Thallinger Team

Research Goals

Our research covers management and processing of high-throughput screening data as well as the development of databases and tools for their computational analysis. Specifically we are interested in the analysis of diverse dataset generated with next generation sequencing technologies, mass spectrometry and the integration of multiple omics datasets in a joint evaluation.

The interdisciplinary team of bioinformaticians, biomedical engineers, chemists, engineers, and mathematicians at our lab builds a creative and inspiring environment to address hot topics in life sciences.

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Current Projects

  • January 2015 - December 2017
    acib industrial project Area 2 - New enzymes for polymer modification

    The in silico screening of genomic databases and own next generation sequencing data is applied to identify novel enzymes acting on polymers and for polymer synthesis. The identified biocatalysts for polymer processing are then engineered for improved technological features.

  • June 2015 – May 2018
    FWF Project P 27843: Comparative phylogeography of co-distributed arboreal mites

    Comparative phylogeographic analyses focusing on distantly related but co-distributed species with proposed different dispersal abilities are an approved strategy to inference the effect of historical and/or contemporaneous processes driving species diversification. The present proposal is a pilot study that shall provide first insights into local- and large-scale phylogeographic patterns by comparing several co-distributed arboreal oribatid mite species with (presumed) different dispersal modes (phoretic versus non-phoretic behavior) in Europe. The use of “traditional” molecular techniques, plus modern next-generation sequencing (NGS) - a new application for population genetics and phylogeography in arachnids – will allow for illuminating recent (gene flow, genetic drift) and past (bottlenecks) evolutionary processes as far as population contractions/expansion and colonization routes, which had important impacts on contemporary intraspecific diversity of species that overlap in time and space.
    This is a joint project coordinated by Dr. Sylvia Schäffer, Institute of Zoology, Karl-Franzens University Graz, and Dr. Ingeborg Klymiuk, ZMF, Medical University of Graz.

  • July 2014 – June 2016
    Land Steiermark Project Molecular Tumour Therapy Selection

    Cancer therapy for patients with progressing metastatis is often hampered by the lack of further evidence based drug routes. This project aims to identify further applicable drugs by molecular analysis of samples from tumor, mestastatis and corresponding tissue of these patients. This is a joint project coordinated by Dr. Karl Kashofer, Institute of Pathology, Medical University of Graz and Dr. Bernhard Wieser, Interuniversitäres Forschungszentrum für Technik, Arbeit und Kultur.

  • October 2013 – December 2018
    Austrian Ministry of Science, Research and Economy - Omics Center Graz

    The Omics Center Graz bundles the expertise and existing infrastructure in genomics, transcriptomics, proteomics, and metabolomics/lipidomics, as well as bioinformatics and administration of research centers in Graz. Special emphasis is put on bioinformatics and measurement capacity, in order to perform more comprehensive omic studies and multi- omic projects. Such organized strategies will facilitate the obtainment of sustainable knowledge from the largest European Biobank which is located in Graz, as well as the implementation of biomarker research in Graz. From this initiative highly profit next to molecular biomedicine, particularly the strong lipid research network and research competence centers with close connection to industry (e.g. ACIB, RCPE), and young researchers finding training in state of the art high end technologies in Graz.

  • July 2013 – June 2016
    FWF Project P 26148: High-Throughput Identification of Lipid Molecular Species in LC-MS/MS Data

    The aim of this project is to develop a versatile and generally applicable method for high throughput determination of lipid structural fatty acid composition from LC-MS/MS data, easily adaptable to different mass spectrometers and experimental setups. The general applicability will be facilitated by a newly developed language for the description of MS/MS fragmentation spectra. Based on this language, a novel algorithm will identify the lipid and its deducible compositional features. The performance of the method will be verified in controlled and biological experiments. Furthermore, we want to supply a graphical user interface for the definition of rules describing the spectra, and supply pre defined rule sets for the most common mass spectrometers. This joint project is coordinated by Dr. Gerhard Thallinger with the partners Dr. Günther Hämmerle, Institute of Molecular Biosciences, Karl-Franzens University Graz, and Dr. Harald Köfeler, ZMF, Medical University of Graz.

  • December 2012 - November 2015
    EU FP7 Project KYROBIO: Grant agreement no: 289646

    The discovery, development and demonstration of biocatalysts for use in the industrial synthesis of chiral chemicals and our interest was to identify a new class of hydroxynitrile lyases. This project is carried out within acib by Dr. Margit Winkler in close collaboration with Prof. Karl Gruber (UniGraz), Prof. Ruth Birner-Grünberger (ZMF and Omics Centre) and Dr. Gerhard Thallinger (TU Graz)

  • January 2011 - June 2016
    FWF Project P 22737: Genomic sequencing of two Lake Tanganyika cichlid fish

    The cichlid fishes of Lake Tanganyika represent the oldest and ecomorphologically most advanced adaptive radiation and several lineages radiated in parallel. We chose the tribe Tropheini to study adaptive evolution and propose to decipher the genomes of two highly divergent members of the Tropheini, the epilithic algae feeder Tropheus moorii, and the unicellular algae comber Petrochromis trewavasae. This is a joint project coordinated by Prof. Christian Sturmbauer, Institute of Zoology, Karl-Franzens University Graz, Dr. Christian Gülly, ZMF, Medical University of Graz and Prof. Christian Schlötterer, Veterenary University Vienna.

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Current Theses

PhD Theses

  • Christoph Fischer: Comparative Genomics of two Cichlids Species from Lake Tanganyika
  • Peter Krempl: Working title: Modeling of the Gene Expresssion Networks of E. coli Productions Strains

MSc Theses

  • Natascha Fladischer: Comparison between Integrative and Traditional Analysis of Omics Data
  • Raphael Hablesreiter: Establishment of an Analysis Pipeline for Public Cancer Gene Expression Sequencing Datasets
  • Simon Kneringer: Genome Characterization of Multiresistant Mycobacterium tuberculosis Strains
  • Rachel Korn: Comparative Genomics and Transcriptomics of Two Closely Related Cichlid Species
  • Tobias Singhania: Reconstruction of Regulatory Networks from Epigenetic and Transcriptomic Data

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Completed Theses

PhD Theses

  • Oana Tomescu: Integrative Analysis of –omics Data
  • Christoph Büschl: Isotopic-Labelling Assisted Metabolomics of Filamentous Fungi: Novel Software Tools for Automated Processing of LC-MS Data (Co-supervisor)
  • Bettina Halwachs: Novel Strategies for the In-depth Analysis of Complex Microbial Communities

MSc Theses

  • Bettina Pucher: Comparison of integrative analysis methods based on simulated and biological data sets
  • Marco Delise: Molecular Stratification of High Grade Serous Ovarian Cancer
  • Josef Höftberger: Reverse Engineering und Erweiterung der Mikrobiom-Analysis Plattform SnoWMAn
  • Lydia Hangelmann: Implementation and Validation of Genome Scale Metabolic Models for E. coli Production Strains
  • Christine Moik: A computational workflow supporting the evaluation of drug efficacy (Co-supervision)
  • Wolfgang Kopp: Correlation Matrices for the Analysis and Integration of Transcriptome and Metabolome Data Sets
  • Bettina Halwachs: Model Driven Software Development with an Application to the Management of Mutein Data
  • Edith Hofer: Component - based Web Development-Integration of JPF into JBoss
  • Kerstin Baumgartner: Tissue Microarray Database Application: Redesign using a "Model Driven Architecture" Approach
  • Michael Guggemoos: Mutein Datenbank (Co-supervisor)
  • Robert Rader: Design and Development of a Database for Protein-Protein Interactions in Crystals
  • Thomas Fuchs: Bayesian Networks in Clinical Decision Support (Co-supervisor)
  • Mathias Kals: Webinterface für YPL.db (Yeast Protein Localization Database)
  • Roland Pieler: Java Tool for Normalization and Analysis of Microarray Data
  • Martin Pirklbauer: Design and Development of a Database for Tissue Micro Array Experiments
  • Thomas Truskaller: Data Integration into a Gene Expression Database
  • Martina Uray: Ein mathematisches Modell zur automatischen Stanzentypisierung in der Immunhistochemie (TMA-Analyse) (Co-supervisor)
  • Edgar Neuherz: Analyse von Proteinarray-Bildersets
  • Robert Molidor: Analyse von Microarray-Bildern

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Selected Publications

Petra Heidinger Hydrogen-driven cofactor regeneration for stereoselective whole-cell C=C bond reduction in Cupriavidus necator Show publication in PURE
Gerhard Thallinger Myristic acid induces proteomic and secretomic changes associated with steatosis, cytoskeleton remodeling, endoplasmic reticulum stress, protein turnover and exosome release in HepG2 cells Show publication in PURE

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Team Leader

Gerhard Thallinger
Dipl.-Ing. Dr.techn.

Team Website

For more information visit our team website