Project Summary Despite their many advantages, single-cell technologies can suffer from the presence of contamination arising from different sources. High levels of contamination can hinder important analyses such as clustering, marker identification, and differential expression. This team has previously developed a tool called decontX that estimates and removes contamination arising from the presence of ambient ……
Category Archives: Featured
24
May
May
Version 1.1 Authors: Joshua Campbell, Rui Hong, Aaron Chevalier, Salam Alabdullatif, Christopher Husted, Yusuke Koga, Yuan Yin, Kelly GeyerDate: 5/4/2022 1. Introduction When developing an R package, the process of adding code that is error free, does the thing that you want it to do, and is maintainable in the long run by other users ……
08
Feb
Feb
The Campbell Lab is participating in an Ancestry Seed Network within the Human Cell Atlas (HCA). This project aims to leverage state-of-the-art techniques to characterize cellular heterogeneity across ancestries and ages in the healthy prostate. This network is led by Franklin Huang at UCSF and a collaboration of investigators from UCSF, University of Texas, and Boston University.
03
Jun
Jun
High-throughput genomic technologies are rapidly evolving including the areas of DNA and RNA sequencing. Novel types of complex data are being quickly generated and require novel methods for quality control and analysis. We are currently focused on developing and/or applying methods for identifying genomic alterations in cancer, quantifying the mutagenic effect of carcinogens, and characterizing ……
03
Jun
Jun
Lung adenocarcinomas and lung squamous cell carcinomas are the most common types of lung cancer and remain major causes of death worldwide despite advances in smoking cessation, early detection, and targeted and immunological therapies. Many patients have lung cancers that do not harbor a known activating mutation and therefore cannot be given targeted therapies. In ……
03
Jun
Jun
Chronic Obstructive Pulmonary Disease (COPD) is the 4th leading cause of death in the world. Our understanding of the molecular mechanisms responsible for the initiation and progression of this disease are limited. By examining expression differences between individuals with and without COPD or differences within a person along a gradient of disease, we hope to ……
27
Jan
Jan
Ryan J. Quinton, Amanda DiDomizio, Marc A. Vittoria, Kristýna Kotýnková, Carlos J. Ticas, Sheena Patel, Yusuke Koga, Jasmine Vakhshoorzadeh, Nicole Hermance, Taruho S. Kuroda, Neha Parulekar, Alison M. Taylor, Amity L. Manning, Joshua D. Campbell & Neil J. Ganem Nature volume 590, pages492–497 (2021)Cite this article Abstract Whole-genome doubling (WGD) is common in human cancers, occurring early in tumorigenesis and generating genetically unstable tetraploid cells that fuel tumour development1,2. Cells that undergo WGD ……
01
Apr
Apr
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 ……
31
Mar
Mar
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 ……
31
Jan
Jan
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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