Liu, Sarah A. Mazzilli, Corry-Anke Brandsma, Maarten van den Berge, Sam M. Janes, Wim Timens, Marc E. Lenburg, Avrum Spira, Joshua D. Campbell*, Jennifer Beane*

Pipeliner: A Nextflow-Based Framework for the Definition of Sequencing Data Processing Pipelines

Anthony Federico, Tanya Karagiannis, Kritika Karri, Dileep Kishore, Yusuke Koga, Joshua D. Campbell, Stefano Monti

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

Zhe Wang, Junming Hu, W. Evan Johnson, Joshua D. Campbell

2018

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, Akinyemi I. Ojesina, Sara Sadeghi, Karen L. Mungall, A. Gordon Robertson, Christopher Benz, Andre Schultz, Rupa S. Kanchi, Carl M. Gay, Apurva Hegde, Lixia Diao, Jing Wang, Wencai Ma, Pavel Sumazin, Hua-Sheng Chiu, Ting-Wen Chen, Preethi Gunaratne, Larry Donehower, Janet S. Rader, Rosemary Zuna, Hikmat Al-Ahmadie, Alexander J. Lazar, Elsa R. Flores, Kenneth Y. Tsai, Jane H. Zhou, Anil K. Rustgi, Esther Drill, Ronglei Shen, Christopher K. Wong, The Cancer Genome Atlas Research Network, Joshua M. Stuart, Peter W. Laird, Katherine A. Hoadley, John N. Weinstein, Myron Peto, Curtis R. Pickering, Zhong Chen, and Carter Van Waes

2017

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

2016

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 Verhaak, Catherine J Wu, Peter S Hammerman, Andrew D Cherniack, Gad Getz, Cancer Genome Atlas Research Network, Maxim N Artyomov, Robert Schreiber, Ramaswamy Govindan* and Matthew Meyerson*