A5047946518- Microbial Metabolic Engineering and Bioproduction
- Bioinformatics and Genomic Networks
- Gene Regulatory Network Analysis
- Protist diversity and phylogeny
- Genomics and Phylogenetic Studies
- Fungal and yeast genetics research
- Photosynthetic Processes and Mechanisms
- Microbial Community Ecology and Physiology
- Gene expression and cancer classification
- Genetics, Bioinformatics, and Biomedical Research
- RNA modifications and cancer
- Algal biology and biofuel production
- RNA and protein synthesis mechanisms
- Metabolomics and Mass Spectrometry Studies
- Biocrusts and Microbial Ecology
- Origins and Evolution of Life
- Advanced Optimization Algorithms Research
- Reinforcement Learning in Robotics
- Chromosomal and Genetic Variations
- Biomedical Text Mining and Ontologies
- Innovative Microfluidic and Catalytic Techniques Innovation
- Industrial Vision Systems and Defect Detection
- Polyamine Metabolism and Applications
- Aquatic Ecosystems and Phytoplankton Dynamics
- Fluid Dynamics and Mixing
Northeastern University
2024
Heinrich Heine University Düsseldorf
2017-2022
University of Vienna
2006-2017
Cluster of Excellence on Plant Sciences
2017
Humboldt-Universität zu Berlin
2014
Leipzig University
2013
Institute of Bioinformatics
2013
Center for Interdisciplinary Studies
2013
Bethesda University
2008
United States Department of Justice
2008
Research on the origin of life is highly heterogeneous. After a peculiar historical development, it still includes strongly opposed views which potentially hinder progress. In 1st Interdisciplinary Origin Life Meeting, early-career researchers gathered to explore commonalities between theories and approaches, critical divergence points, expectations for future. We find that even though classical approaches theories-e.g. bottom-up top-down, RNA world vs. metabolism-first-have been prevalent...
Abstract The SBML ODE Solver Library (SOSlib) is a programming library for symbolic and numerical analysis of chemical reaction network models encoded in the Systems Biology Markup Language (SBML). It written ISO C distributed under open source LGPL license. package employs libSBML structures formula representation associated functions to construct system ordinary differential equations, their Jacobian matrix other derivatives. SUNDIALS' CVODES incorporated integration sensitivity analysis....
When grown in continuous culture, budding yeast cells tend to synchronize their respiratory activity form a stable oscillation that percolates throughout cellular physiology and involves the majority of protein-coding transcriptome. Oscillations batch culture at single cell level support idea these dynamics constitute general growth principle. The precise molecular mechanisms biological functions remain elusive. Fourier analysis transcriptome time series datasets from two different periods...
Amino acid substitutions may substantially alter protein stability and function, but the contribution of arising from alternate translation (deviations genetic code) is unknown. To explore it, we analyzed deep proteomic transcriptomic data over 1,000 human samples, including 6 cancer types 26 healthy tissues. This global analysis identified 60,024 high confidence corresponding to 8,801 unique sites in proteins derived 1,990 genes. Some are shared across while others exhibit strong...
The transcriptomes of several cyanobacterial strains have been shown to exhibit diurnal oscillation patterns reflecting the phototrophic lifestyle organisms. analysis such genome-wide transcriptional oscillations is often facilitated by use clustering algorithms in conjunction with a number pre-processing steps. Biological interpretation usually focused on time and phase expression resulting groups genes. However, microarray technology studies requires normalization data, unclear impact...
Abstract The segmentation of time series and genomic data is a common problem in computational biology. With increasingly complex measurement procedures individual points are often not just numbers or simple vectors which all components the same kind. Analysis methods that capitalize on slopes single real-valued track make explicit use vectorial nature applicable such scenaria. We develop here framework for arbitrary domains only requires minimal notion similarity. Using unsupervised...
In cyanobacteria DNA supercoiling varies over the diurnal cycle and is integrated with temporal programs of transcription replication. We manipulated in Synechocystis sp. PCC 6803 by CRISPRi-based knockdown gyrase subunits overexpression topoisomerase I (TopoI). Cell division was blocked but cell growth continued all strains. The small endogenous plasmids were only transiently relaxed, then became strongly supercoiled TopoI strain. Transcript abundances showed a pronounced 5'/3' gradient...
Prokaryotic transcripts constitute almost always uninterrupted intervals when mapped back to the genome. Split reads, i.e., RNA-seq reads consisting of parts that only map discontiguous loci, are thus disregarded in most analysis pipelines. There are, however, some well-known exceptions, particular, tRNA splicing and circularized small RNAs Archaea as well self-splicing introns. Here, we reanalyze a series published data sets, screening them specifically for non-contiguously mapping reads....
A plethora of data is accumulating from high throughput methods on metabolites, coenzymes, proteins, and nucleic acids their interactions as well the signalling regulatory functions pathways cellular network. The frozen moment viewed in a single discrete time sample requires frequent repetition updating before any appreciation dynamics component interaction becomes possible. Even then derived cell population, time-averaging processes events that occur out-of-phase individuals blur detailed...
A periodic bias in nucleotide frequency with a period of about 11 bp is characteristic for bacterial genomes. This signal commonly interpreted to relate the helical pitch negatively supercoiled DNA. Functions supercoiling-dependent RNA transcription or as ‘structural code’ DNA packaging have been suggested. Cyanobacterial genomes showed especially strong signals and, on other hand, supercoiling and are highly dynamic underlie circadian rhythms these phototrophic bacteria. Focusing this...
The structural dynamics of chromatin have been implicated in the regulation fundamental eukaryotic processes, such as DNA transcription, replication and repair. Although previous studies revealed that landscape, nucleosome remodeling histone modification events are intimately tied into cellular energetics redox state, few undertake defined time-resolved measurements these state variables. Here, we use metabolically synchronous, continuously-grown yeast cultures to measure occupancy track...
Gas-liquid mass transfer is often rate-limiting in laboratory and industrial cultures of aerobic or autotrophic organisms. The volumetric coefficient k(L) a crucial characteristic for comparing, optimizing, upscaling efficiency bioreactors. Reliable dynamic models resulting methods parameter identification are needed quantitative modeling microbial growth dynamics. We describe laboratory-scale stirred tank reactor (STR) with highly efficient aeration system (k(L) ≈ 570 h(-1)). can sustain...
Abstract In cyanobacteria DNA supercoiling varies over the diurnal light/dark cycle and is integrated with circadian transcription program (Woelfle et al. [2007], Vijayan [2009], PNAS). Specifically, Woelfle al . have reported that of an endogenous plasmid became progressively higher during prolonged dark phases in Synechococcus elongatus PCC 7942. This counterintuitive, since levels negative are commonly associated exponential growth high metabolic flux. then reverted interpretation...
The problem of segmenting linearly ordered data is frequently encountered in time-series analysis, computational biology, and natural language processing. Segmentations obtained independently from replicate sets or the same with different methods parameter settings pose computing an aggregate consensus segmentation. This Segmentation Aggregation amounts to finding a segmentation that minimizes sum distances input segmentations. It again can be solved by dynamic programming. aim this...
Abstract Metabolic oscillations are characterized by alternating phases of high and low respiratory activity, associated with transcription genes involved in biosynthetic pathways growth, catabolism stress response. However, the functional consequences transcriptome remain unclear, since most proteins too stable to be affected oscillatory transcript abundances. In this work, we investigate a time series during an unstable state oscillation. Our analyses confirm previous suggestions that...
Abstract In cyanobacteria DNA supercoiling varies over the diurnal light/dark cycle and is integrated with temporal programs of transcription replication. We manipulated in Synechocystis sp. PCC 6803 by CRISPRi-based knock-down gyrase subunits overexpression topoisomerase I (TopoI), characterized phenotypes. Cell division was blocked, most likely due to inhibition genomic but not plasmid growth continued 4-5x wildtype cell volume, metabolic flux redirected towards glycogen TopoI strain....