The pathway coexpression network: revealing pathway relationships
Y Pita-Juárez, G Altschuler, S Kariotis… - PLoS computational …, 2018 - journals.plos.org
A goal of genomics is to understand the relationships between biological processes.
Pathways contribute to functional interplay within biological processes through complex but …
Pathways contribute to functional interplay within biological processes through complex but …
Taking bioinformatics to systems medicine
AHC van Kampen, PD Moerland - Systems medicine, 2016 - Springer
Abstract Systems medicine promotes a range of approaches and strategies to study human
health and disease at a systems level with the aim of improving the overall well-being of …
health and disease at a systems level with the aim of improving the overall well-being of …
PanomiR: a systems biology framework for analysis of multi-pathway targeting by miRNAs
Charting microRNA (miRNA) regulation across pathways is key to characterizing their
function. Yet, no method currently exists that can quantify how miRNAs regulate multiple …
function. Yet, no method currently exists that can quantify how miRNAs regulate multiple …
[HTML][HTML] A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients
The molecular underpinnings of organ dysfunction in acute COVID-19 and its potential long-
term sequelae are under intense investigation. To shed light on these in the context of liver …
term sequelae are under intense investigation. To shed light on these in the context of liver …
Meta-analysis in gene expression studies
This chapter introduces methods to synthesize experimental results from independent high-
throughput genomic experiments, with a focus on adaptation of traditional methods from …
throughput genomic experiments, with a focus on adaptation of traditional methods from …
Integrated analysis of numerous heterogeneous gene expression profiles for detecting robust disease-specific biomarkers and proposing drug targets
Genome-wide expression profiling has revolutionized biomedical research; vast amounts of
expression data from numerous studies of many diseases are now available. Making the …
expression data from numerous studies of many diseases are now available. Making the …
The relative resistance of children to sepsis mortality: from pathways to drug candidates
RB Joachim, GM Altschuler, JN Hutchinson… - Molecular Systems …, 2018 - embopress.org
Attempts to develop drugs that address sepsis based on leads developed in animal models
have failed. We sought to identify leads based on human data by exploiting a natural …
have failed. We sought to identify leads based on human data by exploiting a natural …
[HTML][HTML] Sample level enrichment analysis of KEGG pathways identifies clinically relevant subtypes of glioblastoma
Background: Glioblastoma is the most lethal primary brain tumor in adults. Aberrant signal
transduction pathways, associated with the progression of glioblastoma, have been …
transduction pathways, associated with the progression of glioblastoma, have been …
Multi-level comparative framework based on gene pair-wise expression across three insulin target tissues for type 2 diabetes
S Sun, F Sun, Y Wang - Frontiers in Genetics, 2019 - frontiersin.org
Type 2 diabetes (T2D) is known as a disease caused by gene alterations characterized by
insulin resistance, thus the insulin-responsive tissues are of great interest for T2D study. It's …
insulin resistance, thus the insulin-responsive tissues are of great interest for T2D study. It's …
Understanding cellular function and disease with comparative pathway analysis
Pathway analysis is important in interpreting the functional implications of high-throughput
experimental results, but robust comparison across platforms and species is problematic. A …
experimental results, but robust comparison across platforms and species is problematic. A …