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Meet the instructors: Kathryn Lilley, Cambridge Centre for Proteomics

Meet the instructors: Kathryn Lilley, Cambridge Centre for Proteomics | 'omics | Scoop.it

The Cambridge Centre for Proteomics (CCP) was set up initially with BBSRC funding as part of the Investigating Gene Function Initiative (IGF) to provide a proteomics resource for the UK Arabidopsis and Drosophila communities. CCP now collaborates with numerous investigators from these communities, and the Cambridge research community, in a wide range of proteomic projects. Such collaborations range from small-scale protein identification in purified protein samples, to systematic analysis of significant protein differences in complex mixtures. Details of these collaborations and more information about CCP can be found on our web site.

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Meet the instructors: Leighton Pritchard, The James Hutton Institute

Meet the instructors: Leighton Pritchard, The James Hutton Institute | 'omics | Scoop.it

My research centres around plant-pathogen interactions. Primarily, I aim to understand what it is about microbial plant pathogens that enables them to infect plants, and what it is is about plants that allows microbes to cause disease on them. As a computational biologist, most of my work involves the computational and mathematical analysis of biological data such as genome sequences, microarray gene expression profiles, and networks of metabolic and regulatory processes.

 

Computational biology and bioinformatics.

Oomycete and bacterial plant pathogens.

Systems biology of plant-pathogen interactions.

Comparative genomics of plant pathogens.

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Meet the instructors: Dan MacLean, The Sainsbury Laboratory

Meet the instructors: Dan MacLean, The Sainsbury Laboratory | 'omics | Scoop.it

My role is to provide The Sainsbury Laboratory with cutting edge bioinformatics expertise and resources. Particular areas of expertise include genomics in particular assembly and alignment with high-throughput sequencing data, genetic polymorphism detection, homology search and automatic sequence annotation, transcriptomics (microarray and RNA-seq), statistical analysis, mathematical and systems-biology approaches to modelling and visualising data and large scale phosphoproteomics analysis. I also provide extensive training in bioinformatics from basic computer use and scripting for the new user up to discussion of new techniques and algorithms for working bioinformaticians. I maintain a small library of print and digital training resources and a busy calendar of training events much of which may be viewed online here http://tsltraining.tsl.ac.uk/.

 

My research can be divided into two complementary streams; tool and resource development and systems biology of plant and pathogen interactions.

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Meet the instructors: Alex Jones, The Sainsbury Laboratory

Meet the instructors: Alex Jones, The Sainsbury Laboratory | 'omics | Scoop.it

My role within the Sainsbury Laboratory is to facilitate and support entry level usage of mass spectrometry for the identification of proteins and their post-translational modifications. My post-doctoral experience includes protein purification, several different types of mass spectrometry and two-dimensional gel electrophoresis.

 

I have a strong background in plant pathology and brassica research from my previous posts at Imperial College (www.imperial.ac.uk) (Rossiter, Grant and Feys groups) and CEH, Dorset (www.ceh.ac.uk).

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Meet the instructors: Brendan MacLean, University of Washington Medicine, Seattle

Meet the instructors: Brendan MacLean, University of Washington Medicine, Seattle | 'omics | Scoop.it

Brendan worked at Microsoft for 8 years in the 1990s where he was a lead developer and development manager for the Visual C++/Developer Studio Project. Since leaving Microsoft, Brendan has been the Vice President of Engineering for Westside Corporation, Director of Engineering for BEA Systems, Inc., Sr. Software Engineer at the Fred Hutchinson Cancer Research Center, and a founding partner of LakKey Software. In this last position he was one of the key programmers responsible for the Computational Proteomics Analysis System (CPAS), made significant contributions to the development of X!Tandem and the Trans Proteomic Pipeline, and created the LabKey Enterprise Pipeline. For the last 3 and a half years he has worked as a Sr. Software Engineer within the MacCoss lab and been responsible for all aspects of design, development and support in creating the Skyline Targeted Proteomics Environment and its growing worldwide user community.

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How to apply de Bruijn graphs to genome assembly : Nature Biotechnology : Nature Publishing Group

A mathematical concept known as a de Bruijn graph turns the formidable challenge of assembling a contiguous genome from billions of short sequencing reads into a tractable computational problem.
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An online resource for latest discussions in HTGS

An online resource for latest discussions in HTGS | 'omics | Scoop.it
SEQanswers is a discussion forum and information source for next generation sequencing.
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Meet the instructors: Eric Kemen, Max Planck Institute for Plant Breeding Research

Since new races of pathogens constantly emerge, new disease resistance (R) genes are needed for crop protection. One of the sources which has not been exploited so far is non-host resistance. In most cases pathogens fail on a non-host because their effectors have not been selected to evade recognition by the plant and thus trigger resistance. In order to make use of this kind of resistance it is important to know how pathogens evade recognition or how they suppress the defence reactions.

 

To identify these important suppressors, my goal is to sequence the genomes of three A. candida strains to make them available for computational analysis. The genomes will be assembled from short sequence reads generated by the Solexa technique which allows generating cheaper sequence data compared to other techniques. Since the Solexa technique was not used for de novo sequencing of eukaryotic genomes so far, my current interest is to establish this technique to make it available for de novo sequencing of different sizes of genomes (reaching from prokaryotic to eukaryotic ones).

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This page is in support of the EMBO Course "Plant-Microbe Interaction" held in Norwich, June 2012

This page is in support of the EMBO Course "Plant-Microbe Interaction" held in Norwich, June 2012 | 'omics | Scoop.it

The last 20 years have provided a sophisticated understanding of how plants recognize relatively conserved microbial patterns to activate defence. This workshop will cover broad aspects of the plant-microbe interaction and train methods to study and visualise intracellular interactions during pathogenesis and defence.

 

Organized by The Sainsbury Laboratory http://www.tsl.ac.uk/

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