Prof. Dr. Falk Schreiber


Prof. Dr. Falk Schreiber
Institute of Computer Science
Martin Luther University
Halle-Wittenberg

Von-Seckendorff-Platz 1
06120 Halle, Germany
Bioinformatics
IPK Gatersleben (Leibniz Institute)
Corrensstra▀e 3
06466 Gatersleben, Germany
tel.: +49 345 5524770
falk.schreiber@informatik.uni-halle.de
tel.: +49 39482 5753
schreibe@ipk-gatersleben.de
MLU IPK

Personal Topical Research Teaching Software Publications

 Personal
since 2007 Professor
(Chair for Bioinformatics)

Institute of Computer Science
Martin Luther University Halle-Wittenberg, Germany
and
Coordinator Bioinformatics
Bioinformatics
IPK Gatersleben (Leibniz Institute), Germany
since 2012 Adjunct Professor
Faculty of Information Technology
Monash University (Melbourne), Australia
2006 Habilitation in Computer Science
(Dr. habil.)

2003-2007 Head of Research Group
IPK Gatersleben, Germany
2001-2002 Postdoctoral Research Fellow
and Lecturer

with Prof. Peter Eades
School of Information Technologies
The University of Sydney, Australia
2001 Ph.D. in Computer Science
(Dr. rer. nat.)

1997-2001 Research Fellow and Lecturer (Wissenschaftlicher Mitarbeiter)
with Prof. Dr. Franz J. Brandenburg
Faculty of Mathematics and Computer Science
University of Passau, Germany
1997 Diploma in Computer Science
(minor: Medical Computer Science)
Faculty of Mathematics and Computer Science
University of Passau, Germany
 Topical
Upcoming conferences

Internat. Symp. on Integrative Bioinformatics
12-14 May 2014, Newcastle (UK)

HARMONY 2014: The Hackathon on Resources for Modeling in Biology
22-25 April 2014, Manchester (UK)

COMBINE 2014: The "Computational Modeling in Biology" Network
18-22 August 2014, in Los Angeles (USA)

Books

Analysis of Biological Networks Modeling in Systems Biology

Bioinformatics / Systems Biology books: Analysis of Biological Networks and Modeling in Systems Biology: The Petri Net Approach.

Tools and databases

Vanted
Vanted 2.1 supporting more data analysis, modelling and visualisation pipelines is now available!

SBGN-ED
SBGN-ED for working with the Systems Biology Graphical Notation.
MetaCrop
MetaCrop 2.0 with extended content, new web-services and more is now online!



 Research
Areas of research

My research is focused on

  • Visual computing and visual analytics of biological data
  • Analysis of structure and dynamics of biological processes and networks
  • Modelling and simulation of metabolism
  • Algorithms for network analysis and visualisation
  • Standards for knowledge representation in biology and medicine
  • Data integration of *omics and multimodal data

 Teaching

I have taught computer science and bioinformatics courses at undergraduate and postgraduate levels at the University of Passau (Germany), The University of Sydney (Australia), the Technical University of Dortmund (Germany), the University of Kiel (Germany) and the University of Halle (Germany).


 Software (selected tools)

I have developed/managed the development of several software tools. Major freely available tools are:

Vanted
Analysis and visualisation of multimodal data in the context of biological networks. Extensions based on Vanted address, for example, metabolic modelling (FBA-SimVis), an information system for experimental data (DBE2), and spatial data investigations/image processing (Hive). Vanted is a leading network analysis and visualisation tool used in several projects and collaborations.

SBGN-ED

SBGN-ED & KGML-ED
Editing, validation, and interactive navigation of KEGG pathways and SBGN (Systems Biology Graphical Notation) maps. SBGN-ED has been voted 2010 and 2011 to be the best software for the SBGN standard.

Meta-All & MetaCrop
Databases/information systems for multi-level representation of metabolic processes (Meta-All) and special instance of the system for detailed plant metabolism (MetaCrop). MetaCrop is not only a large collection of manually curated pathways and metabolic information in crop plants, but also a repository for metabolic models.

HTPheno
Image analysis pipeline for high throughput plant phenotyping

MAVisto, CentiBiN & CentiLib
Investigation of structural network properties (motifs, centralities, and global graph properties) especially for biological networks. Initially stand-alone programs, the newer developments are now part of the Vanted toolssuite and further developed there.

BioPath
Representation, visualisation, and exploration of biochemical pathways; an electronic version of the Boehringer pathway chart.


 Publications
Complete list of publications
Selected books
Modeling in Systems Biology

Analysis of Biological Networks

Ina Koch, Wolfgang Reisig and Falk Schreiber: Modeling in Systems Biology: The Petri Net Approach Springer, 2011.
This book deals with modeling of biochemical networks (metabolism, regulation, signaling) based on Petri net theory. It serves as text book for biologists who want to model biochemical systems using Petri nets as well as for computer scientists who are interested in biological applications.

Bj÷rn H. Junker and Falk Schreiber: Analysis of Biological Networks Wiley, 2008.
This book deals with methods for the analysis of biological networks. The first part introduces network analysis algorithms such as centralities, motifs, clustering and general network properties, and the second part studies the usage of these methods for the investigation of different biological networks ranging from molecular networks (gene regulation, protein interaction, metabolism) to ecological and phylogenetical networks.

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