Active Projects

JKU/UAS International PhD Program

Proteomics
Data Mining

JKU/UAS International PhD Program


The aim of this project is to develop algorithms and bioinformatic concepts incorporating de novo identification, blind modification search, and genomics data information for peptide and protein identification in proteomics analyses, exploiting all potential benefits of newly developed machines. A new approach for de novo identification, i.e., for explaining mass spectra in the absence of sequence database information, shall be developed to detect unknown peptides and shall be combined with adequate and fast blind modification search.

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Proteomics
Data Mining

LipoDrop

Image Analysis

LipoDrop


Ziel gegenwärtiger Forschungsarbeiten ist es, zum einen genau diese Vorgänge auf molekularbiologischer Ebene zu verstehen bzw. zum anderen pharmakologisch wirksame Substanzen zu finden, die eine übermäßige Fetteinlagerung und in weiterer Folge die Entstehung der bereits genannten Krankheiten verhindern. Die übergeordneten Ziele dieses Projektes sind deshalb die 1) Weiterentwicklung des bestehenden Assays für die Beantwortung detaillierte molekularbiologischer Fragestellungen, 2) Entwicklung bioinformatischer Tools für eine schnelle Auswertung der komplexen generierten Mikroskopiedaten und 3) Identifikation pharmakologischer Substanzen zur Verhinderung der Triglycerideinlagerung in Lipid Droplets mit Hauptaugenmerk auf phytogene Stoffe.

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Image Analysis

MS Amanda

Proteomics

MS Amanda


The development of the peptide and protein identification algorithm MS Amanda has been started within this project. this scoring system is developed by the Bioinformatics Research Group in close cooperation with the group of Karl Mechtler at IMP Vienna and especially focused on the identification of peptides and proteins of tandem mass spectrometry data.

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Proteomics

Recognition of 3D-objects in images

Image Analysis

Recognition of 3D-objects in images


Ziele sind die einfache Identifizierung von Objekten mittels Foto(s) via Smartphone oder Tablet, einer anschließenden 3D-Bilderkennung, der Zuordnung zu vorhandenen Daten aus Bibliotheken bzw. Datenbanken und die Bereitstellung von zugehörigen Daten bzw. weiterführenden Prozessen (z.B. Bestellung von Ersatzteilen usw.).

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Image Analysis

Screening

Image Analysis
Data Mining

Screening


The consortium of Screening 2.0 aims at the development of a comprehensive concept of non-invasive diagnostic tools for individual, exhaustive, and user-friendly diabetes screening (diabetes as a first step) in combination with e-health applications. It involves a service innovation combined with a product innovation:

 

* Development of a printed qualitative diabetes-screening strip used in a trend analysis for early detection of diabetes

 

* Development of a comprehensive communication concept

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Image Analysis
Data Mining

SESAM

Proteomics
Data Mining

SESAM


The project SESAM is sponsored by the FWF (within the translational research programme) and executed as joint basic research project of the group of Karl Mechtler at IMP Vienna and members of the Bioinformatics Research Group Hagenberg. SESAM continues the research started in the MS Amanda project and pursues the development of the peptide and protein identification algorithm MS Amanda.

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Proteomics
Data Mining

Thrombotherm

Image Analysis
Data Mining

Thrombotherm


Aim of this project is to extend the shelf life of platelet concentrates and to characterize their actual state via real-time analysis. Utilizing high-resolution microscopy techniques on different biochemical surfaces allows monitoring activation-induced changes from the cellular - down to the molecular - level. Physico-chemical parameters during storage will be characterized. Moreover, the project is aimed to classify the interaction reactivity of (transfused) platelets following storage with the cells of the individual receiver.

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Image Analysis
Data Mining

Tomo3D

Image Analysis
Data Mining

Tomo3D


Moderne Fluoreszenz-Bildgebungstechniken gewinnen in allen Forschungsbereichen der Life Sciences, speziell in der biomedizinischen Diagnostik, z.B. in den Bereichen Tissue Engineering und Zell-Analyse im Mikro- und Nanometer-Bereich, kontinuierlich an Bedeutung. Im Rahmen des Projekts TOMO3D soll ein Fluoreszenzmikroskopie-Setup zur 3D Bildgebung an der FH OÖ aufgebaut werden.

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Image Analysis
Data Mining

Transplant

Immunology
Data Mining

Transplant


Im Rahmen des Regio 13 Projekts "Transplant – Marker für humorale und zelluläre Abstoßung nach Nierentransplantation" (Konsortialführer: Blutzentrale des OÖRK) wird erforscht, ob und wie sich Next-Generation Sequencing (NGS) von B- und T-Zell-Rezeptoren dazu eignet, den Zustand von Nierentransplantaten schneller und spezifischer zu untersuchen. Ziel ist eine deutliche Verbesserung des Transplantatmonitorings sowie die Erhöhung der Funktionsdauer von transplantierten Organen.

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Immunology
Data Mining

ImmuneProfiler

Immunology
Data Mining

ImmuneProfiler


Das adaptive Immunsystem (in erster Linie repräsentiert durch B- und T-Zellen) spielt eine lebenswichtige Rolle bei der Erkennung von potenziellen Krankheitserregern, wie z.B. pathogenen Mikroorganismen und Parasiten. Es erzeugt allerdings auch ungewollte Immunreaktionen gegen allografte (gleiche Spezies, unterschiedliches Individuum) bzw. xenografte (unterschiedliche Spezies) Transplantate oder Allergene. In seltenen Fällen kommt es vor, dass das Immunsystem auch körpereigenes Gewebe bzw. Zellen attackiert; man spricht dann von Autoimmunerkrankungen. Die Zusammensetzung der Immunzellpopulationen zu kennen ist daher in der Diagnostik von Autoimmunkrankheiten ebenso von besonderer Bedeutung wie beim Monitoring nach Transplantationen oder bei der Behandlung von Infektionen.

Die aktuelle Problemstellung dabei ist, dass es bisher noch keine Möglichkeit gibt, das Immunsystem bzw. seinen „aktuellen Zustand“ zu beschreiben. Insbesondere existieren derzeit weltweit keine algorithmischen Ansätze, die es der biomedizinischen Forschung ermöglichen, die vorhandenen Daten zu verarbeiten. Ziel dieses Basisfinanzierungsprojekts ist es daher – ähnlich wie auch schon im Bereich Protein-Identifikationsalgorithmen sehr erfolgreich gezeigt – völlig neue algorithmische Grundlagen zu entwickeln, die das B- und T-Zell-Spektrum von Menschen detailliert erfassen, darstellen und analysieren können.

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Immunology
Data Mining

PPI-ID

Proteomics

PPI-ID


Ziel dieses Projekts ist die Entwicklung eines Frameworks zur Identifizierung und Quantifizierung cytosolischer Protein-Protein-Interaktionen in einer Zelle. Sowohl Protein-Protein-Interaktionen als auch deren Blockade sind an einer Vielzahl an Erkrankungen beteiligt (z.B. Tumore oder Allergien). Durch dieses Projekt soll die Erforschung dieser Interaktionen wesentlich erleichtert werden. Das Projekt wird durch die Kooperation der Forschungsgruppe Bioinformatik am Campus Hagenberg, des Protein Interaction Labs am Campus Wels und der Forschungsgruppe Protein Chemistry am Institut für Molekulare Pathologie in Wien ermöglicht.

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Proteomics

Finished Projects

Bio Databases and Analysis Algorithms

Proteomics

Bio Databases and Analysis Algorithms


Development and improvement of basic data structures and analysis algorithms for biomedical applications.

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Proteomics

Bioinformatics Resource Facility Hagenberg

Data Mining
Image Analysis

Bioinformatics Resource Facility Hagenberg


Fluorescence microscopy is going to become one of the core technologies for biomedical research and diagnostics. Therefore, image analysis is an increasing challenge for biomedical researchers. In the proposed project NanoDetect we plan to realize an innovative framework that combines novel image processing with novel machine learning methods in order to allow researchers to solve complex biomedical problems.

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Data Mining
Image Analysis

Biomedical Information Systems

Proteomics

Biomedical Information Systems


In the past few years, the promises of biotechnology - understanding the human body and its intercellular processes, detailed knowledge of health and disease, better diagnostics and treatments - have been driven ever closer to fruition. These insights are accompanied by an unprecedented torrent of biological data streaming out of the research labs. Knowledge-based systems enable their users to manage massive amounts of heterogeneous data in order to obtain deep insight into highly complex interrelationships. 

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Proteomics

Detector/MicroProt

Image Analysis
Data Mining

Detector/MicroProt


The Detector/MicroProt project is dedicated to the analysis of nanoscale microscopy images; we especially focus on the extraction of relevant structures in images and the effect secondary ingredients of plants.

 

Relevant structures found in nanoscale microscopy images are, e.g., cells and single molecules. We analyze and optimize the identification these objects and build statistical models hat describe their relationship as well as their movements. The goal is to find out, which features of these objects can be used for formulating classifiers that predict the presence or the state of certain diseases.

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Image Analysis
Data Mining

GlucoStar

Image Analysis

GlucoStar


High-content Screening Plattform for the Identification and Characterization of insulin-mimetic substances Die steigende Zahl an Menschen die an Typ-2 Diabetes/Insulin Resistenz erkrankt sind stellt die Charakterisierung von etablierten und die Entwicklung neuer Insulin-mimetischer Substanzen in den Fokus der Forschung. Verschiedene Methoden wurden entwickelt um diese Fragestellung zu adressieren. Quantifizierbarkeit und/oder Analyse von lebenden Zellen sind dabei allerdings ein limitierender Faktor. Ein Schlüssel-Molekül für die Charakterisierung von Insulin-mimetischen Substanzen ist der Glukose-Transporter 4 (GLUT4). Dieses Protein ermöglicht die Aufnahme von Glukose in Fett- und Muskelzellen und reduziert so den Blutzuckerspiegel um Hyperglykämie zu vermeiden. In einem basalen Zustand der Zelle ist GLUT4 in intrazellulären Kompartimenten arretiert. Insulin induziert die Translokation von GLUT4 in die Plasmamembran und führt so zur Aufnahme von Glukose. 

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Image Analysis

Laboratory Commission Management System

Data Mining

Laboratory Commission Management System


In context of a research and development cooperation, a laboratory commission management system is developed for a group of test laboratories.

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Data Mining

MAAGYS

Immunology

MAAGYS


Molecular Biological Screening Assay for Gynaecological Smear Diagnostic in Routine Laboratories.

 

 

Recent molecular biological screening methods are only applicable for singular micro-organisms or viruses. Especially for clinical gynaecology, such methods are not only time-intense and expensive, but also unreliable. Moreover, there are up to 200 relevant germs, each one needing an own test. Therefore, an integrated multianalyte assay shall be designed to replace this vast amount of different tests.

 

 

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Immunology

MoPS

Data Mining

MoPS


Mobile Peer Support - Patient Centered Mobile Services for Chronic Disease Management

Chronic diseases often decrease the quality of life and the well-being of patients. The aim of this project is to develop a platform that supports self-help strategies for people with chronic diseases: We plan to design and implement a self-learning, mobile coaching system that uses machine learning to identify how activities and drugs affect patients in the long term. This system shall be able to respond to the needs of patients and suggest activities to relieve symptoms; we so plan to improve the well-being of people suffering from chronic diseases.

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Data Mining

NanoDetect

Image Analysis
Data Mining

NanoDetect


Fluorescence microscopy is going to become one of the core technologies for biomedical research and diagnostics. Therefore, image analysis is an increasing challenge for biomedical researchers.
In the proposed project NanoDetect we plan to realize an innovative framework that combines novel image processing with novel machine learning methods in order to allow researchers to solve complex biomedical problems.

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Image Analysis
Data Mining

OMIS

Data Mining

OMIS


XYZ Project Description

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Data Mining

Opinion Mining and Biomedical Information Retrieval

Data Mining

Opinion Mining and Biomedical Information Retrieval


The goal of this project is to research on methods for biomedical information retrieval and opinion mining. Information retrieval (IR) includes methods for finding relevant information in huge masses of data; biomedical IR methods include text mining and machine learning methods that are used for, e.g., finding relevant publications and clusters of similarly used keywords and papers. In opinion mining the general goal is to develop classification models that are able to estimate the sentiment of statements and opinions (found online in forums or reviews, e.g.). The HeuristicLab framework was in this project applied for developing classification and clustering models using evolutionary algorithms.

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Data Mining

PepSeq - Genome based Diagnostics

Proteomics

PepSeq - Genome based Diagnostics


Concerning the analysis of biological probations one particular thing is very interesting - the combination of proteins. The knowledge of proteins enables one to gain insight into the processes of an organism and creates the foundation of understanding the most simple functions of all living beings. Moreover, the knowledge of existing proteins may allow excellent and detailed comprehension of the innermost procedures in the body but is difficult to identify in general. Proteins are on one side just too complex to be analyzed by chemical methods and on the other side too small to be made visible.

For this reason previous methods shall be thoroughly analyzed and improved resulting in the operating procedure as a whole to become completely automated.

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Proteomics

ProComCure In Silico Validation

Proteomics

ProComCure In Silico Validation


Procomcure targets heterologous protein-protein interactions in host-pathogen interactions, specifically infections caused by multi-drug resistant Staphylococcus aureus. This limited-spectrum approach focusing on severe diseases considers the role of the host in acquisition and dissemination of infections and development of resistance.

 

Procomcure uses a method that exploits qualified host-pathogen protein-protein interactions, using peptides derived from interacting partners, selected for tight binding, as lead structures for new chemical entities.

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Proteomics

WIMAKS

Data Mining

WIMAKS


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Data Mining