Network propagation: a universal amplifier of genetic associations

L Cowen, T Ideker, BJ Raphael, R Sharan - Nature Reviews Genetics, 2017 - nature.com
Biological networks are powerful resources for the discovery of genes and genetic modules
that drive disease. Fundamental to network analysis is the concept that genes underlying the …

Predicting protein–protein interactions from the molecular to the proteome level

O Keskin, N Tuncbag, A Gursoy - Chemical reviews, 2016 - ACS Publications
Identification of protein–protein interactions (PPIs) is at the center of molecular biology
considering the unquestionable role of proteins in cells. Combinatorial interactions result in …

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 …

Identification and rescue of α-synuclein toxicity in Parkinson patient–derived neurons

CY Chung, V Khurana, PK Auluck, DF Tardiff… - Science, 2013 - science.org
The induced pluripotent stem (iPS) cell field holds promise for in vitro disease modeling.
However, identifying innate cellular pathologies, particularly for age-related …

[HTML][HTML] Computational approaches in target identification and drug discovery

T Katsila, GA Spyroulias, GP Patrinos… - Computational and …, 2016 - Elsevier
In the big data era, voluminous datasets are routinely acquired, stored and analyzed with the
aim to inform biomedical discoveries and validate hypotheses. No doubt, data volume and …

The yeast deletion collection: a decade of functional genomics

G Giaever, C Nislow - Genetics, 2014 - academic.oup.com
The yeast deletion collections comprise> 21,000 mutant strains that carry precise start-to-
stop deletions of∼ 6000 open reading frames. This collection includes heterozygous and …

Studying and modelling dynamic biological processes using time-series gene expression data

Z Bar-Joseph, A Gitter, I Simon - Nature Reviews Genetics, 2012 - nature.com
Biological processes are often dynamic, thus researchers must monitor their activity at
multiple time points. The most abundant source of information regarding such dynamic …

Fundamentals of protein interaction network mapping

J Snider, M Kotlyar, P Saraon, Z Yao… - Molecular systems …, 2015 - embopress.org
Studying protein interaction networks of all proteins in an organism (“interactomes”) remains
one of the major challenges in modern biomedicine. Such information is crucial to …

TDP-43 is intrinsically aggregation-prone, and amyotrophic lateral sclerosis-linked mutations accelerate aggregation and increase toxicity

BS Johnson, D Snead, JJ Lee, JM McCaffery… - Journal of Biological …, 2009 - ASBMB
Non-amyloid, ubiquitinated cytoplasmic inclusions containing TDP-43 and its C-terminal
fragments are pathological hallmarks of amyotrophic lateral sclerosis (ALS), a fatal motor …

CRISPR–Cas9 screens in human cells and primary neurons identify modifiers of C9ORF72 dipeptide-repeat-protein toxicity

NJ Kramer, MS Haney, DW Morgens, A Jovičić… - Nature …, 2018 - nature.com
Hexanucleotide-repeat expansions in the C9ORF72 gene are the most common cause of
amyotrophic lateral sclerosis and frontotemporal dementia (c9ALS/FTD). The nucleotide …