Next-generation proteomics: towards an integrative view of proteome dynamics

AFM Altelaar, J Munoz, AJR Heck - Nature Reviews Genetics, 2013 - nature.com
Next-generation sequencing allows the analysis of genomes, including those representing
disease states. However, the causes of most disorders are multifactorial, and systems-level …

Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review

P Csermely, T Korcsmáros, HJM Kiss, G London… - Pharmacology & …, 2013 - Elsevier
Despite considerable progress in genome-and proteome-based high-throughput screening
methods and in rational drug design, the increase in approved drugs in the past decade did …

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 …

Evolution and functional cross‐talk of protein post‐translational modifications

P Beltrao, P Bork, NJ Krogan… - Molecular systems …, 2013 - embopress.org
Protein post‐translational modifications (PTM s) allow the cell to regulate protein activity and
play a crucial role in the response to changes in external conditions or internal states …

Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system

BC Collins, LC Gillet, G Rosenberger, HL Röst… - Nature …, 2013 - nature.com
Protein complexes and protein interaction networks are essential mediators of most
biological functions. Complexes supporting transient functions such as signal transduction …

Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition

JP Lambert, G Ivosev, AL Couzens, B Larsen… - Nature …, 2013 - nature.com
Characterizing changes in protein-protein interactions associated with sequence variants
(eg, disease-associated mutations or splice forms) or following exposure to drugs, growth …

Human diseases through the lens of network biology

LI Furlong - Trends in genetics, 2013 - cell.com
One of the challenges raised by next generation sequencing (NGS) is the identification of
clinically relevant mutations among all the genetic variation found in an individual. Network …

[HTML][HTML] DiffCorr: an R package to analyze and visualize differential correlations in biological networks

A Fukushima - Gene, 2013 - Elsevier
Large-scale “omics” data, such as microarrays, can be used to infer underlying cellular
regulatory networks in organisms, enabling us to better understand the molecular basis of …

[HTML][HTML] Genotype to phenotype via network analysis

H Carter, M Hofree, T Ideker - Current opinion in genetics & development, 2013 - Elsevier
A prime objective of genomic medicine is the identification of disease-causing mutations and
the mechanisms by which such events result in disease. As most disease phenotypes arise …

[HTML][HTML] Topology of molecular interaction networks

W Winterbach, PV Mieghem, M Reinders, H Wang… - BMC systems …, 2013 - Springer
Molecular interactions are often represented as network models which have become the
common language of many areas of biology. Graphs serve as convenient mathematical …