Computational Methods for Single-cell Multi-omics Integration and Alignment.

Recently developed technologies to generate single-cell genomic data have made a revolutionary impact in the field of biology. Multi-omics assays offer even greater opportunities to understand cellular states and biological processes. The problem of integrating different omics data with very different dimensionality and statistical properties remains, however, quite challenging. A growing body of computational tools is being developed for this task, leveraging ideas ranging from machine translation to the theory of networks, and represents another frontier on the interface of biology and data science. Our goal in this review is to provide a comprehensive, up-to-date survey of computational techniques for the integration of single-cell multi-omics data, while making the concepts behind each algorithm approachable to a non-expert audience.

Emerging artificial intelligence applications in Spatial Transcriptomics analysis.

Spatial transcriptomics (ST) has advanced significantly in the last few years. Such advancement comes with the urgent need for novel computational methods to handle the unique challenges of ST data analysis. Many artificial intelligence (AI) methods have been developed to utilize various machine learning and deep learning techniques for computational ST analysis. This review provides a comprehensive and up-to-date survey of current AI methods for ST analysis.

GranatumX: A Community-engaging, Modularized, and Flexible Webtool for Single-cell Data Analysis.

We present GranatumX, a next-generation software environment for single-cell RNA sequencing (scRNA-seq) data analysis. GranatumX is inspired by the interactive webtool Granatum. GranatumX enables biologists to access the latest scRNA-seq bioinformatics methods in a web-based graphical environment. It also offers software developers the opportunity to rapidly promote their own tools with others in customizable pipelines. The architecture of GranatumX allows for easy inclusion of plugin modules, named Gboxes, which wrap around bioinformatics tools written in various programming languages and on various platforms. GranatumX can be run on the cloud or private servers and generate reproducible results. It is a community-engaging, flexible, and evolving software ecosystem for scRNA-seq analysis, connecting developers with bench scientists. GranatumX is freely accessible at http://garmiregroup.org/granatumx/app.

All-Loop Singularities of Scattering Amplitudes in Massless Planar Theories.

In massless quantum field theories the Landau equations are invariant under graph operations familiar from the theory of electrical circuits. Using a theorem on the Y-Δ reducibility of planar circuits we prove that the set of first-type Landau singularities of an n-particle scattering amplitude in any massless planar theory, at any finite loop order, is a subset of those of a certain n-particle ⌊(n-2)^{2}/4⌋-loop "ziggurat" graph. We determine this singularity locus explicitly for n=6 and find that it corresponds precisely to the vanishing of the symbol letters familiar from the hexagon bootstrap in supersymmetric Yang-Mills (SYM) theory. Further implications for SYM theory are discussed.