A5089456984- Biofuel production and bioconversion
- Biodiesel Production and Applications
- Epigenetics and DNA Methylation
- Genomics and Phylogenetic Studies
- Plant Genetic and Mutation Studies
- RNA modifications and cancer
- Cancer-related gene regulation
- Microbial Metabolic Engineering and Bioproduction
- Cancer Genomics and Diagnostics
- Radiomics and Machine Learning in Medical Imaging
- Hepatitis C virus research
- Seed Germination and Physiology
- Meta-analysis and systematic reviews
- Hepatitis B Virus Studies
- Lipid metabolism and biosynthesis
- Genomics and Rare Diseases
- Liver Disease Diagnosis and Treatment
- Chromosomal and Genetic Variations
- Gene Regulatory Network Analysis
- Biomedical Ethics and Regulation
- Gene expression and cancer classification
- Genomics and Chromatin Dynamics
- Bioinformatics and Genomic Networks
- Biomedical Text Mining and Ontologies
- RNA and protein synthesis mechanisms
Austrian Institute of Technology
2014-2021
Innsbruck Medical University
2012-2015
University of Maryland, Baltimore
2013
Johns Hopkins University
2013
Graz University of Technology
2009-2011
Recent advances in genome sequencing technologies provide unprecedented opportunities to characterize individual genomic landscapes and identify mutations relevant for diagnosis therapy. Specifically, whole-exome using next-generation (NGS) is gaining popularity the human genetics community due moderate costs, manageable data amounts straightforward interpretation of analysis results. While and, near future, whole-genome are becoming commodities, still poses significant challenges led...
Abstract The tuatara ( Sphenodon punctatus )—the only living member of the reptilian order Rhynchocephalia (Sphenodontia), once widespread across Gondwana 1,2 —is an iconic species that is endemic to New Zealand 2,3 . A key link now-extinct stem reptiles (from which dinosaurs, modern reptiles, birds and mammals evolved), provides insights into ancestral amniotes 2,4 Here we analyse genome tuatara, which—at approximately 5 Gb—is among largest vertebrate genomes yet assembled. Our analyses...
Abstract Motivation: A large and rapidly growing number of bacterial organisms have been sequenced by the newest sequencing technologies. Cheaper faster technologies make it easy to generate very high coverage genomes, but these advances mean that DNA preparation costs can exceed cost for small genomes. The need contain often results in creation only a single library, which turn introduces new challenges genome assembly methods. Results: We evaluated ability multiple programs assemble...
Microphysiological systems play a pivotal role in progressing toward global paradigm shift drug development. Here, we designed four-organ-chip interconnecting miniaturized human intestine, liver, brain and kidney equivalents. All four organ models were predifferentiated from induced pluripotent stem cells the same healthy donor integrated into microphysiological system. The coculture of autologous tissue one common medium deprived specific growth factors was successful over 14-days. Although...
Tannerella forsythia is the only 'red-complex' bacterium covered by an S-layer, which has been shown to affect virulence. Here, outer membrane vesicles (OMVs) enriched with putative glycoproteins are described as a new addition virulence repertoire of T. forsythia. Investigations this hampered its fastidious growth requirements and recently discovered mismatch available genome sequence (92A2 = ATCC BAA-2717) widely used strain (ATCC 43037). was grown anaerobically in serum-free medium...
Abstract Background Since its introduction quantitative real-time polymerase chain reaction (qPCR) has become the standard method for quantification of gene expression. Its high sensitivity, large dynamic range, and accuracy led to development numerous applications with an increasing number samples be analyzed. Data analysis consists a steps, which have carried out in several different applications. Currently, no single tool is available incorporates storage, management, multiple methods...
The success of widely used oligonucleotide-based experiments, ranging from PCR to microarray, strongly depends on an accurate design. design process involves a number steps, which use specific parameters produce high quality oligonucleotides. Oli2go is efficient, user friendly, fully automated multiplex oligonucleotide tool, performs primer and different hybridization probe designs as well specificity cross dimer checks in single run. main improvement existing web-tools that oli2go combines...
In recent studies, exome sequencing has proven to be a successful screening tool for the identification of candidate genes causing rare genetic diseases. Although underlying targeted methods are well established, necessary data handling and focused, structured analysis still remain demanding tasks. Here, we present cloud-enabled autonomous pipeline, which comprises complete workflow. The pipeline combines several in-house developed published applications perform following steps: (a) initial...
Traditional Sanger sequencing has been used as a gold standard method for genetic testing in clinic to perform single gene test, which cumbersome and expensive test several genes heterogeneous disease such cancer. With the advent of Next Generation Sequencing technologies, produce data on unprecedented speed cost effective manner have overcome limitation sequencing. Therefore, efficient affordable testing, complementary with causing mutation identification confirmation clinical research....
Abstract Animal mitochondrial genomic polymorphism occurs as low-level heteroplasmy and deeply divergent co-existing molecules. The latter is rare, known only in bivalvian mollusks. Here we show two mt-genomes a vertebrate through sequencing of the Tuatara ( Sphenodon punctatus ), sole-representative an ancient reptilian Order. molecules, revealed using combination short-read long-read technologies, differ by 10.4% nucleotide divergence. A single covers entire mt-molecule for both strands....
Abstract Background Recent advances in genomic sequencing have enabled the use of genome standard biological and biotechnological research projects. The challenge is how to integrate large amount data order gain novel insights. One way leverage sequence genome-scale metabolic models. We therefore designed implemented a bioinformatics platform which supports development such Results MEMOSys (MEtabolic MOdel System) versatile for management, storage, It new models by providing built-in version...
Semantic Web has established itself as a framework for using and sharing data across applications database boundaries. Here, we present web-based platform querying biological databases in graphical way. SPARQLGraph offers an intuitive drag & drop query builder, which converts the visual graph into executes it on public endpoint. The tool integrates several publicly available databases, including of just recently released EBI RDF platform. Furthermore, provides predefined template queries...
Increasing economic interest in Jatropha curcas requires a major research focus on the genetic background and geographic origin of this non-edible biofuel crop. To determine worldwide structure species, amplified fragment length polymorphisms, inter simple sequence repeats, novel single nucleotide polymorphisms (SNPs) were employed for large collection 907 J. accessions related species (RS) from three continents, 15 countries 53 regions. PCoA, phenogram, cophenetic analyses separated RS two...
Tannerella forsythia is an oral pathogen implicated in the development of periodontitis. Here, we report draft genome sequence strain ATCC 43037. The previously available this designation (NCBI reference NC_016610.1) was discovered to be derived from a different strain, FDC 92A2 (= BAA-2717).
The diversity of the hepatitis B surface antigen (HBsAg) has a significant impact on performance diagnostic screening tests and clinical outcome infection. Neutralizing or antibodies against HBsAg are directed towards its highly conserved major hydrophilic region (MHR), in particular "a" determinant subdomain. Here, we explored, global scale, genetic MHR large, multi-ethnic cohort randomly selected subjects with HBV infection from four continents. A total 1553 positive blood samples...
Abstract DNA methylation is one of the major epigenetic modifications and has frequently demonstrated its suitability as diagnostic prognostic biomarker. In addition to chip sequencing based epigenome wide profiling methods, targeted bisulfite (TBS) been established a cost-effective approach for routine diagnostics target validation applications. Yet, an easy-to-use tool analysis TBS data in combination with array-based results missing. Consequently, we have developed EPIC-TABSAT,...
Targeted sequencing of PCR amplicons generated from bisulfite deaminated DNA is a flexible, cost-effective way to study methylation sample at single CpG resolution and perform subsequent multi-target, multi-sample comparisons. Currently, no platform specific protocol, support, or analysis solution provided targeted on Personal Genome Machine (PGM). Here, we present novel tool, called TABSAT, for analyzing data Ion Torrent sequencers. The workflow starts with raw data, performs quality...
The MEtabolic MOdel research and development System (MEMOSys) is a versatile database for the management, storage of genome-scale models (GEMs). Since its initial release, has undergone major improvements, new version introduces several features. First, novel concept derived allows users to create model hierarchies that automatically propagate modifications along their order. Second, all stored components can now be easily enhanced with additional annotations directly extracted from supplied...
Background: Bacillus Calmette-Guérin (BCG) immunotherapy, the standard adjuvant intravesical therapy for some intermediate and most high-risk non-muscle invasive bladder cancers (NMIBCs), suffers from a heterogenous response rate. Molecular markers to help guide responses are scarce currently not used in clinical setting. Methods: To identify novel biomarkers pathways involved BCG we performed genome-wide DNA methylation analysis of NMIBCs before therapy. Genome-wide profiles isolated tumors...
It is essential that hepatitis B surface antigen (HBsAg) diagnostic assays reliably detect genetic diversity in the major hydrophilic region (MHR) of HBsAg to avoid false-negative results. Mutations this domain display marked ethno-geographic variation and may lead failure diagnose virus (HBV) infection.Evaluate performance Elecsys® II Qualitative assay a cohort South African HBV-positive blood donors.A total 179 HBsAg- HBV DNA > 100 IU/mL-positive donor samples were included. Samples...
An important requirement for a state-of-the-art hepatitis B surface antigen (HBsAg) screening assay is reliable detection of mutated HBsAg. Currently, there striking shortage data regarding the rates in vivo HBsAg mutations these clinically assays. Therefore, we compared four commercial assays using global cohort 1553 patients from continents with known HBV genotypes. These samples, which represent broadest spectrum and novel major hydrophilic region (MHR) to date, were analyzed presence...
Bisulfite (BS) conversion-based and methylation-sensitive restriction enzyme (MSRE)-based PCR methods have been the most commonly used techniques for locus-specific DNA methylation analysis. However, both advantages limitations. Thus, an integrated approach would be extremely useful to quantify status successfully with great sensitivity specificity. Designing specific optimized primers target regions is critical challenging step in obtaining adequate results using PCR-based methods....