Month Flat Week Day

Tue. 7 Jun, 2016

Thesis Defence - Franziska Bandau

Tue. 7 Jun, 2016 10:00 - 13:00
Thesis Defence Department of Plant Physiology

Franziska Bandau

Title: Importance of tannins for responses of aspen to anthropogenic nitrogen enrichment

Faculty Examiner: Lisbeth Jonsson, professor, Stockholm University,  Department of Ecology, Environment and Plant Sciences

Supervisor: Benedicte Albrectsen.

Room: Lilla hörsalen, KB3A9

Wed. 8 Jun, 2016

Paul C. Rogers - North American Quaking Aspen: functional effects of elk, fire, and climate on long-term resilience

Wed. 8 Jun, 2016 9:00 - 10:00
Paul C. Rogers

Director, Western Aspen Alliance
Department of Wildland Resources
Utah State University

Title: North American Quaking Aspen: functional effects of elk, fire, and climate on long-term resilience

Host: Lars Edenius (VFM, SLU)
Contact: This email address is being protected from spambots. You need JavaScript enabled to view it.

Place: Skogis

Cutting Edge Seminar - Daniel Cosgrove

Wed. 8 Jun, 2016 15:15 - 16:15

UPSC Cutting Edge Seminar

Daniel Cosgrove
Department of Biology

The Pennsylvania State University, University Park, PA, USA

Title: Rethinking the architecture and mechanics of growing plant cell walls and mechanisms of cell wall loosening. Insights from biomechanics, atomic force microscopy and the actions of wall-loosening enzymes.

Host: Stephanie Robert

Place: Lilla Hörsalen, KB3A9

Fri. 10 Jun, 2016

Seminar - Mikko Sillanpää: An efficient genome-wide multilocus epistasis search

Fri. 10 Jun, 2016 13:00 - 14:00
UPSC Seminar

Mikko Sillanpää
Helsinki University, Finland

An efficient genome-wide multilocus epistasis search

Room: Lilla hörsalen, KB3A9

Host: Rosario Garcia Gil


High-throughput laboratory techniques are producing vast amount of genomic marker data – discrete predictors to association studies. Linear regression model is often considered to link study phenotypes and these marker measurements to each other. Number of predictors in multi-marker regression models can easily be much larger than number of observations. Therefore, one needs application of variable selection to find small subset of important predictors out of large number of candidates. Such models can occasionally include also all pairwise locus-by-locus (epistasis) interactions which increases dimensionality of the model very rapidly.

We consider variable selection problem of linear model containing large amount of predictors and all of their pairwise interactions in the model jointly. Our suggested approach (Kärkkäinen et al. 2015) use sure-independence-screening to first drop dimension of the problem by considering marginal importance of each interaction term within the huge loop. Subsequent estimation step then consider Bayesian variable selection approach (Extended Bayesian LASSO – Mutshinda and Sillanpää 2010). We also show that it is important to separate search of main and interaction effects in the algorithm to control number of false positives. Examples illustrates superior performance of our method over PLINK in terms of computation time and empirical power. Our successful examples consider even problem of originally of order of 280,000,000 interactions within a reasonable time frame.


Mutshinda CM, Sillanpää MJ (2010) Extended Bayesian LASSO for multiple quantitative trait loci mapping and unobserved phenotype prediction. Genetics 186: 1067-1075.

Kärkkäinen HP, Li Z, Sillanpää MJ (2015) An efficient genome-wide multilocus epistasis search. Genetics 201: 865-870.

Mon. 13 Jun, 2016

Zander Myburg - Systems genetics of cell wall biology in Eucalyptus

Mon. 13 Jun, 2016 10:00 - 11:00
UPSC Seminar

Zander Myburg

Department of Genetics
Forestry and Agricultural Biotechnology Institute (FABI)
Genomics Research Institute
University of Pretoria

Systems genetics of cell wall biology in Eucalyptus: Fine-scale dissection of gene regulation during xylogenesis

Room: Lilla hörsalen, KB3A9

Host: Hannele Tuominen

Tue. 21 Jun, 2016

Melané Vivier - The whole universe is in a glass of wine

Tue. 21 Jun, 2016 9:00 - 10:00
Speaker: Melané Vivier

Institute for Wine Biotechnology
Department of Viticulture and Oenology
Stellenbosch University, South Africa

Title: The whole universe is in a glass of wine

Host: Izabella Surowiec

Place: KB3A9 Lilla hörsalen


From Richard Feynman: "A poet once said, “The whole universe is in a glass of wine".”

We will probably never know in what sense he said that, for poets do not write to be understood. But it is true that if we look in a glass of wine closely enough we see the entire universe. There are the things of physics: the twisting liquid which evaporates depending on the wind and weather, the reflections in the glass, and our imagination adds the atoms. The glass is a distillation of the earth’s rocks, and in its composition we see the secrets of the universe’s age, and the evolution of the stars. What strange array of chemicals are in the wine? How did they come to be? There are the ferments, the enzymes, the substrates, and the products. There in wine is found the great generalization: all life is fermentation. Nobody can discover the chemistry of wine without discovering the cause of much disease. How vivid is the claret, pressing its existence into the consciousness that watches it! If our small minds, for some convenience, divide this glass of wine, this universe, into parts - physics, biology, geology, astronomy, psychology, and so on - remember that nature does not know it! So let us put it all back together, not forgetting ultimately what it is for. Let us give one more final pleasure: drink it and forget it all!