Adage-based integration of publicly available pseudomonas aeruginosa gene expression data with denoising autoencoders illuminates microbe-host interactions
The increasing number of genome-wide assays of gene expression available from public
databases presents opportunities for computational methods that facilitate hypothesis …
databases presents opportunities for computational methods that facilitate hypothesis …
Bone marrow microenvironments that contribute to patient outcomes in newly diagnosed multiple myeloma: A cohort study of patients in the Total Therapy clinical trials
Background The tumor microenvironment (TME) is increasingly appreciated as an important
determinant of cancer outcome, including in multiple myeloma (MM). However, most …
determinant of cancer outcome, including in multiple myeloma (MM). However, most …
Biclustering methods: biological relevance and application in gene expression analysis
DNA microarray technologies are used extensively to profile the expression levels of
thousands of genes under various conditions, yielding extremely large data-matrices. Thus …
thousands of genes under various conditions, yielding extremely large data-matrices. Thus …
Biclique communities
We present a method for detecting communities in bipartite networks. Based on an
extension of the k-clique community detection algorithm, we demonstrate how modular …
extension of the k-clique community detection algorithm, we demonstrate how modular …
It is time to apply biclustering: a comprehensive review of biclustering applications in biological and biomedical data
Biclustering is a powerful data mining technique that allows clustering of rows and columns,
simultaneously, in a matrix-format data set. It was first applied to gene expression data in …
simultaneously, in a matrix-format data set. It was first applied to gene expression data in …
From protein-protein interactions to protein co-expression networks: a new perspective to evaluate large-scale proteomic data
The reductionist approach of dissecting biological systems into their constituents has been
successful in the first stage of the molecular biology to elucidate the chemical basis of …
successful in the first stage of the molecular biology to elucidate the chemical basis of …
Gene expression profiling of 1200 pancreatic ductal adenocarcinoma reveals novel subtypes
L Zhao, H Zhao, H Yan - BMC cancer, 2018 - Springer
Background Pancreatic ductal adenocarcinoma (PDAC) is the fourth leading cause of
cancer related death in the world with a five-year survival rate of less than 5%. Not all PDAC …
cancer related death in the world with a five-year survival rate of less than 5%. Not all PDAC …
Systems biology of innate immunity
DE Zak, A Aderem - Immunological reviews, 2009 - Wiley Online Library
Systems biology is the comprehensive and quantitative analysis of the interactions between
all of the components of biological systems over time. Systems biology involves an iterative …
all of the components of biological systems over time. Systems biology involves an iterative …
Differential gene regulatory networks in development and disease
Gene regulatory networks, in which differential expression of regulator genes induce
differential expression of their target genes, underlie diverse biological processes such as …
differential expression of their target genes, underlie diverse biological processes such as …
An integrative systems biology approach to understanding pulmonary diseases
Chronic inflammatory pulmonary diseases such as COPD and asthma are highly prevalent
and associated with a major health burden worldwide. Despite a wealth of biologic and …
and associated with a major health burden worldwide. Despite a wealth of biologic and …