Here’s a list of publications where GobyWeb was used for analyses (see more recent citations directly from Google Scholar).

Ritchie, Marylyn D., et al. “Methods of integrating data to uncover genotype-phenotype interactions.” Nature Reviews Genetics 16.2 (2015): 85-97.

Differential gene body methylation and reduced expression of cell adhesion and neurotransmitter receptor genes in adverse maternal environment

J Oh, N Chambwe, S Klein, J Gal, S Andrews… – Translational Psychiatry, 2013 – nature.com

 Bisulfite converted reads were mapped to the mouse genome mm9 with GobyWeb and the last
bisulfite plugin. 30 Methylation rates were estimated with GobyWeb as described in
Supplementary Material. Sample preparation for RNA extraction and RNA-Seq. 

Tmem88a mediates GATA-dependent specification of cardiomyocyte progenitors by restricting WNT signaling

N Novikov, T Evans – Development, 2013 – dev.biologists.org

Summary Biphasic control of WNT signaling is essential during cardiogenesis, but how the
pathway switches from promoting cardiac mesoderm to restricting cardiomyocyte progenitor
fate is unknown. We identified genes expressed in lateral mesoderm that are dysregulated 

Small heat shock proteins Hspb7 and Hspb12 regulate early steps of cardiac morphogenesis

GE Rosenfeld, EJ Mercer, CE Mason, T Evans – Developmental biology, 2013 – Elsevier

 Fastq files were uploaded to the gobyweb application (http://gobyweb.apps.campagnelab.org/). 
Zebrafish cardiomyocyte RNA sample sequence reads were analyzed with gobyweb and aligned
to the zebrafish reference genome (Zv9.61) with the BWA algorithm. 

Altered Epigenetic Regulation of Homeobox Genes in Human Oral Squamous Cell Carcinoma Cells

KM Marcinkiewicz, LJ Gudas – Experimental cell research, 2013 – Elsevier

Abstract To gain insight into oral squamous cell carcinogenesis, we performed deep
sequencing (RNA-Seq) of non-tumorigenic human OKF6-TERT1R and tumorigenic SCC-9
cells. Numerous homeobox genes are differentially expressed between OKF6-TERT1R 

L Fu, G Wang, MM Shevchuk, DM Nanus, LJ Gudas – Cancer research, 2013 – AACR

Abstract Renal cell carcinoma (RCC) is the most common primary cancer arising from the
kidney in adults, with clear cell renal cell carcinoma (ccRCC) representing approximately
75% of all RCCs. Increased expression of the hypoxia-induced factors-1α (HIF1α) and 

Systematic Identification of Molecular Subtype-Selective Vulnerabilities in Non-Small-Cell Lung Cancer

HS Kim, S Mendiratta, J Kim, CV Pecot, JE Larsen et al – Cell, 2013
Summary Context-specific molecular vulnerabilities that arise during tumor evolution
represent an attractive intervention target class. However, the frequency and diversity of
somatic lesions detected among lung tumors can confound efforts to identify these targets.