A5029642674- Genomics and Phylogenetic Studies
- Bioinformatics and Genomic Networks
- Computational Drug Discovery Methods
- Computational Geometry and Mesh Generation
- Protein Structure and Dynamics
- Gene expression and cancer classification
- RNA and protein synthesis mechanisms
- Chromosomal and Genetic Variations
- Algorithms and Data Compression
- Data Visualization and Analytics
- Microbial Metabolic Engineering and Bioproduction
- Gene Regulatory Network Analysis
- Genetics, Bioinformatics, and Biomedical Research
- Genomics and Chromatin Dynamics
- Advanced Graph Theory Research
- RNA modifications and cancer
- Graph Theory and Algorithms
- Genome Rearrangement Algorithms
- Machine Learning in Bioinformatics
- Enzyme Structure and Function
- Constraint Satisfaction and Optimization
- Genetic Associations and Epidemiology
- Advanced Proteomics Techniques and Applications
- Vehicle Routing Optimization Methods
- Metabolomics and Mass Spectrometry Studies
Heinrich Heine University Düsseldorf
2017-2025
Life Science Center Düsseldorf (Germany)
2024
Cluster of Excellence on Plant Sciences
2020-2022
Centrum Wiskunde & Informatica
2008-2017
Brown University
2017
Institut national de recherche en informatique et en automatique
2015-2016
Université Claude Bernard Lyon 1
2013-2016
Institute for Systems Biology
2016
Seattle University
2016
European Bioinformatics Institute
2016
With the exponential growth of expression and protein-protein interaction (PPI) data, frontier research in systems biology shifts more to integrated analysis these large datasets. Of particular interest is identification functional modules PPI networks, sharing common cellular function beyond scope classical pathways, by means detecting differentially expressed regions networks. This requires on one hand an adequate scoring nodes network be identified other availability effective algorithm...
The human genome is diploid, which requires assigning heterozygous single nucleotide polymorphisms (SNPs) to the two copies of genome. resulting haplotypes, lists SNPs belonging each copy, are crucial for downstream analyses in population genetics. Currently, statistical approaches, oblivious direct read information, constitute state-of-the-art. Haplotype assembly, addresses phasing directly from sequencing reads, suffers fact that reads current generation too short serve purposes...
Abstract Read-based phasing allows to reconstruct the haplotypes of a sample purely from sequencing reads. While is an important step for answering questions about population genetics, compound heterozygosity, and aid in clinical decision making, there has been lack accurate, usable standards-based software. WhatsHap production-ready tool highly accurate read-based phasing. It was designed beginning leverage third-generation technologies, whose long reads can span many variants are therefore...
Deregulation of cell signaling pathways plays a crucial role in the development tumors. The identification such requires effective analysis tools that facilitate interpretation expression differences. Here, we present novel and highly efficient method for identifying deregulated subnetworks regulatory network. Given score each node measures degree deregulation corresponding gene or protein, algorithm computes heaviest connected subnetwork specified size reachable from designated root node....
Over the past two decades, several fungal outbreaks have occurred, including high-profile 'Vancouver Island' and 'Pacific Northwest' outbreaks, caused by Cryptococcus gattii, which has affected hundreds of otherwise healthy humans animals. same time period, C. gattii was cause additional case clusters at localities outside tropical subtropical climate zones where species normally occurs. In every case, causative agent belongs to a previously rare genotype called AFLP6/VGII, but origin...
In addition to component-based comparative approaches, network alignments provide the means study conserved topology such as common pathways and more complex motifs. Yet, unlike in classical sequence alignment, comparison of networks becomes computationally challenging, most meaningful assumptions instantly lead NP-hard problems. Most previous algorithmic work on is heuristic nature.We introduce graph-based maximum structural matching formulation for pairwise global alignment. We relate...
Increasing quantity and quality of data in transcriptomics interactomics create the need for integrative approaches to network analysis. Here, we present a comprehensive R-package analysis biological networks including an exact heuristic approach identify functional modules.The BioNet package provides extensive framework integrated R. This includes statistics integration transcriptomic with networks, scoring nodes as well methods search visualization.The tutorial are available from...
Molecular simulation techniques are increasingly being used to study biomolecular systems at an atomic level. Such simulations rely on empirical force fields represent the intermolecular interactions. There many different available—each based a set of assumptions and thus requiring parametrization procedures. Recently, efforts have been made fully automate assignment force-field parameters, including partial charges, for novel molecules. In this work, we focus problem arising in automated...
Next-generation sequencing techniques have facilitated a large-scale analysis of human genetic variation. Despite the advances in speed, computational discovery structural variants is not yet standard. It likely that many remained undiscovered most sequenced individuals.Here, we present novel internal segment size based approach, which organizes all, including concordant, reads into read alignment graph, where max-cliques represent maximal contradiction-free groups alignments. A algorithm...
In the adult heart, epicardium becomes activated after injury, contributing to cardiac healing by secretion of paracrine factors. Here, we analyzed single-cell RNA sequencing combined with in situ hybridization and lineage tracing Wilms tumor protein 1-positive (WT1
Abstract Small molecule machine learning aims to predict chemical, biochemical, or biological properties from molecular structures, with applications such as toxicity prediction, ligand binding, and pharmacokinetics. A recent trend is developing end-to-end models that avoid explicit domain knowledge. These assume no coverage bias in training evaluation data, meaning the data are representative of true distribution. However, applicability rarely considered models. Here, we investigate how...
Abstract Many disciplines, from human genetics and oncology to plant breeding, microbiology virology, commonly face the challenge of analyzing rapidly increasing numbers genomes. In case Homo sapiens , number sequenced genomes will approach hundreds thousands in next few years. Simply scaling up established bioinformatics pipelines not be sufficient for leveraging full potential such rich genomic datasets. Instead, novel, qualitatively different computational methods paradigms are needed. We...
Abstract Resolving genomes at haplotype level is crucial for understanding the evolutionary history of polyploid species and designing advanced breeding strategies. Polyploid phasing still presents considerable challenges, especially in regions collapsing haplotypes.We present WhatsHap polyphase , a novel two-stage approach that addresses these challenges by (i) clustering reads (ii) threading haplotypes through clusters. Our method outperforms state-of-the-art terms quality. Using real...
Abstract Potato is one of the world’s major staple crops, and like many important crop plants, it has a polyploid genome. Polyploid haplotype assembly poses computational challenge. We introduce novel strategy for genomes present an autotetraploid potato cultivar Altus. Our method uses low-depth sequencing data from offspring population to achieve chromosomal clustering phasing on graph. approach generates high-quality assemblies individual chromosomes with haplotype-specific sequence...
The discovery of functional non-coding RNA sequences has led to an increasing interest in algorithms related analysis. Traditional sequence alignment algorithms, however, fail at computing reliable alignments low-homology sequences. spatial conformation largely determines their function, and therefore have take structural information into account. We present a graph-based representation for sequence-structure alignments, which we model as integer linear program (ILP). sketch how compute...
Recently, several classifiers that combine primary tumor data, like gene expression and secondary data sources, such as protein-protein interaction networks, have been proposed for predicting outcome in breast cancer. In these approaches, new composite features are typically constructed by aggregating the levels of genes. The sources employed to guide this aggregation. Although many studies claim approaches improve classification performance over single genes classifiers, gain is difficult...
Abstract Mining large datasets using machine learning approaches often leads to models that are hard interpret and not amenable the generation of hypotheses can be experimentally tested. We present ‘Logic Optimization for Binary Input Continuous Output’ (LOBICO), a computational approach infers small easily interpretable logic binary input features explain continuous output variable. Applying LOBICO cancer cell line panel, we find combinations multiple mutations more predictive drug response...
We present CIDANE, a novel framework for genome-based transcript reconstruction and quantification from RNA-seq reads. CIDANE assembles transcripts efficiently with significantly higher sensitivity precision than existing tools. Its algorithmic core not only reconstructs ab initio, but also allows the use of growing annotation known splice sites, transcription start end or full-length transcripts, which are available most model organisms. supports integrated analysis additional gene-boundary...
Whooping cough is a highly contagious respiratory disease caused by
Numerous applications in psychological research require that a pool of elements is partitioned into multiple parts. While many seek groups are well-separated, is, dissimilar from each other, others the different to be as similar possible. Examples include assignment students parallel courses, assembling stimulus sets experimental psychology, splitting achievement tests parts equal difficulty, and dividing data set for cross-validation. We present anticlust, an easy-to-use free software...
Allogeneic hematopoietic stem cell transplantation (alloHSCT) is a potentially curative treatment for high-risk hematological malignancies, but early mortality within 100 days remains significant challenge, affecting approximately 18% of patients. Identifying patients critical timely interventions. While static risk scores like the Hematopoietic Cell Transplantation-Specific Comorbidity Index (HCT-CI) and Endothelial Activation Stress (EASIX) are valuable, they do not adapt to patients'...