Splits and Tight-Spans of Convex Polytopes
Location: S3.05
Date: 15:30-16:30 8 Nov 2010
Speaker: Dr Sven Herrmann
Institution: School of Computing Sciences, UEA
Abstract: A split of a convex polytope P is a (regular) subdivision with exactly two maximal cells. The tight-span of a subdivision of P is the complex dual to its complex of inner faces. Both concepts were introduced in the case of a very special polytope in order to study decompositions of finite metric spaces. However, we will explain how the concept of splits (and possible generalisations of it) can be used to obtain a better understanding of polytopes and their subdivisions in general. We show that each weight function on the vertices of P admits a unique decomposition into splits with a split prime remainder. Introducing the concept of compatibility of splits gives rise to a finite simplicial complex associated with P, the split complex of P. In the second part of the talk our theory we be used to give examples of applications in different parts of mathematics, one in phylogenetics and another in tropical geometry.
The seminar is in collaboration with the School of Mathematics.

Interfacing with Industry
Location: D'Arcy Thompson Room, School of Computing Sciences, UEA
Date: 14.00-15.00 29 Oct 2010
Speaker: Dr. Dominic Clark
Organiser: Dr. Katharina Huber
Institution: EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton
Abstract: In this presentation, Dr. Clark will describe the various forms of interaction between EMBL-EBI and industrial companies and organisations though the EMBL-EBI Industry Programme and the EMBL-EBI SME Forum. For the Industry Programme, he will describe the principal industry drivers behind the involvement of companies in the Industry Programme and some of the pre-competitive projects that have resulted. For the SME Forum, he will describe the key factors of interest to the smaller sized companies and how interactions are managed.

This week's seminar is replaced by JIC's "Annual Science meeting" held from Oct. 13-15.
Location: John Innes Centre Auditorium
Date: 3 whole days 13 Oct 2010 – 15 Oct 2010
Organiser: Prof. James Brown, JIC
Institution: John Innes Centre
If you would like to attend please contact Samantha Lingwood, JIC

A new algorithm for drawing split networks
Location: D'Arcy Thompson Room, School of Computing Sciences, UEA
Date: 15:00-16:00 20 Sep 2010
Speaker: Dr. Andreas Spillner
Institution: University of Greifswald, Germany
Abstract: Split networks have been developed as a tool to visualize collections of bipartions of a finite set, so called split systems. Such collections arise, for example, in the process of reconstructing the evolutionary history of a set of species. We present a polynomial time algorithm that allows to compute drawings of split networks without crossing edges for a large class of split systems. In addition, we show that the drawings produced by our algorithm are optimal in the sense that any drawing with less edges would necessarily miss out some of the information contained in the given split system.

EMBO Practical Course on Multi-level Modelling of Morphogenesis
Location: JIC Conference Centre G34/35
Date: 22 Jul 2010
Organiser: Drs Stan Marée, Verônica Grieneisen and Professor Enrico Coen Institution: John Innes Centre
Programme:

  • 20th July 15:00 - 16:00 Dr Kirsten ten Tusscher, Utrecht University, The Netherlands: Three-dimensional heart modelling
  • 21st July 15:00 - 16:00 Dr Stan Marée ,John Innes Centre, UK: Modelling T-cell dynamics
  • 22nd July 15:00 - 16:00 Professor Kees Weijer, University of Dundee, UK: Mechanics of cell movement in Dictyostelium and chick development
  • 23rd July 15:00 - 16:00 Professor Martin Howard, John Innes Centre, UK: Fluctuating gradients inside single cells: cell division regulation in fission yeast
  • 24th July 11:30 - 12:30 Dr Nick Monk, University of Nottingham, UK: Root hair positioning
  • 26th July 11:30 - 12:30 Dr Richard Smith, University of Bern, Switzerland: Modelling the shoot apex and morphogenesis with V V
  • 26th July 15:00 - 16:00 Professor Yves Couder, École Normale Supérieure, Paris, France: Phyllotaxis
  • 27th July 15:00 - 16:00 Professor Andrew Bangham, University of East Anglia, UK : Modelling the growth of flowers
  • 28th July 15:00 - 16:00 Dr Kristin Sherrard, University of Chicago, USA: Sequential activation of apical and basolateral contractility drive endoderm invagination in ascidian embryos
  • 29th July 15:00 - 16:00 Professor Isabel Palmeirim, University of Algarve, Portugal: The clock in space and time
  • 30th July 13:45 - 14:45 Dr Nadine Peyriéras, Institut de Neurobiologie Alfred Fessard, Paris, France: Multi-level morphogenesis: a view towards the future

Looking after the neighbourhood: Noise abatement and genome evolution
Location: JIC Conference Centre, G34/35 (Watson & Crick)
Date: 16.00 22 Jun 2010
Speaker: Professor Laurence Hurst
Organiser: Professor Martin Howard
Institution: University of Bath, UK

Scheduling developmental events and its impact on plant form
Location: JIC Auditorium
Date: 11.30 28 May 2010
Speaker: Dr Yuval Eshed
Organiser: Susana Sauret-Gueto
Institution: Weizmann Institute of Science, Israel

The goldilocks principle: from microtubulespatial organisation to plant cell shape
Location: Biffen Annex, Seminar Room 117, JIC
Date: 16.00 11 May 2010
Speaker: Professor Geoffrey Wasteneys
Organiser: Dr Veronica Grieneisen
Institution: The University of British Columbia, Vancouver, BC Canada

DNA and biological relationships
Location: D'Arcy Thompson Room, School of Computing Sciences, UEA
Date: 14.00-15.00 30 Apr 2010
Speaker: Dr. Thomas Haizel
Organiser: Dr. Katharina Huber
Institution: Anglia DNA Services Limited
Abstract: DNA testing is increasingly becoming more poplar. It is used among others to establish paternity and other biological relationships. This talk is designed to give a background in the use of DNA to establish biological relationships. The talk will include the science of DNA analysis, and an overview of the latest advances in DNA testing for the courts and forensic purposes.

Excitement in sexual plant reproduction: the remarkable biology of pollen tubes and their urges for models
Location: (Watson & Crick) JIC Conference Centre
Date: 16.00 27 Apr 2010
Speaker: Professor Jose Feijo
Organiser: Dr Veronica Grieneisen
Institution: Instituto Gulbenkian de Ciencia (IGC)

Phenomenological reconstruction of Danio rerio early embryogenesis
Location: Genome Centre Seminar Room, JIC
Date: 16.00 23 Mar 2010
Speaker: Dr Nadine Peyrieras
Organiser: Dr Stan Maree
Institution: Institut de Neurobiologie Alfred Fessard, Paris, France

Weighted and directed networks in biology
Location: Barton Room, IFR
Date: 14.00 17 Mar 2010
Speaker: Dr Sebastian Ahnert
Organiser: Dr József Baranyi
Institution: Cambridge
Abstract: We introduce a novel way of detecting patterns and correlations in microarray time series and discuss how the correlations between them can be viewed as a weighted network. By measuring the properties of this network, such as the clustering coefficents of its nodes, we can assess the importance of each gene in the biological process underlying the microarray measurements. In addition we also discuss a new way to classify directed networks and show how the properties of several types of real-world networks, including transcription networks and food webs, differ significantly in this classification.

The interwinding nature of protein-protein interfaces
Location: D'Arcy Thompson Room, School of Computing Sciences, UEA
Date: 14.00-15.00 16 Mar 2010
Speaker: Prof. Kei Yura
Organiser: Dr. Katharina Huber
Institution: Ochanomizu University, Tokyo, Japan
The interwinding nature of protein-protein interfaces and its implication for protein complex formation.
Motivation: Structural features at protein-protein interfaces can be studied to understand protein-protein interactions. It was noticed that in a dataset of 45 multimeric proteins the interface could either be described as flat against flat or protruding/interwound. In the latter, residues within one chain were surrounded by those in other chains, whereas in the former they were not.
Results: A simple method was developed that could distinguish between these two types with results that matched those made by a human annotator. Applying this automatic method to a large dataset of 888 structures, chains at interfaces were categorized as non-surrounded or surrounded. It was found that the surrounded set had a significantly lower folding tendency using a sequence based measure, than the non-surrounded set. This suggests that before complexation, surrounded chains are relatively unstable and may be involved in 'fly-casting'. This is supported by the finding that terminal regions are overrepresented in the surrounded set.
Availability

Species, Clusters and the ʽTree of Lifeʼ
Location: D'Arcy Thompson Room, UEA
Date: 14.00-15.00 12 Mar 2010
Speaker: Dr. Taoyang Wu
Organiser: Dr. Katharina Huber
Institution: School of Computing Sciences, UEA
Abstract: A hierarchical structure describing the inter-relationships of species has long been a fundamental concept in systematic biology, from Linnean classification through to the more recent quest for a Tree of Life. In this talk we introduce an approach based on discrete mathematics to address a basic question: Could one delineate this hierarchical structure in nature purely by reference to the genealogy of present-day individuals, which describes how they are related with one another by ancestry through a continuous line of descent? We describe several mathematically precise ways by which one can naturally define collections of subsets of present day individuals so that these subsets are nested (and so form a tree) based purely on the directed graph that describes the ancestry of these individuals. We also explore the relationship between these and related clustering constructions.

Biophysical models of starch breakdown in plant leaves
Location: G34/35 (Watson & Crick) JIC Conference Centre
Date: 16.00 9 Mar 2010
Speaker: Dr Oliver Ebenhoeh
Organiser: Professor Martin Howard
Institution: University of Aberdeen, Scotland

Detecting outliers in latent variable models for categorical responses
Location: D'Arcy Thompson room, University of East Anglia
Date: 14.00 5 Mar 2010
Speaker: Dr. Irini Moustaki
Organiser: Dr. Hywel Williams
Institution: London School of Economics
Abstract: Different approaches for detecting outliers in categorical responses using a latent variable model.
I will discuss different approaches for detecting outliers in categorical responses using a latent variable model. Outliers are considered to be those response patterns that are not fitted by the hypothesized model and they are expected to be generated by secondary response strategies such as guessing. For the first part of my talk I will discuss the forward search algorithm for detecting outliers and for the second part I will present a model that accounts for outliers or over-represented response patterns. The proposed model is an extended latent trait model that models the guessing mechanism through an unobserved pseudo-item. Both methods will be illustrated with simulated and real examples.

Hormonal interaction during root meristem growth
Location: G34/35 (Watson & Crick) JIC Conference Centre
Date: 16.00 hrs 2 Mar 2010
Speaker: Dr Sabrina Sabatini
Organiser: Dr Veronica Grieneisen
Institution: Universita La Sapienza, Rome, Italy

Selection versus Demography: evolutionary history of wild tomatoes
Location: Genome Centre Seminar Room, Norwich Research Park
Date: 11.30 19 Feb 2010
Speaker: Dr. Aurelien Tellier
Organiser: Dr. James Brown
Institution: University of Munich
DSB Seminar Series
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Modelling DivIVA-mediated branching in Streptomyces
Location: G34/35 (Watson & Crick) JIC Conference Centre
Date: 16.00 2 Feb 2010
Speaker: Dr. David Richards, JIC
Organiser: Professor Martin Howard
Institution: John Innes Centre

Short-read de-novo assembly for large genomes
Location: D'Arcy Thompson Room, School of Computing Sciences, UEA
Date: 14.00-15.00 29 Jan 2010
Speaker: Dr. Mario Caccamo, Head of Bioinformatics, TGAC
Organiser: Dr. Katharina Huber
Institution: The Genome Analysis Centre, (TGAC)
Abstract: Next generation sequencing technologies offer an unprecedented wealth of genomic data, but also huge computational challenges. The sheer volume of data requires a new level of software sophistication both to cope with the load, and to analyse it effectively.
We present a new, highly memory-efficient de Bruijn software suite, Cortex, capable of simultaneously loading and analysing short and long reads from multiple genomes. This provides a valuable framework for the efficient implementation of novel algorithms for the analysis of genomic sequences. We have investigated the application of Cortex to the assembly of large eukaryote genomes. The advantages of de Bruijn graph approach to short-read for small genomes is well-documented in the literature. One of the issues in upgrading the current algorithms to longer genomes is the memory usage. In Cortex, this problem is addressed with a combined strategy: optimised memory efficient data structures and a divide-and-conquer approach. These techniques can be modified to be applied to other settings such as transcriptome analysis and metagenomics.
We have also explore the application of this methodology to the discovery and direct analysis of structural variants across whole genomes. Cortex allows us to directly verify shared variation in sequence data from different individuals, in a consistent manner right across the structural variation spectrum from SNPs to large structural variants. The marginal cost of adding individuals reduces, as they contribute fewer new k-mers. We are therefore able to load full genomic datasets from many different individuals in the same data structure, and directly search for sequence differences. One of the strengths of this approach is that does not require a reference sequence or coordinate-based analysis. Cortex has been developed by Zamin Iqbal (University of Oxford, UK) and Mario Caccamo (The Genome Analysis Centre, Norwich, UK).