Principles of ChIP-seq Data Analysis Illustrated with Examples

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Telomeres are the nucleoprotein structures at chromosome ends. Telomeres are particularly sensitive to oxidative stress, which can induce telomere damage, shortening, and premature cellular senescence. How oxidative damage influences telomere structure has ...

Wastewater resulting from human activities must be treated to minimize the impact on the receiving ecosystems. One of such potential impacts in lakes and other water bodies is eutrophication, an excessive increase in their nitrogen and phosphorus content. ...

Chromatin-modifying enzymes target distinct residues within histones to finetune gene expression profiles. SIRT7 is an NAD+-dependent deacylase often deregulated in cancer, which deacetylates either H3 lysine 36 (H3K36) or H3K18 with high specificity withi ...

Circular RNAs (circRNAs) are covalently closed back‐splicing products involved in the regulation of different cellular processes, and their dysregulation has been frequently observed in cancer cells. CircCDYL, a circRNA derived from the back‐splicing of CD ...

The precise control of transcription factor (TF) concentrations is crucial for While TF concentration gradients are well-characterized in model organisms like Drosophila and Caenorhabditis elegans, their quantitative relationship with genomic occupancy in ...

Viral metagenomics is a useful tool for detecting multiple human viruses in urban sewage. However, more refined protocols are required for its effective use in disease surveillance. In this study, we investigated the performance of three different preampli ...

Since Strahl and Allis proposed the "language of covalent histone modifications", a host of experimental studies have shed light on the different facets of chromatin regulation by epigenetic mechanisms. Initially proposed as a concept for controlling gene ...

The control of eukaryotic gene expression is intimately connected to highly dynamic chromatin structures. Gene regulation relies on activator and repressor transcription factors (TFs) that induce local chromatin opening and closing. However, it is unclear ...

Genome-wide chromatin conformation capture assays provide formidable insights into the spatial organization of genomes. However, due to the complexity of the data structure, their integration in multi-omics workflows remains challenging. We present data st ...

Light-controlled transcriptional activation is a commonly used optogenetic strategy that allows researchers to regulate gene expression with high spatiotemporal precision. The vast majority of existing tools are, however, limited to light-triggered inducti ...

Dataset corresponding to the following manuscript: Slagter, A., Setyadji, J.A., Vogt, E.L. et al. Nanoindentation Hardness and Modulus of Al2O3–SiO2–CaO and MnO–SiO2–FeO Inclusions in Iron. Metall Mater Trans A (2024). https://doi.org/10.1007/s11661-024-0 ...

Recently, Pham et al. used an array of model systems to uncover a role for the enzyme methionine adenosyltransferase (MAT) -1A, which is mainly expressed in liver, in both sensing formaldehyde and regulating transcriptional responses that protect against i ...

Aerobic granular sludge (AGS) consists of a microbial consortium that has an important role in wastewater treatment. This study investigates AGS microorganisms cultivated in a laboratory-scale sequencing batch reactor. Metagenomic sequencing was conducted ...

We propose a comparative study of three different methods aimed at optimizing existing groundwater monitoring networks. Monitoring piezometric heads in subsurface porous formations is crucial at regional scales to properly characterize the relevant subsurf ...

This data set contains the data collected during the FNS project Green Piezo (Grant no. 179064) in association with the recent publication entitled “3D printing of customizable transient bioelectronics and sensors”. This work aims to study and demonstrate ...

Understanding the ecological impacts of viruses on natural and engineered ecosystems relies on the accurate identification of viral sequences from community sequencing data. To maximize viral recovery from metagenomes, researchers frequently combine viral ...

Cell fate progression of pluripotent progenitors is strictly regulated, resulting in high human cell diversity. Epigenetic modifications also orchestrate cell fate restriction. Unveiling the epigenetic mechanisms underlying human cell diversity has been di ...

This document contains all the data and the details of the analysis used in the manuscript titled " Control of Ge island coalescence for the formation of nanowires on silicon." https://doi.org/10.1039/D3NH00573A ...

This repository contains microphysics routines, scripts, and processed data from the Weather Research and Forecasting (WRF) model simulations presented in the paper "RaFSIP: Parameterizing ice multiplication in models using a machine learning approach", by ...

This paper presents a novel hybrid framework for generating and updating a synthetic population. We call it hybrid because it combines model-based and data-driven approaches. Existing generators produce a snapshot of synthetic data that becomes outdated ov ...

Principles of ChIP-seq Data Analysis Illustrated with Examples

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Oxidative stress at telomeres triggers internal DNA loops, TRF1 dissociation, and TRF2-dependent R-loops

Modelling the metabolism of the polyphosphate-accumulating organism Candidatus Accumulibacter

Structural basis of SIRT7 nucleosome engagement and substrate specificity

CircCDYL Association With hnRNPL Modulates CDYL Isoform Switching in Breast Cancer Cells

The Regulation of Transcription Factors Binding Site Occupancies by Their Concentrations

Comparison of Three Viral Nucleic Acid Preamplification Pipelines for Sewage Viral Metagenomics

Decoding Chromatin Ubiquitylation: A Chemical Biology Perspective

Individual transcription factors modulate both the micromovement of chromatin and its long-range structure

Orchestrating chromosome conformation capture analysis with Bioconductor

A modular toolbox for the optogenetic deactivation of transcription

Nanoindentation hardness and modulus of Al2O3-SiO2-CaO and MnO-SiO2-FeO inclusions in iron

Formaldehyde regulates one-carbon metabolism and epigenetics

Microbial genome collection of aerobic granular sludge cultivated in sequencing batch reactors using different carbon source mixtures

Data-driven statistical optimization of a groundwater monitoring network

Dataset for '3D printing of customizable transient bioelectronics and sensors'

Benchmarking informatics approaches for virus discovery: caution is needed when combining in silico identification methods

Single-cell epigenomic reconstruction of developmental trajectories from pluripotency in human neural organoid systems

Data set for control of Ge island coalescence for the formation of nanowires on silicon

Data and scripts for the RaFSIP scheme

Hybrid Simulator for Capturing Dynamics of Synthetic Populations