Search Calendar
Thesis Defence - Franziska Bandau
07-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
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
Paul C. Rogers - North American Quaking Aspen: functional effects of elk, fire, and climate on long-term resilience
08-Jun-2016 9:00 - 10:00
Speaker:
Paul C. Rogers
Director, Western Aspen Alliance
Department of Wildland Resources
Utah State University
http://www.western-aspen-alliance.org/
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
Paul C. Rogers
Director, Western Aspen Alliance
Department of Wildland Resources
Utah State University
http://www.western-aspen-alliance.org/
Title: North American Quaking Aspen: functional effects of elk, fire, and climate on long-term resilience
Host: Lars Edenius (VFM, SLU)
Contact:
Place: Skogis
Cutting Edge Seminar - Daniel Cosgrove
08-Jun-2016 15:15 - 16:15
NOTE CHANGED DAY: WEDNESDAY
UPSC Cutting Edge Seminar
Speaker:
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
UPSC Cutting Edge Seminar
Speaker:
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
Seminar - Mikko Sillanpää: An efficient genome-wide multilocus epistasis search
10-Jun-2016 13:00 - 14:00
UPSC Seminar
Speaker:
Mikko Sillanpää
Helsinki University, Finland
Title:
An efficient genome-wide multilocus epistasis search
Room: Lilla hörsalen, KB3A9
Host: Rosario Garcia Gil
Abstract
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.
REFERENCES
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.
Speaker:
Mikko Sillanpää
Helsinki University, Finland
Title:
An efficient genome-wide multilocus epistasis search
Room: Lilla hörsalen, KB3A9
Host: Rosario Garcia Gil
Abstract
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.
REFERENCES
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.
Zander Myburg - Systems genetics of cell wall biology in Eucalyptus
13-Jun-2016 10:00 - 11:00
UPSC Seminar
Speaker:
Zander Myburg
Department of Genetics
Forestry and Agricultural Biotechnology Institute (FABI)
Genomics Research Institute
University of Pretoria
South-Africa
Title:
Systems genetics of cell wall biology in Eucalyptus: Fine-scale dissection of gene regulation during xylogenesis
Room: Lilla hörsalen, KB3A9
Host: Hannele Tuominen
Speaker:
Zander Myburg
Department of Genetics
Forestry and Agricultural Biotechnology Institute (FABI)
Genomics Research Institute
University of Pretoria
South-Africa
Title:
Systems genetics of cell wall biology in Eucalyptus: Fine-scale dissection of gene regulation during xylogenesis
Room: Lilla hörsalen, KB3A9
Host: Hannele Tuominen
Melané Vivier - The whole universe is in a glass of wine
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
Abstract:
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!
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
Abstract:
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!
UPSC Monday Seminar 2016
05-Sep-2016 9:00 - 11:00
UPSC Monday Seminar 2016
Speakers:
David Sundell (PhD student)
Supervisor: Nathaniel Street, Torgeir R Hvidsten
Federica Brunoni (Postdoc)
Supervisor: Karin Ljung, Catherine Bellini
Speakers:
David Sundell (PhD student)
Supervisor: Nathaniel Street, Torgeir R Hvidsten
Federica Brunoni (Postdoc)
Supervisor: Karin Ljung, Catherine Bellini
Cutting Edge Seminar: Jean-Pierre Jacquot
08-Sep-2016 15:00 - 16:00
Cutting Edge Seminar
Speaker: Jean-Pierre Jacquot
University of Lorraine, Nancy, France
Title: Redox regulation of chloroplast enzymes: molecular and evolutionary aspects
Host: Gunnar Wingsle and Göran Samuelsson
Room: KB3A9 Lilla hörsalen
Speaker: Jean-Pierre Jacquot
University of Lorraine, Nancy, France
Title: Redox regulation of chloroplast enzymes: molecular and evolutionary aspects
Host: Gunnar Wingsle and Göran Samuelsson
Room: KB3A9 Lilla hörsalen
UPSC Monday Seminar 2016
12-Sep-2016 9:00 - 11:00
UPSC Monday Seminar 2016
Speakers:
Bastian Schiffthaler (PhD student)
Supervisor: Nathaniel Street
John Baison (Postdoc)
Supervisor: Totte Niittylä
Speakers:
Bastian Schiffthaler (PhD student)
Supervisor: Nathaniel Street
John Baison (Postdoc)
Supervisor: Totte Niittylä
Master thesis defence Álvaro Montiel Jordá
12-Sep-2016 13:00 - 14:00
Master Thesis Defence
Department of Forest Genetics and Plant Physiology
Álvaro Montiel Jordá
Title: The role of the BLADE-ON-PETIOLE genes in flowering
Supervisor: Ove Nilsson and Bo Zhang
Room: KB4C10 Lecture Room
Department of Forest Genetics and Plant Physiology
Álvaro Montiel Jordá
Title: The role of the BLADE-ON-PETIOLE genes in flowering
Supervisor: Ove Nilsson and Bo Zhang
Room: KB4C10 Lecture Room
UPSC Monday Seminar 2016
19-Sep-2016 10:00 - 12:00
UPSC Monday Seminar 2016
Speakers:
Noemi Skorzinski (PhD student)
Supervisor: Markus Schmid
Jihua Ding (Postdoc)
Supervisor: Ove Nilsson, Markus Grebe
Speakers:
Noemi Skorzinski (PhD student)
Supervisor: Markus Schmid
Jihua Ding (Postdoc)
Supervisor: Ove Nilsson, Markus Grebe
Seminar - Peter Marhavy
22-Sep-2016 10:00 - 11:00
Speaker: Peter Marhavy
Department of Plant Molecular Biology (DBMV)
University of Lausanne
Switzerland
Title:
Call for help - or - Short distance cell-to-cell communication in response to wound stress in Arabidopsis root.
Host: Karin Ljung
Place: KB3A9 Lilla hörsalen
Time: 22 september kl 10-11
Department of Plant Molecular Biology (DBMV)
University of Lausanne
Switzerland
Title:
Call for help - or - Short distance cell-to-cell communication in response to wound stress in Arabidopsis root.
Host: Karin Ljung
Place: KB3A9 Lilla hörsalen
Time: 22 september kl 10-11
UPSC Monday Seminar 2016
26-Sep-2016 9:00 - 11:00
UPSC Monday Seminar 2016
Speakers:
Haleh Hayatgheibi (PhD student)
Supervisor: Harry Wu
Hardy Hall (Postdoc)
Supervisor: Hannele Tuominen
Speakers:
Haleh Hayatgheibi (PhD student)
Supervisor: Harry Wu
Hardy Hall (Postdoc)
Supervisor: Hannele Tuominen
Seminar - Daniel Kierzkowski
28-Sep-2016 10:30 - 11:30
Speaker: Daniel Kierzkowski
Max Planck Institute for Plant Breeding Research,
Department of Comparative Development and Genetics,
Cologne, Germany
Title: Understanding morphogenesis: control of organ growth at cellular level
Host: Karin Ljung
Place: KB3B1 Stora hörsalen
Time: 28 september kl 10.30-11.30
Max Planck Institute for Plant Breeding Research,
Department of Comparative Development and Genetics,
Cologne, Germany
Title: Understanding morphogenesis: control of organ growth at cellular level
Host: Karin Ljung
Place: KB3B1 Stora hörsalen
Time: 28 september kl 10.30-11.30
Seminar - Anne-Lise Routier-Kierzkowska
28-Sep-2016 14:00 - 15:00
Speaker: Anne-Lise Routier-Kierzkowska
Max Planck Institute for Plant Breeding Research,
Department of Comparative Development and Genetics,
Cologne, Germany
Title: A new insight into plant mechanics from computational modelling and force measurements.
Host: Karin Ljung
Place: KB3B1 Stora hörsalen
Time: 28 september kl 14-15
Max Planck Institute for Plant Breeding Research,
Department of Comparative Development and Genetics,
Cologne, Germany
Title: A new insight into plant mechanics from computational modelling and force measurements.
Host: Karin Ljung
Place: KB3B1 Stora hörsalen
Time: 28 september kl 14-15
Master thesis defence: Daniel Iglesias Duro
30-Sep-2016 9:00 - 10:00
Master Thesis Defence
Department of Plant Physiology
Daniel Iglesias Duro
Title: CRISPR/Cas9-based transcriptional regulation in Arabidopsis thaliana
Supervisor: Markus Schmid
Room: KB4C10 Lecture Room
Department of Plant Physiology
Daniel Iglesias Duro
Title: CRISPR/Cas9-based transcriptional regulation in Arabidopsis thaliana
Supervisor: Markus Schmid
Room: KB4C10 Lecture Room
UPSC Monday Seminar 2016
03-Oct-2016 9:00 - 10:00
UPSC Monday Seminar 2016
Speakers:
Umut Rende (PhD student)
Supervisor: Totte Niittylä
Suman Paul (Postdoc)
Supervisor: Göran Samuelsson
Speakers:
Umut Rende (PhD student)
Supervisor: Totte Niittylä
Suman Paul (Postdoc)
Supervisor: Göran Samuelsson
Cutting Edge Seminar: Andrew Millar
03-Oct-2016 10:00 - 11:00
Cutting Edge Seminar
Speaker: Andrew Millar
Centre for Synthetic and Systems Biolgy, University of Edinburgh, Scotland, UK
Title: Biological timing, from rhythmic phosphoproteomics to predicting carbon biomass.
Host: Maria Eriksson and Johannes Hanson
Room: KB3A9 Lilla hörsalen
Speaker: Andrew Millar
Centre for Synthetic and Systems Biolgy, University of Edinburgh, Scotland, UK
Title: Biological timing, from rhythmic phosphoproteomics to predicting carbon biomass.
Host: Maria Eriksson and Johannes Hanson
Room: KB3A9 Lilla hörsalen
Thesis Defence: Louise Norén Lindbäck
06-Oct-2016 10:00 - 13:00
Thesis Defence Department of Plant Physiology
Louise Norén Lindbäck
Title: Coordination of two different genomes in response to light and stress.
Faculty Examiner: Dr Antony Dodd, School of Biological Sciences, University of Bristol, UK
Supervisor: Åsa Strand
Room: Lilla hörsalen, KB3A9
Louise Norén Lindbäck
Title: Coordination of two different genomes in response to light and stress.
Faculty Examiner: Dr Antony Dodd, School of Biological Sciences, University of Bristol, UK
Supervisor: Åsa Strand
Room: Lilla hörsalen, KB3A9
UPSC Seminar: Dominique Loqué
06-Oct-2016 15:00 - 16:00
Speaker: Dominique Loqué
Director of Cell Wall Engineering at the Joint BioEnergy Institute, UC Berkeley, CA, USA
Title: Synthetic Biology and Bioengineering to Optimize Energy Crops
Host: Totte Niittylä
Room: KB3B1 Stora hörsalen
Director of Cell Wall Engineering at the Joint BioEnergy Institute, UC Berkeley, CA, USA
Title: Synthetic Biology and Bioengineering to Optimize Energy Crops
Host: Totte Niittylä
Room: KB3B1 Stora hörsalen
UPSC Monday Seminar 2016
10-Oct-2016 9:00 - 11:00
UPSC Monday Seminar 2016
Speakers:
Johanna Carlsson (PhD student)
Supervisor: Ulrika Egertsdotter
Hailiang Mao (Postdoc)
Supervisor: Markus Grebe, Ove Nilsson
Speakers:
Johanna Carlsson (PhD student)
Supervisor: Ulrika Egertsdotter
Hailiang Mao (Postdoc)
Supervisor: Markus Grebe, Ove Nilsson
Seminar: Paul Dijkwel
10-Oct-2016 14:00 - 15:00
Speaker: Paul Dijkwel
Institute of Fundamental Sciences
Massey University
New Zealand
Title: Eternal youth in plants: reuse, reduce, and discard!
Host: Stefan Jansson
Place: KB3A9 Lilla hörsalen
Time: 14.00
Thesis Defence: Erik Edlund
11-Oct-2016 10:00 - 13:00
Thesis Defence Department of Plant Physiology
Erik Edlund
Title: Regulatory Control of Autumn Senescence in Populus tremula.
Faculty Examiner: Paul Dijkwel, Institute of Fundamental Sciences, Massey University, New Zealand
Supervisor: Stefan Jansson
Room: Stora hörsalen, KB3B1
Erik Edlund
Title: Regulatory Control of Autumn Senescence in Populus tremula.
Faculty Examiner: Paul Dijkwel, Institute of Fundamental Sciences, Massey University, New Zealand
Supervisor: Stefan Jansson
Room: Stora hörsalen, KB3B1
UPSC Seminar: Marek Mutwil
12-Oct-2016 14:00 - 15:00
UPSC Seminar
Speaker: Marek Mutwil
Max-Planck-Institut für Molekulare Pflanzenphysiologie Golm, Potsdam, Germany
Title: Beyond genomics: studying evolution with gene networks.
Host: Totte Niittylä
Room: KB3A9 Lilla hörsalen
Speaker: Marek Mutwil
Max-Planck-Institut für Molekulare Pflanzenphysiologie Golm, Potsdam, Germany
Title: Beyond genomics: studying evolution with gene networks.
Host: Totte Niittylä
Room: KB3A9 Lilla hörsalen
Thesis Defence: Marie Holmgren
14-Oct-2016 14:00 - 17:00
Thesis Defence Department of Plant Physiology
Marie Holmgren
Title: Trametes versicolor as biodegrader of lignocellulose and biocatalyst during ethanol fermentation.
Faculty Examiner: Mohammad Taherzadeh, professor in Bioprocess Technology, Swedish Centre of Resource Recovery University of Borås.
Supervisor: Anita Sellstedt
Room: Lilla hörsalen, KB3A9
Marie Holmgren
Title: Trametes versicolor as biodegrader of lignocellulose and biocatalyst during ethanol fermentation.
Faculty Examiner: Mohammad Taherzadeh, professor in Bioprocess Technology, Swedish Centre of Resource Recovery University of Borås.
Supervisor: Anita Sellstedt
Room: Lilla hörsalen, KB3A9
UPSC Monday Seminar 2016
17-Oct-2016 9:00 - 11:00
UPSC Monday Seminar 2016
Speakers:
Chanaka Mannapperuma (PhD student)
Supervisor: Nathaniel Street
Bo Zhang (Postdoc)
Supervisor: Ove Nilsson
Speakers:
Chanaka Mannapperuma (PhD student)
Supervisor: Nathaniel Street
Bo Zhang (Postdoc)
Supervisor: Ove Nilsson
Honory doctor lecture: Norman Hüner
21-Oct-2016 14:00 - 15:00
UPSC Seminar
Honory doctor lecture by Norman Hüner
Department of Biology, Western University, Ontario, Canada
Honorary doctor at Umeå University
Title: Photosynthesis, cold acclimation and crop productivity
Host: Gunnar Öquist
Room: KB.E3.01 Lilla hörsalen (formerly KB3A9)
More information about Norman Hüner
Honory doctor lecture by Norman Hüner
Department of Biology, Western University, Ontario, Canada
Honorary doctor at Umeå University
Title: Photosynthesis, cold acclimation and crop productivity
Host: Gunnar Öquist
Room: KB.E3.01 Lilla hörsalen (formerly KB3A9)
More information about Norman Hüner
UPSC Monday Seminar 2016
24-Oct-2016 9:00 - 11:00
UPSC Monday Seminar 2016
Speakers:
Daniel Decker (PhD student)
Supervisor: Leszek Kleczkowski
Kerstin Richau (Postdoc)
Supervisor: Nathaniel Street
Speakers:
Daniel Decker (PhD student)
Supervisor: Leszek Kleczkowski
Kerstin Richau (Postdoc)
Supervisor: Nathaniel Street