Genome interpretation using in silico predictors of variant impact

P Katsonis, K Wilhelm, A Williams, O Lichtarge - Human genetics, 2022 - Springer
Estimating the effects of variants found in disease driver genes opens the door to
personalized therapeutic opportunities. Clinical associations and laboratory experiments …

Cancer stem cell regulated phenotypic plasticity protects metastasized cancer cells from ferroptosis

M Wu, X Zhang, W Zhang, YS Chiou, W Qian… - Nature …, 2022 - nature.com
Cancer cells display phenotypic equilibrium between the stem-like and differentiated states
during neoplastic homeostasis. The functional and mechanistic implications of this …

[HTML][HTML] A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA

M Cesana, D Cacchiarelli, I Legnini, T Santini… - Cell, 2011 - cell.com
Recently, a new regulatory circuitry has been identified in which RNAs can crosstalk with
each other by competing for shared microRNAs. Such competing endogenous RNAs …

Computational identification of transcriptional regulatory elements in DNA sequence

D GuhaThakurta - Nucleic acids research, 2006 - academic.oup.com
Identification and annotation of all the functional elements in the genome, including genes
and the regulatory sequences, is a fundamental challenge in genomics and computational …

On the immortality of television sets:“function” in the human genome according to the evolution-free gospel of ENCODE

D Graur, Y Zheng, N Price, RBR Azevedo… - Genome biology and …, 2013 - academic.oup.com
A recent slew of ENCyclopedia Of DNA Elements (ENCODE) Consortium publications,
specifically the article signed by all Consortium members, put forward the idea that more …

Atheroprotective communication between endothelial cells and smooth muscle cells through miRNAs

E Hergenreider, S Heydt, K Tréguer, T Boettger… - Nature cell …, 2012 - nature.com
The shear-responsive transcription factor Krüppel-like factor 2 (KLF2) is a critical regulator of
endothelial gene expression patterns induced by atheroprotective flow. As microRNAs …

LincRNA-Gm4419 knockdown ameliorates NF-κB/NLRP3 inflammasome-mediated inflammation in diabetic nephropathy

H Yi, R Peng, L Zhang, Y Sun, H Peng, H Liu, L Yu… - Cell death & …, 2017 - nature.com
Diabetic nephropathy (DN) as the primary cause of end-stage kidney disease is a common
complication of diabetes. Recent researches have shown the activation of nuclear factor …

MatInspector and beyond: promoter analysis based on transcription factor binding sites

K Cartharius, K Frech, K Grote, B Klocke… - …, 2005 - academic.oup.com
Motivation: Promoter analysis is an essential step on the way to identify regulatory networks.
A prerequisite for successful promoter analysis is the prediction of potential transcription …

NALP1 in Vitiligo-Associated Multiple Autoimmune Disease

Y Jin, CM Mailloux, K Gowan, SL Riccardi… - … England Journal of …, 2007 - Mass Medical Soc
Background Autoimmune and autoinflammatory diseases involve interactions between
genetic risk factors and environmental triggers. We searched for a gene on chromosome …

NF-κB–YY1–miR-29 regulatory circuitry in skeletal myogenesis and rhabdomyosarcoma

H Wang, R Garzon, H Sun, KJ Ladner, R Singh… - Cancer cell, 2008 - cell.com
Studies support the importance of microRNAs in physiological and pathological processes.
Here we describe the regulation and function of miR-29 in myogenesis and …