Issue 16 - December 2012
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1) Software Spotlight
Head of Cheminformatics and Metabolism, European Bioinformatics Institute, Hinxton, Cambridge, UK
Christoph Steinbeck received his diploma and doctoral degree in chemistry from the University of Bonn. After a postdoc at Tufts University in Boston, MA, USA, Dr. Steinbeck led the Structural Chem- and Bioinformatics Workgroup at the newly founded Max-Planck-Institute of Chemical Ecology in Jena, Germany. In the Fall of 2002, he moved to the Cologne University Bioinformatics Center (CUBIC) as head of the Research Group for Molecular Informatics. In December 2003, he received his "Habilitation" in Organic Chemistry from Friedrich-Schiller-University in Jena, Germany.
Dr. Steinbeck is editor-in-chief of the Journal of Cheminformatics, a director of the Metabolomics Society, lifetime member of the World Association of Theoretically Oriented Chemists (WATOC), past chairman of the Computers-Information-Chemistry (CIC) division of the German Chemical Society, and member of various editorial boards and committees.
Today, he is Head of Cheminformatics and Metabolism at the European Bioinformatics Institute (EBI) in Hinxton, Cambridge, UK. His group develops open chemistry databases for the biosciences, such as ChEBI, the dictionary and ontology of Chemical Entities of Biological Interest, the EnzymePortal, and the MetaboLights database, a repository and reference database for Metabolomics. They further develop a number of the leading open source software packages in chem- and bioinformatics, including the Chemistry Development Kit (CDK), a Java library for chem- and bioinformatics.
The Steinbeck group’s research is dedicated to natural products research, the elucidation of metabolomes by means of computer-assisted structure elucidation and other prediction methods, the reconstruction of metabolic networks, and algorithm development in cheminformatics.
3) Biomarker Beacon
4) Metabolomics Current Contents
|16 Nov 2012
New whale shark study used metabolomics to help understand shark and ray health
New research from Georgia Aquarium and Georgia Institute of Technology provides evidence that a suite of techniques called "metabolomics" can be used to determine the health status of whale sharks (Rhincodon typus), the world's largest fish species. The study, led by Dr. Alistair Dove, Director of Research & Conservation at Georgia Aquarium and an adjunct professor at Georgia Tech, found that the major difference between healthy and unhealthy sharks was the concentration of homarine in their in serum—indicating that homarine is a useful biomarker of health status for the species.
The paper, "Biomarkers of whale shark health: a metabolomic approach", which is published in the journal PLOS ONE, is especially significant to the veterinary science community because the study documents the results of a rare opportunity to collect and analyze blood from whale sharks. The paper also comprises the only work yet carried out on biochemistry of the world's largest fish. "This research and its resulting findings are vitally important to ensuring Georgia Aquarium's and the scientific community's care, knowledge, and understanding of not only whale sharks, but similar species of sharks and rays," said Dr. Greg Bossart, Senior Vice President of Animal Health, Research & Conservation and Chief Veterinary Officer at Georgia Aquarium. "The publishing of this clinical research provides a greater opportunity for scientists and Zoological professionals to understand the Animals in our care and can be used to help wild populations, which puts us ahead of the curve in the integrated understanding of animal biology."
|14 Nov 2012
New centre to bring metabolomics to the clinic
Imperial College London has set up a new research centre, called the Imperial Clinical Phenome Centre, that will apply the latest metabolomics technology to the real-time diagnosis of disease.
The new centre will look to develop novel technologies and methods for analysing the metabolites in bodily fluids such as blood and urine as a way to diagnose disease and determine its progression, as disease can have an important effect on metabolite composition. These novel technologies and methods with be based on liquid chromatography, capillary electrophoresis, mass spectrometry and NMR spectroscopy. However, they will be adapted for use in the clinic or operating theatre, providing physicians and surgeons with useful, real-time diagnostic information.
For example, Zoltan Takats, a reader in medical mass spectrometry at Imperial, is developing an 'intelligent knife' that can analyse the smoke produced when an electrically-heated surgical blade cuts into tissue during an operation. Research shows that the profile of the chemicals in the smoke can provide detailed information about the disease state of the tissue, such as whether it is cancerous, or otherwise diseased or non-viable.
"These analytical technologies are now very mature and are immensely powerful for telling us about someone's physical condition and disease state," said Jeremy Nicholson, head of the Department of Surgery and Cancer at Imperial. "Bringing them fully into the clinical setting will help doctors make a more informed diagnosis, choose the best treatment based on the individual characteristics of the patient, and monitor their progress more precisely. It is the dawn of a new age of 'precision medicine'."
The centre is being jointly funded by the National Institute for Health Research (NIHR), the Imperial Biomedical Research Centre and the analytical instrument companies Waters and Bruker. It will be equipped with three nuclear magnetic resonance spectrometers and six mass spectrometers, and will work closely with the existing Medical Research Council-NIHR Phenome Centre, which uses metabolomics data for population screening.
Several researchers involved with the new centre, including Nicholson and Takats, have written a review that appears in the latest edition of Nature highlighting the promise of metabolomics for disease diagnosis.
|9 Nov 2012
Salk's $300M Campaign to Fuel Genomic Medicine, Replace Waning NIH Funds
The Salk Institute for Biological Sciences has launched a campaign to raise $300 million in private funding to support a new genomic medicine initiative, as well as new cancer, aging, and neuroscience programs.
Speaking at a press conference yesterday, Salk's Chair of the Board of Trustees, Irwin Jacobs, said the institute has already raised $150 million from private individuals and foundations during a quiet phase of campaign fundraising that began in 2009.
This six-year effort, the first such campaign in the institute's 53-year history, is aimed at bridging the gap left by flagging funding from the National Institutes of Health. Nine years ago, NIH funding made up two-thirds of the Salk's budget, but now it accounts for less than 50 percent, the institute said.
The Campaign for Salk will support research efforts across a wide range of the institute's missions, including Alzheimer's disease, Parkinson's, obesity and diabetes, spinal cord injuries, crop studies, and others.
The Genomic Medicine Initiative that Salk plans to fund will focus on research in three general areas: metabolism and physiology, cancer, and stem cells.
"This type of initiative is going to be transformative to the Salk — to the present as well as in the future," Ron Evans, a professor in the Salk Gene Expression Laboratory, said during the press briefing.
Evans said the initiative "is really underpinned by our interest in wanting to understand the nature of chronic disease and chronic illnesses ... [including] diabetes, heart disease, cancer, neurodegeneration."
"We will delve into the genome, and use cutting-edge, state-of-the-art technologies to try to understand the nature of stress, and the impact of stress on our genes, and how our bodies respond to the environment when things go wrong," Evans added.
The Genomic Medicine Initiative will create several new core facilities at Salk focused on genome sequencing, proteomics, chemical and systems biology, bioinformatics, and metabolomics, as well as a therapeutics development resource for pursuing new drug targets in preclinical and proof-of-principal trials.
The genome sequencing core facility will provide complete genomics solutions and services for use in next-generation projects involving de novo genome sequencing, targeted re-sequencing, metagenomics, transcriptome profiling, and epigenetic marker sequencing.
The bioinformatics core facility will house both genome sequencing and computing capacities, and it will host databases and biostatisticians for storing and analyzing genomic data.
The metabolomics core will provide mass spectrometers and chromatography tools and expertise for use in studies of lipids, metabolites, and metabolic pathways.
The metabolism and physiology studies will involve metabolomic profiling, studies of the aging genome, epigenetics studies of chronic inflammation and angiogenesis, and they will focus on important pathways and molecules that could be used in new treatments.
Salk's stem cell initiative will focus on identifying gene regulatory networks that control stem cell development and on determining how these genes can be manipulated to make stem cells useful as model systems or as treatments. Researchers also will perform genome sequencing-based studies of the role of DNA modification in reprogramming and generating stem cells.
Through the cancer initiative, Salk researchers will seek to define cancer genomes and the mutations involved in cancer development and disease progression — an effort that will produce knowledge that will be integrated into the stem cell and metabolomics initiatives.
"Our goals are to build on our current strengths and expand into new areas that have been opened up by the human genome sequence and by new imaging technologies," explained Tony Hunter, Salk professor of molecular and cell biology.
"We will continue to build more accurate models of human cancers, like glioblastoma and lung cancer, to study the process of metastasis, and test our ideas for new cancer drugs," Hunter said.
|3-6 Dec 2012||
Metabonomics Shortcourse 2012 - Metabolic
Phenotyping in Disease Diagnosis & Personalised
For more information, please contact:
|27 Jan-1 Feb 2013||
Gordon Research Conference on Plant Lipids:
Structure, Metabolism & Function
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
|25 Feb-1 Mar 2013||
EMBO Practical Course on Metabolomics:
Bioinformatics for Life Scientists
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||
2nd International 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/.
|1-4 Jul 2013||
9th Annual International Meeting of the
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
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 (firstname.lastname@example.org).
Job postings will be carried for a maximum of 4
issues (8 weeks) unless the position is filled prior to that
|Job Title||Employer||Location||Date Posted||Source|
||Human Metabolome Technologies
||Cambridge, MA, USA||20-Nov-2012||Human Metabolome Technologies|
||Stemina Biomarker Discovery
||Madison, WI, USA||10-Nov-2012||naturejobs.com
Officer in NMR Metabolite Analysis
||University of Birmingham||Birmingham, UK
of Laboratory Operations
||Durham, NC, USA||29-Oct-2012||Metabolomics
positions in Advanced Metabolomics
||NIH West Coast Metabolomics Center, UC Davis||Davis, CA, USA
Position in Metabolomics
||Georgetown University||Washington, DC, USA
Inflammation and Malnutrition Using Metabolomics - Open
||The Pennsylvania State University||University Park, PA, USA
Professor of Biology
||University of Virginia
||Charlottesville, VA, USA
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