A guide to conquer the biological network era using graph theory

M Koutrouli, E Karatzas, D Paez-Espino… - … in bioengineering and …, 2020 - frontiersin.org
Networks are one of the most common ways to represent biological systems as complex sets
of binary interactions or relations between different bioentities. In this article, we discuss the …

A copy number variation map of the human genome

M Zarrei, JR MacDonald, D Merico… - Nature reviews …, 2015 - nature.com
A major contribution to the genome variability among individuals comes from deletions and
duplications—collectively termed copy number variations (CNVs)—which alter the diploid …

Mapping genomic loci implicates genes and synaptic biology in schizophrenia

V Trubetskoy, AF Pardiñas, T Qi, G Panagiotaropoulou… - Nature, 2022 - nature.com
Schizophrenia has a heritability of 60–80%, much of which is attributable to common risk
alleles. Here, in a two-stage genome-wide association study of up to 76,755 individuals with …

Senescence atlas reveals an aged-like inflamed niche that blunts muscle regeneration

V Moiseeva, A Cisneros, V Sica, O Deryagin, Y Lai… - Nature, 2023 - nature.com
Tissue regeneration requires coordination between resident stem cells and local niche
cells,. Here we identify that senescent cells are integral components of the skeletal muscle …

KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis

D Bu, H Luo, P Huo, Z Wang, S Zhang, Z He… - Nucleic acids …, 2021 - academic.oup.com
Gene set enrichment (GSE) analysis plays an essential role in extracting biological insight
from genome-scale experiments. ORA (overrepresentation analysis), FCS (functional class …

[HTML][HTML] Spatially confined sub-tumor microenvironments in pancreatic cancer

BT Grünwald, A Devisme, G Andrieux, F Vyas, K Aliar… - Cell, 2021 - cell.com
Intratumoral heterogeneity is a critical frontier in understanding how the tumor
microenvironment (TME) propels malignant progression. Here, we deconvolute the human …

[HTML][HTML] gprofiler2--an R package for gene list functional enrichment analysis and namespace conversion toolset g: Profiler

L Kolberg, U Raudvere, I Kuzmin, J Vilo… - …, 2020 - ncbi.nlm.nih.gov
Abstract g: Profiler (https://biit. cs. ut. ee/gprofiler) is a widely used gene list functional
profiling and namespace conversion toolset that has been contributing to reproducible …

p21 produces a bioactive secretome that places stressed cells under immunosurveillance

I Sturmlechner, C Zhang, CC Sine, EJ van Deursen… - Science, 2021 - science.org
INTRODUCTION Complex multicellular organisms are subject to a myriad of cellular
stresses, which can be managed through cell-intrinsic adaptation and repair mechanisms …

[HTML][HTML] A proteogenomic portrait of lung squamous cell carcinoma

S Satpathy, K Krug, PMJ Beltran, SR Savage, F Petralia… - Cell, 2021 - cell.com
Lung squamous cell carcinoma (LSCC) remains a leading cause of cancer death with few
therapeutic options. We characterized the proteogenomic landscape of LSCC, providing a …

Proteomics of SARS-CoV-2-infected host cells reveals therapy targets

D Bojkova, K Klann, B Koch, M Widera, D Krause… - Nature, 2020 - nature.com
A new coronavirus was recently discovered and named severe acute respiratory syndrome
coronavirus 2 (SARS-CoV-2). Infection with SARS-CoV-2 in humans causes coronavirus …