Past courses
2013
Genomics and Clinical Microbiology 20-25 January 2013
The study of bacterial genomes is revolutionising clinical microbiology, and the clinical microbiologists of the future will have to process and interpret data very different from that provided by the agar-centric clinical microbiology labs of the 20th century. This laboratory-based training course combines practical hands-on laboratory and bioinformatics work with a set of faculty lectures by leaders in this exciting area. The principal aim is to equip clinical scientists, specialist registrars, and consultants in medical microbiology (including joint medical microbiology and infectious diseases) with sufficient understanding of these areas to meet these challenges in the future. The course will concentrate on techniques that are currently practicable but will also look to the likely application of ‘next generation’ sequencing approaches to clinical microbiology.
Course instructors
Professor Martin Maiden (University of Oxford)
Professor Stephen Gillespie (University of St Andrews)
Dr Cath Arnold (Health Protection Agency)
Mathematical Models for Infectious Disease Dynamics 4-15 February 2013
Over the last two decades, mathematical models have seen a huge development in all aspects of infectious diseases, from microbiology to epidemiology and evolution. Professionals in these fields are now exposed to a wide range of models, often without receiving appropriate training.
This intensive, two-week course is aimed at any life scientist, public health officer, or medical or veterinary professional with an interest in quantitative approaches to infectious disease dynamics and control in humans or animals. The programme will cover introductory and advanced concepts in mathematical modelling of infectious diseases.
Course instructors
Olivier Restif, Ellen Brooks Pollock, Andrew Conlan, TJ McKinley, Cerian Webb (University of Cambridge, Department of Veterinary Medicine)
Ken Eames (London School of Hygiene and Tropical Medicine)
Nik Cunniffe, Matt Castle and James Cox (University of Cambridge, Department of Plant Sciences)
Malaria Experimental Genetics 3-9 March 2013
This laboratory-based advanced course will give participants a working knowledge of and practical experience in cutting edge Plasmodium experimental genetics techniques, from designing gene targeting vectors and creating transgenic parasites to phenotyping the strains that result. The goal is to facilitate the participants’ own research careers by exposing them to state-of-the-art experimental approaches, while discussing the advantages and limitations of each approach.
The week-long practical course will cover experimental approaches to both the human parasite (Plasmodium falciparum) and the rodent parasite (Plasmodium berghei). The practical work will include several novel technological approaches, including production of gene targeting constructs using recombineering, which eliminates the need for PCR and restriction enzyme based ligation, and advanced molecular phenotyping approaches including next generation RNA sequencing and comparative mass spectrometry. The laboratory-based programme will be complemented by specific lectures in topical areas as well as a panel of distinguished guest speakers, who will present the latest research in the field.
Course instructors
Oliver Billker (Wellcome Trust Sanger Institute, Hinxton, UK)
Julian Rayner (Wellcome Trust Sanger Institute, Hinxton, UK)
2012
Genomics and Clinical Microbiology 22-27 January 2012
The study of bacterial genomes is revolutionising clinical microbiology, and the clinical microbiologists of the future will have to process and interpret data very different from that provided by the agar-centric clinical microbiology labs of the 20th century.This laboratory-based training course combines practical hands-on laboratory and bioinformatics work with a set of faculty lectures by leaders in this exciting area. The principal aim is to equip clinical scientists, specialist registrars, and consultants in medical microbiology (including joint medical microbiology and infectious diseases) with sufficient understanding of these areas to meet these challenges in the future.The course will concentrate on techniques that are currently practicable but will also look to the likely application of ‘next generation’ sequencing approaches to clinical microbiology.
Course instructors
Professor Martin Maiden (University of Oxford)
Professor Stephen Gillespie (University of St Andrews)
Dr Cath Arnold (Health Protection Agency)
Mathematical Models for Infectious Disease Dynamics 13-24 February 2012
Over the last two decades, mathematical models have seen a huge development in all aspects of infectious diseases, from microbiology to epidemiology and evolution. Professionals in these fields are now exposed to a wide range of models, often without receiving appropriate training.
This intensive, two-week course is aimed at any life scientist, public health officer, or medical or veterinary professional with an interest in quantitative approaches to infectious disease dynamics and control in humans or animals. The programme will cover introductory and advanced concepts in mathematical modelling of infectious diseases.
Course instructors
Olivier Restif, Ellen Brooks Pollock, Andrew Conlan, TJ McKinley, Cerian Webb (University of Cambridge, Department of Veterinary Medicine)
Ken Eames (London School of Hygiene and Tropical Medicine)
Nik Cunniffe, Matt Castle and James Cox (University of Cambridge, Department of Plant Sciences)
Malaria Experimental Genetics 4-10 March 2012
This laboratory-based advanced course will give participants a working knowledge of and practical experience in cutting edge Plasmodium experimental genetics techniques, from designing gene targeting vectors and creating transgenic parasites to phenotyping the strains that result. The goal is to facilitate the participants’ own research careers by exposing them to state-of-the-art experimental approaches, while discussing the advantages and limitations of each approach.
The week-long practical course will cover experimental approaches to both the human parasite (Plasmodium falciparum) and the rodent parasite (Plasmodium berghei). The practical work will include several novel technological approaches, including production of gene targeting constructs using recombineering, which eliminates the need for PCR and restriction enzyme based ligation, and advanced molecular phenotyping approaches including next generation RNA sequencing and comparative mass spectrometry. The laboratory-based programme will be complemented by specific lectures in topical areas as well as a panel of distinguished guest speakers, who will present the latest research in the field.
Course instructors
Oliver Billker (Wellcome Trust Sanger Institute, Hinxton, UK)
Julian Rayner (Wellcome Trust Sanger Institute, Hinxton, UK)
Exome Sequencing 15-24 April 2012
This new, laboratory-based training course provides a comprehensive overview of exome sequencing, also known as pulldown, sequence capture and targeted sequencing. Participants will gain practical laboratory experience as well as training in downstream data analysis, interpretation and validation.
Solution hybrid capture is used to enrich for all known exon sequences (the exome) or for customised regions from genomic DNA for the purpose of sequencing the regions of interest. The enriched targets are sequenced using next generation technology to a high coverage and analysed for variants.
Course instructors
Dr Cordelia Langford (Wellcome Trust Sanger Institute, Cambridge)
Dr Peter Ellis (Wellcome Trust Sanger Institute, Cambridge)
Dr Robert Andrews (Wellcome Trust Sanger Institute, Cambridge)
Dr Matthew Breen (North Carolina State University, USA)
Joint EMBL-EBI-Wellcome Trust Course: In silico Systems Biology 23-27 April 2012
Systems biology can now be considered an established and fundamental field in life sciences. It has facilitated the move from the identification of molecular ‘parts lists’ for living organisms towards synthesising information from different ‘omics’-based approaches to generate and test new hypotheses about how biological systems work. This joint EMBL-EBI-Wellcome Trust course will combine lectures and led discussions to identify the key challenges, opportunities and bottlenecks, with practical sessions on network analysis and network-based modelling.
Scientific Organising Committee
Nicolas Le Novere (EMBL-EBI, UK)
Julio Saez-Rodriguez (EMBL-EBI, UK)
Vicky Schneider (EMBL-EBI, UK)
Virus Discovery in the Clinical Setting 13-18 May 2012
This unique, laboratory-based training course focuses on how to investigate an evolving outbreak of an infectious disease. Theoretical and practical sessions are integrated around a theme of using modern laboratory and epidemiological methods to identify the source of an outbreak. There will be daily morning update sessions analysing the results from the previous day and exploring the next steps in both investigating the cause and managing the clinical situation.
It will provide training for specialty trainees in virology, medical microbiology and infectious diseases, veterinary sciences and health care scientists in the application of current molecular and serological techniques in identifying and characterising a novel virus in a clinical setting.
Course organisers
Dr Kevin Brown (Health Protection Agency)
Dr Mark Zuckerman (Health Protection Agency and King’s College Hospital)
Functional Genomics and Systems Biology 13-22 June 2012
This intensive laboratory and computer-based training course introduces participants to a wide range of post-genome techniques including practical experience in performing RNAi experiments, expression profiling using the latest platforms, yeast 2-hybrid analyses and hands on experience with sample preparation procedures for Illumina high throughput sequencing. Laboratory work will be complemented by training in state-of-the-art approaches to data analysis and interpretation through the use of a range of bioinformatics resources and systems biology tools, including R, Bioconductor, network analysis (e.g. BioLayout Express3D) and pathway modelling. Particular emphasis will be placed upon the integration of complementary approaches to ask specific biological questions.
Course instructors
Andrew Fraser (University of Toronto, Canada)
Tom Freeman (The Roslin Institute, Edinburgh, UK)
David Markie (Dunedin School of Medicine, New Zealand)
Ioannis Ragoussis (Wellcome Trust Centre for Human Genetics, Oxford, UK)
Anton Enright (European Bioinformatics Institute, Hinxton, UK)
Practical Aspects of Small Molecule Drug Discovery: At the interface of biology, chemistry and pharmacology
17-22 June 2012
A growing number of investigators in leading research institutions and small and medium-sized companies are expanding from their strength in disease biology into early-stage drug discovery. However, this move requires successfully combining the disciplines of biochemistry, medicinal chemistry, pharmacokinetics and pharmacology, the breadth of which can present organisational, knowledge and competence challenges for institutions and investigators. This residential course aims to give researchers of any discipline a broad introduction to the theoretical, practical and organisational aspects of small molecule drug discovery. Each topic will include a lecture together with discussion sessions or case histories to develop key aspects highlighted in the lectures. In addition there will be practical sessions to illustrate the beginnings of drug discovery programmes, including the production of target product profiles, project plans and milestones, compound progression criteria and scientific strategy.
Course organisers
Professor Paul Wyatt (Drug Discovery Unit, University of Dundee, UK)
Dr Mary Donnelly (MDPharmasolutions Ltd, Hertford, UK)
Human Genome Analysis: Genetic Analysis of Multifactorial Diseases 11-17 July 2012
This advanced course covers statistical methods currently used to map disease susceptibility genes, with an emphasis on (but not limited to) methods that can analyse family data or a combination of families and individuals. Discussions of the latest statistical methodology are complemented by practical hands-on computer exercises using state-of-the-art software. The statistical basics behind each method will be carefully explained so that participants with a non-statistical background can understand.
Course instructors
Daniel Weeks (University of Pittsburgh, USA)
Heather Cordell (Institute of Genetic Medicine, Newcastle University, UK)
Janet Sinsheimer (University of California, Los Angeles, USA)
Eric Sobel (University of California, Los Angeles, USA)
Chad Garner (University of California, Irvine, USA)
Simon Heath (Centre Nacional d’Anàlisi Genòmica (CNAG), Barcelona, Spain)
Protein Interactions and Networks 19-25 August 2012
This popular lab-based course provides training in the latest laboratory techniques and bioinformatics tools necessary to discover protein interactions and understand protein function.
The week-long course will combine practical work with computer-based data analysis. The practical programme will be complemented by specific lectures in topical areas as well as a panel of distinguished guest speakers, who will present the latest research in the field.
Course instructors
Jyoti Choudhary (Wellcome Trust Sanger Institute, Hinxton, UK)
Chris Sanderson (University of Liverpool, UK)
Gavin Wright (Wellcome Trust Sanger Institute, Hinxton, UK)
Anton Enright (European Bioinformatics Institute, Hinxton, UK)
Design and Analysis of Genetic-based Association Studies 24-28 September 2012
This Advanced Course aims to give researchers involved in disease studies a firm grounding in the use of the latest statistical methods and software for analysis of genetic association studies. The course will cover both theoretical and practical aspects of the design and analysis of such studies. Each topic will include a lecture followed by a practical session in which state-of-the-art statistical software will be applied to relevant datasets. The practical sessions will illustrate the ideas presented in the lectures. All the software used will be freely available so skills learnt can be applied to the datasets after the course.
Course Instructors
Dr Heather Cordell (Institute of Genetic Medicine, Newcastle University, UK)
Dr Andrew Morris (Wellcome Trust Centre for Human Genetics, University of Oxford, UK)
Dr Jonathan Marchini (Department of Statistics, University of Oxford, UK)
Next Generation Sequencing 8-16 October 2012
Next-generation sequencing has become the premier tool in genetic and genomic analysis. This laboratory-based course is directed at scientists who will be generating and interpreting sequence information in their research and wish to gain a better understanding of the techniques involved and their applications. This course is not meant to replace the manufacturers’ training normally supplied with new instruments, nor is it intended to be a training course for those solely interested in next-generation sequencing bioinformatics.
The course will include theoretical and practical information on all of the next-generation sequencing systems available and those on the near horizon. The laboratory element will cover a mix of technologies that will be determined nearer the time, but will be chosen from platforms like the Ion Torrent, PacBio and Illumina Miseq / HiSeq. One aim of the course is to allow participants to make informed decisions about which technology to apply to solve specific research questions they may face in the future. A variety of applications will be covered as time permits, e.g., RNA-Seq, target enrichment, bacterial sequencing, cancer genomics, human variation analysis, etc. All the basic techniques of post-sequencing analysis will be covered, QC, alignment, assembly, variant calling, etc.
Course Instructors
Harold Swerdlow (Wellcome Trust Sanger Institute, Cambridge, UK)
Carol Churcher (Wellcome Trust Sanger Institute, Cambridge, UK)
Tony Cox (Wellcome Trust Sanger Institute, Cambridge, UK)
Genetic Manipulation of ES Cells 5-18 November 2012
This laboratory-based training course will provide a comprehensive overview and practical laboratory experience of the genetic manipulation of mouse ES cells for a broad range of applications. Recent advances in genome informatics, recombineering, transposon technology and uses of conditional gene targeting will be covered in lectures by both instructors and invited expert speakers and through interactive demonstrations.Laboratory work will focus on the culture and transfection of ES cells, design and construction of gene targeting vectors from BACs by recombineering, genotyping of gene targeting events, and the use of site-specific nucleases (TALENs/ZFNs) to facilitate gene targeting. Participants will also be trained in the informatics and practical use of public gene targeting resources being produced by the IKMC (International Knockout Mouse Consortium).
Course instructors
Professor Francis Stewart (Dresden University of Technology, Dresden, Germany)
Dr William Skarnes (Wellcome Trust Sanger Institute, Cambridge, UK)
Dr Pentao Liu (Wellcome Trust Sanger Institute, Cambridge, UK)
Dr Barry Rosen (Wellcome Trust Sanger Institute, Cambridge, UK)
Molecular Pathology and Diagnosis of Cancer 9-14 December 2012
A joint initiative of the Wellcome Trust and the Royal College of Pathologists and aimed primarily at trainee pathologists or haematologists, this inaugural residential course aims to introduce participants to the rapidly evolving field of the molecular diagnosis of cancer.
Molecular techniques in current use, as well as the hurdles to the introduction of these new approaches into routine clinical practice, will be covered. In addition, the ethical, societal and practical implications of introducing genome-wide genetic analyses to the clinic will be considered.
The course will host a number of leading national and international speakers who will give lectures on the molecular pathology of a number of cancers, including lung, colorectal, leukaemia, myeloma and others.
Course instructors
George Vassiliou (Wellcome Trust Sanger Institute, Hinxton, UK)
Anthony Bench (Addenbrooke’s Hospital, Cambridge, UK)
Bridget Manasse (Addenbrooke’s Hospital, Cambridge, UK)
Harold Swerdlow (Wellcome Trust Sanger Institute, Hinxton, UK)
Peter Ellis (Wellcome Trust Sanger Institute, Hinxton, UK)
Michael Quail (Wellcome Trust Sanger Institute, Hinxton, UK)
Serena Nik-Zainal (Wellcome Trust Sanger Institute, Hinxton, UK)
Jeffrey Barrett (Wellcome Trust Sanger Institute, Hinxton, UK)
Elli Papaemmanuil (Wellcome Trust Sanger Institute, Hinxton, UK)
2011
Genomics and Clinical Microbiology 23-28 January 2011
The study of bacterial genomes is revolutionising clinical microbiology, and the clinical microbiologists of the future will have to process and interpret data very different from that provided by the agar-centric clinical microbiology labs of the 20th century. This course combines practical hands-on laboratory and bioinformatics work with a set of faculty lectures by leaders in this exciting area. The principal aim is to equip clinical scientists, specialist registrars, and consultants in medical microbiology (including joint medical microbiology and infectious diseases) with sufficient understanding of these areas to meet these challenges in the future. The course will concentrate on techniques that are currently practicable but will also look to the likely application of ‘next generation’ sequencing approaches to clinical microbiology.
Course instructors
Professor Martin Maiden (University of Oxford)
Professor Stephen Gillespie (University of St Andrews)
Dr Cath Arnold (Health Protection Agency)
Mathematical Models for Infectious Disease Dynamics 14-25 February 2011
Over the last two decades, mathematical models have seen a huge development in all aspects of infectious diseases, from microbiology to epidemiology and evolution. Professionals in these fields are now exposed to a wide range of models, often without receiving appropriate training.
This intensive, two-week course is aimed at any life scientist, public health officer, or medical or veterinary professional with an interest in quantitative approaches to infectious disease dynamics and control in humans or animals. The programme will cover introductory and advanced concepts in mathematical modelling of infectious diseases.
Course instructors
Olivier Restif, Andrew Conlan, TJ McKinley, Cerian Webb (University of Cambridge, Department of Veterinary Medicine)
Ken Eames (London School of Hygiene and Tropical Medicine)
Roberto Saenz, Johann von Kirchbach (University of Cambridge, Department of Applied Mathematics)
Nik Cunniffe and Matt Castle (University of Cambridge, Department of Plant Sciences)
Malaria Experimental Genetics 20-26 February 2011
This laboratory-based advanced course will give participants a working knowledge of and practical experience in cutting edge Plasmodium experimental genetic techniques, from designing gene targeting vectors and creating transgenic parasites to phenotyping the strains that result. The goal is to facilitate the participants’ own research careers by exposing them to state-of-the-art experimental approaches, while discussing the advantages and limitations of each approach.
The week-long practical course will cover experimental approaches to both the human parasite (Plasmodium falciparum) and the rodent parasite (Plasmodium berghei). The practical work will include several novel technological approaches, including production of gene targeting constructs using recombineering, which eliminates the need for PCR and restriction enzyme based ligation, and advanced molecular phenotyping approaches including next generation RNA sequencing and comparative mass spectrometry. The laboratory-based programme will be complemented by specific lectures in topical areas as well as a panel of distinguished guest speakers, who will present the latest research in the field.
Course instructors
Oliver Billker (Wellcome Trust Sanger Institute, Hinxton, UK)
Julian Rayner (Wellcome Trust Sanger Institute, Hinxton, UK)
Exome Sequencing, Genotyping and ArrayCGH: Technologies for Genome Analysis 7-16 March 2011
This new laboratory-based course provides a comprehensive overview of three cutting edge technologies used for the analysis of structural variation in vertebrate genomes.Participants will gain practical, laboratory-based experience of a number of platforms, as well as training in aspects of data analysis such as quality control, data formatting, variation calling and visualisation.Meaningful biological data will be generated first-hand, and a sound theoretical knowledge of all leading technologies will be gained for a broad understanding of the field.
The hands-on, laboratory- and computer—based programme is designed for researchers whose aim might be to employ these methods alone or collectively, to gain a multifaceted understanding of genome structure and its influences on function.
Course instructors
Dr Cordelia Langford (Wellcome Trust Sanger Institute, Cambridge)
Dr Peter Ellis (Wellcome Trust Sanger Institute, Cambridge)
Dr Robert Andrews (Wellcome Trust Sanger Institute, Cambridge)
Dr Matthew Breen (North Carolina State University, USA)
Computational Molecular Evolution 10-21 April 2011
This joint Wellcome Trust-EMBL-EBI advanced course aims to provide researchers with the theoretical knowledge and practical skills required to carry out molecular evolutionary analysis on their own data, as well as on data drawn from sequence databases. The course will combine basic assumptions and ideas fundamental to the field with discussion of cutting-edge methodologies, and is therefore relevant to researchers with a range of different experience levels.
Course instructors
Nick Goldman (European Bioinformatics Institute, Hinxton, UK)
Ziheng Yang (University College London, UK)
Aidan Budd (European Molecular Biology Laboratory, Heidelberg, Germany)
Alexandros Stamatakis (Heidelberg Institute for Theoretical Studies)
Molecular Basis of Bacterial Infection: Basic and Applied Research Approaches 8-14 May 2011
This course will introduce participants to concepts and techniques currently used in studies on the molecular basis of bacterial infection. Several themes will run throughout the week and these will provide a framework for bench experiments, demonstrations, supporting lectures and discussion groups. Core themes will include tissue-based assays, reporters, tissue culture assays, and microscopy (fluorescent and scanning/transmission electron microscopy).
Course instructors
Professor Gordon Dougan (Wellcome Trust Sanger Institute)
Dr Rob Kingsley (Wellcome Trust Sanger Institute)
Functional Genomics and Systems Biology 13-22 June 2011
This intensive laboratory and computer-based training course introduces participants to a wide range of post-genome techniques including hands-on experience in performing RNAi experiments in worms and mammalian cells, expression profiling using the latest platforms, yeast 2-hybrid analyses and hands on experience with sample preparation procedures for Illumina high throughput sequencing. Laboratory work will be complemented by training in state-of-the-art approaches to data analysis and interpretation through the use of a range of bioinformatics resources and systems biology tools, including R, Bioconductor, network analysis e.g. BioLayout Express3D and pathway modelling. Particular emphasis will be placed upon the integration of complementary approaches to ask specific biological questions.
Course instructors
Andrew Fraser (University of Toronto, Canada)
Tom Freeman (The Roslin Institute, Edinburgh, UK)
David Markie (Dunedin School of Medicine, New Zealand)
Ioannis Ragoussis (Wellcome Trust Centre for Human Genetics, Oxford, UK)
Anton Enright (European Bioinformatics Institute, Hinxton, UK)
Human Genome Analysis: Genetic Analysis of Multifactorial Diseases 23-29 July 2011
This advanced course covers statistical methods currently used to map disease susceptibility genes, with an emphasis on (but not limited to) methods that can analyse family data or a combination of families and individuals. Discussions of the latest statistical methodology are complemented by practical hands-on computer exercises using state-of-the-art software. The statistical basics behind each method will be carefully explained so that participants with a non-statistical background can understand.
Course Instructors
Daniel Weeks (University of Pittsburgh, USA)
Mark Lathrop (Centre National de Genotypage, Evry, France)
Heather Cordell (Institute of Human Genetics, University of Newcastle upon Tyne, UK)
Janet Sinsheimer (University of California, Los Angeles, USA)
Eric Sobel (University of California, Los Angeles, USA)
Joe Terwilliger (Columbia University, New York, USA)
Chad Garner (University of California, Irvine, USA)
Simon Heath (Centre Nacional d’Anàlisi Genòmica (CNAG), Barcelona, Spain)
Design and Analysis of Genetic-based Association Studies 26-30 September 2011
This residential workshop aims to give researchers involved in disease studies a firm grounding in the use of the latest statistical methods and software for analysis of genetic association studies. The course will cover both theoretical and practical aspects of the design and analysis of such studies. Each topic will include a lecture followed by a practical session in which state-of-the-art statistical software will be applied to relevant datasets. The practical sessions will illustrate the ideas presented in the lectures. All the software used will be freely available so skills learnt can be applied to the datasets after the course.
Course Instructors
Dr Heather Cordell (Institute of Genetic Medicine, Newcastle University, UK)
Dr Andrew Morris (Wellcome Trust Centre for Human Genetics, University of Oxford, UK)
Dr Jonathan Marchini (Department of Statistics, University of Oxford, UK)
Next Generation Sequencing 2-10 October 2011
In recent years, nucleic acid sequencing using next generation methods has emerged as a major transformative tool in the genomics field. This laboratory-based course is directed at scientists who will be generating and interpreting sequence information in their research and wish to gain a better understanding of the techniques involved and their applications. This course is not meant to replace the manufacturers’ training normally supplied with new instruments, nor is it intended to be a training course for those solely interested in next-generation sequencing bioinformatics.
The course will consist of a mix of theoretical and practical elements focused on Solexa Sequencing on the Illumina platform. However, the course will familiarise participants with other technologies, allowing them to make informed decisions about which technology to apply to solve specific research questions they may face in the future.
Course Instructors
Harold Swerdlow, Head of Sequencing Technology, The Wellcome Trust Sanger Institute, Cambridge, UK
Carol Churcher, Head of Sequencing Operations, The Wellcome Trust Sanger Institute, Cambridge, UK
Tony Cox, Head of Sequencing Informatics, The Wellcome Trust Sanger Institute, Cambridge, UK
Genetic Manipulation of ES Cells 31 October-13 November 2011
This course will provide a comprehensive overview and practical laboratory experience of the genetic manipulation of mouse ES cells for a broad range of applications. Recent advances in genome informatics, recombineering, transposon technology and uses of conditional gene targeting will be covered in lectures by both instructors and invited expert speakers and through interactive demonstrations.Laboratory work will focus on the culture and transfection of ES cells, design and construction of gene targeting vectors from BACs by recombineering, genotyping of gene targeting events and the practical use of transposon technology. Participants will also be trained in the informatics and practical use of public gene targeting resources being produced by the IKMC ( International Knockout Mouse Consortium).
Course instructors
Professor Francis Stewart (Dresden University of Technology, Dresden, Germany)
Dr William Skarnes (Wellcome Trust Sanger Institute, Cambridge, UK)
Dr Pentao Liu (Wellcome Trust Sanger Institute, Cambridge, UK)
Dr Barry Rosen (Wellcome Trust Sanger Institute, Cambridge, UK)
Protein Interactions and Networks 11-17 December 2011
This advanced course will provide training in the laboratory techniques and bioinformatics tools necessary to discover protein interactions and understand protein function.
The week-long course will combine laboratory-based practical work with computer-based data analysis. The practical programme will be complemented by specific lectures in topical areas as well as a panel of distinguished guest speakers, who will present the latest research in the field.
Course instructors
Jyoti Choudhary (Wellcome Trust Sanger Institute, Hinxton, UK)
Chris Sanderson (University of Liverpool, UK)
Gavin Wright (Wellcome Trust Sanger Institute, Hinxton, UK)
Anton Enright (European Bioinformatics Institute, Hinxton, UK)
2010
Genomics and Clinical Microbiology 24-29 January 2010
The overall aim of this course is to provide practical, laboratory-based training for clinical scientists, specialist registrars and consultants in medical microbiology (including joint medical microbiology and infectious diseases) in the application of current genetic techniques to the general medical microbiology laboratory.
The course will be planned around a theme of using genetic techniques to identify the source of an outbreak. Bacteriology (rather than virology) will be the focus. The course programme will consist of hands-on laboratory training complemented by lectures and guest-speaker seminars.
Course Instructors
Professor Martin Maiden (University of Oxford)
Professor Stephen Gillespie (University College London)
Dr Cath Arnold (Health Protection Agency)
Mathematical Models for Infectious Disease Dynamics 15-26 February 2010
Over the last two decades, mathematical models have seen a huge development in all aspects of infectious diseases, from microbiology to epidemiology and evolution. Professionals in these fields are now exposed to a wide range of models, often without receiving appropriate training.
This intensive, two-week course is aimed at any life scientist, public health officer, medical or veterinary professional with an interest in quantitative approaches to infectious disease dynamics and control in humans or animals. The programme will cover introductory and advanced concepts in mathematical modelling of infectious diseases.
Course instructors
Olivier Restif, Andrew Conlan, TJ McKinley, Cerian Webb (University of Cambridge Department of Veterinary Medicine)
Ken Eames (London School of Hygiene and Tropical Medicine)
Joshua Ross (Kings College, Cambridge)
Roberto Saenz, Johann von Kirchbach (University of Cambridge, Department of Applied Mathematics)
Nik Cunniffe (University of Cambridge, Department of Plant Sciences)
Colin Russell (University of Cambridge, Department of Zoology)
Virus Discovery in the Clinical Setting 7-12 March 2010
This course will provide training for health care scientists, specialist registrars and consultants in virology (including joint medical microbiology and infectious diseases) in the application of current molecular and serological techniques in identifying and characterising a novel virus in a clinical setting.
Course Instructors
Dr Kevin Brown (Health Protection Agency)
Dr Mark Zuckerman (Health Protection Agency and King’s College Hospital)
Technologies and Applications for Genome Analysis 18-27 April 2010
The course will provide a comprehensive overview and practical experience of the production and uses of DNA microarrays and related high-throughput methods for a broad range of applications in genome analysis.
Course Instructors
Dr David Vetrie (University of Glasgow, UK)
Dr Cordelia Langford (Wellcome Trust Sanger Institute)
Dr Peter Ellis (Wellcome Trust Sanger Institute
Dr Robert Andrews (Wellcome Trust Sanger Institute)
Molecular Basis of Bacterial Infection: Basic and Applied Research Approaches 9-15 May 2010
This course will introduce participants to concepts and techniques currently used in studies on the molecular basis of bacterial infection. Several themes will run throughout the week and these will provide a framework for bench experiments, demonstrations, supporting lectures and discussion groups.Core themes will include tissue-based assays, reporters, tissue culture assays, and microscopy (fluorescent and scanning/transmission electron microscopy).
Course Instructors
Professor Gordon Dougan (Wellcome Trust Sanger Institute)
Dr Rob Kingsley (Wellcome Trust Sanger Institute)
Dr Tim Foster (Trinity College, Dublin)
Dr Christine Hale (Wellcome Trust Sanger Institute)
Dr Simon Clare (Wellcome Trust Sanger Institute)
Dr Angela Jansen (Wellcome Trust Sanger Institute)
Functional Genomics and Systems Biology 16-25 June 2010
This intensive laboratory and computer-based training course introduces participants to a wide range of post-genome techniques including hands-on experience in performing RNAi experiments in worms and mammalian cells, expression profiling using the latest platforms, yeast 2-hybrid analyses and hands on experience with sample preparation procedures for Illumina high throughput sequencing . Laboratory work will be complemented by training in state-of-the-art approaches to data analysis and interpretation through the use of a range of bioinformatics resources and systems biology tools, including R, Bioconductor, network analysis e.g. BioLayout Express3D and pathway modelling. Particular emphasis will be placed upon the integration of complementary approaches to ask specific biological questions.
Course Instructors
Andrew Fraser (Wellcome Trust Sanger Institute)
Tom Freeman (Division of Pathway Medicine, Edinburgh)
David Markie (Dunedin School of Medicine, New Zealand)
Ioannis Ragoussis (Wellcome Trust Centre for Human Genetics, Oxford)
Anton Enright (Wellcome Trust Sanger Institute)
Molecular Neurology and Neuropathology 19-26 June 2010
This is an intensive, discussion-based course that offers the unique opportunity to learn the latest concepts and methodologies associated with the study of human neurological disorders such as Alzheimer's, Parkinson's, Amyotrophic Lateral Sclerosis, Stroke, Prion diseases and Spinocerebellar Ataxias. Participants will discuss in detail the strengths and weaknesses of the accumulated experimental evidence underlying our current understanding of these diseases.
Many of these diseases can be approached by first understanding human genetics, and so the course will discuss both mendelian traits and more complex situations including recent examples of the application of genome wide association studies (GWAS) to sporadic disease. The course will examine why many of these disorders share apparently common features of protein aggregation, specific vulnerability of certain classes of neuron, long incubation period and will discuss to what extent these features reflect common pathological mechanisms. The course will further explore how the underlying mechanisms may be targeted for potential diagnostic and therapeutic gain, applying lessons from genetic knowledge to inherited and sporadic diseases.
These fundamental questions will be discussed in the context of identifying the best experimental approaches to finding answers. These will include consideration of clinical and pathological data from human subjects through the use of experimental models including molecular approaches, cell biological and imaging studies, transgenic animal models including vertebrate and invertebrate models.
Extended seminars and discussion by a wide range of leading investigators will further illuminate developments in the rapidly moving field. Participation in the course will provide an essential conceptual and methodological framework for anyone intending to pursue rigorous research.
Course Instructors
Dr Mark Cookson (National Institute on Aging, USA)
Professor Beverly Davidson (University of Iowa, USA)
Professor Harry Orr (University of Minnesota, USA)
Professor Nicholas Wood (Institute of Neurology, London, UK)
Practical Aspects of Small Molecule Drug Discovery: at the interface of biology, chemistry and pharmacology 4-9 July 2010
A growing number of investigators in leading research institutions and small and medium-sized companies are expanding from their strength in disease biology into early-stage drug discovery. However, this move requires successfully combining the disciplines of biochemistry, medicinal chemistry, pharmacokinetics and pharmacology, the breadth of which can present organisational, knowledge and competence challenges for institutions and investigators. This residential course aims to give researchers of any discipline a broad introduction into the theoretical, practical and organisational aspects of small molecule drug discovery. Each topic will include a lecture together with discussion sessions or case histories to develop key aspects highlighted in the lectures. In addition there will be practical sessions to illustrate the beginnings of drug discovery programmes, including the production of project plans and milestones, compound progression criteria and scientific strategy based on screening results.
Course Instructors
Professor Paul Wyatt (Drug Discovery Unit, University of Dundee, UK)
Dr Richard Davis (Technology Transfer Division, The Wellcome Trust)
Next Generation Sequencing 18-24 July 2010
In recent years, nucleic acid sequencing using next generation methods has emerged as a major transformative tool in the genomics field. This laboratory-based course is directed at scientists who will be generating and interpreting sequence information in their research and wish to gain a better understanding of the techniques involved and their applications. This course is not meant to replace the manufacturers’ training normally supplied with new instruments.
The course will consist of a mix of theoretical and practical elements focused on Solexa Sequencing on the Illumina platform. However, the course will familiarise participants with other technologies, allowing them to make informed decisions about which technology to apply to solve specific research questions they may face in the future.
Course instructors
Harold Swerdlow, Head of Sequencing Technology, The Wellcome Trust Sanger Institute, Cambridge, UK
Carol Churcher, Head of Sequencing Operations, The Wellcome Trust Sanger Institute, Cambridge, UK
Tony Cox, Head of Sequencing Informatics, The Wellcome Trust Sanger Institute, Cambridge, UK
Human Genome Analysis: Genetic Analysis of Multifactorial Diseases 21-27 July 2010
This Advanced Course covers statistical methods based on linkage and association used to map disease susceptibility genes, with an emphasis on family-based designs. Discussions of the methodology are complemented by practical hands-on computer exercises. We will discuss issues of power to detect linkage, optimal study design, use of software, and proper statistical analyses. Our interactive and intensive educational program will enable one to better carry out sophisticated statistical analyses of genetic data, and will also improve one's interpretation and understanding of the results.
Course Instructors
Daniel Weeks (University of Pittsburgh, USA)
Mark Lathrop (Centre National de Genotypage, Evry, France)
Heather Cordell (Institute of Human Genetics, University of Newcastle upon Tyne, UK)
Janet Sinsheimer (University of California, Los Angeles, USA)
Eric Sobel (University of California, Los Angeles, USA)
Joe Terwilliger (Columbia University, New York, USA)
Chad Garner (University of California, Irvine, USA)
Simon Heath (Centre Nacional d’Anàlisi Genòmica (CNAG), Barcelona, Spain)
Design and Analysis of Genetic-based Association Studies 23-27 August 2010
This residential workshop aims to give researchers involved in disease studies a firm grounding in the use of the latest statistical methods and software for analysis of genetic association studies. The course will cover both theoretical and practical aspects of the design and analysis of such studies. Each topic will include a lecture followed by a practical session in which state-of-the-art statistical software will be applied to relevant datasets. The practical sessions will illustrate the ideas presented in the lectures. All the software used will be freely available so skills learnt can be applied to the datasets after the course.
Course Instructors
Dr Heather Cordell (Institute of Human Genetics, University of Newcastle upon Tyne, UK)
Dr Andrew Morris (Wellcome Trust Centre for Human Genetics, University of Oxford, UK)
Dr Jonathan Marchini (Department of Statistics, University of Oxford, UK)
Protein Interactions and Networks 17-23 October 2010
This advanced course will provide training in the laboratory techniques and bioinformatics tools necessary to discover protein interactions and understand protein function.
The week-long course will combine laboratory-based practical work with computer-based data analysis. The practical programme will be complemented by specific lectures in topical areas as well as a panel of distinguished guest speakers, who will present the latest research in the field.
Course instructors
Jyoti Choudhary (Wellcome Trust Sanger Institute, Hinxton, UK)
Chris Sanderson (University of Liverpool, UK)
Gavin Wright (Wellcome Trust Sanger Institute, Hinxton. UK)
Anton Enright (European Bioinformatics Institute, Hinxton, UK)
Genetic Manipulation of ES Cells 15-28 November 2010
This course will provide a comprehensive overview and practical laboratory experience of the genetic manipulation of mouse ES cells for a broad range of applications. Recent advances in genome informatics, BAC recombineering, transposon technology and conditional gene targeting will be covered in theoretical sessions and demonstrations.Laboratory work will focus on the culture and transfection of ES cells, construction of gene targeting vectors, genotyping of gene targeting events and the derivation of mouse iPS cells.
Course Instructors
Professor Francis Stewart (Dresden University of Technology, Dresden)
Dr William Skarnes (Wellcome Trust Sanger institute, Cambridge)
Dr Pentao Liu (Wellcome Trust Sanger Institute, Cambridge)
Dr Barry Rosen (Wellcome Trust Sanger Institute, Cambridge)
Genome-wide Approaches with Fission Yeast 11-18 December 2010
Increasingly, researchers using S. pombe as a model organism want to apply functional genomic and computational approaches for their research, due to the availability of the complete genome and various tools and resources such as microarrays, next-generation sequencing and close/mutant collections. At present, however, only a handful of fission yeast laboratories are pursuing genome-wide projects.
This intensive, laboratory-based training course is aimed at introducing participants to both practical methodologies and concepts for the global analysis of large-scale data sets. This course should help the participants acquire the necessary skills to pursue large-scale methods routinely in their own laboratories.
Course Instructors
Jürg Bähler (Department of Genetics, Evolution & Environment, University College London)
Juan Mata (Department of Biochemistry, Cambridge University)