Research Activities at the Centre
General
The DFG-funded Bioinformatics Initiative Leipzig pursues an interdisciplinary
approach bringing together experimental bioscientists (i.e.
cell biologists, biochemists, pathologists, clinicians involved
in basic research) and experts trained in the analysis of complex
data and formal modelling of structures and processes (i.e.
computer scientists, biostatisticians, biomathematicians). The
particular local research profile and the request for bioinformatics
support led us to select two major fields of research.
(1) In Genetic Evolution we pursue projects to analyse
genetic diversity and to use this knowledge to identify evolutionary
relationships among species (i.e. phylogeny reconstruction),
compare humans and chimpanzees, and obtain an understanding
of the complexities of biological processes (e.g. the evolution
of genetic regulation).
(2) In Tissue Formation and Cellular Signal Transduction
we concentrate on understanding genotype and phenotype dependency
in tissue formation and function. Several projects are planned
to elucidate the mechanisms of the spatial formation of tissues
(e.g. epithelia, tumours, engineered tissues), to investigate
the architecture of signal transduction and genetic regulatory
networks, and to analyse high-dimensional genomic and molecular
data from manipulated normal and diseased tissues (e.g. gene
expression analysis).
Regarding the teaching of bioinformatics, the objective of the
DFG Bioinformatics Initiative Leipzig is to build up a curriculum
for about 30 students annually.
In 2002 the DFG Bioinformatics Initiative Leipzig achieved the
following:
(1) An interacting network of local partners was established
which contributes to the teaching, research and functioning
of our infrastructures. It involves scientists from five faculties
of Universität Leipzig, the Max Planck Institutes of Evolutionary
Anthropology (MPI EVA) and Mathematics in the Natural Sciences
(MPI MIS), and new centres such as the BBZ Biotechnology-Biomedicine
Centre, the Interdisciplinary Centre for Clinical Research (IZKF)
and the Clinical Trials Coordinating Centre (KKSL, both funded
by the German Ministry of Education and Research).
(2) The Interdisciplinary Centre for Bioinformatics (IZBI)
was established as a key infrastructural element. Consequently,
it has its own staff, premises and administration. It became
fully functional by the end of 2002. IZBI employs core research
staff, one junior research group, temporary personnel for project
groups, and doctoral students. IZBI assists its partners on
selected joint R&D projects. Service projects (e.g. for
data analyses or database developments) are handled on a consultancy
or contract basis. The first projects have reached publication
status and the first grants are in preparation.
(3) A C4 professorship in Bioinformatics was established as
a second important infrastructural unit. Prof Peter Stadler
joined the faculty of Mathematics and Computer Science in September
2002. His group is now operative.
Research concept
IZBI offers its partners a novel approach to research management
in order to meet their demands as efficiently as possible.
Projects: IZBI is designed to support cooperating scientists
on a project basis. Projects can be either research projects (with
a scientific aim) or service projects (designed to develop a technology
or routine data analysis). A project is headed by a principal
investigator. For each project we request a project proposal detailing
the objective, work plan, project team (including the responsibilities
of IZBI's staff and the personnel from the participating partners)
and budget plan (IZBI resources required, other resources, grants).
Depending on the complexity of the task IZBI can support the project
with resources ranging from short-term student employment or a
temporary task force to a full scale team involving several experts
for many months. The scientific coordinators discuss the quality,
feasibility and compatibility of the project proposals with the
principal investigators. The proposals are evaluated by the board
of directors and external reviewers. Scientific quality, consistency
with the research profile and financial feasibility are the key
criteria for deciding whether to support a project.
Any researcher from the university (including the IZBI members
themselves) and the supporting MPIs can submit a project proposal
at any time. The projects selected are supported whenever possible
with IZBI funds.
Working groups: To establish an interactive interface
with partners and to bring together the expertise at IZBI, it
was decided to organise the personnel into working groups. Working
groups consist of IZBI research staff members and scientists from
the participating institutes. They have regular meetings, discuss
research results, invite guests, discuss new project proposals,
and conduct courses and seminars. Scientific coordinators stimulate
and coordinate these activities and supervise the progress of
projects and of skills. Four working groups have been implemented:
Working Group 1 (Data Base and Data Integration; coordinator
Prof Rahm) focuses particularly on design projects for data
warehouses for genomic and molecular data and related annotations.
Being a methodological working group, it works together with
all the other working groups. It was set up in autumn 2001 and
has two core staff members.
Working Group 2 (Tissue Organisation; coordinator Dr
Drasdo) focuses on understanding spatial tissue formation. It
pursues projects using simulation models and the 3D image reconstruction
of microscopy data. Two specialists were employed in 2002 as
core staff researchers.
Working Group 3 (Signal Transduction and Gene Expression;
coordinator Prof Horn) was set up in summer 2002. It addresses
gene expression analysis and cellular signal transduction. A
junior research group is associated with WG3:
Junior Research Group (Complex Regulatory Networks;
PD Dr Bornholdt) This group studies the dynamics and function
of complex regulatory network systems. Examples range from the
molecular level of gene regulation and signal transduction networks
to cellular systems such as the immune system and the brain.
The group's goal is to develop methods, models and strategies
for studying the dynamics of complex regulatory network systems.
Working Group 4 (Genetic Evolution; coordinator
since September 2002 Prof Stadler) began its first projects in
autumn 2002.
Research projects
Databases and Data Integration (WG1)
Project: Data warehouse design and implementation
to support gene expression analysis
Rahm, Do, Kirsten
Tissue Organisation (WG2)
Project 1: 3D characterisation of the invasion front of
human cervical carcinoma
Einenkel, Braumann, Kuska, Horn, Drasdo, Höckel
Project 2: 3D morphological analysis of vascular structures
in artificial tissues
Kuska, Frerich
Project 3: Generic single-cell based model of interacting
cells to describe spatial epithelial tissue formation
Drasdo, Galle, Löffler
Project 4: Spatial dynamics of growing tumour spheroids
Drasdo, Höhme
Gene expression and cellular signal transduction (WG3)
This working group dedicated its efforts to a key project on
gene expression (GE), providing a service and research platform
for future projects. A second project was devoted to signal
transduction modelling.
Project 1: Platform for gene expression analysis
Horn, Boriss, Binder, Hasenclever, Kropf, Krohn, Läuter,
Löffler, Paschke, Wagner
Project 2: Optimising strategies for the identification
of transcriptional networks in haemopoietic progenitor cells
Drasdo , Cross, Missal, Löffler
Junior Research Group: Complex Regulatory Networks
Dr Bornholdt
Project: Estimates of recombination from human
polymorphism data
Ptak, Przeworski
In addition, two pilot-study projects on functional nucleic acid
structures in two distinct virus groups have just been approved
by the IZBI board: "Translation from polycistronic mRNAs:
RNA secondary structure analysis to identify conserved structural
elements" and "Analysis of secondary RNA structure of
infectious bursal disease virus (IBDV) genome segment B"
(Mueller, Stadler, Johne, Raue).
|
Home 
