Doctoral Program Bioinformatics and Genome Research (no new applicants accepted)

General | Aims | Structure | Application | Documents | Contact
Students | Faculty | International Faculty | History | Alumni

 

General

The PhD program Bioinformatics and Genome Research has expired in February 2014. It has been replaced by the doctoral program Bioinformatics.

The program was coordinated by the International Graduate School in Bioinformatics and Genome Research and was devoted to top-level research in bioinformatics and molecular biology. It offered a structured PhD-level education in English language for students with excellent qualifications. No new applicants will be accepted here. Further information about the new PhD program Bioinformatics will follow here. The program is coordinated by the International Reserach Training Group Computational Methods for the Analysis of the Diversity and Dynmaics of Genomes.

Aims

High throughput experimental techniques in genome research - such as DNA sequencing, expression arrays, proteomics - present manifold challenges for algorithmic data analysis and data management. Scientific progress and industrial exploitation of experimental data are dependent on the availability and quality of appropriate bioinformatic techniques. The doctoral program Bioinformatics and Genome Research therefore combines the fields of experimental genome research and bioinformatics.

Structure

In addition to the scientific research work, PhD students complete a study program consisting of a total of 30 ECTS credit points, taking into account the scientific background of the students and the subject of the doctoral thesis. The student may choose the study program in accordance with the supervisors. Typically these will be courses from master programs at Bielefeld University, but courses offered elsewhere may also be acceptable. In addition, credit points can be earned for teaching assistance, the organization of and participation in workshops, publications, and soft skill training. Details can be found in the study regulations.

Moreover, students of this program have the option to participate in scientific retreats and in the Bioinformatics Research and Education Workshop (BREW), an international workshop for first-year PhD students that is jointly organized and attended by students from different bioinformatics graduate schools in northern Europe.

Application

Currently we can not offer PhD scholarships for new students. Students with external funding can apply to be associated to the school. In such cases, please contact the dean of studies.

Documents

Contact

Bielefeld University
Faculty of Technology
Doctoral program Bioinformatics
P.O. Box 10 01 31
33501 Bielefeld
Germany

Contact person/Dean of studies: Prof. Dr. Jens Stoye

Examination office: Christian Haupt

Students

  • Hoffmann, Nils
  • Willing, Eyla

Faculty

The PhD program and Grduate School in Bioinformatics and Genome Research offers a stimulating research environment. The faculty members listed below offer projects and supervise PhD students at the Graduate School on a regular basis.

  • Baake, Ellen
  • Dietz, Karl-Josef
  • Eichenlaub, Rudolf
  • Flaschel, Erwin
  • Giegerich, Robert
  • Hofestädt, Ralf
  • Kalinowski, Jörn
  • Kandlbinder, Andrea
  • Küster, Helge
  • Merkle, Thomas
  • Michel, Klaus-Peter
  • Nattkemper, Tim
  • Niehaus, Karsten
  • Pühler, Alfred
  • Ragg, Hermann
  • Sagasser, Martin
  • Schlüter, Andreas
  • Schneiker-Bekel, Susanne
  • Sewald, Norbert
  • Staiger, Dorothee
  • Stoye, Jens
  • Tauch, Andreas
  • Weidner, Stefan
  • Weisshaar, Bernd

International Faculty

The members of the International Faculty of the PhD program and Graduate School are researchers of international renown that have their research groups in other countries. They visit the Graduate School on a regular basis to give lectures, conduct workshops on cutting edge science and advise the PhD students in their projects.

  • William R. Atchley. Department of Genetics and Center for Computation Biology. North Carolina State University, Raleigh, NC, USA.
  • Volker Brendel. Department of Genetics, Development and Cell Biology. Iowa State University, USA.
  • Douglas Cook. Plant Pathology. University of California, Davis, USA.
  • Gene Myers. Howard Hughes Medical Institute, Janelia Farm Research Campus.
  • Ross Overbeek. Argonne National Labs. Chicago, IL, USA.
  • Christoph Sensen. Biochemistry and Molecular Biology, University of Calgary, Canada.
  • Andreas Dress. CAS-MPG Partner Institute for Computational Biology. Shanghai, PR China.

 

History

Bielefeld University established its reputation in excellent PhD education of interdisciplinary science with the establishment of the DFG Research Training Group 231 "Structure Formation Processes" in 1996. The mission of this program was to bring together mathematicians and computer scientists to work together with biologists, chemists, physicists, linguists and economists on the mathematical modelling of pattern formation processes. It has catalyzed the cooperation between mathematics, molecular biology, biochemistry, and computer science.

When bioinformatics gained momentum as a new discipline (rather than a field of interdisciplinary research), this gave rise to the DFG Research Training Group 635 "Bioinformatics" reflecting that the needs of the day were most urgently directed towards software and algorithmics to handle and interpret the upcoming large amounts of genomic data. A number of joint activities resulting from this point have turned Bielefeld into one of the leading bioinformatic sites in Germany and beyond, as visible from the success in the DFG Bioinformatics Initiative in 2000 and the endowment with the International NRW Graduate School in Bioinformatics and Genome Research in 2001 by the Ministry for Science and Research (MWF) of the State of North Rhine-Westphalia (NRW).

In October 2013, a new graduate program has been established: The International DFG Research Training Group "Computational Methods for the Analysis of the Diversity and Dynmaics of Genomes" in cooperation with Simon Fraser University in Canada. Besides its research program, it also involves a broad qualification program including teaching, workshops, key skill seminars, and, most notably, extensive exchange of students and faculty between the partner institutions. To accommodate the computer science focus of the graduate program, the study regulations have been updated to the new version "Bioinformatics".

Historical documents:

 

Alumni

  • Alves jun., Leonardo: Prediction, validation and functional analysis of miRNA targets in Arabidopsis thaliana
  • Amgarten Quitzau, José Augusto: Biological Application for de Bruijn Subgraphs and Interval Group Testing
  • Barsch, Aiko: Establishment of metabolite profiling methods for the comprehensive metabolite analysis of the symbiotic interaction between Sinorhizobium meliloti and its host plant Medicago sativa
  • Baumbach, Jan: CoryneRegNet - A reference database and analysis platform for corynebaterial gene regulatory networks
  • Bednarz, Hanna: Etablierung einer Transposon-basierten Methode zur fluoreszenten Markierung und mikroskopischen Aufklärung subzellulärer Proteinlokalisierungen in Sinorhizobium meliloti Rm1021
  • Brinkrolf, Karina: Das transkrptionelle Regulationsnetzwerk von Corynebacterium glutamicum unter Einbeziehung des Lacl/GalR-Regulators UriR
  • Cavalcanti de Lucena, Daniella Karine: Characterization of Sigma Factors of Sinorhizobium meliloti involved in Stress Response
  • Chandran, Vijayendran: Proteome, transcriptome and metabolome plasticity in closely related strain of Escherichia coli - K12 and its diversity during molecular evolution processes
  • Chao, Tzu-Chiao: Charakterisierung der globalen Regulation durch die metallabhängigen Repressoren Fur und RirA in dem symbiontischen Bakterium Sinorhizobium meliloti Rm 1021
  • de Carvalho jun., Sergio Anibal: Algorithms for Improving the Design and Production of Oligonucelotide Microarrays
  • Diaz Solorzano, Naryttza Namelly: Taxonomic classification of genomic sequences: from whole genomes to environmental genomic fragments
  • Ding, Jia: Genome-wide prediction of development enhancers and analysis of evolutionary plasticity in Drosophila
  • Dondrup, Michael: EMMA2: AMAGE-Compliant System for the Analysis of Microarray Data in Integrated Functional Genomics
  • Drepper, Carsten: Identifizierung und Charakterisierung des krankheitsauslösenden Gens in einem Mausmodell für humane Motoneuronerkrankungen
  • Fritzilas, Epameinondas: Combinatorial Aspects of Low-Rank Matrix Factorization and Two Applications in Bioinformatics
  • Gaus, Katharina: Synthetic Peptide Ligands of Proteins and DNA - Structure and Function
  • Gerlach, Wolfgang: Taxonomic Classification of Metagenomic Sequences
  • Guthöhrlein, Eckhart: Effiziente Konformationsanalyse von Peptiden
  • Hauenschild, Arne: In silico Analysis of Polycomb/Trithorax Response Elements in Drosophila and Mammals Based on DynScan: An Alignment Independent Sensitivity Increasing Framework for Cross-species Prediction of Regulatory Elements
  • Heinen, Robert: Validierung von miRNA-Zielgen-Interaktionen und ihre Charakterisierung bei Motoneuronerkrankunge
  • Henckel, Kolja: Development of a software infrastructure to mine GeneChip expression data and to combine datasets from different Medicago truncatula expression profiling platforms
  • Herms, Inke: Probabilistic Arithmetic Automata - Applications of a Stochastic Computational Framework in Biological Sequence Analysis
  • Herold, Julia: A Data Mining Approach for High-Content Fluorescence Microscopy Images of Tissue Samples
  • Höchsmann, Matthias: The Tree Alignment Model: Algorithms, Implementations, and Applications
  • Husemann, Peter: Bioinformatic Approaches for Genome Finishing
  • Ishihara, Hirofumi: Analysis of Two Single Trait Loci Affecting Flavonol Glycoside Accumulations in Arabidopsis thaliana Natural Variation
  • Jahn, Katharina: Approximate Common Intervals Based Gene Cluster Models
  • Jochmann, Nina: Die transkriptionellen Regulationsnetzwerke von LexA und PdxR aus Corynebacterium glutamicum
  • Kaltenbach, Hans-Michael: Statistics and Algorithms for Peptide Mass Fingerprinting
  • Kleindt, Christiane Katja: Combining bioinformatic approaches and transcriptomics to study powdery mildew infection and flavonoid biosynthesis in Arabidopsis thaliana
  • Koch, Daniel: Elucidation of the sulfonate utilization and its regulation in Corynebacterium glutamicum
  • Kohl, Thomas: The GlxR regulation of the amino acid producer Corynebacterium glutamicum: in silico and in vitro detection of DNA binding sites of a global transcriptional regulator
  • Krause, Lutz: From Single Genomes to Natural Microbial Communities: Novel Methods for the High-Throughput Analysis of Genomic Sequence
  • Lee, Hang-Mao: Bioinformatics pre-selection of thioredoxin/glutaredoxin target proteins for the construction of cellular regulatory network
  • Lipsmeiner, Florian: Rare event simulation for probabilistic models of T-cell activation
  • Martin, Christian: Visual data mining in intrinsic hierarchical complex biodata
  • Möller, Mark: A Hybrid Algorithm for the Simulation of Biochemical Reactions and Diffusion
  • Naus, Silvia: Identification of ADAM8 substrates involved in neurodegeneration and immune response
  • Neuweger, Heiko: MeltDB A software platform for the analysis and integration of metabolomics experiment data
  • Niemeier, Sandra: Etablierung und Optimierung der synthetischen primär-microRNA Technik für funktionale Genomanalysen in Arabidopsis thaliana
  • Oehm, Sebastian: Comparing Organisms on the Level of Metabolism
  • Oelze, Marie-Luise: Towards Systems Biology of the Chloroplast under Stress: Linking Transcription to the Metabolic State
  • Oleson, Björn: Integrative Simulation Framework for Modeling Dynamic Cellular Phenomena in 3D over Time
  • Pobigaylo, Nataliya: Identification of genes in Sinorhizobium meliloti relevant to symbiosis and competitiveness using signature tagged transposons
  • Reeder, Janina: Locomotif – a Graphical Programming System for RNA Motif Search
  • Rubiano Castellanos, Claudia Consuelo: Nuclear Export Signals (NESs) in Arabidopsis thaliana Development and experimental validation of a prediction tool
  • Rückert, Christian: Functional Genome and Expression Analysis of Sulfur Metabolism in Corynebacterium glutamicum
  • Sauthoff, Georg: Bellmans's GAP: A 2nd Generation Language and System for Algebraic Dynamic Programming
  • Schirmer, Stefanie: Comparing Forests
  • Schmidt, Thomas: Efficient Algorithms for Gene Cluster Detection in Prokaryotic Genomes
  • Schriek, Sarah: Interrelationship of photosynthesis, respiration and L-arginine metabolism in the cyanobacterium Synechocycstis sp. PCC6803
  • Schürmann, Klaus-Bernd: Suffix Arrays in Theory and Practice
  • Skusa, Andre: Reconstruction and analysis of intercellular signaling networks
  • Sommer, Björn:CELLmicrocosmos - Integrative Cell Modeling at the molecular, mesoscopic and functional Level
  • Stiens, Michael: Characterisation and Complete Nucleotide Sequence Analysis of Accessory Plasmids, Isolated from the Dominant Indigenous Sinorhizobium mellioti Strain SM11 Identified during a Long-Term Field Release Experiment
  • Ströher, Elke: Exploring components of the chloroplast thiol-disulphide redox network in Arabidopsis thaliana
  • Syed, Intikhab-Alam: Integration Approaches to Protein Homology Search
  • Taher, Leila: Computational Methods for Splice Site Prediction
  • Timm, Wiebke: Peak Intensity Prediction in Mass Spectra unsing Machine Learning Methods
  • von Wangenheim, Ute: Single-crossover recombination and ancestral recombination trees
  • Voß, Björn: Advanced Tools for RNA Secondary Structure Analysis
  • Wei, Ning: ???
  • Whitehead, Dion: Reconstructing Gene Function and Gene Regulatory Networks in Prokaryotes
  • Wittkop, Tobias: Clustering Biological Date by Unraveling Hidden Transitive Substructures
  • Wittler, Roland: Phylogeny-based Analysis of Gene Clusters
  • Zakotnik, Julia: The Double Cut and Join Operation and its Applications to Genome Rearrangements