Integrative approaches for finding modular structure in biological networks

K Mitra, AR Carvunis, SK Ramesh, T Ideker - Nature Reviews Genetics, 2013 - nature.com
A central goal of systems biology is to elucidate the structural and functional architecture of
the cell. To this end, large and complex networks of molecular interactions are being rapidly …

Integration of 'omics' data in aging research: from biomarkers to systems biology

J Zierer, C Menni, G Kastenmüller, TD Spector - Aging cell, 2015 - Wiley Online Library
Age is the strongest risk factor for many diseases including neurodegenerative disorders,
coronary heart disease, type 2 diabetes and cancer. Due to increasing life expectancy and …

Molecular choreography of acute exercise

K Contrepois, S Wu, KJ Moneghetti, D Hornburg… - Cell, 2020 - cell.com
Acute physical activity leads to several changes in metabolic, cardiovascular, and immune
pathways. Although studies have examined selected changes in these pathways, the system …

Network integration of parallel metabolic and transcriptional data reveals metabolic modules that regulate macrophage polarization

AK Jha, SCC Huang, A Sergushichev, V Lampropoulou… - Immunity, 2015 - cell.com
Macrophage polarization involves a coordinated metabolic and transcriptional rewiring that
is only partially understood. By using an integrated high-throughput transcriptional …

NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data

J **a, EE Gill, REW Hancock - Nature protocols, 2015 - nature.com
Meta-analysis of gene expression data sets is increasingly performed to help identify robust
molecular signatures and to gain insights into underlying biological processes. The …

Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes

A Heintz-Buschart, P May, CC Laczny, LA Lebrun… - Nature …, 2016 - nature.com
The gastrointestinal microbiome is a complex ecosystem with functions that shape human
health. Studying the relationship between taxonomic alterations and functional …

Sex differences and immune correlates of Long Covid development, symptom persistence, and resolution

RE Hamlin, SM Pienkos, L Chan, MA Stabile… - Science Translational …, 2024 - science.org
Sex differences have been observed in acute coronavirus disease 2019 (COVID-19) and
Long Covid (LC) outcomes, with greater disease severity and mortality during acute infection …

The role of Arabidopsis ABA receptors from the PYR/PYL/RCAR family in stomatal acclimation and closure signal integration

M Dittrich, HM Mueller, H Bauer, M Peirats-Llobet… - Nature Plants, 2019 - nature.com
Stomata are microscopic pores found on the surfaces of leaves that act to control CO2
uptake and water loss. By integrating information derived from endogenous signals with …

Reduced insulin production relieves endoplasmic reticulum stress and induces β cell proliferation

M Szabat, MM Page, E Panzhinskiy, S Skovsø… - Cell metabolism, 2016 - cell.com
Pancreatic β cells are mostly post-mitotic, but it is unclear what locks them in this state.
Perturbations including uncontrolled hyperglycemia can drive β cells into more pliable states …

SLICE: determining cell differentiation and lineage based on single cell entropy

M Guo, EL Bao, M Wagner, JA Whitsett… - Nucleic acids …, 2017 - academic.oup.com
A complex organ contains a variety of cell types, each with its own distinct lineage and
function. Understanding the lineage and differentiation state of each cell is fundamentally …