Gene regulatory network inference resources: A practical overview

D Mercatelli, L Scalambra, L Triboli, F Ray… - Biochimica et Biophysica …, 2020 - Elsevier
Transcriptional regulation is a fundamental molecular mechanism involved in almost every
aspect of life, from homeostasis to development, from metabolism to behavior, from reaction …

Sex-dimorphic and age-dependent organization of 24-hour gene expression rhythms in humans

L Talamanca, C Gobet, F Naef - Science, 2023 - science.org
The circadian clock modulates human physiology. However, the organization of tissue-
specific gene expression rhythms and how these depend on age and sex is not defined in …

HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis

IV Kulakovskiy, IE Vorontsov, IS Yevshin… - Nucleic acids …, 2018 - academic.oup.com
We present a major update of the HOCOMOCO collection that consists of patterns
describing DNA binding specificities for human and mouse transcription factors. In this …

Glucocorticoids promote breast cancer metastasis

MMS Obradović, B Hamelin, N Manevski, JP Couto… - Nature, 2019 - nature.com
Diversity within or between tumours and metastases (known as intra-patient tumour
heterogeneity) that develops during disease progression is a serious hurdle for therapy …

Collagen density regulates the activity of tumor-infiltrating T cells

DE Kuczek, AMH Larsen, ML Thorseth… - … for immunotherapy of …, 2019 - Springer
Background Tumor progression is accompanied by dramatic remodeling of the surrounding
extracellular matrix leading to the formation of a tumor-specific ECM, which is often more …

The tumor microenvironment underlies acquired resistance to CSF-1R inhibition in gliomas

DF Quail, RL Bowman, L Akkari, ML Quick… - Science, 2016 - science.org
INTRODUCTION Therapies targeted against the tumor microenvironment (TME) represent a
promising approach for treating cancer. This appeal arises in part from the decreased …

Liver-fibrosis-activated transcriptional networks govern hepatocyte reprogramming and intra-hepatic communication

A Loft, AJ Alfaro, SF Schmidt, FB Pedersen… - Cell metabolism, 2021 - cell.com
Liver fibrosis is a strong predictor of long-term mortality in individuals with metabolic-
associated fatty liver disease; yet, the mechanisms underlying the progression from the …

[HTML][HTML] Dynamics in transcriptomics: advancements in RNA-seq time course and downstream analysis

D Spies, C Ciaudo - Computational and structural biotechnology journal, 2015 - Elsevier
Abstract Analysis of gene expression has contributed to a plethora of biological and medical
research studies. Microarrays have been intensively used for the profiling of gene …

Primate-specific transposable elements shape transcriptional networks during human development

J Pontis, C Pulver, CJ Playfoot, E Planet, D Grun… - Nature …, 2022 - nature.com
The human genome contains more than 4.5 million inserts derived from transposable
elements (TEs), the result of recurrent waves of invasion and internal propagation …

Deletion of SNX9 alleviates CD8 T cell exhaustion for effective cellular cancer immunotherapy

MP Trefny, N Kirchhammer, P Auf der Maur… - Nature …, 2023 - nature.com
Tumor-specific T cells are frequently exhausted by chronic antigenic stimulation. We here
report on a human antigen-specific ex vivo model to explore new therapeutic options for T …