BayeSMART: Bayesian clustering of multi-sample spatially resolved transcriptomics data.

The field of spatially resolved transcriptomics (SRT) has greatly advanced our understanding of cellular microenvironments by integrating spatial information with molecular data collected from multiple tissue sections or individuals. However, methods for multi-sample spatial clustering are lacking, and existing methods primarily rely on molecular information alone. This paper introduces BayeSMART, a Bayesian statistical method designed to identify spatial domains across multiple samples.

NetMIM: network-based multi-omics integration with block missingness for biomarker selection and disease outcome prediction.

Compared with analyzing omics data from a single platform, an integrative analysis of multi-omics data provides a more comprehensive understanding of the regulatory relationships among biological features associated with complex diseases. However, most existing frameworks for integrative analysis overlook two crucial aspects of multi-omics data. Firstly, they neglect the known dependencies among biological features that exist in highly credible biological databases.

An interpretable Bayesian clustering approach with feature selection for analyzing spatially resolved transcriptomics data.

Recent breakthroughs in spatially resolved transcriptomics (SRT) technologies have enabled comprehensive molecular characterization at the spot or cellular level while preserving spatial information. Cells are the fundamental building blocks of tissues, organized into distinct yet connected components. Although many non-spatial and spatial clustering approaches have been used to partition the entire region into mutually exclusive spatial domains based on the SRT high-dimensional molecular profile, most require an ad hoc selection of less interpretable dimensional-reduction techniques.

iIMPACT: integrating image and molecular profiles for spatial transcriptomics analysis.

Current clustering analysis of spatial transcriptomics data primarily relies on molecular information and fails to fully exploit the morphological features present in histology images, leading to compromised accuracy and interpretability. To overcome these limitations, we have developed a multi-stage statistical method called iIMPACT. It identifies and defines histology-based spatial domains based on AI-reconstructed histology images and spatial context of gene expression measurements, and detects domain-specific differentially expressed genes.

Automatic block-wise genotype-phenotype association detection based on hidden Markov model.

Background: For detecting genotype-phenotype association from case-control single nucleotide polymorphism (SNP) data, one class of methods relies on testing each genomic variant site individually. However, this approach ignores the tendency for associated variant sites to be spatially clustered instead of uniformly distributed along the genome. Therefore, a more recent class of methods looks for blocks of influential variant sites.

Cu-catalyzed oxygenation of alkene-tethered amides with O unactivated C[double bond, length as m-dash]C bond cleavage: a direct approach to cyclic imides.

The transformations of unactivated alkenes through C[double bond, length as m-dash]C bond double cleavage are always attractive but very challenging. We report herein a chemoselective approach to valuable cyclic imides by a novel Cu-catalyzed geminal amino-oxygenation of unactivated C[double bond, length as m-dash]C bonds. O was successfully employed as the oxidant as well as the O-source and was incorporated into alkenyl amides C[double bond, length as m-dash]C bond cleavage for the efficient preparation of succinimide or glutarimide derivatives.

Selective Aerobic Oxygenation of Tertiary Allylic Alcohols with Molecular Oxygen.

Aerobic epoxidation of tertiary allylic alcohols remains a significant challenge. Reported here is an efficient and highly chemoselective copper-catalyzed epoxidation and semipinacol rearrangement reaction of tertiary allylic alcohols with molecular oxygen. The solvent 1,4-dioxane activates dioxygen, thereby precluding the addition of a sacrificial reductant.

Oxygenation of Simple Olefins through Selective Allylic C-C Bond Cleavage: A Direct Approach to Cinnamyl Aldehydes.

A novel metal-free allylic C-C σ-bond cleavage of simple olefins to give valuable cinnamyl aldehydes is reported. 1,2-Aryl or alkyl migration through allylic C-C bond cleavage occurs in this transformation, which is assisted by an alkyl azide reagent. This method enables O-atom incorporation into simple unfunctionalized olefins to construct cinnamyl aldehydes.

Cs CO -Catalyzed Aerobic Oxidative Cross-Dehydrogenative Coupling of Thiols with Phosphonates and Arenes.

An efficient Cs CO -catalyzed oxidative coupling of thiols with phosphonates and arenes that uses molecular oxygen as the oxidant is described. These reactions provide not only a novel alkali metal salt catalyzed aerobic oxidation, but also an efficient approach to thiophosphates and sulfenylarenes, which are ubiquitously found in pharmaceuticals and pesticides. The reaction proceeds under simple and mild reaction conditions, tolerates a wide range of functional groups, and is applicable to the late-stage synthesis and modification of bioactive molecules.