Conormal bundles, contact homology and knot invariants

We summarize recent work on a combinatorial knot invariant called knot contact homology. We also discuss the origins of this invariant in symplectic topology, via holomorphic curves and a conormal bundle naturally associated to the knot.Comment: This is the version published by Geometry & Topology Monographs on 22 April 200

A topological introduction to knot contact homology

This is a survey of knot contact homology, with an emphasis on topological, algebraic, and combinatorial aspects.Comment: 38 pages, based on lectures at the Contact and Symplectic Topology Summer School in Budapest, July 2012; v2: fixed typos, updated references, version to be publishe

TFBSTools: an R/bioconductor package for transcription factor binding site analysis.

Summary: The ability to efficiently investigate transcription factor binding sites (TFBSs) genome-wide is central to computational studies of gene regulation. TFBSTools is an R/Bioconductor package for the analysis and manipulation of TFBSs and their associated transcription factor profile matrices. TFBStools provides a toolkit for handling TFBS profile matrices, scanning sequences and alignments including whole genomes, and querying the JASPAR database. The functionality of the package can be easily extended to include advanced statistical analysis, data visualization and data integration. Availability and implementation: The package is implemented in R and available under GPL-2 license from the Bioconductor website (http://bioconductor.org/packages/TFBSTools/). Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online