Future events

THURSDAY Biostatistical Seminar: Robin Andersson

Thursday, April 27, 2017 - 14:30

Speaker: Robin Andersson, Assistant Professor, The Bioinformatics Centre, University of Copenhagen, Denmark

Title: Characterisation of regulatory activities and active chromatin architectures from transcription initiation events

Note: This biostatistics seminar is jointly organised with the Sven Furberg Seminars in Bioinformatics and Statistical Genomics. At the end of the seminar simple food and refreshments will be served.

Abstract: The correct activities of gene regulatory elements and their interplay are essential for the correct coordinated transcriptional activities within a cell. Transcription is regulated in part by events at gene promoters and at gene-distal transcriptional enhancers, whose activities are influenced by local chromatin characteristics and favourable chromatin architectures bringing distant enhancers close to their target promoters in three-dimensional space.

In this talk, I will describe our efforts to characterise the inherent transcriptional activities at regulatory elements using Cap Analysis of Gene Expression (CAGE) and how such data can be used as a proxy to infer the regulatory activities of a cell. I will further present our work on modelling regulatory architectures by decomposition of expression data into positionally dependent and independent components. The independent component carries information about promoter-localised and expression-level associated effects. The positional component is highly reflective of chromatin organisation, revealing chromatin compartments, boundaries of transcriptionally active topologically associating domains, and proximity interactions as defined by chromatin conformation capture data. In all, our work demonstrates a close relationship between transcription and higher order regulatory organisations.

Organizer: Oslo Centre for Biostatistics and Epidemiology (OCBE), Research group in Statistics and Biostatistics, Dept. of Mathematics, UiO, Big Insight and the Sven Furberg Seminars in Bioinformatics and Statistical Genomics

Location: 
Forskningsparken (Oslo Science Park), HAGEN 3

Wednesday Lunch: TBA

Wednesday, May 3, 2017 - 12:00

Speaker: TBA

The lunch starts at 12:00, and the talk will start around 12:20.

 

NB: Wednesday BigInsight Lunches are open to staff and students from any of the BigInsight partners, including UiO, but not to others

Location: 
Spiseriet, Norwegian Computing Center

THURSDAY Biostatistical Seminar: Jukka Corander

Thursday, May 4, 2017 - 14:15

Speaker: Jukka Corander, Professor, Oslo Centre for Biostatistics and Epidemiology, Dept. of Biostatistics, University of Oslo

Title: Fast inference for intractable ultra high-dimensional Potts models for genome sequence data

Coffee/tea served from 14:15 and the talk will start around 14:30.

Abstract: The potential for genome-wide modeling of epistasis has recently surfaced given the possibility of sequencing densely sampled populations and the emerging families of statistical interaction models. Direct coupling analysis (DCA) has earlier been shown to yield valuable predictions for single protein structures, and has recently been extended to genome-wide analysis of bacteria, identifying novel interactions in the co-evolution between resistance, virulence and core genome elements. However, earlier computational DCA methods have not been scalable to enable model fitting simultaneously to 104-105 polymorphisms, representing the upper bound of variation observed in genomic analyses of many bacterial species. We will introduce a novel inference method (SuperDCA) which employs a new scoring principle, efficient parallelization, optimization and filtering on phylogenetic information to achieve scalability for up to 105 polymorphisms. Using large population samples of Streptococcus pneumoniae, we demonstrate the ability of SuperDCA to make significant biological findings about this major human pathogen. We also show that our method can uncover weak signals of selection that are not detectable by genome-wide association analysis, even though our analysis does not require phenotypic measurements. SuperDCA thus holds considerable potential in building understanding about numerous organisms at a systems biological level.

Organizer: Oslo Centre for Biostatistics and Epidemiology (OCBE), Research group in Statistics and Biostatistics, Dept. of Mathematics, UiO and Big Insight

Location: 
Domus Medica, room 2240 (Dep. of Biochemistry)

TUESDAY Statistics Seminar: Willi Sauerbrei

Tuesday, May 9, 2017 - 14:15

Speaker: Willi Sauerbrei (Institute for Medical Biometry and Statistics, University of Freiburg)

Title: Regression model-building with continuous variables – multivariable fractional polynomials, with extensions for interactions

Abstract: In the analysis of studies in clinical epidemiology, the number of candidate variables for a regression model is often too large and a more parsimonious model is sought. Another key issue is the determination of appropriate dose-response functions for continuous covariates. Often, continuous predictors are either categorized or linearity is assumed. However, both approaches can have major disadvantages and models incorporating non-linear functions may markedly improve the fit. The method of multivariable fractional polynomials (MFP) simultaneously determines suitable functional forms for continuous covariates and eliminates uninfluential covariates (1,2,3). The method also allows categorical and binary covariates.

By analysing data in the framework of linear, logistic and Cox regression models, we discuss model-building issues with an emphasis on MFP. Extensions of MFP have been developed to investigate for interactions between continuous covariates and treatment (MFPI), between two continuous covariates (MFPIgen) and for interactions with time (non-proportional hazards, MFPT) in a Cox model (3,4,5). Using data from a large cohort study, we show that mis-modelling non-linear main effects can introduce spurious interactions between two continuous covariates. In RCTs, we illustrate that our approach has power to identify differential treatment effects, and demonstrate how to estimate and plot a continuous treatment-effect function. In a large simulation studies we could show that MFPI has advantages to several alternative approaches (5).

We conclude that MFP and its extensions for interactions are useful in multivariable model-building with continuous and categorical variables. MFP software for Stata, SAS and R is generally available (6).

Joint work with Patrick Royston (MRC Clinical Trials Unit, London, UK). For more details see http://mfp.imbi.uni-freiburg.de/

References:

  1. Royston P and Altman DG (1994): Regression using fractional polynomials of continuous covariates: parsimonious parametric modelling (with disc.) Applied Statistics, 43: 429-467
  2. Sauerbrei W and Royston P (1999): Building multivariable prognostic and diagnostic models: transformation of the predictors using fractional polynomials. Journal of the Royal Statistical Society, Series A, 162: 71-94
  3. Royston P, Sauerbrei, W (2008): ‘Multivariable Model-Building – A pragmatic approach to regression analysis based on fractional polynomials for modelling continuous variables’. Wiley.
  4. Sauerbrei W, Royston P, Look M (2007): A new proposal for multivariable modelling of time-varying effects in survival data based on fractional polynomial time-transformation. Biometrical Journal, 49: 453-473
  5. Royston P., Sauerbrei W. (2014): Interaction of treatment with a continuous variable: simulation study of power for several methods of analysis. Statistics in Medicine, 33: 4695-4708
  6. Sauerbrei W, Meier-Hirmer C, Benner A, Royston P (2006): Multivariable regression model building by using fractional polynomials: description of SAS, STATA and R programs, Computational Statistics and Data Analysis, 50: 3464-3485
Location: 
Department of Mathematics, room Sverdrups plass (lunch area) on the 8th floor of Niels Henrik Abels hus

THURSDAY Biostatistical Seminar: Cristopher Yau

Thursday, May 18, 2017 - 14:30

Speaker: Cristopher Yau, Reader in Computational Biology, Centre for Computational Biology, University of Birmingham, UK

Title: TBA

Note: This biostatistics seminar is jointly organised with the Sven Furberg Seminars in Bioinformatics and Statistical Genomics. At the end of the seminar simple food and refreshments will be served.

Abstract: TBA

Organizer: Oslo Centre for Biostatistics and Epidemiology (OCBE), Research group in Statistics and Biostatistics, Dept. of Mathematics, UiO, Big Insight and the Sven Furberg Seminars in Bioinformatics and Statistical Genomics

Location: 
TBA

Wednesday Lunch: TBA

Wednesday, May 24, 2017 - 12:00

Speaker: TBA

The lunch starts at 12:00, and the talk will start around 12:20.

 

NB: Wednesday BigInsight Lunches are open to staff and students from any of the BigInsight partners, including UiO, but not to others

Location: 
Sverdrups plass (lunch area), 8th floor N. H. Abels hus, Department of Mathematics

THURSDAY Biostatistical Seminar: Roderic Guigò

Thursday, June 22, 2017 - 14:30

Speaker: Roderic Guigò, Professor, Centre de Regualció Genòmica, Barcelona, Spain

Title: TBA

Note: This biostatistics seminar is jointly organised with the Sven Furberg Seminars in Bioinformatics and Statistical Genomics. At the end of the seminar simple food and refreshments will be served.

Abstract: TBA

Organizer: Oslo Centre for Biostatistics and Epidemiology (OCBE), Research group in Statistics and Biostatistics, Dept. of Mathematics, UiO, Big Insight and the Sven Furberg Seminars in Bioinformatics and Statistical Genomics

Location: 
TBA