A5021859801- Genomics and Chromatin Dynamics
- Genomics and Phylogenetic Studies
- Epigenetics and DNA Methylation
- RNA and protein synthesis mechanisms
- Single-cell and spatial transcriptomics
- Gene expression and cancer classification
- RNA Research and Splicing
- Molecular Biology Techniques and Applications
- Biomedical Text Mining and Ontologies
- Genetics, Bioinformatics, and Biomedical Research
- Cell Image Analysis Techniques
- Embedded Systems Design Techniques
- Chromosomal and Genetic Variations
- VLSI and FPGA Design Techniques
- Amphibian and Reptile Biology
- Turtle Biology and Conservation
- Species Distribution and Climate Change
- Scientific Computing and Data Management
- RNA regulation and disease
- Spider Taxonomy and Behavior Studies
- Computational Physics and Python Applications
- DNA and Nucleic Acid Chemistry
- Low-power high-performance VLSI design
- Cancer Genomics and Diagnostics
- Optimism, Hope, and Well-being
Utrecht University
2024
Hubrecht Institute for Developmental Biology and Stem Cell Research
2020-2024
Royal Netherlands Academy of Arts and Sciences
2022-2024
Oncode Institute
2022-2024
University Medical Center Utrecht
2024
Manipal University Jaipur
2024
Netaji Subhas University of Technology
2023
Max Planck Institute of Immunobiology and Epigenetics
2015-2021
Intel (United Kingdom)
2021
Intel (Malaysia)
2021
We present an update to our Galaxy-based web server for processing and visualizing deeply sequenced data. Its core tool set, deepTools, allows users perform complete bioinformatic workflows ranging from quality controls normalizations of aligned reads integrative analyses, including clustering visualization approaches. Since we first described deepTools Galaxy in 2014, have implemented new solutions many requests the community users. Here, introduce significant enhancements tools further...
Despite an abundance of new studies about topologically associating domains (TADs), the role genetic information in TAD formation is still not fully understood. Here we use our software, HiCExplorer (hicexplorer.readthedocs.io) to annotate >2800 high-resolution (570 bp) boundaries Drosophila melanogaster. We identify eight DNA motifs enriched at boundaries, including a motif bound by M1BP protein, and two boundary motifs. In contrast mammals, CTCF only on small fraction flanking inactive...
Abstract Motivation Generating publication ready plots to display multiple genomic tracks can pose a serious challenge. Making desirable and accurate figures requires considerable effort. This is usually done by hand or using vector graphic software. Results pyGenomeTracks (PGT) modular plotting tool that easily combines tracks. It enables reproducible standardized generation of highly customizable images. Availability implementation PGT available through graphical interface on...
Galaxy HiCExplorer is a web server that facilitates the study of 3D conformation chromatin by allowing Hi-C data processing, analysis and visualization. With server, users with little bioinformatic background can perform every step in one workflow: mapping raw sequence data, creation contact matrices, quality assessment, correction matrices identification topological associated domains (TADs) A/B compartments. Users create publication ready plots matrix, compartments, TADs on selected...
The primary problem with the explosion of biomedical datasets is not data, computational resources, and required storage space, but general lack trained skilled researchers to manipulate analyze these data. Eliminating this requires development comprehensive educational resources. Here we present a community-driven framework that enables modern, interactive teaching data analytics in life sciences facilitates training materials. key feature our system it static continuously improved...
Due to the rapidly increasing scale and diversity of epigenomic data, modular scalable analysis workflows are wide interest. Here we present snakePipes, a workflow package for processing downstream data from common assays: ChIP-seq, RNA-seq, Bisulfite-seq, ATAC-seq, Hi-C single-cell RNA-seq. snakePipes enables users assemble variants each easily install upgrade underlying tools, via its simple command-line wrappers yaml files.snakePipes can be installed conda: `conda -c mpi-ie bioconda...
Scientists routinely use images to display data. Readers often examine figures first; therefore, it is important that are accessible a broad audience. Many resources discuss fraudulent image manipulation and technical specifications for acquisition; however, data on the legibility interpretability of scarce. We systematically examined these factors in non-blot published top 15 journals 3 fields; plant sciences, cell biology, physiology ( n = 580 papers). Common problems included missing...
Abstract Post-translational histone modifications modulate chromatin activity to affect gene expression. How states underlie lineage choice in single cells is relatively unexplored. We develop sort-assisted single-cell immunocleavage (sortChIC) and map active (H3K4me1 H3K4me3) repressive (H3K27me3 H3K9me3) the mouse bone marrow. During differentiation, hematopoietic stem progenitor (HSPCs) acquire mediated by cell-type-specifying transcription factors, which are unique for each lineage. By...
MOF (MYST1, KAT8) is the major H4K16 lysine acetyltransferase (KAT) in Drosophila and mammals essential for embryonic development. However, little known regarding role of specific cell lineages. Here we analyze differential proliferating terminally differentiated tissues at steady state under stress conditions. In cells, directly binds maintains expression genes required cycle progression. contrast, dispensable differentiated, postmitotic glomerular podocytes physiological response to...
Aggregating low numbers of mouse embryonic stem cells (mESCs) and inducing Wnt signalling generates ‘gastruloids’, self-organising complex structures that display an anteroposterior organisation cell types derived from all three germ layers. Current gastruloid protocols considerable heterogeneity between experiments in terms morphology, elongation efficiency, type composition. We therefore investigated whether altering the mESC pluripotency state would provide more consistent results. By...
Abstract Eukaryotic chromatin is partitioned into domains called TADs that are broadly conserved between species and virtually identical among cell types within the same species. Previous studies in mammals have shown DNA binding protein CTCF cohesin contribute to a fraction of TAD boundaries. Apart from this, molecular mechanisms governing this partitioning remain poorly understood. Using our new software, HiCExplorer, we annotated high-resolution (570 bp) boundaries flies identified eight...
Abstract Primate-specific Alus harbor different regulatory features, including miRNA targets. In this study, we provide evidence for miRNA-mediated modulation of transcript isoform levels during heat-shock response through exaptation Alu-miRNA sites in mature mRNA. We performed genome-wide expression profiling coupled with functional validation target within exonized Alus, and analyzed conservation these targets across primates. observed that two miRNAs (miR-15a-3p miR-302d-3p) elevated...
By aggregating low numbers of mouse embryonic stem cells (mESCs) followed by exposure to Wnt activation, structures termed gastruloids are produced that display an anteroposterior organisation cell types derived from all three germ layers. Since current gastruloid protocols considerable heterogeneity between experiments in terms morphology, elongation efficiency, and type composition, we investigated whether optimised mESC pluripotency state would provide more consistent results. growing...
Extensive scientific investigation is necessary because every government wants to construct smart cities. This why examining how researchers approach this area of study critical. investigates global research trends in cities and the Internet Things (IoT) by analyzing 14,309 articles from Scopus database (2010–2024). Using text mining latent semantic analysis (LSA) via KNIME tool, identifies key areas city development. The k-means clustering algorithm predicts future directions, highlighting...
Abstract The position, shape and number of transcription start sites (TSS) are critical determinants gene regulation. Most methods developed to detect TSSs study promoter usage are, however, limited use in studies that demand quantification expression changes between two or more groups. In this study, we combine high-resolution detection differential analysis using a simplified TSS protocol, MAPCap (Multiplexed Affinity Purification Capped RNA) along with the software icetea . Applying on...
Abstract The primary problem with the explosion of biomedical datasets is not data itself, computational resources, and required storage space, but general lack trained skilled researchers to manipulate analyze these data. Eliminating this requires development comprehensive educational resources. Here we present a community-driven framework that enables modern, interactive teaching analytics in life sciences facilitates training materials. key feature our system it static continuously...
Abstract Epigenetic mechanisms, such as histone modifications, are key regulators of transcription and maintenance cell identity. While our knowledge concerning type-specific modifications has constantly increased, we still know little about the interplay between epigenetics at level individual cell. To gain an understanding this process, developed T-ChIC (Transcriptome + Chromatin ImmunoCleavage), a method allowing for detection full-length transcripts in same single We applied technique to...
Nucleosomal organization at gene promoters is critical for transcription, with a nucleosome-depleted region (NDR) transcription start sites (TSSs) being required initiation. How NDRs and the precise positioning of +1 nucleosomes are maintained on active genes remains unclear. Here, we report that Drosophila nonspecific lethal (NSL) complex necessary to maintain this stereotypical nucleosomal promoters. Upon NSL1 depletion, invade TSSs NSL-bound genes. NSL member NSL3 binds TATA-less in...
We describe here the draft genome sequence of Sporosarcina pasteurii, a urease-producing bacterium with potential applications in biocement production.
A large repertoire of gene-centric data has been generated in the field zebrafish biology. Although bulk these are available public domain, most them not readily accessible or nonstandard formats. One major challenge is to unify and integrate widely scattered sources. We tested hypothesis that active community participation could be a viable option address this challenge. present here our approach create standards for assimilation sharing information system open database intercommunication....
Long-term perturbation of de novo chromatin assembly during DNA replication has profound effects on epigenome maintenance and cell fate. The early mechanistic origin these defects is unknown. Here, we combine acute degradation Chromatin Assembly Factor 1 (CAF-1), a key player in assembly, with single-cell genomics, quantitative proteomics, live-microscopy to uncover initiating mechanisms human cells. CAF-1 loss immediately slows down speed renders nascent hyper-accessible. A rapid cellular...
Abstract Emerging single-cell sequencing protocols allow researchers to study multiple layers of epigenetic regulation while resolving tissue heterogeneity. However, despite the rising popularity such epigenomics assays, lack easy-to-use computational tools that flexible quality control and data exploration hinders their broad adoption. We introduce Single-Cell Informatics ( sincei ) toolkit. provides an easy-to-use, command-line interface for from a wide range (epi)genomics directly aligned...