Summer Meeting 2011

Friday 10th June 2011

Scientific Session, Presentation of IBS Honorary Life Membership to Robert Curnow & Excursion

National University of Ireland Galway

This one-day event will be hosted by NUI Galway and will combine a programme of talks with an excursion and a chance to experience the unique landscape and flora of the west of Ireland. We hope that it will be a very special and enjoyable day including a talk from Ray Carroll and the presentation of an IBS Honorary Life Membership to Robert Curnow,

To reserve your place, please email John Hinde (

The cost, including a light lunch and refreshements, is €10 (members) and €30 (non-members) payable on the day.


The presentions will given in the Martin Ryan Institute Lecture Theatre - this is on level 2 in the new Ryan Institute extension. The Ryan Institute is directly in front of the main University Quadrangle Building, along the tree-lined avenue, and the extension is the new building on the right.


There are good rail and coach links from Dublin and Dublin airport to Galway. It is also possible to fly directly to Galway from Southend and Luton with Aer Arann:


There is a wide range of accommodation options in Galway. If need be, we can send you a list.


 Document downloads for IBS members.
Join us now.
09:30 - 10:00Registration

In the foyer of the Ryan Institute Lecture Theatre, see map


10:00 - 10:30Time-varying parameters in the study of fish population dynamics

Coilin Minto (Galway-Mayo Institute of Technology)

Recruitment, the process whereby new individuals enter a given stage of a fish population is a key concern in fisheries ecology and resource management. Traditional approaches to statistical modelling of recruitment have largely focussed on constant parameter estimation. While this approach has proven useful, it ignores the potential for inter-annual parameter change. The maximum reproductive rate is a parameter of central importance to recruitment. It determines, amongst others, the intrinsic rate of population growth, productivity, overfishing limits and management reference points. Allowing the maximum reproductive rate to follow a stochastic process provides an opportunity to track changes in productivity through time.

In this talk, I give an overview of previous foundational single-population applications using dynamic linear models estimated via a Kalman filter. The estimation is then extended to the multivariate case, where the covariance structure of the trends in productivity across taxa and geographic regions is also of interest. Example applications to marine fish species and communities across the North Atlantic are provided.

10:30 - 11:00Clustering time-course microarray data using the linear mixed effects model

Norma Coffey (NUIG)

Time-course microarray analyses involve measuring the expression levels of thousands of genes repeatedly through time. Multivariate clustering methods such as principal components analysis, k-means clustering, finite mixture models etc.  have difficulties handling missing values, require uniform sampling for all genes, fail to account for the correlation between measurements made on the same gene or do not facilitate the removal of noise from the measured data thus ignoring any smoothness that may be evident in the expression profiles. This talk proposes the use of curve-based clustering, which can handle the latter issues. We use the linear mixed effects model representation of penalized spline smoothing to estimate the gene expression curves which provides a framework for simultaneously determining a smooth estimate of the mean expression profile in each cluster, determining estimates of the gene-specific expression profiles within a cluster through the use of additional random effects and clustering expression profiles using mixtures of mixed effects models.

11:00 - 11.15Coffee
11:15 - 12:00Powerful Methods for Understanding Gene-Environment Interactions

Raymond J. Carroll (Texas A & M University, USA)

We consider population-based case-control studies of gene-environment interactions using prospective logistic regression models. Data sets like this arise when studying pathways based on haplotypes as well as in multistage genome wide association studies (GWAS). In a typical case-control study, logistic regression is used and there is little power for detecting interactions. However, in many cases it is reasonable to assume that, for example, genotype and environment are independent in the population, possibly conditional on factors to account for population stratification. In such as case, we have developed an extremely statistically powerful semiparametric approach for this problem, showing that it leads to much more efficient estimates of gene-environment interaction parameters and the gene main effect than the standard approach: decreases of standard errors for the former are often by factors of 50% and more. 

I am going to review case-control studies, and show a new look at them that allows new methods to handle gene-environment interactions. Illustrations with various data sets will be made.


12:00 - 12:15IBS Honorary Life Membership Award to Robert Curnow
12:15 - 13:00Lunch
13:00 - 18:00Excursion

Visit to Carna Research Station  the NUIGalway Ryan Institute’s base for large scale, exploratory aquatic investigations, and both applied and basic research, on existing and novel species for aquaculture. We will also take in  Mace Head Atmospheric Research Station, a site for aerosol measurements since 1958.. Both of these are located in Connemara about an hour from Galway city. This will provide a chance to appreciate the wild setting of the West of Ireland and to see a diversity of applied research.



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