Category Archives: News

Award: Methods and Software for Decontamination of Single-Cell Data

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 ……

New Funding

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. 

New funding from NCI

New funding from NCI – The Campbell lab has received a new U01 from the NCI’s ITCR program to develop novel methods and software for mutational signature inference in collaboration with the Yajima and Huggins labs at BU. Additionally, the lab has received a new R01 from the NCI’s Center to Reduce Cancer Health Disparities to ……

ExperimentSubset accepted for publication in Bioinformatics

ExperimentSubset is an R package to manage subsets of Bioconductor Experiment objects during an analysis workflow. The package boasts features such as efficient memory management and provenance tracking while keeping data redundancy at minimum. This work was led by lab member Irzam Sarfraz and was recently accepted for publication in Oxford Bioinformatics. The package is ……

Unique vulnerabilities in tumors that have undergone whole-genome doubling

A study led by Neil Ganem and his graduate student Ryan Quinton was published in Nature. Genomic characteristics of tumors that have undergone whole-genome doubling (WGD) were explored and a novel vulnerability was identified in the gene KIF18A using the Broad’s Dependency Map data. KIF18A encodes a mitotic kinesin protein and was required for viability of tumors with WGD. Yusuke Koga and Josh Campbell contributed to the study by aiding ……