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Full-Text Articles in Biochemistry, Biophysics, and Structural Biology
A Framework For Application Of Metabolic Modeling In Yeast To Predict The Effects Of Nssnv In Human Orthologs, Hayley Dingerdissen, Daniel S. Weaver, Peter D. Karp, Yang Pan, Vahan Simonyan, Raja Mazumder
A Framework For Application Of Metabolic Modeling In Yeast To Predict The Effects Of Nssnv In Human Orthologs, Hayley Dingerdissen, Daniel S. Weaver, Peter D. Karp, Yang Pan, Vahan Simonyan, Raja Mazumder
Biochemistry and Molecular Medicine Faculty Publications
Background
We have previously suggested a method for proteome wide analysis of variation at functional residues wherein we identified the set of all human genes with nonsynonymous single nucleotide variation (nsSNV) in the active site residue of the corresponding proteins. 34 of these proteins were shown to have a 1:1:1 enzyme:pathway:reaction relationship, making these proteins ideal candidates for laboratory validation through creation and observation of specific yeast active site knock-outs and downstream targeted metabolomics experiments. Here we present the next step in the workflow toward using yeast metabolic modeling to predict human metabolic behavior resulting from nsSNV.
Results
For the …
Non-Synonymous Variations In Cancer And Their Effects On The Human Proteome: Workflow For Ngs Data Biocuration And Proteome-Wide Analysis Of Tcga Data, Charles Cole, Konstantinos Krampis, Konstantinos Karagiannis, Jonas Almeida, William J. Faison, Mona Motwani, Quan Wan, Anton Golikov, Yang Pan, Vahan Simonyan, Raja Mazumder
Non-Synonymous Variations In Cancer And Their Effects On The Human Proteome: Workflow For Ngs Data Biocuration And Proteome-Wide Analysis Of Tcga Data, Charles Cole, Konstantinos Krampis, Konstantinos Karagiannis, Jonas Almeida, William J. Faison, Mona Motwani, Quan Wan, Anton Golikov, Yang Pan, Vahan Simonyan, Raja Mazumder
Biochemistry and Molecular Medicine Faculty Publications
Background
Next-generation sequencing (NGS) technologies have resulted in petabytes of scattered data, decentralized in archives, databases and sometimes in isolated hard-disks which are inaccessible for browsing and analysis. It is expected that curated secondary databases will help organize some of this Big Data thereby allowing users better navigate, search and compute on it.
Results
To address the above challenge, we have implemented a NGS biocuration workflow and are analyzing short read sequences and associated metadata from cancer patients to better understand the human variome. Curation of variation and other related information from control (normal tissue) and case (tumor) samples will …