SPP 1530: Flowering Time Control - from Natural Variation to Crop Improvement

Summer School and Mini-Conference on Next Generation Sequencing in Plant Research

Zwei Studenten und eine Tasse Kaffee

The purpose of this summer school is to develop an understanding of the potential, the challenges, and the pitfalls of next-generation sequencing (NGS) in plant research with a special focus on bioinformatics issues. Advantages and disadvantages of current sequencing technologies and their implications on data analysis will be discussed. Real-life datasets from RNA and DNA sequencing projects will be used throughout the summer school, and the participants will be enabled to perform important analyses of these data by themselves. Moreover, the participants will be trained on understanding their NGS data, on finding potential problems and errors therein, and finally on performing their data analysis. The layout of the summer school is adapted to the needs of beginners in the field of NGS bioinformatics and allows scientists with no or little background in computer science to get a first hands-on experience in this new and rapidly evolving research field. The summer school is followed by a two-day mini-conference with 21 national and international speakers who will provide an overview over a broad spectrum of novel applications, unexpected challenges, and emerging trends of next generation sequencing in plant research.

Summer School: July 4-6, 2016

Mini Conference: July 6-8, 2016

Venue: Martin Luther University Halle-Wittenberg, Institute of Computer Science, Von-Seckendorff-Platz 1, 06120 Halle (Saale)



Registration for summer school: closed
Registration for mini-conference: open until July 4, 2016, 12 pm

Getting there


Zwei Studenten und eine Tasse Kaffee


Keynote speakers

  • Elliot Meyerowitz (California Institute of Technology, Pasadena, USA)
  • Matt Weirauch (University of Cincinnati, USA)
  • David Ardell (University of California, Merced, USA) 




Program (PDF)

Summer school: Preliminary program

Room: 3.02 (PC-Pool)

Monday, July 4, 2016:

9-10.30: Introduction to Linux (David Langenberger, Mario Fasold, ecSeq Bioinformatics)

10.30-11.00: Coffee break

11.00-12.30: Introduction to NGS technologies and data analysis (David Langenberger, Mario Fasold, ecSeq Bioinformatics)

12.30-14.00: Lunch (Mensa)

14.00-15.30: NGS notations and terminology (David Langenberger, Mario Fasold, ecSeq Bioinformatics)

15.30-16.00: Coffee break

16.00-17.30: Quality control and pre-processing of raw data (David Langenberger, Mario Fasold, ecSeq Bioinformatics)

18.00: Welcome reception


Tuesday, July 5, 2016:

9.00-10.30: Read mapping (David Langenberger, Mario Fasold, ecSeq Bioinformatics)

10.30-11.00: Coffee break

11.00-12.30: Statistics and visualization of mapped reads (David Langenberger, Mario Fasold, ecSeq Bioinformatics)

12.30-14.00: Lunch (Mensa)

14.00-15.30: Quantification of gene expression (Alexander Gabel, Claus Weinholdt, Ioana Lemnian, MLU Halle-Wittenberg)

15.30-16.00: Coffee break

16.00-17.30: Detection of differentially expressed genes (Alexander Gabel, Claus Weinholdt, Ioana Lemnian, MLU Halle-Wittenberg)

18.00: Discussions and food


Wednesday, July 6, 2016:

9.00-10.30: SNP calling (Martin Porsch, Ioana Lemnian, MLU Halle-Wittenberg)

10.30-11.00: Coffee break

11.00-12.30: Genome wide association study (Bettina Konte, Martin Porsch, MLU Halle-Wittenberg)

12.30-13.45: Lunch (Mensa)


Mini-Conference: preliminary program

Room: 3.04

Wednesday, July 6, 2016:

13.45-14.00: Welcome address

14.00-15.00: Keynote lecture: Elliot Meyerowitz (California Institute of Technology, USA): Gene expression in plant stem cells: the Arabidopsis shoot apical meristem

15.00-15.30: Marcel Quint (Martin-Luther University Halle-Wittenberg, DE): Post-embryonic hourglass patterns mark ontogenetic transitions in plant development

15.30-16.00: Coffee break

16.00-16.30: Markus Schmid (University of Umea, SE): Integration of flowering time signals in Arabidopsis thaliana

16.30-17.00: Nadine Dally (Christian-Albrechts University Kiel, DE): Genomic and transcriptomic approaches to identify flowering time regulators in crops

17.00-17.30: Klaus Pillen (Martin-Luther University Halle-Wittenberg, DE): Next-generation sequencing to characterize the region containing the domestication gene threshability-1 (thresh-1) in the barley nested association mapping population HEB-25

18.00: Welcome reception


Thursday, July 7, 2016:

9.00-10.00: Keynote lecture: Matt Weirauch (University of Cincinnatti, USA): Functional genomics approaches for plant gene regulation

10.00-10.30: Jan Grau (Martin-Luther University Halle-Wittenberg, DE): Methods for motif analysis of ChIP-seq data

10.30-11.00: Coffee break

11.00-11.30: Dorothee Staiger (Bielefeld University, DE): Towards ribonomics to decipher RNA-based regulation in Arabidopsis

11.30-12.00: Selma Gago (Leibniz Institute of Plant Biochemistry Halle, DE): The expanding world of long non-condign RNAs in plants

12.00-12.30: Sven-Erik Behrens (Martin-Luther University Halle-Wittenberg, DE): Screen for small interfering RNAs effective in antiviral RNA silencing in plants

12.30-14.00: Lunch break

14.00-14.30: Jens Keilwagen (Julius Kühn-Institut Quedlinburg, DE): Improving homology-based gene prediction by RNA-seq data

14.30-15.00: Holger Deising (Martin-Luther University Halle-Wittenberg, DE): PAMP modulation in infection structures of the maize pathogen Colletotrichum graminicola is required for the establishment of compatibility

15.00-15.30: Christoph Schuster (Sainsbury Laboratory, Cambridge, UK): Diversity and evolution of the developmental transcriptome in flowering plants

15.30-16.00: Coffee break

16.00-16.30: Martin Mascher (Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, DE): Barley diversity now and 6000 years ago

16.30-17.00: Bernd Weisshaar (Bielefeld University, DE): Mapping by sequencing based on phenotypic pooling for rapeseed

17.00-17.30: Günter Theissen (University of Jena, DE): Floral quartets link flower development and evolution

18.00: Guided tour through historical building of the University of Halle

19.30: Conference dinner


Friday, July 8, 2016: 

9.00-10.00: Keynote lecture: David Ardell (University of California, USA): The origin of plastids from cyanobacteria from tRNA signatures

10.00-10.30: Hans-Wilhelm Nützmann (John Innes Centre, Norwich, UK): Gene order and chromatin signatures in plant metabolism

10.30-11.00: Coffee break

11.00-11.30: Katrin Hoffmann (Martin-Luther University Halle-Wittenberg, DE): Identification of disease-causing sequence variants

11.30-12.00:Dan Rujescu (Martin-Luther University Halle-Wittenberg, DE): Genetics of neuropsychiatric diseases

12.00-12.30: Helene Kretzmer (University of Leipzig, DE): Integrative DNA methylation analysis in lymphoma

12.30: Closing remarks



  • Martina Blümel
  • Alexander Gabel
  • Jan Grau
  • Ivo Grosse
  • Kathleen Kletsch
  • Ioana Lemnian
  • Martin Porsch
  • Claus Weinholdt



Martina Blümel
Christian Albrechts University Kiel
Plant Breeding Institute
Am Botanischen Garten 1-9
D-24118 Kiel
Phone: +49 431 880 2135
Email: m.bluemel@plantbreeding.uni-kiel.de

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