Hunting for Promoters with NGS data

Genome-wide epigenetic analysis
Downloadable poster in PDF

   Deadline for applications: Oct 10th 2014
   Notification of acceptance in 72 hours after application
   Acceptance on meeting requirements for up to 20 seats
   Course date: Oct 13th - Oct 15th 2014


Edgar Wingender started his career with an education as chemist and trained biochemist at the Technical University of Braunschweig, Germany. After 17 years of experimental work in different areas of molecular biology, mostly gene regulation problems, he fully dedicated himself to bioinformatics since 1993 when he was heading the research group Bioinformatics at the former German Research Centre for Biotechnology (GBF), now Helmholtz Center for Infection Research (HZI), in Braunschweig, Germany. He was coordinator of one of first eight research clusters funded by the German Ministry of Research and Technology. One of the major achievements of these early days was the TRANSFAC database on transcriptional regulation. Since then, he participated in and coordinated a number of national and international research consortia. In 1998, he founded the company BIOBASE, which he was heading as President and CSO until 2010. Later that year, he established geneXplain GmbH together with Alexander Kel, where he acts as CEO since. On the academic side, he accepted a call from the University Medical Center of Georg August University in Goettingen (Germany) in 2002 where he is now professor and director of the Institute of Bioinformatics. His major research interest here is on the identification of regulatory signals in the human genome and the re-construction and analysis of regulatory networks. He is also concurrent professor at Nanjing University, China. E. Wingender has authored about 150 peer-reviewed scientific articles and 2 books.

Affiliation: University Medical Center Göttingen, Göttingen, DE and geneXplain GmbH, Wolfenbuettel, DE
Edgar Wingender's Personal homepage

Philip Stegmaier studied Biology at the Technical University Braunschweig. In more than ten years of experience in the biotech industry, he has taken-on roles as scientific and technical support, project manager as well as product manager, where his activities included organization of training courses at international institutes. His scientific work has yielded peer-reviewed publications as well as talks, lectures and poster presentations at conferences, workshops and colloquia.

Affiliation: geneXplain GmbH, Wolfenbuettel, DE
Course description:

This course is set-up to review the basic principles of gene regulation and the corresponding bioinformatic problems. It will start with the computational prediction of promoters and distant enhancers and will deal with the analysis of the structure of such regions by identifying binding sites for transcription factors. The most intriguing parts of genomes, still not completely understood, are the gene regulatory regions - mostly promoters and enhancers. A complete annotation of a newly sequenced genome has to address the identification of these regions in addition to the classical task of finding genes in terms of coding regions. Regulatory regions define when, where and under what conditions genes become active and, thus, are part of the fundamental function of a gene. In this course, we will overview some of the experimental methods such as next generation sequencing (NGS) techniques for genome-wide epigenetic analysis such as ChIP-seq, which have revolutionized our ways for studying the gene regulatory mechanisms. The attendees will learn about several techniques of finding promoters and enhancers and the principles on which these methods are based on. In the "hands on" exercises, several analytical tools will be introduced and the results critically evaluated to assess their reliability.


The course will consist of lectures that lay out the conceptual framework as needed and and "hands on" exercises, which will provide the practical insight on the use of the methods, gradually, in order to produce skills that can be used with a relatively high degree of independence. Participants will learn how to set-up some of the programs, and use publicly available servers for more complex analytical jobs, in an informed fashion, so that they fully understand the output generated and how its quality can be assessed. Participants will also learn the novel principles of organization of gene regulatory regions, which will help them to interpret their results of genomic and transcriptomic studies.

Target Audience:

The course addresses researchers in biology, bioinformatics, biochemistry and medicine with interest in gene regulation and related topics.

Course Pre-requisites:

Basic biochemistry. Elementary computing skills. Background knowledge in basic bioinformatics is not absolutely necessary, but may be instrumental.

Please note that the PathProt brainstorming event takes place right after this course. You will need to register for PathProt separately, though. Please use the specific website for PathProt

Detailed Program

Instituto Gulbenkian de Ciência,

Apartado 14, 2781-901 Oeiras, Portugal

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Last updated:  September 18th 2014