Differentiable biology: using deep learning for biophysics-based and data-driven modeling of molecular mechanisms

M AlQuraishi, PK Sorger - Nature methods, 2021 - nature.com
Deep learning using neural networks relies on a class of machine-learnable models
constructed using 'differentiable programs'. These programs can combine mathematical …

Nuclear receptor crosstalk—defining the mechanisms for therapeutic innovation

K De Bosscher, SJ Desmet, D Clarisse… - Nature Reviews …, 2020 - nature.com
Nuclear receptor crosstalk can be defined as the interplay between different nuclear
receptors or between their overlapping signalling pathways. A subset of nuclear receptors …

Gelsolin: the tail of a molecular gymnast

S Nag, M Larsson, RC Robinson, LD Burtnick - Cytoskeleton, 2013 - Wiley Online Library
Gelsolin superfamily members are Ca2+‐dependent, multidomain regulators of the actin
cytoskeleton. Calcium binding activates gelsolin by inducing molecular gymnastics (large …

Protein-protein interaction networks: probing disease mechanisms using model systems

U Kuzmanov, A Emili - Genome medicine, 2013 - Springer
Protein-protein interactions (PPIs) and multi-protein complexes perform central roles in the
cellular systems of all living organisms. In humans, disruptions of the normal patterns of PPIs …

A protein interaction between β-catenin and Dnmt1 regulates wnt signaling and DNA methylation in colorectal cancer cells

J Song, Z Du, M Ravasz, B Dong, Z Wang… - Molecular Cancer …, 2015 - AACR
Aberrant activation of the Wnt signaling pathway is an important step in the initiation and
progression of tumor development in diverse cancers. The central effector of canonical Wnt …

The identification of novel protein-protein interactions in liver that affect glucagon receptor activity

J Han, M Zhang, S Froese, FF Dai, M Robitaille… - PloS one, 2015 - journals.plos.org
Glucagon regulates glucose homeostasis by controlling glycogenolysis and
gluconeogenesis in the liver. Exaggerated and dysregulated glucagon secretion can …

Applications of CRISPR-Cas technologies to proteomics

G Dolgalev, E Poverennaya - Genes, 2021 - mdpi.com
CRISPR-Cas-based genome editing is a revolutionary approach that has provided an
unprecedented investigational power for the life sciences. Rapid and efficient, CRISPR-Cas …

How do oncoprotein mutations rewire protein–protein interaction networks?

EH Bowler, Z Wang, RM Ewing - Expert review of proteomics, 2015 - Taylor & Francis
The acquisition of mutations that activate oncogenes or inactivate tumor suppressors is a
primary feature of most cancers. Mutations that directly alter protein sequence and structure …

Characterization of molecules binding to the 70K N-terminal region of fibronectin by IFAST purification coupled with mass spectrometry

SF Moussavi-Harami, DS Annis, W Ma… - Journal of proteome …, 2013 - ACS Publications
Fibronectin (Fn) is a large glycoprotein present in plasma and extracellular matrix and is
important for many processes. Within Fn the 70 kDa N-terminal region (70k-Fn) is involved in …

Studying epigenetic complexes and their inhibitors with the proteomics toolbox

D Weigt, C Hopf, G Médard - Clinical Epigenetics, 2016 - Springer
Some epigenetic modifier proteins have become validated clinical targets. With a few small
molecule inhibitors already approved by national health administrations and many more in …