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1
Job announcements / Fellowship: Newcastle University (UK)
Last post by Kat Burton -
The 2020 Newcastle University Academic Track Fellowship Scheme, is now open for applications with a closing date of 6th March 2020.  Anyone within the ECN who is interested should contact Prof. John Mathers (email: john.mathers@ncl.ac.uk ) in the first instance to let him know if they are interested in applying.  John will be delighted to give more background to the application process and the University to the potential candidate.
 

This is an excellent opportunity for talented researchers in nutrigenomics to develop towards an independent career.
 
NUAcT Clinical Fellows will join a thriving cohort of talented early career researchers across the NUAcT Scheme and across the whole University.
A candidate briefing pack for those applying to the Medicine and Biological Sciences panel is attached.
 
What does the NUAcT programme offer?
   • Five years' salary (or five years FTE equivalent if working part time)
   • Initial fixed term appointment with progression to an open-ended contract subject to review
   • Research expenses (up to £50k, subject to research programme needs)
   • Funding for a PhD studentship associated with the research project
   • Dedicated mentors with world class expertise and significant research management experience
   • The opportunity to join and participate in our world-class interdisciplinary research centres
   • A bespoke personal development plan and extensive training opportunities
   • Peer support from a cross disciplinary cohort of talented early career researchers
 
Further details about how to apply can be found by following this link.
 
A direct link to the recruitment portal for the NUAcT Clinical Fellowship can be reached by clicking here:https://jobs.ncl.ac.uk/job/Newcastle-NUAcT-%28Newcastle-Unviversity-Academic-Track%29-Fellowship-Scheme-Clinical-Research/579516901/.
4
External training / Free course on molecular biological pathways and networks
Last post by Kat Burton -
Interested in pathway analysis?

Check out a free course on molecular biological pathways and networks that the BiGCaT department of Bioinformatics at Maastricht University created for the Helis Academy.

“Learn create and curate pathways, put them on WikiPathways and use them for omics analysis or as the start of biological networks that can be used for more advanced types of analysis”.

Course date: 30-31  March 2020
Further information and registration details at:
https://www.eventbrite.co.uk/e/helis-academy-omics-data-analysis-course-registration-93267516653
5
General Discussion / HPLC Sample filtration?
Last post by gregopim -
Hello everyone :)
Do anyone filter their blood/urine/food_extract samples before injection in their LC-MS system?
We are hesitating about which type of filter to use (reg cellulose, nylon, PFTE, ...) and the porosity (0.2 or 0.45 micron).
We are planning to analyse 700+ samples of milk or yoghurt for untargeted metabolomics and want to avoid damaging our column (it is a 1.8 micron column)
Do you have some recomendations?
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PhD/training funding / NuGO training grants
Last post by Kat Burton -
6th Nutrition Winter School 27-31 January 2020,Levi, Finnish Lapland

Title: Diet and Microbes: Gut health for the brain and body
Date: 27-31 January 2020, Levi, Lapland, Finland

Course Website: https://www.helsinki.fi/en/conferences/nutrition-winter-school/nutrition-winter-school-2020

Grants: NuGO will make 4 course grants available for PhDs and postdocs (< 3 years after obtaining the PhD) covering the course fee of 550€. For more details about the grant and how to apply please visit: grants Winterschool Lapland 2020

Deadline grant application: 31 October 2019.

For detailed infomation about this symposium please visit the programme
8
External training / The 6th Nutrition Winter School
Last post by Kat Burton -

Diet and Microbes: Gut health for the brain and body
27.1. – 31.1.2020, Levi, Lapland, Finland
 
Nutrition Winter School is a scientific seminar aimed at young post docs and PhD students from the fields of nutrition, medicine, and biochemistry. Ever since we organized this event for the first time in 2009, our goal has been to gather early-career scientists and top researchers from various backgrounds to enjoy scientific lectures and fruitful discussions under the magical atmosphere of the Finnish Lapland.
 
The 6th Nutrition Winter School will take place in Lapland at Levi, Kittilä, Finland from January 27th to 31st, 2020. This time the theme of the seminar is Diet and Microbes: Gut health for the brain and body. This theme is covered by internationally renowned experts from a clinical, experimental, and molecular biological point-of-view.
 
Confirmed speakers include:
Prof. Robert-Jan Brummer, Örebro University                                   Dr Federica Facciotti, European Institute of Oncology
Prof. Karl-Heinz Herzig, University of Oulu                                         Dr Jonna Jalanka, University of Helsinki
Prof. Stefan Kiechl, Medical University of Innsbruck                        Prof. Eero Mervaala, University of Helsinki
Dr Milla Pietiäinen, University of Helsinki                                           Dr Justus Reunanen, University of Oulu
Dr Anu Ruusunen, University of Eastern Finland                              Prof Seppo Salminen, University of Turku        
Prof Michael Schemann, Technical University of München              Dr Filip Scheperjans, Helsinki University Hospital       
Prof. Magnus Simrén, University of Gothenburg

 
Check out the preliminary program:
https://www.helsinki.fi/en/conferences/nutrition-winter-school/nutrition-winter-school-2020/seminar-program
 
Early Bird registration and call for abstracts are now open! Be fast and book your place today!
Registration: https://www.helsinki.fi/en/conferences/nutrition-winter-school/registration
 
9
ECN webinars 2019 / Re: 6th September 2019- ECN multivariate statistics webinar 2
Last post by Kat Burton -
The recorded webinar is now available at:

https://vimeo.com/358591917

Extra Q and As from Claus:

What other omics integration tools have you tested on your datasets (DIABLO, MINT, sMBPLS...)?
 
This particular data set is more than 10 years old. I think Le Cao had published some of her papers by then, but the mixOmics package didn’t exist yet and neither did DIABLO and MINT. In a way doing this seminar was one way for me get into these packages a bit more. At that time we used the ade4 and made4 packages, which I think are pre-runners of omicade4. I wasn’t aware of the sMBPLS package, but it looks very interesting so will check it out. I think there are slightly different cultures depending on which omics data you deal with. The metabolomics world seems very strong on variants of PLS, whereas the Gene Expression folk seem to love network analysis (which you can regard as multivariate analysis too, but is very different).
 
 
Is there any rule for a maximum number of variables that can be assessed according to the number of samples (when the number of variables is huge but the number of subjects do not exceed a few hundreds)?
 

No, I don’t think so. The number of variables will only ever grow in comparison to the number of samples and saying there is a maximum number would imply we (as statisticians) refuse to accept our responsibility to deal with that. Statistics has developed rapidly in this area in the last 20 years, and the best and most successful methods tend to make use of the high-dimensionality rather than seeing it as a curse.

A pdf copy of the webinar presentation is available in the attachment to this message for ECN members.
 
10
ECN webinars 2019 / 6th September 2019- ECN multivariate statistics webinar 2
Last post by Kat Burton -
The ECN committee are pleased to announce the second webinar in our series on multivariate statistics that will be delivered by Dr Claus Mayer:

Sparse multivariate methods and integration of omics data sets

Friday 6th September, 16:00-17:00 CET

Multivariate methods like principle component analysis (PCA) or partial least squares (PLS) are essential in revealing structure in high-dimensional omics type data, where the number of variables is typically much larger than the number of samples (p>>n). As useful as these methods are to study the relationship between samples the high number of variables obscures the interpretation which genes, proteins or metabolites contribute to the patterns we see. Sparse methods enforce the loadings of most variables to be 0, while still explaining much of the variation in the data and thus enable an easier biological interpretation of the results. Dr Mayer will introduce sparse versions of some commonly used multivariate methods and illustrate their use in data examples.
In a second part he will present methods that simultaneously analyse two (or more) data sets like Canonical Correlation Analysis (CCA) or Co-Inertia Analysis (CIA). These tools allow to study the joint influence of two sets of variables (eg. a transcriptomic and a proteomic data set) on the variation within samples while showing the relationship between the data sets at the same time.


Dr Claus Mayer is a senior statistician working for Biomathematics and Statistics Scotland. His main area of research in recent years has been the analysis of high-dimensional genomics data with a particular emphasis on gene expression studies (microarrays, RNAseq) and related areas (proteomics, methylation studies. Dr Mayer has worked on methods of integrating/combining such omics data sets from different sources like combining high-dimensional  data from different stages of an experiment in a group-sequential setting, conducting meta-analysis of comparable gene expression studies or integrating different types of omics data collected from the same samples. Dr Mayer has also investigated ways of quickly calculating overall summary statistics of pairwise (cross-) correlations within one or more high-dimensional data sets and has studied ways of turning such (partial) correlation structures into sparse biologically interpretable networks.

Sign up for the webinar at:

https://attendee.gotowebinar.com/register/5674949347539367939