A systematic integrated analysis of brain expression profiles reveals YAP1 and other prioritized hub genes as important upstream regulators in Alzheimer's disease
M Xu, DF Zhang, R Luo, Y Wu, H Zhou, LL Kong… - Alzheimer's & …, 2018 - Elsevier
Introduction Profiling the spatial-temporal expression pattern and characterizing the
regulatory networks of brain tissues are vital for understanding the pathophysiology of …
regulatory networks of brain tissues are vital for understanding the pathophysiology of …
Prenatal phthalates, maternal thyroid function, and risk of attention-deficit hyperactivity disorder in the Norwegian mother and child cohort
Background: There is growing concern that phthalate exposures may have an impact on
child neurodevelopment. Prenatal exposure to phthalates has been linked with externalizing …
child neurodevelopment. Prenatal exposure to phthalates has been linked with externalizing …
Classifiers and their metrics quantified
JB Brown - Molecular informatics, 2018 - Wiley Online Library
Molecular modeling frequently constructs classification models for the prediction of two‐
class entities, such as compound bio (in) activity, chemical property (non) existence, protein …
class entities, such as compound bio (in) activity, chemical property (non) existence, protein …
Alternative empirical Bayes models for adjusting for batch effects in genomic studies
Background Combining genomic data sets from multiple studies is advantageous to
increase statistical power in studies where logistical considerations restrict sample size or …
increase statistical power in studies where logistical considerations restrict sample size or …
A merged lung cancer transcriptome dataset for clinical predictive modeling
Abstract The Gene Expression Omnibus (GEO) database is an excellent public source of
whole transcriptomic profiles of multiple cancers. The main challenge is the limited …
whole transcriptomic profiles of multiple cancers. The main challenge is the limited …
Comparison of statistical methods and the use of quality control samples for batch effect correction in human transcriptome data
A Espín-Pérez, C Portier, M Chadeau-Hyam… - PloS one, 2018 - journals.plos.org
Batch effects are technical sources of variation introduced by the necessity of conducting
gene expression analyses on different dates due to the large number of biological samples …
gene expression analyses on different dates due to the large number of biological samples …
Identifying and correcting epigenetics measurements for systematic sources of variation
F Perrier, A Novoloaca, S Ambatipudi, L Baglietto… - Clinical …, 2018 - Springer
Background Methylation measures quantified by microarray techniques can be affected by
systematic variation due to the technical processing of samples, which may compromise the …
systematic variation due to the technical processing of samples, which may compromise the …
In vitro pluripotent stem cell differentiation to hepatocyte ceases further maturation at an equivalent stage of E15 in mouse embryonic liver development
R Raju, D Chau, T Notelaers, CL Myers… - Stem Cells and …, 2018 - liebertpub.com
Hepatocyte-like cells (HLCs) can be derived from pluripotent stem cells (PSCs) by
sequential treatment of chemical cues to mimic the microenvironment of embryonic liver …
sequential treatment of chemical cues to mimic the microenvironment of embryonic liver …
[HTML][HTML] Identifying differentially expressed genes from cross-site integrated data based on relative expression orderings
H Cai, X Li, J Li, Q Liang, W Zheng… - … Journal of Biological …, 2018 - ncbi.nlm.nih.gov
It is a basic task in high-throughput gene expression profiling studies to identify differentially
expressed genes (DEGs) between two phenotypes. But the weakly differential expression …
expressed genes (DEGs) between two phenotypes. But the weakly differential expression …
Detecting hidden batch factors through data-adaptive adjustment for biological effects
Motivation Batch effects are one of the major source of technical variations that affect the
measurements in high-throughput studies such as RNA sequencing. It has been well …
measurements in high-throughput studies such as RNA sequencing. It has been well …