Preserving biological heterogeneity with a permuted surrogate variable analysis for genomics batch correction
Motivation: Sample source, procurement process and other technical variations introduce
batch effects into genomics data. Algorithms to remove these artifacts enhance differences …
batch effects into genomics data. Algorithms to remove these artifacts enhance differences …
[HTML][HTML] YuGene: a simple approach to scale gene expression data derived from different platforms for integrated analyses
Gene expression databases contain invaluable information about a range of cell states, but
the question “Where is my gene of interest expressed?” remains one of the most difficult to …
the question “Where is my gene of interest expressed?” remains one of the most difficult to …
[HTML][HTML] Dysfunctional HIV-specific CD8+ T cell proliferation is associated with increased caspase-8 activity and mediated by necroptosis
Summary Decreased HIV-specific CD8+ T cell proliferation is a hallmark of chronic infection,
but the mechanisms of decline are unclear. We analyzed gene expression profiles from …
but the mechanisms of decline are unclear. We analyzed gene expression profiles from …
Removing batch effects for prediction problems with frozen surrogate variable analysis
Batch effects are responsible for the failure of promising genomic prognostic signatures,
major ambiguities in published genomic results, and retractions of widely-publicized …
major ambiguities in published genomic results, and retractions of widely-publicized …
Batch effect confounding leads to strong bias in performance estimates obtained by cross-validation
Background With the large amount of biological data that is currently publicly available,
many investigators combine multiple data sets to increase the sample size and potentially …
many investigators combine multiple data sets to increase the sample size and potentially …
Natural genetic variation impacts expression levels of coding, non‐coding, and antisense transcripts in fission yeast
M Clément‐Ziza, FX Marsellach, S Codlin… - Molecular systems …, 2014 - embopress.org
Our current understanding of how natural genetic variation affects gene expression beyond
well‐annotated coding genes is still limited. The use of deep sequencing technologies for …
well‐annotated coding genes is still limited. The use of deep sequencing technologies for …
Selective inhibition of pancreatic ductal adenocarcinoma cell growth by the mitotic MPS1 kinase inhibitor NMS-P715
RB Slee, BR Grimes, R Bansal, J Gore… - Molecular cancer …, 2014 - AACR
Most solid tumors, including pancreatic ductal adenocarcinoma (PDAC), exhibit structural
and numerical chromosome instability (CIN). Although often implicated as a driver of tumor …
and numerical chromosome instability (CIN). Although often implicated as a driver of tumor …
Comparison of gene expression microarray data with count-based RNA measurements informs microarray interpretation
AC Richard, PA Lyons, JE Peters, D Biasci, SM Flint… - BMC genomics, 2014 - Springer
Background Although numerous investigations have compared gene expression microarray
platforms, preprocessing methods and batch correction algorithms using constructed spike …
platforms, preprocessing methods and batch correction algorithms using constructed spike …
Microarray‐based RNA profiling of breast cancer: batch effect removal improves cross‐platform consistency
Microarray is a powerful technique used extensively for gene expression analysis. Different
technologies are available, but lack of standardization makes it challenging to compare and …
technologies are available, but lack of standardization makes it challenging to compare and …
Gene expression profiling in asthma
J Sordillo, BA Raby - Heterogeneity in Asthma, 2014 - Springer
Transcriptomics (gene expression profiling) refers to the quantitative and qualitative
characterization of the collection of ribose nucleic acid (RNA) elements expressed in a …
characterization of the collection of ribose nucleic acid (RNA) elements expressed in a …