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1. SEraster: a rasterization preprocessing framework for scalable spatial omics data analysis

   https://doi.org/10.1093/bioinformatics/btae412  

   Aihara, Gohta; Clifton, Kalen; Chen, Mayling; Li, Zhuoyan; Atta, Lyla; Miller, Brendan_F; Satija, Rahul; Hickey, John_W; Fan, Jean; Martelli, ed., Pier_Luigi (June 2024, Bioinformatics)

   Abstract MotivationSpatial omics data demand computational analysis but many analysis tools have computational resource requirements that increase with the number of cells analyzed. This presents scalability challenges as researchers use spatial omics technologies to profile millions of cells. ResultsTo enhance the scalability of spatial omics data analysis, we developed a rasterization preprocessing framework called SEraster that aggregates cellular information into spatial pixels. We apply SEraster to both real and simulated spatial omics data prior to spatial variable gene expression analysis to demonstrate that such preprocessing can reduce computational resource requirements while maintaining high performance, including as compared to other down-sampling approaches. We further integrate SEraster with existing analysis tools to characterize cell-type spatial co-enrichment across length scales. Finally, we apply SEraster to enable analysis of a mouse pup spatial omics dataset with over a million cells to identify tissue-level and cell-type-specific spatially variable genes as well as spatially co-enriched cell types that recapitulate expected organ structures. Availability and implementationSEraster is implemented as an R package on GitHub (https://github.com/JEFworks-Lab/SEraster) with additional tutorials at https://JEF.works/SEraster. 

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2. Inferring neuron-neuron communications from single-cell transcriptomics through NeuronChat

   https://doi.org/10.1038/s41467-023-36800-w  

   Zhao, Wei; Johnston, Kevin G.; Ren, Honglei; Xu, Xiangmin; Nie, Qing (February 2023, Nature Communications)

   Abstract Neural communication networks form the fundamental basis for brain function. These communication networks are enabled by emitted ligands such as neurotransmitters, which activate receptor complexes to facilitate communication. Thus, neural communication is fundamentally dependent on the transcriptome. Here we develop NeuronChat, a method and package for the inference, visualization and analysis of neural-specific communication networks among pre-defined cell groups using single-cell expression data. We incorporate a manually curated molecular interaction database of neural signaling for both human and mouse, and benchmark NeuronChat on several published datasets to validate its ability in predicting neural connectivity. Then, we apply NeuronChat to three different neural tissue datasets to illustrate its functionalities in identifying interneural communication networks, revealing conserved or context-specific interactions across different biological contexts, and predicting communication pattern changes in diseased brains with autism spectrum disorder. Finally, we demonstrate NeuronChat can utilize spatial transcriptomics data to infer and visualize neural-specific cell-cell communication. 

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3. Supervised capacity preserving mapping: a clustering guided visualization method for scRNA-seq data

   https://doi.org/10.1093/bioinformatics/btac131  

   Zhai, Zhiqian; Lei, Yu L.; Wang, Rongrong; Xie, Yuying; Mathelier, ed., Anthony (March 2022, Bioinformatics)

   Abstract MotivationThe rapid development of scRNA-seq technologies enables us to explore the transcriptome at the cell level on a large scale. Recently, various computational methods have been developed to analyze the scRNAseq data, such as clustering and visualization. However, current visualization methods, including t-SNE and UMAP, are challenged by the limited accuracy of rendering the geometric relationship of populations with distinct functional states. Most visualization methods are unsupervised, leaving out information from the clustering results or given labels. This leads to the inaccurate depiction of the distances between the bona fide functional states. In particular, UMAP and t-SNE are not optimal to preserve the global geometric structure. They may result in a contradiction that clusters with near distance in the embedded dimensions are in fact further away in the original dimensions. Besides, UMAP and t-SNE cannot track the variance of clusters. Through the embedding of t-SNE and UMAP, the variance of a cluster is not only associated with the true variance but also is proportional to the sample size. ResultsWe present supCPM, a robust supervised visualization method, which separates different clusters, preserves the global structure and tracks the cluster variance. Compared with six visualization methods using synthetic and real datasets, supCPM shows improved performance than other methods in preserving the global geometric structure and data variance. Overall, supCPM provides an enhanced visualization pipeline to assist the interpretation of functional transition and accurately depict population segregation. Availability and implementationThe R package and source code are available at https://zenodo.org/record/5975977#.YgqR1PXMJjM. Supplementary informationSupplementary data are available at Bioinformatics online. 

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4. Nonnegative spatial factorization applied to spatial genomics

   https://doi.org/10.1038/s41592-022-01687-w  

   Townes, F. William; Engelhardt, Barbara E. (December 2022, Nature Methods)

   Abstract Nonnegative matrix factorization (NMF) is widely used to analyze high-dimensional count data because, in contrast to real-valued alternatives such as factor analysis, it produces an interpretable parts-based representation. However, in applications such as spatial transcriptomics, NMF fails to incorporate known structure between observations. Here, we present nonnegative spatial factorization (NSF), a spatially-aware probabilistic dimension reduction model based on transformed Gaussian processes that naturally encourages sparsity and scales to tens of thousands of observations. NSF recovers ground truth factors more accurately than real-valued alternatives such as MEFISTO in simulations, and has lower out-of-sample prediction error than probabilistic NMF on three spatial transcriptomics datasets from mouse brain and liver. Since not all patterns of gene expression have spatial correlations, we also propose a hybrid extension of NSF that combines spatial and nonspatial components, enabling quantification of spatial importance for both observations and features. A TensorFlow implementation of NSF is available fromhttps://github.com/willtownes/nsf-paper. 

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5. BioModME for building and simulating dynamic computational models of complex biological systems

   https://doi.org/10.1093/bioadv/vbae023  

   Womack, Justin A.; Shah, Viren; Audi, Said H.; Terhune, Scott S.; Dash, Ranjan K.; Lengauer, ed., Thomas (February 2024, Bioinformatics Advances)

   Abstract SummaryMolecular mechanisms of biological functions and disease processes are exceptionally complex, and our ability to interrogate and understand relationships is becoming increasingly dependent on the use of computational modeling. We have developed “BioModME,” a standalone R-based web application package, providing an intuitive and comprehensive graphical user interface to help investigators build, solve, visualize, and analyze computational models of complex biological systems. Some important features of the application package include multi-region system modeling, custom reaction rate laws and equations, unit conversion, model parameter estimation utilizing experimental data, and import and export of model information in the Systems Biology Matkup Language format. The users can also export models to MATLAB, R, and Python languages and the equations to LaTeX and Mathematical Markup Language formats. Other important features include an online model development platform, multi-modality visualization tool, and efficient numerical solvers for differential-algebraic equations and optimization. Availability and implementationAll relevant software information including documentation and tutorials can be found at https://mcw.marquette.edu/biomedical-engineering/computational-systems-biology-lab/biomodme.php. Deployed software can be accessed at https://biomodme.ctsi.mcw.edu/. Source code is freely available for download at https://github.com/MCWComputationalBiologyLab/BioModME. 

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