Michiel de Hoon
A5037842288- Cancer-related molecular mechanisms research
- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Genomics and Chromatin Dynamics
- Particle accelerators and beam dynamics
- Magnetic confinement fusion research
- Genomics and Phylogenetic Studies
- Advanced biosensing and bioanalysis techniques
- MicroRNA in disease regulation
- Gene expression and cancer classification
- Genetics, Bioinformatics, and Biomedical Research
- Molecular Biology Techniques and Applications
- Bioinformatics and Genomic Networks
- Bacterial Genetics and Biotechnology
- Laser-Plasma Interactions and Diagnostics
- Particle Accelerators and Free-Electron Lasers
- RNA Interference and Gene Delivery
- DNA and Nucleic Acid Chemistry
- Gene Regulatory Network Analysis
- Kruppel-like factors research
- CRISPR and Genetic Engineering
- Epigenetics and DNA Methylation
- Circular RNAs in diseases
- Protein Degradation and Inhibitors
RIKEN Center for Integrative Medical Sciences
2016-2025
CLS Technology (Norway)
2015-2017
Genomic Health (United States)
2017
CE Technologies (United Kingdom)
2015
Columbia University
2007-2010
Roslin Institute
2009
University of Edinburgh
2009
The University of Queensland
2009
University of Algarve
2009
Liverpool School of Tropical Medicine
2009
Abstract Summary: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for wide range bioinformatics problems. includes modules reading and writing different sequence file formats multiple alignments, dealing with 3D macro molecular structures, interacting common tools such as BLAST, ClustalW EMBOSS, accessing key online databases, well numerical methods statistical learning. Availability: freely available,...
Abstract Summary: We have implemented k-means clustering, hierarchical clustering and self-organizing maps in a single multipurpose open-source library of C routines, callable from other C++ programs. Using this library, we created an improved version Michael Eisen's well-known Cluster program for Windows, Mac OS X Linux/Unix. In addition, generated Python Perl interface to the Clustering Library, thereby combining flexibility scripting language with speed C. Availability: The Library...
Abstract The FANTOM5 project investigates transcription initiation activities in more than 1,000 human and mouse primary cells, cell lines tissues using CAGE. Based on manual curation of sample information development an ontology for classification, we assemble the resulting data into a centralized resource ( http://fantom.gsc.riken.jp/5/ ). This contains web-based tools data-access points research community to search extract related samples, genes, promoter activities, factors enhancers...
Although it is generally accepted that cellular differentiation requires changes to transcriptional networks, dynamic regulation of promoters and enhancers at specific sets genes has not been previously studied en masse. Exploiting the fact active are transcribed, we simultaneously measured their activity in 19 human 14 mouse time courses covering a wide range cell types biological stimuli. Enhancer RNAs, then messenger RNAs encoding transcription factors, dominated earliest responses....
DBTBS, first released in 1999, is a reference database on transcriptional regulation Bacillus subtilis, summarizing the experimentally characterized transcription factors, their recognition sequences and genes they regulate.Since previous release, original content was extended by addition of data contained 569 new publications, total which now reaches 947.The number B. subtilis promoters annotated more than doubled to 1475.In addition, 463 validated operons terminators have been...
Animal microRNA sequences are subject to 3′ nucleotide addition. Through detailed analysis of deep-sequenced short RNA data sets, we show adenylation and uridylation miRNA is globally present conserved across Drosophila vertebrates. To better understand function, after knockdown nucleotidyltransferase enzymes. The PAPD4 adenylates a wide range loci, but does not appear affect stability on genome-wide scale. Adenine addition appears reduce effectiveness targeting mRNA transcripts while...
While several studies have focused on the relationship between individual miRNA loci or classes of small RNA with human Argonaute (AGO) proteins, a comprehensive, global analysis content associating different AGO proteins has yet to be performed. We compared deep sequenced extracted from immunoprecipitation experiments AGO1, AGO2, and AGO3 proteins. Consistent previous observations, sequence tags derived globally associate in approximately equivalent amounts AGO3. Exceptions include miR-182,...
The FANTOM web resource (http://fantom.gsc.riken.jp/) was developed to provide easy access the data produced by project. It contains most complete and comprehensive sets of actively transcribed enhancers promoters in human mouse genomes. We determined transcription activities these regulatory elements CAGE (Cap Analysis Gene Expression) for both steady dynamic cellular states all major some rare cell types, consecutive stages differentiation responses stimuli. have expanded employing...
In prokaryotes, genes belonging to the same operon are transcribed in a single mRNA molecule. Transcription starts as RNA polymerase binds promoter and continues until it reaches transcriptional terminator. Some terminators rely on presence of Rho protein, whereas others function independently Rho. Such Rho-independent consist an inverted repeat followed by stretch thymine residues, allowing us predict their directly from DNA sequence. Unlike Escherichia coli, protein is dispensable Bacillus...
Next-generation sequencing experiments have shown that microRNAs (miRNAs) are expressed in many different isoforms (isomiRs), whose biological relevance is often unclear. We found mature miR-21, the most widely researched miRNA because of its importance human disease, produced two prevalent isomiR forms differ by 1 nt at their 3' end, and moreover end miR-21 posttranscriptionally adenylated noncanonical poly(A) polymerase PAPD5. PAPD5 knockdown caused an increase expression level, suggesting...
MicroRNAs (miRNAs) are short (20–23 nt) RNAs that sequence-specific mediators of transcriptional and post-transcriptional regulation gene expression. Modern high-throughput technologies enable deep sequencing such RNA species on an unprecedented scale. We find the analysis small deep-sequencing libraries can be affected by cross-mapping, in which sequences originating from one locus inadvertently mapped to another. Similar cross-hybridization microarrays, cross-mapping is prevalent among...
Abstract Mammalian genomes encode tens of thousands noncoding RNAs. Most transcripts exhibit nuclear localization and several have been shown to play a role in the regulation gene expression chromatin remodeling. To investigate function such RNAs, methods massively map genomic interacting sites multiple developed; however, these some limitations. Here, we introduce RNA And DNA Interacting Complexes Ligated sequenced (RADICL-seq), technology that maps genome-wide RNA–chromatin interactions...
Naturally occurring regulatory T (Treg) cells, which specifically express the transcription factor forkhead box P3 (Foxp3), are engaged in maintenance of immunological self-tolerance and homeostasis. By transcriptional start site cluster analysis, we assessed here how genome-wide patterns DNA methylation or Foxp3 binding sites were associated with Treg-specific gene expression. We found that hypomethylated regions closely Treg up-regulated clusters, whereas had no significant correlation...
The FANTOM5 consortium utilised cap analysis of gene expression (CAGE) to provide an unprecedented insight into transcriptional regulation in human cells and tissues. In the current study, we have used CAGE-based profiling on extended dense time course response monocyte-derived macrophages grown macrophage colony-stimulating factor (CSF1) bacterial lipopolysaccharide (LPS). We propose that this system provides a model for differentiation adaptation monocytes entering intestinal lamina...
Big leaps in science happen when scientists from different backgrounds interact. In the past 15 years, FANTOM Consortium has brought together fields to analyze and interpret genomic data produced with novel technologies, including mouse full-length cDNAs and, more recently, expression profiling at single-nucleotide resolution by cap-analysis gene expression. The provided most comprehensive cDNA collection for functional studies extensive maps of human transcriptome comprising promoters,...