Showing papers by "Saurabh Srivastava published in 2017"
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TL;DR: A computational method, the Temporal Pathway Synthesizer (TPS), is presented, to discover missing pathway elements by modeling temporal phosphoproteomic data andhibiting predicted active kinases supports the TPS pathway model.
Abstract: Advances in proteomics reveal that pathway databases fail to capture the majority of cellular signaling activity. Our mass spectrometry study of the dynamic epidermal growth factor (EGF) response demonstrates that over 89% of significantly (de)phosphorylated proteins are excluded from individual EGF signaling maps, and 63% are absent from all annotated pathways. We present a computational method, the Temporal Pathway Synthesizer (TPS), to discover missing pathway elements by modeling temporal phosphoproteomic data. TPS uses constraint solving to exhaustively explore all possible structures for a signaling pathway, eliminating structures that are inconsistent with protein-protein interactions or the observed phosphorylation event timing. Applied to our EGF response data, TPS connects 83% of the responding proteins to receptors and signaling proteins in EGF pathway maps. Inhibiting predicted active kinases supports the TPS pathway model. The TPS algorithm is broadly applicable and also recovers an accurate model of the yeast osmotic stress response.
5 citations
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17 Jan 2017
TL;DR: In this paper, the authors provide compositions and methods for the biosynthetic production of acetaminophen, p-aminophenol, and paminobenzoic acid.
Abstract: The present disclosure provides compositions and methods for the biosynthetic production of acetaminophen, p-aminophenol, and p-aminobenzoic acid and the purification of biologically derived acetaminophen.
2 citations
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17 Jan 2017
TL;DR: In this paper, the authors provide compositions and methods for the biosynthetic production of choline, ethanolamine, phosphoethanolamine, and phosphocholine, as well as methods for synthesizing choline derivatives.
Abstract: The present disclosure provides compositions and methods for the biosynthetic production of choline, ethanolamine, phosphoethanolamine, and phosphocholine.
1 citations