A5021716093- Genomics and Chromatin Dynamics
- Genomic variations and chromosomal abnormalities
- Genomics and Phylogenetic Studies
- Gene expression and cancer classification
- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- Chromosomal and Genetic Variations
- RNA modifications and cancer
- Epigenetics and DNA Methylation
- Neutrophil, Myeloperoxidase and Oxidative Mechanisms
- Immune Response and Inflammation
- Machine Learning in Bioinformatics
- Cancer-related molecular mechanisms research
- Trypanosoma species research and implications
- Genetics, Bioinformatics, and Biomedical Research
- Immune Cell Function and Interaction
- Bioinformatics and Genomic Networks
- Immune cells in cancer
- Autism Spectrum Disorder Research
- Genomics and Rare Diseases
- Obsessive-Compulsive Spectrum Disorders
Warsaw University of Technology
2021-2025
University of Warsaw
2021-2025
University of Copenhagen
2024
Abstract The dynamic three-dimensional (3D) organization of the human genome (the “4D Nucleome”) is closely linked to function. Here, we integrate a wide variety genomic data generated by 4D Nucleome Project provide detailed view 3D in widely used embryonic stem cells (H1-hESCs) and immortalized fibroblasts (HFFc6). We extensive benchmarking mapping assays these diverse datasets annotate spatial features across scales. reveal rich complexity chromatin domains their sub-nuclear positions,...
Abstract Chromosome Conformation Capture (3 C) methods, including Hi-C (a high-throughput variation of 3 C), detect pairwise interactions between DNA regions, enabling the reconstruction chromatin architecture in nucleus. HiChIP is a modification experiment that includes immunoprecipitation (ChIP) step, allowing genome-wide identification contacts mediated by protein interest. In mammalian cells, cohesin complex one major players establishment loops. We present an improved experimental...
Abstract Modeling 3D genome organisation has been booming in the last years thanks to availability of experimental datasets genomic contacts. However, field is currently missing standardisation methods and metrics compare predictions experiments. We present 3DGenBench, a web server available at https://inc-cost.eu/benchmarking/, that allows benchmarking computational models Genomics. The benchmark performed using manually curated dataset 39 capture Hi-C profiles wild type genome-edited mouse...
Prediction of chromatin interactions from DNA sequence has been a significant research challenge in the last couple years. Several solutions have proposed, most which are based on encoder-decoder architecture, where 1D is convoluted, encoded into latent representation, and then decoded using 2D convolutions Hi-C pairwise spatial proximity matrix. Those methods, while obtaining high correlation scores improved metrics, produce matrices that artificial - they blurred due to deep learning model...
Abstract Prediction of chromatin interactions from DNA sequence has been a significant research challenge in the last couple years. Several solutions have proposed, most which are based on encoder-decoder architecture, where 1D is convoluted, encoded into latent representation, and then decoded using 2D convolutions Hi-C pairwise spatial proximity matrix. Those methods, while obtaining high correlation scores improved metrics, produce matrices that artificial - they blurred due to deep...
The challenge of modelling the spatial conformation chromatin remains an open problem. While multiple data-driven approaches have been proposed, each has limitations. This work introduces two image-driven methods based on Molecular Dynamics Flexible Fitting (MDFF) approach: force method and correlational method. Both already used successfully in protein modelling. We propose a novel way to employ them for building models directly from 3D images. approach is termed Additionally, we introduce...
Abstract Summary The detection of the structural variants (SVs) using Illumina sequencing human DNA is not an easy task. Multiple approaches have been proposed; however, all methods their limitations. In this article, we present ConsensuSV pipeline that aids research in complex variant detection. By consensus meta-approach, eight independent SV callers are being used to identify a uniform set high-quality SVs. works raw data and performs necessary steps automatically, significantly reducing...
There have been multiple attempts to predict the expression of genes based on sequence, epigenetics, and various other factors. To improve those predictions, we decided investigate adding protein-specific 3D interactions that play a significant role in condensation chromatin structure cell nucleus. achieve this, used architecture one state-of-the-art algorithms, ExPecto, investigated changes model metrics upon spatially relevant data. We ChIA-PET are mediated by cohesin (24 lines), CTCF (4...
Emergency granulopoiesis is the enhanced and accelerated production of granulocytes that occurs during acute infection. The contribution hematopoietic stem cells (HSCs) to this process was reported; however, how HSCs participate in emergency remains elusive. Here, using a mouse model we observe transcriptional changes as early 4 h after lipopolysaccharide (LPS) administration. We HSC identity changed towards myeloid-biased show CD201 enriched lymphoid-biased HSCs. While expression under...
Background With the development of rapid and cheap sequencing techniques, cost whole‐genome (WGS) has dropped significantly. However, complexity human genome is not limited to pure sequence—and additional experiments are required learn genome’s influence on complex traits. One most exciting aspects for scientists nowadays spatial organisation genome, which can be discovered using ( e.g. , Hi‐C, ChIA‐PET). The information about contacts helps in analysis brings new insights into our...
The 2 m-long human DNA is tightly intertwined into the cell nucleus of size 10 μm. packing explained by folding chromatin fiber. This leads to formation such hierarchical structures as: chromosomal territories, compartments; densely-packed genomic regions known as Topologically Associating Domains (TADs), or Chromatin Contact (CCDs), and loops. We propose models dynamical genome components in lymphoblastoid, stem cell, fibroblast lines. Our are based on explosive percolation theory....
Abstract Chromosome Conformation Capture (3C) methods, including Hi-C (a high-throughput variation of 3C), detect pairwise interactions between DNA regions, enabling the reconstruction chromatin architecture in nucleus. HiChIP is a modification experiment, which includes immunoprecipitation step (ChIP), allowing genome-wide identification contacts mediated by protein interest. In mammalian cells, cohesin complex one major players establishment loops. We present an improved experimental...
Gilles de la Tourette syndrome (GTS) is a neurodevelopmental psychiatric disorder with complex and elusive etiology significant role of genetic factors. The aim this study was to identify structural variants that could be associated familial GTS. group comprised 17 multiplex families 80 patients. Structural were identified from whole-genome sequencing data followed by co-segregation bioinformatic analyses. localization these used select candidate genes create gene sets, which subsequently...
The improvements in sequencing technology make the development of new tools for detection structural variance more and common. However, available long-read Oxford Nanopore are limited, it is hard to choose one, which best. That why there a need create tool based on consensus that combines existing work order discover set high-quality, reliable variants can be used further downstream analysis. field has also been subject revolution machine learning techniques, especially deep learning. In...
Abstract The 2m-long human DNA is tightly intertwined into the cell nucleus of size 10μm. packing explained by folding chromatin fiber. This leads to formation such hierarchical structures as: chromosomal territories, compartments; densely packed genomic regions known as Chromatin Contact Domains (CCDs), and loops. We propose models dynamical genome components in lymphoblastoid, stem cell, fibroblast lines. Our are based on explosive percolation theory. chromosomes modeled graphs where CTCF...
There have been multiple attempts to predict the expression of genes based on sequence, epigenetics, and various other factors. To improve those predictions, we decided investigate adding protein-specific 3D interactions that play a major role in compensation chromatin structure cell nucleus. achieve this, used architecture one state-of-the-art algorithms, ExPecto (J. Zhou et al., 2018), investigated changes model metrics upon spatially relevant data. We ChIA-PET are mediated by cohesin (24...