A5046982519- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Genomics and Chromatin Dynamics
- RNA modifications and cancer
- Chromosomal and Genetic Variations
- Gene expression and cancer classification
- Genomic variations and chromosomal abnormalities
- Cell Image Analysis Techniques
- RNA Research and Splicing
- Single-cell and spatial transcriptomics
- Click Chemistry and Applications
- Computational Drug Discovery Methods
- Bioinformatics and Genomic Networks
- Protein Degradation and Inhibitors
- Data Visualization and Analytics
- Heat Transfer and Optimization
- Genetic Mapping and Diversity in Plants and Animals
- Advanced Image and Video Retrieval Techniques
- Data Analysis with R
- Computer Graphics and Visualization Techniques
- Spacecraft and Cryogenic Technologies
- Infections and bacterial resistance
- Algorithms and Data Compression
- Microbial Applications in Construction Materials
- Biotechnology and Related Fields
University of Vienna
2015-2023
Harvard University
2017-2022
Boston Public Library
2018
University of Copenhagen
2013-2014
Since its initial release in 2000, the human reference genome has covered only euchromatic fraction of genome, leaving important heterochromatic regions unfinished. Addressing remaining 8% Telomere-to-Telomere (T2T) Consortium presents a complete 3.055 billion–base pair sequence T2T-CHM13, that includes gapless assemblies for all chromosomes except Y, corrects errors prior references, and introduces nearly 200 million base pairs containing 1956 gene predictions, 99 which are predicted to be...
We present HiGlass, an open source visualization tool built on web technologies that provides a rich interface for rapid, multiplex, and multiscale navigation of 2D genomic maps alongside 1D tracks, allowing users to combine various data types, synchronize multiple modalities, share fully customizable views with others. demonstrate its utility in exploring different experimental conditions, comparing the results analyses, creating interactive snapshots collaborators broader public. HiGlass...
Abstract Motivation: The secondary structure of RNA is integral to the variety functions it carries out in cell and its depiction allows researchers develop hypotheses about which nucleotides base pairs are functionally relevant. Current approaches visualizing provide an adequate platform for conversion static text-based representations 2D images, but limited their offer interactivity as well ability display larger structures, multiple structures pseudoknotted structures. Results: In this...
Existing human genome assemblies have almost entirely excluded repetitive sequences within and near centromeres, limiting our understanding of their organization, evolution, functions, which include facilitating proper chromosome segregation. Now, a complete, telomere-to-telomere assembly (T2T-CHM13) has enabled us to comprehensively characterize pericentromeric centromeric repeats, constitute 6.2% the (189.9 megabases). Detailed maps these regions revealed multimegabase structural...
Abstract In 2001, Celera Genomics and the International Human Genome Sequencing Consortium published their initial drafts of human genome, which revolutionized field genomics. While these updates that followed effectively covered euchromatic fraction heterochromatin many other complex regions were left unfinished or erroneous. Addressing this remaining 8% Telomere-to-Telomere (T2T) has finished first truly complete 3.055 billion base pair (bp) sequence a representing largest improvement to...
Abstract Summary The visualization and analysis of genomic repeats is typically accomplished using dot plots; however, the emergence telomere-to-telomere assemblies with multi-megabase requires new strategies. Here, we introduce StainedGlass, which can generate publication-quality figures interactive visualizations that depict identity orientation tandem repeat structures at a genome-wide scale. tool rapidly reveal higher-order improve inference evolutionary history for some most complex...
Abstract The 4D Nucleome (4DN) Network aims to elucidate the complex structure and organization of chromosomes in nucleus impact their disruption disease biology. We present 4DN Data Portal ( https://data.4dnucleome.org/ ), a repository for datasets generated network relevant external datasets. Datasets were with wide range experiments, including chromosome conformation capture assays such as Hi-C other innovative sequencing microscopy-based probing architecture. All together, data portal...
Intermolecular interactions of ncRNAs are at the core gene regulation events, and identifying full map these bears crucial importance for ncRNA functional studies. It is known that RNA-RNA built up by complementary base pairings between interacting RNAs high level complementarity two RNA sequences a powerful predictor such interactions. Here, we present RIsearch2, large-scale interaction prediction tool enables quick localization potential near-complementary given query target sequences. In...
The three-dimensional conformation of a genome can be profiled using Hi-C, technique that combines chromatin capture with high-throughput sequencing. However, structural variations often yield features mistaken for chromosomal interactions. Here, we describe computational method HiNT (Hi-C copy Number variation and Translocation detection), which detects number interchromosomal translocations within Hi-C data breakpoints at single base-pair resolution. We demonstrate outperforms existing...
Achromobacter xylosoxidans is an environmental opportunistic pathogen, which infects increasing number of immunocompromised patients. In this study we combined genomic analysis a clinical isolated A. strain with phenotypic investigations its important pathogenic features. We present complete assembly the genome NH44784-1996, isolate from cystic fibrosis patient obtained in 1996. The NH44784-1996 contains approximately 7 million base pairs 6390 potential protein-coding sequences. identified...
A 3D model of RNA structure can provide information about its function and regulation that is not possible with just the sequence or secondary structure. Current models suffer from low accuracy long running times either neglect presume knowledge long-range interactions which stabilize tertiary Our coarse-grained, helix-based, operates only a few degrees freedom compared all-atom while preserving ability to sample structures given It strikes balance between precision an simplicity...
This paper presents an interactive visualization interface-HiPiler-for the exploration and of regions-of-interest in large genome interaction matrices. Genome matrices approximate physical distance pairs regions on to each other can contain up 3 million rows columns with many sparse regions. Regions interest (ROIs) be defined, e.g., by sets adjacent columns, or specific visual patterns matrix. However, traditional matrix aggregation pan-and-zoom interfaces fail supporting search, inspection,...
Modern DNA sequencing methods produce vast amounts of data that often requires mapping to a reference genome. Most existing programs use the number mismatches between read and genome as measure quality. This approach is without statistical foundation can for some types result in many wrongly mapped reads. Here we present probabilistic method based on position-specific scoring matrices, which take into account not only quality scores reads but also user-specified models evolution...
<ns4:p>We present <ns4:italic>forgi</ns4:italic>, a Python library to analyze the tertiary structure of RNA secondary elements. Our representation an molecule is centered on elements (stems, bulges and loops). By fitting cylinder helix axis, these are carried over into coarse-grained 3D representation. Integration with Biopython allows for handling all-atom information. <ns4:italic>forgi</ns4:italic> can deal variety file formats including dotbracket strings, PDB MMCIF files. We handle...
Abstract We present HiGlass, an open source visualization tool built on web technologies that provides a rich interface for rapid, multiplex, and multiscale navigation of 2D genomic maps alongside 1D tracks, allowing users to combine various data types, synchronize multiple modalities, share fully customizable views with others. demonstrate its utility in exploring different experimental conditions, comparing the results analyses, creating interactive snapshots collaborators broader public....
We present Scalable Insets, a technique for interactively exploring and navigating large numbers of annotated patterns in multiscale visualizations such as gigapixel images, matrices, or maps. Exploration many but sparsely-distributed is challenging visual representations change across zoom levels, context navigational cues get lost upon zooming, navigation time consuming. Our visualizes too small to be identifiable at certain levels using insets, i.e., magnified thumbnail views the...
We present forgi, a Python library to analyze the tertiary structure of RNA secondary elements. Our representation an molecule is centered on elements (stems, bulges and loops). By fitting cylinder helix axis, these are carried over into coarse-grained 3D representation. Integration with Biopython allows for handling all-atom information. forgi can deal variety file formats including dotbracket strings, PDB MMCIF files. handle modified residues, missing cofold multifold structures as well...
Abstract Existing human genome assemblies have almost entirely excluded highly repetitive sequences within and near centromeres, limiting our understanding of their sequence, evolution, essential role in chromosome segregation. Here, we present an extensive study newly assembled peri/centromeric representing 6.2% (189.9 Mb) the first complete, telomere-to-telomere assembly (T2T-CHM13). We discovered novel patterns repeat organization, variation, evolution at both large small length scales....
Abstract The 4D Nucleome (4DN) Network aims to elucidate the complex structure and organization of chromosomes in nucleus impact their disruption disease biology. We present 4DN Data Portal ( https://data.4dnucleome.org/ ), a repository for datasets generated network relevant external datasets. Datasets were with wide range experiments, including chromosome conformation capture assays such as Hi-C other innovative sequencing microscopy-based probing architecture. All together, data portal...
Abstract This paper presents an interactive visualization interface—HiPiler—for the exploration and of regions-of-interest in large genome interaction matrices. Genome matrices approximate physical distance pairs regions on to each other can contain up 3 million rows columns with many sparse regions. Regions interest (ROIs) be defined, e.g., by sets adjacent columns, or specific visual patterns matrix. However, traditional matrix aggregation pan-and-zoom interfaces fail supporting search,...
Understanding RNA folding at the level of secondary structures can give important insights concerning function a molecule. We are interested to learn how change dynamically during transcription, as well whether particular form already or only after transcription. While different approaches exist simulate cotranscriptional folding, current strategies for visualization lagging behind. New, more suitable necessary help with exploring generated data from simulations.
Abstract We present Scalable Insets , a technique for interactively exploring and navigating large numbers of annotated patterns in multiscale visualizations such as gigapixel images, matrices, or maps. Exploration many but sparsely-distributed is challenging visual representations change across zoom levels, context navigational cues get lost upon zooming, navigation time consuming. Our visualizes too small to be identifiable at certain levels using insets, i.e., magnified thumbnail views...