Biotechnology Forum: Charting Unknown Territories – reverse QSARs, random forests, in-silico spectra
| Days and times: | November 16, 2010 – 11am – 12pm |
| Lead Instructors: | Dr. Tobias Kind, researcher Metabolomics Laboratory at UC Davis Genome Center |
| Facility: | UC Davis Genome Center, Room 4202 |
We will have a Bioinformatics Technology Forum (BTF) presentation on “Charting unknown territories – reverse QSARs, random forests, in-silico spectra – and the hunt for the holy grail in mass spectrometry” presented by Dr. Tobias Kind, Tuesday (November 16, 2010) at 11am-12pm in room 4202, GBSF, Davis, CA.
Genetic imperialism – fact or fiction? The cost of a large GWAS (genome wide association study) can account for more expenses than the yearly funding for metabolomics by the NSF or NIH. For example the breast cancer genes BRCA1 and BRCA2 are only causative for 5% of the high risk breast cancer cases, other causes remain unknown. Yet the influences of small molecules from food sources and the environment on diseases are not well understood and need to be investigated in more detail using metabolic profiling techniques.
Mass spectrometry based metabolomics can be used to obtain a very fine-grained view at all small molecules and can be used with genomics, transcriptomics and proteomics in systems-wide approaches. The drawback is that small molecules can not be sequenced like genes and proteins, but each molecule requires on average one year and one researcher for complete structural elucidation. Many of the algorithms do not scale well on Hadoop MapReduce or cloud services, because there are actually no algorithms to deduce the correct structure from mass spectral signals.
The holy grail of mass spectrometry, the deduction of the correct structures from mass spectral information can only be found with systematic approaches and a wide range of modern cheminformatics and bioinformatics software tools. The talk focuses in more detail how reverse QSARs, random forests, genetic algorithms and in-silico spectra can be used for fishing in the sea of 10^200 possible molecules and which direction to steer on the voyage to the holy grail of mass spectrometry.
Tobias Kind is a researcher at the Metabolomics Laboratory (FiehnLab) at the UC Davis Genome Center. His interests are mass spectrometric based metabolic profiling methods and their application to fundamental disease and plant research.
The purpose of the Bioinformatics Technology Forum (BTF) meeting series at the Genome Center is to provide a campus-wide venue to show and tell how bioinformatics tools or related information technology actually work. To present your practical problems and ask bioinformatics help is also an appropriate thing to do. In the meeting, people are encouraged to do live demonstrations as well as brief introductions of their work or problems. All talks are informal (although introduction slides are often helpful) and active interactions are expected. BTF is operating by a committee, which consists of Kyoungmi Kim and Dawei Lin. If you want to talk at the BTF, please send an email to lhslin@ucdavis.edu to schedule your talk. You may subscribe to the Bioinformatics mailing list for up-to-date news and follow us on twitter at @ucd_biorhythm.
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Email Dawei Lin
Dr. Dawei Lin received his PhD from Peking University, China in Computational and Structural Biology. He started his career at the Protein Data Bank (PDB) at Brookhaven National Laboratory, a worldwide repository for macromolecular structures. He is currently the Bioinformatics Core Director at the UC Davis Genome Center. In his current position, he is leading his team to provide expertise and infrastructure to carry out acquisition curation, and distribution of complex data sets as well as to develop and perform computations, analyses and simulations addressing a wide variety of biological questions from genomics to network biology.