The Lung Cancer Research Foundation (LCRF) is a leading organization that funds research leading towards improvement of outcome for people with lung cancer. LCRF during its 15th Anniversary Celebration event announced the recipients of the 2020 Scientific Grant Program. As a part of the 2020 Disparities in Lung Cancer Research Grant Program, Joshua D. Campbell and Umit Tapan were awarded their proposal entitled “Determining differences ……
Author Archives: admin
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Our Bayesian method for identifying and removing contamination from single cell data was recently published in Genome Biology. This work was led by Iris Yang in collaboration with Masanao Yajima. This method is available in the Celda R package.
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Rui Hong is a graduate student in the BU Bioinformatics program. He has joined the Campbell lab to work on single cell software and methods development.
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Yusuke Koga, Hanbing Song, Zachary R. Chalmers, Justin Newberg, Eejung Kim, Jian Carrot-Zhang, Daphnee Piou, Paz Polak, Sarki A. Abdulkadir, Elad Ziv, Matthew Meyerson, Garrett M. Frampton, Joshua D. Campbell and Franklin W. Huang. Abstract Purpose: African American (AFR) men have the highest mortality rate from prostate cancer (PCa) compared with men of other racial/ancestral groups. Differences in the spectrum of somatic genome alterations in tumors between AFR men and other populations have not been well-characterized due to a lack of inclusion of significant ……
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Shiyi Yang, Sean E. Corbett, Yusuke Koga, Zhe Wang, W. Evan Johnson, Masanao Yajima, Joshua D. Campbell. Abstract Droplet-based microfluidic devices have become widely used to perform single-cell RNA sequencing (scRNA-seq). However, ambient RNA present in the cell suspension can be aberrantly counted along with a cell’s native mRNA and result in cross-contamination of transcripts between different ……
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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* Abstract The advent of high-throughput sequencing technologies has led to the ……
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Anthony Federico, Tanya Karagiannis, Kritika Karri, Dileep Kishore, Yusuke Koga, Joshua D. Campbell, Stefano Monti. Abstract The advent of high-throughput sequencing technologies has led to the need for flexible and user-friendly data preprocessing platforms. The Pipeliner framework provides an out-of-the-box solution for processing various types of sequencing data. It combines the Nextflow scripting language and Anaconda package ……
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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 ……
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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, ……
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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, ……