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Q1: What are the evolutionary forces that have shaped the genomes of contemporary organisms and how can we infer the relevant parameters from multiple sequence alignments?
Q2: Can we develop mathematical, statistical and computational tools that help to analyse big data as generated by high throughput technologies in molecular biology?
Mathematical Models and efficient bioinformatics tools are the cornerstones to work on both questions. We develop such models and turn them into applicable software products for a wide user community. To understand the evolutionary forces, we are developing complex models of sequence evolution that in conjunction with tree reconstruction algorithms provide a comprehensive picture about the historical relationship of organisms and the changes that occur in a gene over time. Our approaches to Q2 are more diverse and are tailored to the special needs of high throughput technologies. We are interested in developing “stand-alone tools”, that can infer all relevant parameters from the input data.
Arndt von Haeseler's birthday is in 1959.
CIBIV-Website: www.cibiv.at
We developed an efficient tree reconstruction algorithm to take the patchy structure of genomic alignments into account and to infer large phylogenetic trees. These methods have been included in the widely used software tool IQ-TREE (http://www.iqtree.org).
We tackled the following problem: For NGS experiments using unique molecular identifiers (UMIs), molecules that are lost entirely during sequencing cause under-estimation of the molecule count, and amplification artifacts like PCR chimeras cause over-estimation. TRUmiCount corrects UMI data for both types of errors, thus improving the accuracy of measured molecule counts considerably (https://cibiv.github.io/trumicount/).
ModelFinder: fast model selection for accurate phylogenetic estimates.
Kalyaanamoorthy, Subha; Minh, Bui Quang; Wong, Thomas K F; von Haeseler, Arndt; Jermiin, Lars S
TRUmiCount: Correctly counting absolute numbers of molecules using unique molecular identifiers.
Pflug, Florian G; von Haeseler, Arndt
Next-generation sequencing diagnostics of bacteremia in septic patients.
Grumaz, Silke; Stevens, Philip; Grumaz, Christian; Decker, Sebastian O; Weigand, Markus A; Hofer, Stefan; Brenner, Thorsten; von Haeseler, Arndt; Sohn, Kai
NextGenMap: fast and accurate read mapping in highly polymorphic genomes.
Sedlazeck, Fritz J; Rescheneder, Philipp; von Haeseler, Arndt
The von Haeseler group participates in the special Doctoral Program "RNA Biology" reviewed and funded by the Austrian Research Fund FWF.
The Group Von Haeseler participates in the Special Research Area (SFB) "RNA-Reg - RNA regulation of the transcriptome" funded by the Austrian Science Fund FWF. SFB's are peer-reviewed, highly interactive research networks, established to foster long-term, interdisciplinary co-operation of local research groups working on the frontiers of their thematic areas.
The FWF project "Parallel computing for phylogenetic interference" funds an international collaborative effort to optimize and improve bioinformatic analysis methods for molecular data. The final aim of the project is to implement those new methods and models to be scalable on all modern multi-core, accelerator and supercomputer architectures.
The Group von Haeseler is an associated member of the special Doctoral Program "Signaling Mechanisms in Cellular Homeostasis" reviewed and funded by the Austrian Research Fund FWF.
Nutrient-regulated control of lysosome function by signaling lipid conversion
Shedding Light on the Dark Side of Terrestrial Ecosystems: Assessing Biogeochemical Processes in Soils
Protein homeostasis and lifelong cell maintenance
Dissecting the turgor sensing mechanisms in the blast fungus Magnaporthe oryzae
Pikobodies: What does it take to bioengineer NLR immune receptor-nanobody fusions
When all is lost? Measuring historical signals
Gene regulatory mechanisms governing human development, evolution and variation
Regulation of Cerebral Cortex Morphogenesis by Migrating Cells
Phage therapy for treating bacterial infections: a double-edged sword
Suckers and segments of the octopus arm
Using the house mouse radiation to study the rapid evolution of genes and genetic processes
CRISPR jumps ahead: mechanistic insights into CRISPR-associated transposons
SLiMs and SHelMs: Decoding how short linear and helical motifs direct PPP specificity to direct signaling
Title to be announced
Visualising mitotic chromosomes and nuclear dynamics by correlative light and electron microscopy
Enigmatic evolutionary origin and multipotency of the neural crest cells - major drivers of vertebrate evolution
Engineered nanocarriers for imaging of small proteins by CryoEM
Bacterial cell envelope homeostasis at the (post)transcriptional level
Title to be announced
Hydrologic extremes alter mechanisms and pathways of carbon export from mountainous floodplain soils
Dissecting post-transcriptional gene expression regulation in humans and viruses
Polyploidy and rediploidisation in stressful times
Prdm9 control of meiotic synapsis of homologs in intersubspecific hybrids
Title to be announced
RNA virus from museum specimens
Programmed DNA double-strand breaks during meiosis: Mechanism and evolution
Title to be announced