Canonical, Stable, General Mapping using Context Schemes

Motivation: Sequence mapping is the cornerstone of modern genomics. However, most existing sequence mapping algorithms are insufficiently general. Results: We introduce context schemes: a method that allows the unambiguous recognition of a reference base in a query sequence by testing the query for substrings from an algorithmically defined set. Context schemes only map when there is a unique best mapping, and define this criterion uniformly for all reference bases. Mappings under context schemes can also be made stable, so that extension of the query string (e.g. by increasing read length) will not alter the mapping of previously mapped positions. Context schemes are general in several senses. They natively support the detection of arbitrary complex, novel rearrangements relative to the reference. They can scale over orders of magnitude in query sequence length. Finally, they are trivially extensible to more complex reference structures, such as graphs, that incorporate additional variation. We demonstrate empirically the existence of high performance context schemes, and present efficient context scheme mapping algorithms. Availability and Implementation: The software test framework created for this work is available from https://registry.hub.docker.com/u/adamnovak/sequence-graphs/. Contact: [email protected] Supplementary Information: Six supplementary figures and one supplementary section are available with the online version of this article.Comment: Submission for Bioinformatic

Loop Spaces and Connections

We examine the geometry of loop spaces in derived algebraic geometry and extend in several directions the well known connection between rotation of loops and the de Rham differential. Our main result, a categorification of the geometric description of cyclic homology, relates S^1-equivariant quasicoherent sheaves on the loop space of a smooth scheme or geometric stack X in characteristic zero with sheaves on X with flat connection, or equivalently D_X-modules. By deducing the Hodge filtration on de Rham modules from the formality of cochains on the circle, we are able to recover D_X-modules precisely rather than a periodic version. More generally, we consider the rotated Hopf fibration Omega S^3 --> Omega S^2 --> S^1, and relate Omega S^2-equivariant sheaves on the loop space with sheaves on X with arbitrary connection, with curvature given by their Omega S^3-equivariance.Comment: Revised versio

Derived Algebraic Geometry

This text is a survey of derived algebraic geometry. It covers a variety of general notions and results from the subject with a view on the recent developments at the interface with deformation quantization.Comment: Final version. To appear in EMS Surveys in Mathematical Science

Algebraic K-theory of quasi-smooth blow-ups and cdh descent

We construct a semi-orthogonal decomposition on the category of perfect complexes on the blow-up of a derived Artin stack in a quasi-smooth centre. This gives a generalization of Thomason's blow-up formula in algebraic K-theory to derived stacks. We also provide a new criterion for descent in Voevodsky's cdh topology, which we use to give a direct proof of Cisinski's theorem that Weibel's homotopy invariant K-theory satisfies cdh descent.Comment: 24 pages; to appear in Annales Henri Lebesgu