John Brothers II


Working towards a Ph.D. in Bioinformatics at Boston University

Undergraduate Degree: Bachelor of Science in Bioinformatics, College of Science, Rochester Institute of Technology

Research Interests:

Currently, I have been focusing on two major projects:


First, I have been working on a large number of mRNA-seq lung tissue datasets (currently >50 samples out of an eventual 400, with over 200 billion base pairs having been sequenced so far) that the Spira lab has been producing as part of the Lung Genome Research Consortium. In particular I have been working on identifying which transcripts and genes have sufficient digital signal for futher downstream analysis, identifying alternative splicing events (such as isoform switching and changes the which isoforms are dominant) between different lung diseases (specifically ILD and COPD), identifying novel expressed regions of the lung genome that have not been previously annotated, and eventually working with integrating the other genomic, epigenetic, and transcriptomic aspects of the LGRC data (with particular interest in methylation on my part) with the mRNA-seq data. I have been doing a majority of this work with Becky Kusko and Jennifer Beane. I am extremely excited about working with Becky and Jen and about the prospects this data has for redefining what we know about the lung transcriptome.


Secondly, I have been working on identifying methylation events (assays run by Sarah Neumann and others in the Kobor lab at Vancouver) in lung tissue samples (from the Jim Hogg group at Vancouver) that appear to associate with severity of emphysema as well as gene expression that associates with severity of emphysema. I have presented this work in poster and oral presentation form and am currently having the results validated via pyrosequencing by Sarah Neumann. This work has the potential to identify methylation as a potential mechanism of gene expression changes that associate with emphysema severity in multiple lung tissue samples from the same lungs of six COPD patients and two control donors.


Previously, I have looked at the effects of eSNPs and MeDIP-chip methylation patterns on gene expression. I had been exploring various techniques and data analysis steps in processing and analyzing MeDIP-chip NimbleGen arrays and correlating the methylation signal from those chips with Affymetrix expression data from the same set of smoking and never smoking patient samples. This analysis has been in collaboration with the Sidransky and Irizarry groups at Johns Hopkins University. I have also started preliminary work on examining miRNA and mRNA data (predominantly examining lung cancer cell lines that have acquired erlotinib resistance) in collaboration with researchers from the Dubinett lab at UCLA. I have also helped with identifying eSNPs associated with lung cancer in the airway epithelium of smokers at risk for lung cancer. I am primarily interested in exploring and utilizing data analysis of the output of high throughput datasets and techniques to identify differences in clinical factors such as disease, prognosis, and age of patients.

Selected Publications:

Wang X, Chorley BN, Pittman GS, Kleeberger SR, Brothers J II, et al. 2010. Genetic Variation and Antioxidant Response Gene Expression in the Bronchial Airway Epithelium of Smokers at Risk for Lung Cancer. PLoS ONE 5(8): e11934. doi:10.1371/journal.pone.0011934 (Link)


Gower AC, Steiling K, Brothers JF, Lenburg ME, Spira A. Transcriptomic studies of the airway ‘field of injury’ associated with smoking-related lung disease. Proc Am Thorac Soc, 2011; 8(2):173-179.