Issue 17 - January 2013
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1) Initiative Spotlight
| Professor and Co-Director,
Center for Translational Biomedical Research, University
of North Carolina at Greensboro, Kannapolis, USA
Dr. Wei Jia is Professor and Co-Director of the Center for Translational Biomedical Research, the University of North Carolina at Greensboro. He also serves as Director of the Metabolomics Core Lab at the David H Murdock Research Institute, Kannapolis, North Carolina. Dr. Jia was previously Professor and Vice Dean, School of Pharmacy, Shanghai Jiao Tong University in China, and has worked nearly a decade on biochemical profiling of botanical preparations and metabolomics. Professor Jia's current research focuses on mass spectrometry (MS)-based metabolomics profiling technologies to investigate metabolic phenotypes and metabolic transformation in cancer and metabolic disorders.
3) Biomarker Beacon
|7 Jan 2013
Navigating by cloud atlas: Using cloud plots to visualize metabolomics data
Cloud plots should be the first port of call when analysing complex metabolomic datasets, says Gary Siuzdak at the Scripps Research Institute in California, US. As an early demonstration of their ability, Siuzdak has used them to uncover novel biomarkers for the onset of life-threatening sepsis.
Siuzdak and his colleagues came up with cloud plots when looking for an effective way to display the complex datasets produced when using liquid chromatography-mass spectrometry (LC-MS) to determine the metabolites in two related samples, such as healthy and diseased samples. They wanted to incorporate such a display technique into their new web-based MS data processing and analysis platform, known as XCMS Online (see Metabolomics for all), alongside more conventional data analysis techniques such as principal component analysis.
The need for such a display technique is driven by the complexity of metabolomic datasets, which often comprise thousands of different peaks. This complexity means that it is simply not practical to try to identify all the metabolites responsible for the thousands of peaks, as this often requires in-depth tandem mass spectrometry (MS/MS). So scientists need a way to identify the most interesting peaks in these datasets and then focus their attention on them.
Cloud plots offer a way to do this. '[They] provide a statistical assessment of the global metabolomic data and ultimately allow a scientist to effectively decide which metabolites need to be confirmed with MS/MS analysis,' explains Siuzdak.
Article in press: Analytical Chemistry: "A view from above: Cloud plots to visualize global metabolomic data"
|18 Dec 2012
Agilent Technologies' Thought Leader Award Supports Dr. Robert Gerszten's Work in Metabolomic Research at Massachusetts General Hospital
Agilent Technologies Inc. today announced that Dr. Robert Gerszten, a recognized leader in cardiovascular research and biomarker discovery, has received an Agilent Thought Leader Award.
Dr. Gerszten is the director of clinical and translational research at Massachusetts General Hospital's Institute for Heart, Vascular and Stroke Care. The award will provide his laboratory with funding for personnel. Agilent will also provide technical and scientific expertise in metabolomics, automation and integrated biology in support of Dr. Gerszten's metabolite profiling study of well-phenotyped human populations, including his work with the Framingham Heart Study.
"Our goal is to identify new metabolites and proteins that mark disease activity, signal disease progression, and ultimately provide targets for therapeutic intervention," said Dr. Gerszten. "We are grateful that Agilent supports our research and is helping us in our quest to advance translational cardiology."
"Agilent is proud to support Dr. Gerszten's research in this pivotal project and further advance progress in the important field of cardiometabolic diseases," said Agilent CTO Darlene Solomon, the executive sponsor of the award. "By providing support and cutting-edge technologies to leading translational researchers like Dr. Gerszten, we aim to facilitate innovative research and to progress the fields of metabolomics and integrated biology toward improved patient outcomes."
The Agilent Thought Leader Award program promotes fundamental advances by contributing philanthropic financial support, products and expertise to the research of thought leaders in the life sciences and chemical analysis. Information about previous recipients is available at www.agilent.com/univ_relation/TLP/index.shtml.
|10 Dec 2012
Agilent Technologies' New Pathway Architect Software to Include SRI Internationalís BioCyc Pathway Database Collection
Agilent Technologies Inc. and SRI International today announced they have signed a licensing agreement to offer laboratory research customers a package that combines Agilentís latest release of GeneSpring GX, GeneSpring NGS, Mass Profiler Professional and Pathway Architect version 12.5 with SRI Internationalís complete BioCyc Pathway Database Collection. The integrated package will allow scientists to access, combine, visualize and analyze biological data sets across multiple "omics" experiments (genomics, transcriptomics, proteomics and metabolomics).
"We are pleased to join forces with SRI to provide this advanced product offering," said Nick Roelofs, president of Agilent's Life Sciences Group. "By combining SRI's rich BioCyc pathway content with our fully-integrated laboratory technologies, we are providing researchers with a complete solution for designing more informed experiments, free of the cumbersome technical challenges of traditional multi-omics research. We chose to work with SRI because of the companyís breadth of coverage of organisms and excellent curation."
The new software package will enable researchers to display biological pathway data generated by Agilentís suite of instruments, software and reagents. Agilent solutions include microarrays and next-generation sequencing technology, as well as LC/MS, GC/MS, ICP/MS and NMR systems. Agilent is the sole global provider of world-class instruments, consumables and software for all four "omics" disciplines.
"SRI's databases in the BioCyc Pathway collection will offer Agilent customers the high level of curation needed to accurately interpret their large-scale datasets," said Peter Karp, Ph.D., director of the Bioinformatics Research Group at SRI International. "Our EcoCyc and MetaCyc databases have been curated from 23,000 and 35,000 publications, respectively. Along with other BioCyc databases, they help speed research in myriad domains, including biofuels, agroscience, pharmaceuticals and consumer products."
SRI's BioCyc is a collection of 2,038 Pathway/Genome Databases including 497 complete bacterial genomes from the Human Genome Microbiome Project. Each of the databases in the collection describes the genome and metabolic pathways of a single organism. SRI continues to expand the BioCyc collection with new types of data, curation, genomes and associated pathway predictions.
"Researchers are excited about the extraordinary capabilities they will have with this pathway-driven technology," said Steven Fischer, Agilentís marketing manager for metabolomics and proteomics. "Some of them, for example, may be doing genomics experiments and then realize that their next step should really be a metabolomics experiment. Either way, Agilent's comprehensive suite of integrated technologies provides the hardware, software and consumables required to complete multiple cycles of experiments in multiple disciplines. As each experiment informs the next, they can quickly redesign, collect, measure and analyze new sets of data at a much faster rate than ever before."
Agilent's combined hardware/software and informatics solutions are fueling the next generation of pathway-centric multi-omics research and yielding valuable information about drug responses, drug resistance, diagnostic markers and fundamental disease/toxicity pathways. To learn more about Agilent's complete portfolio of integrated biology solutions, click here.
Source: Lab Manager Magazine
6) Metabolomics Events
|27 Jan-1 Feb 2013
Gordon Research Conference
on Plant Lipids: Structure, Metabolism &
For the first time, a pre-conference Gordon Research Seminar (GRS) , January 26-27, 2013 at the same location, is being organized by investigators at the graduate student and postdoctoral levels for investigators at the graduate student and postdoctoral levels. This seminar is intended to provide (1) background that will enhance understanding of science presented at the subsequent conference, (2) opportunities to share research and to network with peers and experts in the field, and (3) peer and expert feedback and supportive suggestions about ongoing research.
For more information, visit http://www.metabolomicssociety.org/scientific_events and http://www.grc.org/programs.aspx?year=2013&program=plantlipid
|1 Feb 2013
Metabolic Determinants of
Stem Cell Pluripotency and Cell Fate
*Reception to follow.
This event will also be broadcast as a webinar; registration is required.
*Please note: Transmission of presentations via the webinar is subject to individual consent by the speakers. The Introduction (Dr. Gross) and first Keynote Presentation (Dr. Peter Carmeliet) will not be included in the webinar transmission for this symposium, and the anticipated webinar start time is 10:30 AM Eastern Time. To access all speakers' presentations in full, we invite you to attend the live event in New York City.
For more information, visit http://www.nyas.org/events/Detail.aspx?cid=3ca63506-9a4b-413b-96b7-7a127c4e2813
|9-13 Feb 2013
MSACL 2013 - Mass
Spectrometry Applications to the Clinical
For more information, visit https://www.msacl.org/
|25 Feb-1 Mar 2013
EMBO Practical Course on
Metabolomics: Bioinformatics for Life
Is it right for me?
This course is aimed at advanced PhD students and post-doctoral researchers who are planning to improve their ability or learn new techniques in metabolomics and applying optimal data analysis methods using various bioinformatics tools in their research. The aim of this course is to familiarize the participants with advanced data analysis and data fusion methodologies and provide hands-on training on the latest analytical approaches and abilities to visualized and map metabolic changes on the relevant pathways.
What will I learn?
Lectures will give insight into how biological knowledge can be generated from metabolomics experiments and illustrate different ways of analyzing such data using variety of open source and freely available tools. Practicals will consist of computer exercises that will enable the participants to apply statistical methods and different analytical and data processing software to the analysis of metabolomics data under the guidance of the lecturers and teaching assistants. Familiarity with the technology such as data acquisition with NMR and MS is required. Ideally also some experience with R/Bioconductor (basic understanding of the syntax and ability to manipulate R objects) and the Unix/Linux operating system.
What will it cover?
The course covers optimal study design for metabolomics experiments, various data analysis methods, usage of online databases and resource as well theoretical a practical approaches on data fusion. Other topics will include: visualization of metabolomics data on metabolic pathways, methods of identification of unknown compounds, differential expression, data quality and reproducibility assessment using statistical analysis and optimal experimental study design.
For more information, visit http://www.ebi.ac.uk/training/course/embo-practical-course-metabolomics-bioinformatics-life-scientists.
|8-10 Apr 2013
Conference and Exhibition on Metabolomics
& Systems Biology
Metabolomics-2013 is a remarkable event which brings together a unique and International mix of large and medium pharmaceutical, biotech and diagnostics companies, leading universities and clinical research institutions making the conference a perfect platform to share experience, foster collaborations across industry and academia, and evaluate emerging technologies across the globe.
2nd International Conference and Exhibition on Metabolomics & Systems Biology will serve as a catalyst for the advances in the study of Metabolomics & Systems Biology by connecting scientists within and across disciplines at sessions and exhibition held at the venue, creates an environment conducive to information exchange, generation of new ideas, and acceleration of applications that benefit research in Metabolomics & Systems Biology.
For more information, visit http://omicsgroup.com/conferences/metabolomics-systems-biology-2013/.
|14-19 Apr 2013
54th ENC Conference
Preliminary Program: http://www.enc-conference.org/ConferenceDetails/Program/tabid/63/Default.aspx
For more information, visit http://www.enc-conference.org/.
|1-7 June 2013
GRC on Computational NMR
and Associated Seminar on Metabolomic NMR
The meeting is the eighth GRC on Computational NMR and the first to include a dedicated Seminar for graduate students and postdocs. The focus of the GRS is to discuss new contributions in computational Nuclear Magnetic Resonance to the growing field of metabolomics and will feature a keynote talk by David Wishart, University of Alberta, and discussions led by experts in metabolomic NMR as a complement to oral presentations by graduate students and postdocs.
For more information: http://www.grc.org/programs.aspx?year=2013&program=grs_bionmr
For registration: http://www.grc.org/application.aspx?id=15572
We do hope that you will both consider attending and provide this information to your students and postdocs and encourage them join us in Vermont for what we anticipate will be an enjoyable and stimulating meeting.
|1-4 Jul 2013
9th Annual International
Meeting of the Metabolomics Society
We expect this to be the 'must attend' meeting in 2013 for researchers from around the world, where the best speakers in the world and rising stars of the future will present their work in a mixture of plenary and parallel sessions. The Metabolomics Society came into being with the development of the Metabolomics as a discipline and as a result provides a focus for the most varied aspects of the subject ranging from microbes to man. As a result of this it brings together a diverse mixture of scientists from many disciplines, which produces very stimulating meetings.
One of the main aims of the conference will be to create a unique platform for young scientists. Come and listen and talk to the top experts in the field. Find out about the latest exciting technologies that can advance your own research, but most of all come and enjoy Scotland's largest and most vibrant city and the beautiful countryside around it.
We look forward to welcoming you to Glasgow in 2013!
Chair, Local Organising Committee
Metabolomics Glasgow 2013
For more information, visit http://www.metabolomics2013.org/.
|13-17 Aug 2013
Metabolic Signaling &
Disease: From Cell to Organism
Daniel Kelly, Sanford-Burnham Medical Research Institute
Mitchell Lazar, University of Pennsylvania
Susanne Mandrup, University of Southern Denmark
We are pleased to announce the first Cold Spring Harbor meeting on Metabolic Signaling & Disease: From Cell to Organism which will begin on Tuesday evening, August 13 and end at noon on Saturday, August 17, 2013.
Metabolic regulation is at the intersection of many scientific fields, ranging from basic biochemistry and molecular biology to physiology, to the study of disease pathogenesis. Currently, a major challenge for these diverse fields is to define commonalities and differences in metabolic pathways and their regulation, and determine the role of these processes for physiology and disease states. This meeting will fill an important gap by bringing together outstanding researchers focused on diverse pathways, cell types, or diseases with a common theme of understanding how metabolism is regulated in physiology and disease states.
For more information, visit http://meetings.cshl.edu/meetings/2013/metab13.shtml.
7) Metabolomics Jobs
This is a resource for
advertising positions in metabolomics. If you have a job
you would like posted in this newsletter, please email
Ian Forsythe (email@example.com).
Job postings will be carried for a maximum of 4
issues (8 weeks) unless the position is filled prior to
Position in Chemical Ecology/Metabolomics
|University of Utah
|Salt Lake City, Utah, USA
fellowship in metabolomics of cancer models
Institute for Medical Research (NIMR)
National Institute for Medical Research
Position in Lipidomics / Metabolomics
|University of Pennsylvania
|Philadelphia, PA, USA
position in biostatistical methods
|University of Calgary
|Calgary, Alberta, Canada
Ian J. Forsythe, M.Sc.MetaboNews
Department of Computing Science
University of Alberta
221 Athabasca Hall
Edmonton, AB, T6G 2E8, Canada
This newsletter is produced by The Metabolomics Innovation Centre (TMIC, http://www.metabolomicscentre.ca/) for the benefit of the worldwide metabolomics community.
A single source destination for fee-for-service metabolic profiling including comprehensive metabolite identification, quantification, and analysis