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Full Project Catalog


Bachelor Projects

Genomic Epidemiology
  • 07/06-2013 - Exploring tools for the prediction of polypharmacology
  • 21/01-2013 - Benchmarking of a method for species identification from whole genome sequencing data
  • 14/07-2012 - Antibody related functional studies of Influenza Hemagglutinin protein
  • 30/06-2011 - Validation of predictors of discontinous B-cell epitopes using homology modelled 3-D protein structures
  • 30/06-2011 - Prediction of the immunogenicity of therapeutic antibodies
  • 15/06-2011 - Validtion of multi-layer multi-valued neural networks
  • 10/12-2010 - Immunological pressure and molecular evolution of Influenza A virus
  • 01/07-2010 - Pan-genome Analysis of the Clostridia Family
  • 20/12-2009 - Molecular Evolution of Influenza A Virus
  • 18/12-2009 - Comparative Microbial Genomics for Staphylococcus Aureus
  • 26/06-2009 - Selection and Validation of CTL Responding Peptides by Bioinformatics Methods
  • 07/05-2009 - Structural Properties of MHC Class II Ligands
  • 23/01-2009 - Molecular Evolution of Influenza A Virus
  • 19/12-2008 - Implementation and validation of a stabilization matrix method for peptide:MHC binding predictions
  • 30/06-2008 - Peptide binding based substitution matrices in epitope prediction
Immunoinformatics and Machine Learning
  • 01/12-2011 - A novel method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion
  • 15/06-2011 - Validtion of multi-layer multi-valued neural networks
Integrative Systems Biology
  • 15/07-2012 - Large-scale text-mining of PubMed abstracts to identify trait causing genes
  • 08/07-2009 - A Drug - Protein Interaction Network Related to Psychotic Diseases
  • 30/06-2008 - Expression Evidence for Loss of Function Mutations in Key Cancer Genes of Diffuse Large B-Cell Lymphoma (DLBL) Patients
Metagenomics
  • 06/07-2012 - Analysis of functional protein variations across several completed yeast genomes
Cancer Genomics
  • 01/06-2014 - Evaluation of automatic data analysis of flow cytometry data



Master Projects

Disease Intelligence and Molecular Evolution
  • 01/02-2012 - Protein complexes affected by differential expression and copy number variations in CLL patient subsets
  • 14/10-2011 - Integrative data analysis of chronic lymphocytic leukemia patient subsets
  • 22/08-2011 - Improved protein homology modelling using structure specific gap penalties and multiple templates
  • 20/11-2009 - Neural Network Based Computational Prediction of MicroRNA Targets
  • 03/03-2009 - Structure-guided Prediction of MHC-II Ligand Binding
  • 06/08-2007 - Prediction of local structure elements using artificial neural networks
Genomic Epidemiology
  • 01/06-2014 - Construction and Benchmarking of Methods for Whole Genome based Phylogeny
  • 03/03-2014 - Sequence based sub-typing of Listeria monocytogenes
  • 31/08-2013 - Comparative genomics of Mycoplasma
  • 28/03-2013 - Searching for the Identity of Unknown Bacterial Species found in the Human Gut
  • 14/01-2013 - Imprints on the T cell epitope repertoire from self-nonself proteomic overlaps
  • 22/10-2012 - Identification of genetic markers for prediction of bacterial lifestyle characteristics
  • 10/07-2012 - Development of an automated approach to FACS data analysis
  • 31/05-2012 - Analysis of overlap between pathogenic and human peptides in MHC binding and presentation
  • 07/11-2011 - Peptide overlap between humans and human pathogens
  • 24/10-2011 - Comparison of probiotic bacterial core genes in Human Microbiome Samples
  • 22/08-2011 - Improved protein homology modelling using structure specific gap penalties and multiple templates
  • 20/08-2011 - Sequence-based Classification of Prokaryotes
  • 15/04-2011 - Evaluation of HIV-1 CCR5/CXCR4 Tropism in Danish HIV Infected Patients
  • 31/03-2011 - Analysis of B-cell epitopes based on structural analysis of 3D antigen-antibody interactions
  • 25/03-2011 - Define Optimal Conditions for Assaying of Low-affinity TCR-MHC Interactions Using MHC Multimers
  • 15/03-2011 - Analysis of Individual and Mixtures of Antibodies
  • 14/02-2011 - In Silico Immunogenicity Evaluation and Commercialisation of a Protein Drug
  • 06/12-2010 - Predicting the Function of Bacterial Proteins
  • 01/10-2010 - Biofilm Formation of Achromobacter Xylosoxidans - an Emerging Cystic Fibrosis Pathogen
  • 30/09-2010 - Bioinformatic analysis of Mycobacterium avium subsp. paratuberculosis Ejlskov 2007
  • 09/08-2010 - Design of an Enterobacteriaceae Pangenome Microarray Chip
  • 30/06-2010 - In Silico Prediction of T Cell Receptor Specificity
  • 01/03-2010 - Analysis of Malaria Proteins
  • 14/12-2009 - Using Bioinformatics Tools to Study Mycobacterium Avium Subsp. Paratuberculosis Ejlskov 2007
  • 30/06-2009 - In Silico Prediction of Bacterial Pathogenicity
  • 03/03-2009 - Structure-guided Prediction of MHC-II Ligand Binding
  • 20/08-2007 - Computational Mapping of Antibody Binding Sites in HIV
  • 06/08-2007 - Prediction of local structure elements using artificial neural networks
  • 06/07-2007 - Feature based discrimination of antigenes in Malaria
  • 31/07-2006 - Implementation and Evaluation of Protein Potentials: Applications to Immunological Problems
  • 28/07-2006 - Epitope prediction in arenaviruses
  • 01/04-2005 - Development of diagnostic assays for detection of retinal diseases
Immunoinformatics and Machine Learning
  • 22/03-2014 - Bayesian modelling of MHC peptide binding
  • 23/02-2014 - Improvement of the pan MHC class I prediction method, PickPocket, through SMM optimisation and development of an alternative picking algorithm
  • 01/03-2013 - AnnDecode, a method for artificial neural network decoding
  • 14/01-2013 - Imprints on the T cell epitope repertoire from self-nonself proteomic overlaps
  • 21/12-2012 - Predicting stability of peptide:MHC complexes; impacts for epitope discovery
  • 31/05-2012 - Analysis of overlap between pathogenic and human peptides in MHC binding and presentation
  • 19/09-2011 - Identification of position specific receptor-ligant interactions by use of artificial neural network decomposition. An investigation of interactions in the MHC:peptide system
  • 22/08-2011 - Improved protein homology modelling using structure specific gap penalties and multiple templates
  • 31/03-2011 - Analysis of B-cell epitopes based on structural analysis of 3D antigen-antibody interactions
  • 15/03-2011 - Analysis of Individual and Mixtures of Antibodies
  • 14/02-2011 - In Silico Immunogenicity Evaluation and Commercialisation of a Protein Drug
  • 31/07-2009 - Swine SLA Clustering Using Sequence and Specificity Similariity
Integrative Systems Biology
  • 21/09-2014 - Epigenetic and transcriptional regulation of LINE1 elements in Embryonic Stem Cells
  • 01/08-2014 - Using mass cytometry and computational methods to identify cellular stages in cancer
  • 21/04-2014 - Quantifying Influenza Impact from Diverse Surveillance Data
  • 30/09-2013 - Centralized Workflow Manager to simplify sharing and deployment of scientific software
  • 01/07-2013 - Data Mining of Drug Side Effects Extracted from Electronic Medical Records: a Case from Psychiatry with Focus on Epilepsy
  • 22/04-2013 - Automation of data mining for applications in vaccinology
  • 01/11-2012 - Data mining system for the development of universal influenza vaccine
  • 30/06-2011 - The Genetic Basis for Comorbidity
  • 01/02-2011 - An Integrated Computational Platform for Vaccine Target Discovery in Flavivirus spp.
  • 12/06-2009 - Analysis of the Pharmacological Space Based on PubChem Bioassay Data
  • 10/03-2008 - Tools to study transcriptional regulation of the cell-cycle
  • 05/10-2007 - Development of a Chemoinformatics database and tool for the Prediction of Compounds that could act as Leads in the Drug Development Pipeline
  • 01/07-2007 - Degradome project: A Bioinformatics approach to intracellular protein degradation
  • 22/07-2005 - Toxicity classification from NMR metabonomic data using artificial neural networks
  • 15/07-2005 - Scoring functions for protein-protein docking
  • 04/07-2005 - Prediction of spliceosomal introns in humane pre-mRNA
  • 01/04-2005 - Development of diagnostic assays for detection of retinal diseases
Metagenomics
  • 26/06-2014 - Metagenomic gene extensions
  • 02/04-2014 - Machine Learning Approach to Cytochrome P450 Identification
  • 26/08-2013 - Detecting life in next-generation sequencing data
  • 28/03-2013 - Searching for the Identity of Unknown Bacterial Species found in the Human Gut
  • 24/10-2011 - Comparison of probiotic bacterial core genes in Human Microbiome Samples
  • 22/08-2011 - Improved protein homology modelling using structure specific gap penalties and multiple templates
  • 31/07-2010 - Neural Network Based Computational Prediction of Chitinases in Microbial Communities
  • 20/11-2009 - Population Differentiation of SNP Affecting Post-translational Modification Sites in Disease-associated Proteins
Cancer Genomics
  • 22/05-2014 - Immunological selection and HLA allele-specific expression in human tumors
  • 01/10-2012 - Identification of cell type gene expression signatures
  • 29/08-2011 - OCELOT: A novel on-line cancer analysis tool to collect, integrate and analyse gene expression and clinical data



Special Courses

Disease Intelligence and Molecular Evolution
  • 01/03-2011 - A Systems View on Chronic Lymphocytic Leukemia
Genomic Epidemiology
  • 20/06-2014 - Tracing microorganisms in Human Kidney biopsies
  • 14/02-2014 - Characterization of a Georgian Bacteriophage Cocktail
  • 22/01-2014 - Analysis of structural changes in B-cell epitopes upon Antibody complex formation
  • 06/12-2013 - Transcription Factors in pathogenic and non-pathogenic E. coli genomes
  • 15/11-2013 - Optimization of construction of phylogenetic trees based on whole genome data
  • 11/10-2013 - Benchmarking of a method for species identification from whole genome sequencing data
  • 01/09-2013 - Investigation of Transcriptional Factors in Lactic Acid Bacteria
  • 15/08-2013 - Specific primer identification for clonal vancomycin resistant Enterococcus differentiation
  • 28/06-2013 - Benchmarking of a method for species identification from whole genome sequencing data
  • 07/06-2013 - Genomic difference between Salmonella causing Typhoidal and Non-Typhoidal Salmonellosis
  • 01/06-2013 - B-cell epitopes in polymorphic regions of human proteins
  • 31/05-2013 - Comparative study of transcription factors in E. coli
  • 17/05-2013 - Cellular and humoral immune response in mice; test for single epitope responses selected by bioinformatics
  • 16/05-2013 - Comparing immunogenicity of biopharmaceuticals to SNPs in MHCII epitopes
  • 16/05-2013 - Python for bioinformaticians
  • 25/04-2013 - Building a prediction tool for HIV Protease cleavage sites using artificial neural networks
  • 21/12-2012 - Bioinformatics Programming Using Python
  • 20/12-2012 - Writing a scientific paper based on bachelor project
  • 22/11-2012 - MHCcluster, an interactive web-based method for functional clustering of MHC molecules
  • 30/03-2012 - Identification of genetic markers relevant to bacterial optimum temperature
  • 15/02-2012 - SCCmec conservation in S.aureus genomes
  • 01/02-2012 - HLA allele specific dominant effects determined using verified HIV CTL epitopes
Immunoinformatics and Machine Learning
  • 23/12-2013 - Improving the PickPocket method for predicting MHC class II ligands using different PSSM approaches
  • 01/07-2013 - Exploring simultaneous peptide clustering and neural network training for predicting peptide affinities to multiple MHC alleles
  • 25/04-2013 - Building a prediction tool for HIV Protease cleavage sites using artificial neural networks
  • 22/11-2012 - MHCcluster, an interactive web-based method for functional clustering of MHC molecules
  • 01/02-2012 - HLA allele specific dominant effects determined using verified HIV CTL epitopes
Integrative Systems Biology
  • 31/01-2014 - ChIP-Seq Data Analysis
  • 30/10-2013 - Bioinformatics analysis of second generation sequencing data for the identification of structural variation in cancer
  • 30/09-2013 - Advanced Immunoinformatics
  • 30/08-2013 - Advanced Microarray studies
  • 22/04-2013 - Analysis and mapping of aneuploidy genome data to protein complexes in breast cancer
  • 15/04-2013 - Analysis and mapping of aneuploidy genome data to protein complexes in breast cancer
  • 09/10-2012 - Independent development of high performance statistical software pipelines and dynamic web-interfaces
  • 01/07-2012 - Benchmarking of Text-mining Methods
  • 01/02-2012 - Advanced Immunoinformatics
Metagenomics
  • 24/01-2014 - Introduction to bioinformatics
  • 01/01-2014 - Insilico prediction of characteristics of metagenomic habitats
  • 07/10-2013 - De novo assembly of Eucalyptus cladocalyx and identification of CYP79 gene clusters
  • 16/03-2012 - Introduction to Systems Biology
Cancer Genomics
  • 01/01-2014 - Predicting tumor origin from mutation patterns using the random forest algorithm
  • 06/09-2013 - HLA downregulation in human tumors
  • 22/04-2013 - Analysis and mapping of aneuploidy genome data to protein complexes in breast cancer
  • 15/04-2013 - Analysis and mapping of aneuploidy genome data to protein complexes in breast cancer



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