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.
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.
Nils Hoffmann, Joel Rein, Timo Tobias Sachsenberg, Jürgen Hartler, Kenneth Haug, Gerhard Mayer, Oliver Alka, Saravanan Dayalan, Jake Thomas Midwinter Pearce, Philippe Rocca-Serra, Da Qi, Martin Eisenacher, Yasset Perez-Riverol, Juan Antonio Vizcaíno, Reza M Salek, Steffen Neumann and Andrew R JonesmzTab-M: a data standard for sharing quantitative results in mass spectrometry metabolomicsShow publication in PURE
Tomislav Cernava, Armin Erlacher, Jung Soh, Christoph W Sensen, Martin Grube and Gabriele BergEnterobacteriaceae dominate the core microbiome and contribute to the resistome of arugula (Eruca sativa Mill.)Show publication in PURE
Nils Hoffmann, Jürgen Hartler and Robert AhrendsjmzTab-M: A Reference Parser, Writer and Validator for the Proteomics Standards Initiative mzTab 2.0 Metabolomics StandardShow publication in PURE
Emilian Jungwirth, Katrin Panzitt, Hanns-Ulrich Marschall, Martin Wagner and Gerhard G ThallingerA Comprehensive FXR Signaling Atlas Derived from Pooled ChIP-seq DataShow publication in PURE
Leen Assil Companioni, Sandy Schmidt, Petra Heidinger, Helmut Schwab and Robert KouristHydrogen-driven cofactor regeneration for stereoselective whole-cell C=C bond reduction in Cupriavidus necatorShow publication in PURE
Katrin Pansy, Julia Feichtinger, Barbara Ehall, Barbara Uhl, Miriam Sedej, David Roula, Beata Pursche, Axel Wolf, Manuel Zoidl, Elisabeth Steinbauer, Verena Gruber, Hildegard T Greinix, Katharina T Prochazka, Gerhard G Thallinger, Akos Heinemann, Christine Beham-Schmid, Peter Neumeister, Tanja M Wrodnigg, Karoline Fechter and Alexander Ja DeutschThe CXCR4-CXCL12-Axis Is of Prognostic Relevance in DLBCL and Its Antagonists Exert Pro-Apoptotic Effects In VitroShow publication in PURE
Gyöngyi Cinege, Zita Lerner, Lilla B Magyar, Bálint Soós, Renáta Tóth, Ildikó Kristó, Péter Vilmos, Gábor Juhász, Attila L Kovács, Zoltán Hegedűs, Christoph W Sensen, Éva Kurucz and István AndóCellular Immune Response Involving Multinucleated Giant Hemocytes with Two-Step Genome Amplification in the Drosophilid Zaprionus indianusShow publication in PURE
Blaž Burja, Julia Feichtinger, Katja Lakota, Gerhard G Thallinger, Snezna Sodin-Semrl, Tadeja Kuret, Žiga Rotar, Rok Ješe, Polona Žigon, Saša Čučnik, Polonca Mali, Sonja Praprotnik, Matija Tomšič and Alojzija HočevarUtility of serological biomarkers for giant cell arteritis in a large cohort of treatment-naïve patientsShow publication in PURE
Tadeja Kuret, Blaž Burja, Julia Feichtinger, Gerhard G Thallinger, Mojca Frank-Bertoncelj, Katja Lakota, Polona Žigon, Snezna Sodin-Semrl, Saša Čučnik, Matija Tomšič and Alojzija HočevarGene and miRNA expression in giant cell arteritis-a concise systematic review of significantly modified studiesShow publication in PURE
Bettina M Pucher, Oana A Zeleznik and Gerhard G ThallingerComparison and evaluation of integrative methods for the analysis of multilevel omics dataShow publication in PURE
Gerhard Thallinger, Bettina Pucher, Natascha Fladischer and Oana Alina ZeleznikDimension Reduction for the Integrative Analysis of Multilevel Omics DataDimension Reduction for the Integrative Analysis of Multilevel Omics DataShow publication in PURE
Giulia Speziali, Laura Liesinger, Juergen Gindlhuber, Christina Leopold, Bettina Pucher, Jessica Brandi, Annalisa Castagna, Tamara Tomin, Petra Krenn, Gerhard G Thallinger, Oliviero Olivieri, Nicola Martinelli, Dagmar Kratky, Matthias Schittmayer, Ruth Birner-Gruenberger and Daniela CecconiMyristic acid induces proteomic and secretomic changes associated with steatosis, cytoskeleton remodeling, endoplasmic reticulum stress, protein turnover and exosome release in HepG2 cellsShow publication in PURE
Thomas Vogl, Lukas Sturmberger, Pia C Fauland, Patrick Hyden, Jasmin Elgin Fischer, Christian Schmid, Gerhard G Thallinger, Martina Geier and Anton GliederMethanol independent induction in Pichia pastoris by simple derepressed overexpression of single transcription factorsShow publication in PURE
B Burja, T Kuret, S Sodin-Semrl, K Lakota, Ž Rotar, R Ješe, K Mrak-Poljšak, P Žigon, G G Thallinger, J Feichtinger, S Čučnik, M Tomšič, S Praprotnik and A HočevarA concise review of significantly modified serological biomarkers in giant cell arteritis, as detected by different methodsShow publication in PURE
Maximilian Malek and Christoph W SensenInstant Feedback Rapid Prototyping for GPU-Accelerated Computation, Manipulation, and Visualization of Multidimensional DataShow publication in PURE
Tomislav Cernava, Ines Aschenbrenner, Jung Soh, Christoph Wilhelm Sensen, Martin Grube and Gabriele BergPlasticity of a holobiont: desiccation induces fasting-like metabolism within the lichen microbiotaShow publication in PURE
Erika Iveth Cedillo-Gonzálaz, Virginia Barbieri, Letiticia M. Torres-Martínez, Paolo Falcaro, Isaías Juárez-Ramírez, Laura Villanova, Monica Montecchi and Luca PasqualiInfluence of domestic and environmental weathering in the self-cleaning performance and durability of TiO2 photocatalytic coatingsShow publication in PURE
Julia J Unterluggauer, Katharina Prochazka, Peter V Tomazic, Heinrich J Huber, Rita Seeboeck, Karoline Fechter, Elisabeth Steinbauer, Verena Gruber, Julia Feichtinger, Martin Pichler, Marc A Weniger, Ralf Küppers, Heinz Sill, Rudolf Schicho, Peter Neumeister, Christine Beham-Schmid, Alexander J A Deutsch and Johannes HaybaeckExpression profile of translation initiation factor eIF2B5 in diffuse large B-cell lymphoma and its correlation to clinical outcomeShow publication in PURE
Karoline Fechter, Julia Feichtinger, Katharina Prochazka, Julia Judith Unterluggauer, Katrin Pansy, Elisabeth Steinbauer, Martin Pichler, Johannes Haybaeck, Andreas Prokesch, Hildegard T Greinix, Christine Beham-Schmid, Peter Neumeister, Gerhard G Thallinger and Alexander J A DeutschCytoplasmic location of NR4A1 in aggressive lymphomas is associated with a favourable cancer specific survivalShow publication in PURE
Bhupesh K Prusty, Nitish Gulve, Sheila Govind, Gerhard R F Krueger, Julia Feichtinger, Lee Larcombe, Richard Aspinall, Dharam V Ablashi and Carla T ToroActive HHV-6 Infection of Cerebellar Purkinje Cells in Mood DisordersShow publication in PURE
Iker Irisarri, Pooja Singh, Stephan Koblmüller, Julián Torres-Dowdall, Frederico Henning, Paolo Franchini, Christoph Fischer, Alan R Lemmon, Emily Moriarty Lemmon, Gerhard G Thallinger, Christian Sturmbauer and Axel MeyerPhylogenomics uncovers early hybridization and adaptive loci shaping the radiation of Lake Tanganyika cichlid fishesShow publication in PURE
Sylvia Schäffer, Stephan Koblmüller, Ingeborg Klymiuk and Gerhard G ThallingerThe mitochondrial genome of the oribatid mite Paraleius leontonychusShow publication in PURE
P V Tomazic, L Liesinger, B Pucher, G G Thallinger, A Leitner, S Spoerk, C Gerstenberger, D Lang-Loidolt and R Birner-GruenbergerComparison of tear proteome in allergic rhinoconjunctivitis patients and controls with respect to pollen seasonShow publication in PURE
Tamara Tomin, Katarina Fritz, Juergen Gindlhuber, Linda Waldherr, Bettina Pucher, Gerhard G Thallinger, Daniel K Nomura, Matthias Schittmayer and Ruth Birner-GruenbergerDeletion of Adipose Triglyceride Lipase Links Triacylglycerol Accumulation to a More-Aggressive Phenotype in A549 Lung Carcinoma CellsShow publication in PURE
Katja Lakota, Julia Feichtinger, Blaž Burja, Tadeja Kuret, Polona Žigon, Žiga Rotar, Rok Ješe, Snezna Sodin-Semrl, Saša Čučnik, Gerhard G Thallinger, Matija Tomšič and Alojzija HočevarUtility of serological biomarkers for giant cell arteritis in a large cohort of treatment-naïve patientsUtility of serological biomarkers for giant cell arteritis in a large cohort of treatment-naïve patients219Show publication in PURE
Holly Stolterfoht, Daniel Schwendenwein, Christoph Wilhelm Sensen, Florian Rudroff and Margit WinklerFour distinct types of E.C. 18.104.22.168 enzymes can catalyze the reduction of carboxylic acids to aldehydesShow publication in PURE
Alexander Triebl, Jürgen Hartler, M. Trötzmüller and Harald C. KöfelerLipidomics: Prospects from a technological perspectiveShow publication in PURE
Alexander Triebl, M. Trötzmüller, Jürgen Hartler, Tatjana Stojakovic and Harald C. KöfelerLipidomics by ultrahigh performance liquid chromatography-high resolution mass spectrometry and its application to complex biological samplesShow publication in PURE
Jürgen Hartler, Alexander Triebl, Andreas Ziegl, Martin Trötzmüller, Gerald N Rechberger, Oana Alina Zeleznik, Kathrin A Zierler, Federico Torta, Amaury Cazenave-Gassiot, Markus R Wenk, Alexander Fauland, Craig E Wheelock, Aaron M Armando, Oswald Quehenberger, Qifeng Zhang, Michael JO Wakelam, Guenter Haemmerle, Friedrich Spener, Harald C Köfeler and Gerhard G ThallingerDeciphering lipid structures based on platform-independent decision rulesShow publication in PURE
Martin Trötzmüller, Alexander Triebl, Amra Ajsic, Jürgen Hartler, Harald Köfeler and Werner RegittnigDetermination of the Isotopic Enrichment of 13C- and 2H-Labeled Tracers of Glucose Using High-Resolution Mass SpectrometryShow publication in PURE
Josch K Pauling, Martin Hermansson, Jürgen Hartler, Klaus Christiansen, Sandra F Gallego, Bing Peng, Robert Ahrends and Christer S EjsingProposal for a common nomenclature for fragment ions in mass spectra of lipidsShow publication in PURE
Elisa Lanfranchi, Tea Pavkov-Keller, Eva-Maria Koehler, Matthias Diepold, Kerstin Steiner, Barbara Darnhofer, Jürgen Hartler, Tom Van Den Bergh, Henk-Jan Joosten, Mandana Gruber-Khadjawi, Gerhard G Thallinger, Ruth Birner-Gruenberger, Karl Gruber, Margit Winkler and Anton GliederErratumShow publication in PURE
Bettina Halwachs, Nandhitha Madhusudhan, Robert Krause, R Henrik Nilsson, Christine Moissl-Eichinger, Christoph Högenauer, Gerhard G Thallinger and Gregor GorkiewiczCritical Issues in Mycobiota AnalysisShow publication in PURE
Christoph Bueschl, Bernhard Kluger, Nora K N Neumann, Maria Doppler, Valentina Maschietto, Gerhard G Thallinger, Jacqueline Meng-Reiterer, Rudolf Krska and Rainer SchuhmacherMetExtract IIShow publication in PURE
Ingeborg Klymiuk, Ceren Bilgilier, Alexander Stadlmann, Jakob Thannesberger, Marie-Theres Kastner, Christoph Högenauer, Andreas Püspök, Susanne Biowski-Frotz, Christiane Schrutka-Kölbl, Gerhard G Thallinger and Christoph SteiningerThe Human Gastric Microbiome Is Predicated upon Infection with Helicobacter pyloriShow publication in PURE
Alexander J A Deutsch, Beate Rinner, Martin Pichler, Katharina Prochazka, Katrin Pansy, Marco Bischof, Karoline Fechter, Stefan Hatzl, Julia Feichtinger, Kerstin Wenzl, Marie-Therese Frisch, Verena Stiegelbauer, Andreas Prokesch, Anne Krogsdam, Heinz Sill, Gerhard G Thallinger, Hildegard T Greinix, Chenguang Wang, Christine Beham-Schmid and Peter NeumeisterNR4A3 Suppresses Lymphomagenesis through Induction of Proapoptotic GenesShow publication in PURE
Martin Grube, Tomislav Cernava, J. Soh, S. Fuchs, Ines Aschenbrenner, C. Lassek, U Wegener, K Riedel, Christoph Wilhelm Sensen and Gabriele BergExploring functional contexts of symbiotic sustain within lichen-associated bacteria by comparative omicsShow publication in PURE
Julie Beauregard-Racine, Cédric Bicep, Klaus Schliep, Philippe Lopez, François-Joseph Lapointe and Eric BaptesteOf woods and websShow publication in PURE
Yan Boucher, Otto X Cordero, Alison Takemura, Dana E Hunt, Klaus Schliep, Eric Bapteste, Philippe Lopez, Cheryl L Tarr and Martin F PolzLocal mobile gene pools rapidly cross species boundaries to create endemicity within global Vibrio cholerae populationsShow publication in PURE