The Local Edge Machine: inference of dynamic models of gene regulation

We present a novel approach, the Local Edge Machine, for the inference of regulatory interactions directly from time-series gene expression data. We demonstrate its performance, robustness, and scalability on in silico datasets with varying behaviors, sizes, and degrees of complexity. Moreover, we demonstrate its ability to incorporate biological prior information and make informative predictions on a well-characterized in vivo system using data from budding yeast that have been synchronized in the cell cycle. Finally, we use an atlas of transcription data in a mammalian circadian system to illustrate how the method can be used for discovery in the context of large complex networks.Department of Applied Mathematic

Mapping genetic variations to three- dimensional protein structures to enhance variant interpretation: a proposed framework

The translation of personal genomics to precision medicine depends on the accurate interpretation of the multitude of genetic variants observed for each individual. However, even when genetic variants are predicted to modify a protein, their functional implications may be unclear. Many diseases are caused by genetic variants affecting important protein features, such as enzyme active sites or interaction interfaces. The scientific community has catalogued millions of genetic variants in genomic databases and thousands of protein structures in the Protein Data Bank. Mapping mutations onto three-dimensional (3D) structures enables atomic-level analyses of protein positions that may be important for the stability or formation of interactions; these may explain the effect of mutations and in some cases even open a path for targeted drug development. To accelerate progress in the integration of these data types, we held a two-day Gene Variation to 3D (GVto3D) workshop to report on the latest advances and to discuss unmet needs. The overarching goal of the workshop was to address the question: what can be done together as a community to advance the integration of genetic variants and 3D protein structures that could not be done by a single investigator or laboratory? Here we describe the workshop outcomes, review the state of the field, and propose the development of a framework with which to promote progress in this arena. The framework will include a set of standard formats, common ontologies, a common application programming interface to enable interoperation of the resources, and a Tool Registry to make it easy to find and apply the tools to specific analysis problems. Interoperability will enable integration of diverse data sources and tools and collaborative development of variant effect prediction methods

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Radical Anion Complexes of Tris(1,3-diphenyltriazenido)aluminum More About This Article Radical Anion Complexes of Tis( 1,3-diphenyltiazenido)aluminum

Abstract: Electrochemical studies of Al(dpt)3 (Hdpt = 1,3-diphenyltriazene) by cyclic voltammetry in THF solution reveal three successive pseudo reversible one-electron reduction waves (E112 = -1.50, -1.84, and -2.16 V). The chemical reduction of Al(dpt)3 by sodium metal in THF allows for the isolation of the radical anion complexes [Na(THF)x]n[Al(dpt)3], n = 1 ( l ) , 1 (2), and 3 (3). Characterization by EPR, NMR, UV-visible, and X-ray photoelectron (XP) spectroscopy, in addition to the X-ray structural determination of [PPN] [Al(dpt)3] (4), supports the formation of the f i s t homologous series of ligand-centered aluminum(II1) radical anion complexes. Analogous electrochemical reduction series are observed for the p-methyl-and p-methoxy-substituted triazenides. The dependence of the complex reduction potentials is discussed with respect to the UV-visible spectra of the unreduced complex and the ligand's Hammett substituent constant (a). In contrast, irreversible electrochemical reduction (-1.5 to -2.2 V) occurs for the pentafluoro-and p-fluoro-, p-chloro-, and p-bromo-substituted triazenido complexes. Irreversible reduction also occurs for the alkyl and aryloxide compounds Al(R)z(dpt) (R = 'Bu, 'Bu), Al('Bu)(dpt)z, Al(BHT)z-(dpt), and Al(BHT)(dpt)z (BHT-H = 2,6-di-tert-butyl-4-methylphenol). Ab initio molecular orbital calculations have been carried out on the model compounds Al(HNNNH)3 and [Al(HNNNH)3I3-. The identity of the frontier molecular orbitals and calculated structures are considered in relation to experimental data