Publications related to Non-coding variants impact cis-regulatory coordination in a cell type-specific manner

Related publications (12)

ChromatinHD connects single-cell DNA accessibility and conformation to gene expression through scale-adaptive machine learning

Bart Deplancke, Olga Pushkarev, Wouter Jozef L Saelens

Gene regulation is inherently multiscale, but scale-adaptive machine learning methods that fully exploit this property in single-nucleus accessibility data are still lacking. Here, we develop ChromatinHD, a pair of scale-adaptive models that uses the raw a ...

Nature Research2025

Specific Stimulation and Multiplex Secretion Analysis of T Cells Using a Suspendable Hydrogel Platform Enables Immunophenotyping at the Single-Cell Scale

Théo Nass

The ability to characterize and separate cells based on their surface marker expression profiles using flow cytometry revolutionized our understanding of the immune system at the level of single cells. However, the use of surface protein quantification to ...

American Chemical Society (ACS)2025

The Fip 1.0 Data Set: Highly Resolved Annotated Image Time Series of 4,000 Wheat Plots Grown in 6 Years

Xiaoran Chen

Background Understanding genotype-environment interactions of plants is crucial for crop improvement, yet limited by the scarcity of quality phenotyping data. This Data Note presents the Field Phenotyping Platform 1.0 data set, a comprehensive resource for ...

OXFORD UNIV PRESS2025

The role of the NF-kappaB pathway in Amyotrophic lateral sclerosis pathogenesis

Emma Charlotta Källstig

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative motor disorder, which results in death within a few years of diagnosis. While the cause of most cases of ALS is unknown, 10% of cases are familial (fALS), and associated with mutations in one of ov ...

EPFL2023

Genetic features and genomic targets of human KRAB-zinc finger proteins

Didier Trono, Priscilla Turelli, Julien Léonard Duc, Sandra Eloise Kjeldsen, Jonas Caspar De Tribolet-Hardy, Jacques Fellay, Michaël Imbeault, Alexandre Coudray, Cyril David Son-Tuyên Pulver, Evaristo Jose Planet Letschert, Christian Axel Wandall Thorball, Romain Forey

Krüppel-associated box (KRAB) domain-containing zinc finger proteins (KZFPs) are one of the largest groups of transcription factors encoded by tetrapods, with 378 members in human alone. KZFP genes are often grouped in clusters reflecting amplification by ...

2023

Sphingolipids accumulate in aged muscle, and their reduction counteracts sarcopenia

Johan Auwerx, Maroun Bou Sleiman, Peiling Luan, Davide D'Amico, Pirkka-Pekka Untamo Laurila, Martin Rainer Wohlwend, Sébastien Robert Victor Herzig, Tanes Imamura de Lima, Qi Wang

Age-related muscle dysfunction and sarcopenia are major causes of physical incapacitation in older adults and currently lack viable treatment strategies. Here we find that sphingolipids accumulate in mouse skeletal muscle upon aging and that both genetic a ...

2022

LncRNA Ctcflos orchestrates transcription and alternative splicing in thermogenic adipogenesis

Bart Deplancke, Petra Catalina Schwalie

The recruitment of thermogenic brite adipocytes within white adipose tissue attenuates obesity and metabolic comorbidities, arousing interest in understanding the underlying regulatory mechanisms. The molecular network of brite adipogenesis, however, remai ...

WILEY2021

Targeted protein degradation through cytosolic delivery of monobody binders using bacterial toxins

Oliver Hantschel, Nadine Eliane Schmit, Katyayanee Neopane

Monobodies are small engineered binding proteins that, upon expression in cells, can inhibit signaling of cytosolic oncoproteins with outstanding selectivity. Efficacy may be further increased by inducing degradation of monobody targets through fusion to t ...

2019

The effects of mitochondrial- and histone stress on the C. elegans transcriptome

Johan Auwerx, Maroun Bou Sleiman, Olli Juhani Matilainen, Pedro Moral Quiros

The aim of this study was to explore whether mitochondrial- and histone stress cause any common changes in global gene expression. For this experiment, we performed RNA sequencing from control RNAi, cco-1 RNAi (mitochondrial stress) and his-3 RNAi (histone ...

EPFL Infoscience2017

The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data

Philipp Bucher, Giovanna Ambrosini, René Dreos

ChIP-seq and related high-throughput chromatin profilig assays generate ever increasing volumes of highly valuable biological data. To make sense out of it, biologists need versatile, efficient and user-friendly tools for access, visualization and itegrati ...

2016

Assessing Recent Selection and Functionality at Long Noncoding RNA Loci in the Mouse Genome

Anamaria Necsulea

Long noncoding RNAs (lncRNAs) are one of the most intensively studied groups of noncoding elements. Debate continues over what proportion of lncRNAs are functional or merely represent transcriptional noise. Although characterization of individual lncRNAs h ...

Oxford Univ Press2015

An integrative genomics approach toward deciphering the regulatory logic of phase-specific circadian transcription in the mouse liver

Irina Krier

EPFL2014