James Christopher Wright (![[info]](http://p-stat.livejournal.com/img/userinfo.gif){kind=small} bifo) wrote,@ 2006-03-27 12:51:00 |
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GENOMES to SYSTEMS Manchester 2006
Well I spent most of last week at the Genomes to Systems conference in the GMEX here in Manchester. There was a good turnout about 900 people quite a few I knew as well - everyone from the exUMIST/Manchester Bioinformatics, the guys from Protein Functions Group in Liverpool, a few people from my Post Genomes MSc course, the guys from GAPSIA and even a few of my colleges from AstraZeneca.
In general there was a lot of interesting talks although as always happens at these events alot of the talks went a bit off topic but there was a lot of choice in what I went to see.
Day 1 - Wednesday 22nd March
Opening Lecture by Bernhard Palsson (San Diego University) - "The Human Metabolic Network"
An interesting talk on how they had been rebuilding the the human metabolic network using two different methods - a bottom up method which basically uses high througput methods (search a whole genome analysis methods) to identify lots of metabolites, their associated proteins, sub cellular location and their interactions, generally very inaccurate but is good for discovery of new metabolic pathways. Secondly they used a top down approach in which they compile published and validated data to create a network that is confirmed experimentally and has no errors. Was filled with lots of complex diagrams of pathways.
The was then the choice of lecture sessions either: Structural Genomics of Disease (Chaired by Samar Hasnain) or Proteomics for Systems Biology (Chaired by Rob Beynon [my primary supervisor!!])
So I went to the Proteomics session:
A. Brian Chait (Rockefeller, New York) - "Proteomic tools for Dissecting Cellular Processes"
This lecture ended up being more structural than proteomics but was a quite interesting look a the transport proteins that cross the nuclear membrane in cells (Then central bit that contains the DNA)
B. Alistair Hetherington (Lancaster Uni) - "The Use of Proteomics to Dissect the Plant Guard Cell Signalling Network"
Again not much in the way of proteomics and twas plant biology..! Was not that bad in the end though and I do have some interest in cellular signalling as I did my masters project on protein phosphatases which are used to degrade cellular signals
C. Al Burlingame (San Francisco Uni) - "Toward Defining Epigenetic Protein Signatures in Cellular Networks by Electron Capture Dissociation (ECD) and Methods of Tandem Mass Spectrometry"
By far the longest title of any talk!! A good example of the application of ECD and MS/MS in systems biology
D. Simon Gaskel (CISB, Manchester Uni was head of my Post Genome Masters Course) - "Convergent Analytical Stratagies for Quantitative Proteomics"
Simon gave a good summary of the various technologies that are being applied in Mass Spectrometry in Manchester, protein labelling and post translational modifications as well as co-analysing proteins to compare relative abundance in a sample
LUNCH - not very nice so James K and I went to Pizza Hut for all you can eat!!
Another choice of sessions here: Metabolomics in Health and Disease, Advances in Biosensors and instrumentation, Comparative and enviromental genomics in action
I didn't really have much I wanted to see in these sessions so I wandered from session to session, the biosensors lecture seemed to be mostly sales lectures by companies trying to promote their new instruments, there was a really good talk on "Metabolic profiling in Diabetes" Chris Newgad (Duke) which showed how as rats put on weight and became obese their beta-islets (the clusters of cells that produce insulin in the pancreas) replicated and grew in size to try and compensate for increased sugar intake but after doing this for so long they seemed to loose control and fall apart hence to on set of diabetes as the cells couldn't produce enough insulin any more. Several other lectures went into the idea of personalised medice based on a metabolite analysis - quite and interesting future for medical treatments
POSTER SESSION and SHOWCASES
Closing Lecture - Julie Ahringer (Cambridge University) - "Global Analyses of Gene Function using RNAi"
A very good lecture on the use of RNAi (Short strands of RNA that are designed to complement the mRNA for a particular gene and interfere with the production of a particular protein via the translation process) to systematically interfere with each protein in c.elegans (Worms) and classify each protein as lethal or by the phenotypic (appearance) effects and hence try to work out which proteins work together and what their function is.
EVENING MEAL AND NETWORKING EVENT
Day 2 - Thursday 23nd March
Opening Lecture by Michael Snyder (Yale University) - "Genomes and Proteomes"
An interesting summary of how we can intergrate all the various data in to large scale networks linking proteins with genes and their regulation at various levels
First Parralel sessions: Disease Proteomics, High-throughput Functional Genomics and Gene Manipulation, Public Population projects in Medicine
I attended the Disease Proteomics Session chaired by Simon Gaskell
A. Ron Heeren (Amsterdam Uni) - "Mass Spectrometric Imaging for Proteome Analysis"
This was one of the best talks I attended, disscussing how MALDI (Matrix Assisted Laser Desorbtion Ionisation - The instrument I have been trained to use over in Liverpool) mass spectrometers can be used as microscopes to image cells and tissues on a molecular level. Gave some examples of its use of brain tissue!!
B. Albert Heck (Utrecht) - "A Quantitative Proteomics approach to Drosophila Early Embryonic Development and Embryonic stem cell differentiation"
A great talk on manipulation of stem cells, not much on proteomic methods but had some cool pictures of Drosophila (Fruit Flies) that had various protein stimulated in various stem cells during the embryonic stage and had grown multiple eyes all over their bodies..even on their knees!!!
C. Pierre Thibault (Montreal Uni) - "Comprehensive Detection of Unlabelled Peptides for Targeted Identification of Key Cell Signalling Events"
A lecture on various methods for identifying relative abundance on peptides without use of a radioactive or mass label again focussed of kinases and phosphatases
D. Tony Whetton (Patterson Cancer Research, Manchester Uni) - "Normal and Malignant Stem Cell Proteomics"
Tony discussed the major diffences in the proteomes of normal and malignant stem cells and how cancers could be treated by targeting malignant stem cells
LUNCH - better today (sweet and sour veg, rice + salad)
EMBL-EBI - Uniprot demonstration - latest improvements to Swissprot and TrEMBL protein sequence databases
2nd parallel session - Engineering Approaches to Biological systems, Pharmacogenomics - personalised medicine, Progress in Standards for Reporting 'Omics Data'
I attended the Progress in Standards for Reporting 'Omics Data'
A. Chris Taylor (EMBL-EBI, European Bioinformatics Institute) - "A coordinated Multi-'omics view of data standards"
A disscusion of how the EBI are setting up and implementing data standards for proteomics and Metabolomics in the hope of making data from different labs and instuments more comparable
B. Jason Snape (NERC, Astrazeneca SHE) - "Importance of data standards to facillitate the uptake of Genomic science outputs into science based policy and regulation"
Mainly focussed on Astrazeneca buisness implementation of research and how they regulated their data
C. Charlotte Capener (BBSRC) "The BBSRC data-sharing policy"
A lot about how the BBSRC decide on funding allocation
D. Herbert Thiele (Bruker Daltronics, Bremen) - "The HUPO Brain Proteome Project"
A interesting and relevant talk about automated proteomics and reverse database searching using various software
POSTER SESSION
Closing Lecture - Matthias Uhlen (Stockholm) A Human Protein Atlas for Normal and Cancer cells - Biomarker discovery by Antibody-based proteomics
Day 3 - Friday 24th March
No opening lecture!
parallel session- From Models to cells, Nanoscale Technologies in bioscience, Transcriptomics and Expression Microarrays A promise Delivered?
Again didn't want to see anything in particular so just wandered from lecture to lecture some interesting stuff in the nanoscale technologies lectures.
Closing Lecture Denis Noble (Oxford) "Principles of Systems Biology Using the virtual Heart"
A totally awesome lecture describe how they have created a computational model of a virtual heart on the cellular level modelling all the electronic signals and transport proteins and well as the muscle contraction twas very impressive
LUNCH - Packed lunch
END
All in All twas a great seminar look forward to its next incarnation in a few years time.
Well I spent most of last week at the Genomes to Systems conference in the GMEX here in Manchester. There was a good turnout about 900 people quite a few I knew as well - everyone from the exUMIST/Manchester Bioinformatics, the guys from Protein Functions Group in Liverpool, a few people from my Post Genomes MSc course, the guys from GAPSIA and even a few of my colleges from AstraZeneca.
In general there was a lot of interesting talks although as always happens at these events alot of the talks went a bit off topic but there was a lot of choice in what I went to see.
Day 1 - Wednesday 22nd March
Opening Lecture by Bernhard Palsson (San Diego University) - "The Human Metabolic Network"
An interesting talk on how they had been rebuilding the the human metabolic network using two different methods - a bottom up method which basically uses high througput methods (search a whole genome analysis methods) to identify lots of metabolites, their associated proteins, sub cellular location and their interactions, generally very inaccurate but is good for discovery of new metabolic pathways. Secondly they used a top down approach in which they compile published and validated data to create a network that is confirmed experimentally and has no errors. Was filled with lots of complex diagrams of pathways.
The was then the choice of lecture sessions either: Structural Genomics of Disease (Chaired by Samar Hasnain) or Proteomics for Systems Biology (Chaired by Rob Beynon [my primary supervisor!!])
So I went to the Proteomics session:
A. Brian Chait (Rockefeller, New York) - "Proteomic tools for Dissecting Cellular Processes"
This lecture ended up being more structural than proteomics but was a quite interesting look a the transport proteins that cross the nuclear membrane in cells (Then central bit that contains the DNA)
B. Alistair Hetherington (Lancaster Uni) - "The Use of Proteomics to Dissect the Plant Guard Cell Signalling Network"
Again not much in the way of proteomics and twas plant biology..! Was not that bad in the end though and I do have some interest in cellular signalling as I did my masters project on protein phosphatases which are used to degrade cellular signals
C. Al Burlingame (San Francisco Uni) - "Toward Defining Epigenetic Protein Signatures in Cellular Networks by Electron Capture Dissociation (ECD) and Methods of Tandem Mass Spectrometry"
By far the longest title of any talk!! A good example of the application of ECD and MS/MS in systems biology
D. Simon Gaskel (CISB, Manchester Uni was head of my Post Genome Masters Course) - "Convergent Analytical Stratagies for Quantitative Proteomics"
Simon gave a good summary of the various technologies that are being applied in Mass Spectrometry in Manchester, protein labelling and post translational modifications as well as co-analysing proteins to compare relative abundance in a sample
LUNCH - not very nice so James K and I went to Pizza Hut for all you can eat!!
Another choice of sessions here: Metabolomics in Health and Disease, Advances in Biosensors and instrumentation, Comparative and enviromental genomics in action
I didn't really have much I wanted to see in these sessions so I wandered from session to session, the biosensors lecture seemed to be mostly sales lectures by companies trying to promote their new instruments, there was a really good talk on "Metabolic profiling in Diabetes" Chris Newgad (Duke) which showed how as rats put on weight and became obese their beta-islets (the clusters of cells that produce insulin in the pancreas) replicated and grew in size to try and compensate for increased sugar intake but after doing this for so long they seemed to loose control and fall apart hence to on set of diabetes as the cells couldn't produce enough insulin any more. Several other lectures went into the idea of personalised medice based on a metabolite analysis - quite and interesting future for medical treatments
POSTER SESSION and SHOWCASES
Closing Lecture - Julie Ahringer (Cambridge University) - "Global Analyses of Gene Function using RNAi"
A very good lecture on the use of RNAi (Short strands of RNA that are designed to complement the mRNA for a particular gene and interfere with the production of a particular protein via the translation process) to systematically interfere with each protein in c.elegans (Worms) and classify each protein as lethal or by the phenotypic (appearance) effects and hence try to work out which proteins work together and what their function is.
EVENING MEAL AND NETWORKING EVENT
Day 2 - Thursday 23nd March
Opening Lecture by Michael Snyder (Yale University) - "Genomes and Proteomes"
An interesting summary of how we can intergrate all the various data in to large scale networks linking proteins with genes and their regulation at various levels
First Parralel sessions: Disease Proteomics, High-throughput Functional Genomics and Gene Manipulation, Public Population projects in Medicine
I attended the Disease Proteomics Session chaired by Simon Gaskell
A. Ron Heeren (Amsterdam Uni) - "Mass Spectrometric Imaging for Proteome Analysis"
This was one of the best talks I attended, disscussing how MALDI (Matrix Assisted Laser Desorbtion Ionisation - The instrument I have been trained to use over in Liverpool) mass spectrometers can be used as microscopes to image cells and tissues on a molecular level. Gave some examples of its use of brain tissue!!
B. Albert Heck (Utrecht) - "A Quantitative Proteomics approach to Drosophila Early Embryonic Development and Embryonic stem cell differentiation"
A great talk on manipulation of stem cells, not much on proteomic methods but had some cool pictures of Drosophila (Fruit Flies) that had various protein stimulated in various stem cells during the embryonic stage and had grown multiple eyes all over their bodies..even on their knees!!!
C. Pierre Thibault (Montreal Uni) - "Comprehensive Detection of Unlabelled Peptides for Targeted Identification of Key Cell Signalling Events"
A lecture on various methods for identifying relative abundance on peptides without use of a radioactive or mass label again focussed of kinases and phosphatases
D. Tony Whetton (Patterson Cancer Research, Manchester Uni) - "Normal and Malignant Stem Cell Proteomics"
Tony discussed the major diffences in the proteomes of normal and malignant stem cells and how cancers could be treated by targeting malignant stem cells
LUNCH - better today (sweet and sour veg, rice + salad)
EMBL-EBI - Uniprot demonstration - latest improvements to Swissprot and TrEMBL protein sequence databases
2nd parallel session - Engineering Approaches to Biological systems, Pharmacogenomics - personalised medicine, Progress in Standards for Reporting 'Omics Data'
I attended the Progress in Standards for Reporting 'Omics Data'
A. Chris Taylor (EMBL-EBI, European Bioinformatics Institute) - "A coordinated Multi-'omics view of data standards"
A disscusion of how the EBI are setting up and implementing data standards for proteomics and Metabolomics in the hope of making data from different labs and instuments more comparable
B. Jason Snape (NERC, Astrazeneca SHE) - "Importance of data standards to facillitate the uptake of Genomic science outputs into science based policy and regulation"
Mainly focussed on Astrazeneca buisness implementation of research and how they regulated their data
C. Charlotte Capener (BBSRC) "The BBSRC data-sharing policy"
A lot about how the BBSRC decide on funding allocation
D. Herbert Thiele (Bruker Daltronics, Bremen) - "The HUPO Brain Proteome Project"
A interesting and relevant talk about automated proteomics and reverse database searching using various software
POSTER SESSION
Closing Lecture - Matthias Uhlen (Stockholm) A Human Protein Atlas for Normal and Cancer cells - Biomarker discovery by Antibody-based proteomics
Day 3 - Friday 24th March
No opening lecture!
parallel session- From Models to cells, Nanoscale Technologies in bioscience, Transcriptomics and Expression Microarrays A promise Delivered?
Again didn't want to see anything in particular so just wandered from lecture to lecture some interesting stuff in the nanoscale technologies lectures.
Closing Lecture Denis Noble (Oxford) "Principles of Systems Biology Using the virtual Heart"
A totally awesome lecture describe how they have created a computational model of a virtual heart on the cellular level modelling all the electronic signals and transport proteins and well as the muscle contraction twas very impressive
LUNCH - Packed lunch
END
All in All twas a great seminar look forward to its next incarnation in a few years time.
