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Abstract MotivationThe increasing availability of complete genomes demands for models to study genomic variability within entire populations. Pangenome graphs capture the full genomic similarity and diversity between multiple genomes. In order to understand them, we need to see them. For visualization, we need a human-readable graph layout: a graph embedding in low (e.g. two) dimensional depictions. Due to a pangenome graph’s potential excessive size, this is a significant challenge. ResultsIn response, we introduce a novel graph layout algorithm: the Path-Guided Stochastic Gradient Descent (PG-SGD). PG-SGD uses the genomes, represented in the pangenome graph as paths, as an embedded positional system to sample genomic distances between pairs of nodes. This avoids the quadratic cost seen in previous versions of graph drawing by SGD. We show that our implementation efficiently computes the low-dimensional layouts of gigabase-scale pangenome graphs, unveiling their biological features. Availability and implementationWe integrated PG-SGD in ODGI which is released as free software under the MIT open source license. Source code is available at https://github.com/pangenome/odgi. 

Abstract Cp*Rh(III)‐catalyzed chelation‐assisted direct C−H bond functionalization of 1‐(2‐pyridyl)‐2‐pyridones with internal alkynes that can be controlled to give three different products in good yields has been realized. Depending on the reaction conditions, solvents and additives, the reaction pathway can be switched between alkenylation, alkenylation/directing group migration and rollover annulation. These reaction manifolds allow divergent access to a variety of valuable C6‐alkenylated 1‐(2‐pyridyl)‐2‐pyridones, (Z)‐6‐(1,2‐diaryl‐2‐(pyridin‐2‐yl)vinyl)pyridin‐2(1H)‐ones and 10H‐pyrido[1,2‐a][1,8]naphthyridin‐10‐ones from the same starting materials. These protocols exhibit excellent regio‐ and stereoselectivity, broad substrate scope, and good tolerance of functional groups. A combination of experimental and computational approaches have been employed to uncover the key mechanistic features of these reactions.