Managing batch effects in microbiome data
Y Wang, KA LêCao - Briefings in bioinformatics, 2020 - academic.oup.com
Microbial communities have been increasingly studied in recent years to investigate their
role in ecological habitats. However, microbiome studies are difficult to reproduce or …
role in ecological habitats. However, microbiome studies are difficult to reproduce or …
Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts
It is estimated that 350 million individuals worldwide suffer from rare diseases, which are
predominantly caused by mutation in a single gene. The current molecular diagnostic rate is …
predominantly caused by mutation in a single gene. The current molecular diagnostic rate is …
[HTML][HTML] SFARI genes and where to find them; modelling Autism Spectrum Disorder specific gene expression dysregulation with RNA-seq data
MNT Arpi, TI Simpson - Scientific Reports, 2022 - nature.com
Abstract Autism Spectrum Disorders (ASD) have a strong, yet heterogeneous, genetic
component. Among the various methods that are being developed to help reveal the …
component. Among the various methods that are being developed to help reveal the …
An efficient approach to screening epigenome‐wide data
Screening cytosine‐phosphate‐guanine dinucleotide (CpG) DNA methylation sites in
association with some covariate (s) is desired due to high dimensionality. We incorporate …
association with some covariate (s) is desired due to high dimensionality. We incorporate …
Mutational landscape and gene expression patterns in adult acute myeloid leukemias with monosomy 7 as a sole abnormality
Monosomy of chromosome 7 is the most frequent autosomal monosomy in acute myeloid
leukemia (AML), where it associates with poor clinical outcomes. However, molecular …
leukemia (AML), where it associates with poor clinical outcomes. However, molecular …
Molecular profiles of matched primary and metastatic tumor samples support a linear evolutionary model of breast cancer
The interpretation of accumulating genomic data with respect to tumor evolution and cancer
progression requires integrated models. We developed a computational approach that …
progression requires integrated models. We developed a computational approach that …
Identification of Let-7 miRNA activity as a prognostic biomarker of SHH medulloblastoma
Simple Summary Medulloblastoma is the most common malignant pediatric brain tumor. It
can be divided into four molecular subgroups with clear biological and clinical differences …
can be divided into four molecular subgroups with clear biological and clinical differences …
[HTML][HTML] Unifying and generalizing methods for removing unwanted variation based on negative controls
Unwanted variation, including hidden confounding, is a well-known problem in many fields,
but particularly in large-scale gene expression studies. Recent proposals to use control …
but particularly in large-scale gene expression studies. Recent proposals to use control …
dbMDEGA: a database for meta-analysis of differentially expressed genes in autism spectrum disorder
S Zhang, L Deng, Q Jia, S Huang, J Gu, F Zhou… - BMC …, 2017 - Springer
Background Autism spectrum disorders (ASD) are hereditary, heterogeneous and
biologically complex neurodevelopmental disorders. Individual studies on gene expression …
biologically complex neurodevelopmental disorders. Individual studies on gene expression …
A robust data-driven genomic signature for idiopathic pulmonary fibrosis with applications for translational model selection
R Ammar, P Sivakumar, G Jarai, JR Thompson - PLoS One, 2019 - journals.plos.org
Idiopathic pulmonary fibrosis (IPF) is a chronic and progressive lung disease affecting~ 5
million people globally. We have constructed an accurate model of IPF disease status using …
million people globally. We have constructed an accurate model of IPF disease status using …