Machine learning for integrating data in biology and medicine: Principles, practice, and opportunities

M Zitnik, F Nguyen, B Wang, J Leskovec… - Information …, 2019 - Elsevier
New technologies have enabled the investigation of biology and human health at an
unprecedented scale and in multiple dimensions. These dimensions include a myriad of …

Transcriptional regulation by Polycomb group proteins

L Di Croce, K Helin - Nature structural & molecular biology, 2013 - nature.com
Polycomb group (PcG) proteins are epigenetic regulators of transcription that have key roles
in stem-cell identity, differentiation and disease. Mechanistically, they function within …

Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks

DR Kelley, J Snoek, JL Rinn - Genome research, 2016 - genome.cshlp.org
The complex language of eukaryotic gene expression remains incompletely understood.
Despite the importance suggested by many noncoding variants statistically associated with …

hnRNPK recruits PCGF3/5-PRC1 to the **st RNA B-repeat to establish polycomb-mediated chromosomal silencing

G Pintacuda, G Wei, C Roustan, BA Kirmizitas… - Molecular cell, 2017 - cell.com
The Polycomb-repressive complexes PRC1 and PRC2 play a key role in chromosome
silencing induced by the non-coding RNA **st. Polycomb recruitment is initiated by the …

Competition between DNA methylation and transcription factors determines binding of NRF1

S Domcke, AF Bardet, P Adrian Ginno, D Hartl… - Nature, 2015 - nature.com
Eukaryotic transcription factors (TFs) are key determinants of gene activity, yet they bind only
a fraction of their corresponding DNA sequence motifs in any given cell type. Chromatin has …

Variant PRC1 complex-dependent H2A ubiquitylation drives PRC2 recruitment and polycomb domain formation

NP Blackledge, AM Farcas, T Kondo, HW King… - Cell, 2014 - cell.com
Chromatin modifying activities inherent to polycomb repressive complexes PRC1 and PRC2
play an essential role in gene regulation, cellular differentiation, and development. However …

A double take on bivalent promoters

P Voigt, WW Tee, D Reinberg - Genes & development, 2013 - genesdev.cshlp.org
Histone modifications and chromatin-associated protein complexes are crucially involved in
the control of gene expression, supervising cell fate decisions and differentiation. Many …

Mammalian SWI/SNF continuously restores local accessibility to chromatin

M Iurlaro, MB Stadler, F Masoni, Z Jagani, GG Galli… - Nature …, 2021 - nature.com
Chromatin accessibility is a hallmark of regulatory regions, entails transcription factor (TF)
binding and requires nucleosomal reorganization. However, it remains unclear how …

CellNet: network biology applied to stem cell engineering

P Cahan, H Li, SA Morris, EL Da Rocha, GQ Daley… - Cell, 2014 - cell.com
Somatic cell reprogramming, directed differentiation of pluripotent stem cells, and direct
conversions between differentiated cell lineages represent powerful approaches to engineer …

Targeting Polycomb systems to regulate gene expression: modifications to a complex story

NP Blackledge, NR Rose, RJ Klose - Nature reviews Molecular cell …, 2015 - nature.com
Polycomb group proteins are transcriptional repressors that are essential for normal gene
regulation during development. Recent studies suggest that Polycomb repressive …