A benchmark study of simulation methods for single-cell RNA sequencing data

The impact of dropouts in scRNAseq dense neighborhood analysis

Single cell RNA sequencing (scRNAseq) provides the possibility to investigate transcriptomic profiles on a single cell level. However, the data show unique challenges in comparison to bulk transcriptomic data, one being high dropout rates, which yields high sparsity data. Many classical analysis and preprocessing pipelines are based on the assumption that poor data can be counteracted by quantity and that similar cells (samples) are close to each other in space. Clustering is commonly used to detect clusters (dense local cell neighborhoods) under the assumption that similar cells are close to each other in space (where close is dependent on the (distance) metric used). The most commonly used clustering methodologies to detect dense local neighborhoods are based on graph clustering on a nearest neighbor graph. However, high dropout rates may break this assumption and make it difficult to reliably detect such dense local neighborhoods. We assess the cluster homogeneity and stability under increasing degrees of dropouts in one of the most popular clustering pipelines (dimensionality reduction + graph based clustering), as provided by scRNAseq analyses packages Seurat and Scanpy. Our study showcases that while the default pipeline performs well in terms of cluster homogeneity (i.e., cells in a cluster are of the same type), also with increasing dropout rates, the stability of clusters (i.e., cell pairs consistently being in the same cluster) decreases. This implies that sub-populations within cell types are increasingly difficult to identify under increasing dropout rates because observations are not consistently close. Our results challenge the current practice of using default clustering pipelines and the general assumption of identifiable local neighborhoods on high dropout data. Hence, these results suggest that careful consideration in interpretation and downstream analysis need to be made when relying on local neighborhoods and clusters on scRNAseq data. In addition, these results call for extensive benchmarking, to identify and provide methods robust in their local neighborhood relationships on data containing low to high dropout rates.

Multi-task benchmarking of spatially resolved gene expression simulation models

BACKGROUND

Computational methods for spatially resolved transcriptomics (SRT) are often developed and assessed using simulated data. The effectiveness of these evaluations relies on the ability of simulation methods to accurately reflect experimental data. However, a systematic evaluation framework for spatial simulators is currently lacking.

RESULTS

Here, we present SpatialSimBench, a comprehensive evaluation framework that assesses 13 simulation methods using ten distinct STR datasets. We introduce simAdaptor, a tool that extends single-cell simulators by incorporating spatial variables, enabling them to simulate spatial data. SimAdaptor ensures SpatialSimBench is backwards compatible, facilitating direct comparisons between spatially aware simulators and existing non-spatial single-cell simulators through the adaption. Using SpatialSimBench, we demonstrate the feasibility of leveraging existing single-cell simulators for SRT data and highlight performance differences among methods. Additionally, we evaluate the simulation methods based on a total of 35 metrics across data property estimation, various downstream analyses, and scalability. In total, we generated 4550 results from 13 simulation methods, ten spatial datasets, and 35 metrics.

CONCLUSIONS

Our findings reveal that model estimation can be influenced by distribution assumptions and dataset characteristics. In summary, our evaluation framework provides guidelines for selecting appropriate methods for specific scenarios and informs future method development.

Deep learning in single-cell and spatial transcriptomics data analysis: advances and challenges from a data science perspective

The development of single-cell and spatial transcriptomics has revolutionized our capacity to investigate cellular properties, functions, and interactions in both cellular and spatial contexts. Despite this progress, the analysis of single-cell and spatial omics data remains challenging. First, single-cell sequencing data are high-dimensional and sparse, and are often contaminated by noise and uncertainty, obscuring the underlying biological signal. Second, these data often encompass multiple modalities, including gene expression, epigenetic modifications, metabolite levels, and spatial locations. Integrating these diverse data modalities is crucial for enhancing prediction accuracy and biological interpretability. Third, while the scale of single-cell sequencing has expanded to millions of cells, high-quality annotated datasets are still limited. Fourth, the complex correlations of biological tissues make it difficult to accurately reconstruct cellular states and spatial contexts. Traditional feature engineering approaches struggle with the complexity of biological networks, while deep learning, with its ability to handle high-dimensional data and automatically identify meaningful patterns, has shown great promise in overcoming these challenges. Besides systematically reviewing the strengths and weaknesses of advanced deep learning methods, we have curated 21 datasets from nine benchmarks to evaluate the performance of 58 computational methods. Our analysis reveals that model performance can vary significantly across different benchmark datasets and evaluation metrics, providing a useful perspective for selecting the most appropriate approach based on a specific application scenario. We highlight three key areas for future development, offering valuable insights into how deep learning can be effectively applied to transcriptomic data analysis in biological, medical, and clinical settings.

MOSim: bulk and single-cell multilayer regulatory network simulator

As multi-omics sequencing technologies advance, the need for simulation tools capable of generating realistic and diverse (bulk and single-cell) multi-omics datasets for method testing and benchmarking becomes increasingly important. We present MOSim, an R package that simulates both bulk (via mosim function) and single-cell (via sc_mosim function) multi-omics data. The mosim function generates bulk transcriptomics data (RNA-seq) and additional regulatory omics layers (ATAC-seq, miRNA-seq, ChIP-seq, Methyl-seq, and transcription factors), while sc_mosim simulates single-cell transcriptomics data (scRNA-seq) with scATAC-seq and transcription factors as regulatory layers. The tool supports various experimental designs, including simulation of gene co-expression patterns, biological replicates, and differential expression between conditions. MOSim enables users to generate quantification matrices for each simulated omics data type, capturing the heterogeneity and complexity of bulk and single-cell multi-omics datasets. Furthermore, MOSim provides differentially abundant features within each omics layer and elucidates the active regulatory relationships between regulatory omics and gene expression data at both bulk and single-cell levels. By leveraging MOSim, researchers will be able to generate realistic and customizable bulk and single-cell multi-omics datasets to benchmark and validate analytical methods specifically designed for the integrative analysis of diverse regulatory omics data.

Crafted experiments to evaluate feature selection methods for single-cell RNA-seq data

While numerous methods have been developed for analyzing scRNA-seq data, benchmarking various methods remains challenging. There is a lack of ground truth datasets for evaluating novel gene selection and/or clustering methods. We propose the use of crafted experiments, a new approach based upon perturbing signals in a real dataset for comparing analysis methods. We demonstrate the effectiveness of crafted experiments for evaluating new univariate distribution-oriented suite of feature selection methods, called GOF. We show GOF selects features that robustly identify crafted features and perform well on real non-crafted data sets. Using varying ways of crafting, we also show the context in which each GOF method performs the best. GOF is implemented as an open-source R package and freely available under GPL-2 license at https://github.com/siyao-liu/GOF. Source code, including all functions for constructing crafted experiments and benchmarking feature selection methods, are publicly available at https://github.com/siyao-liu/CraftedExperiment.

Interpretable single-cell factor decomposition using sciRED

Single-cell RNA sequencing maps gene expression heterogeneity within a tissue. However, identifying biological signals in this data is challenging due to confounding technical factors, sparsity, and high dimensionality. Data factorization methods address this by separating and identifying signals in the data, such as gene expression programs, but the resulting factors must be manually interpreted. We developed Single-Cell Interpretable REsidual Decomposition (sciRED) to improve the interpretation of scRNA-seq factor analysis. sciRED removes known confounding effects, uses rotations to improve factor interpretability, maps factors to known covariates, identifies unexplained factors that may capture hidden biological phenomena, and determines the genes and biological processes represented by the resulting factors. We apply sciRED to multiple scRNA-seq datasets and identify sex-specific variation in a kidney map, discern strong and weak immune stimulation signals in a PBMC dataset, reduce ambient RNA contamination in a rat liver atlas to help identify strain variation and reveal rare cell type signatures and anatomical zonation gene programs in a healthy human liver map. These demonstrate that sciRED is useful in characterizing diverse biological signals within scRNA-seq data.

scCobra allows contrastive cell embedding learning with domain adaptation for single cell data integration and harmonization

The rapid advancement of single-cell technologies has created an urgent need for effective methods to integrate and harmonize single-cell data. Technical and biological variations across studies complicate data integration, while conventional tools often struggle with reliance on gene expression distribution assumptions and over-correction. Here, we present scCobra, a deep generative neural network designed to overcome these challenges through contrastive learning with domain adaptation. scCobra effectively mitigates batch effects, minimizes over-correction, and ensures biologically meaningful data integration without assuming specific gene expression distributions. It enables online label transfer across datasets with batch effects, allowing continuous integration of new data without retraining. Additionally, scCobra supports batch effect simulation, advanced multi-omic integration, and scalable processing of large datasets. By integrating and harmonizing datasets from similar studies, scCobra expands the available data for investigating specific biological problems, improving cross-study comparability, and revealing insights that may be obscured in isolated datasets.

Characterizing the omics landscape based on 10,000+ datasets

The characteristics of data produced by omics technologies are pivotal, as they critically influence the feasibility and effectiveness of computational methods applied in downstream analyses, such as data harmonization and differential abundance analyses. Furthermore, variability in these data characteristics across datasets plays a crucial role, leading to diverging outcomes in benchmarking studies, which are essential for guiding the selection of appropriate analysis methods in all omics fields. Additionally, downstream analysis tools are often developed and applied within specific omics communities due to the presumed differences in data characteristics attributed to each omics technology. In this study, we investigate over ten thousand datasets to understand how proteomics, metabolomics, lipidomics, transcriptomics, and microbiome data vary in specific data characteristics. We were able to show patterns of data characteristics specific to the investigated omics types and provide a tool that enables researchers to assess how representative a given omics dataset is for its respective discipline. Moreover, we illustrate how data characteristics can impact analyses at the example of normalization in the presence of sample-dependent proportions of missing values. Given the variability of omics data characteristics, we encourage the systematic inspection of these characteristics in benchmark studies and for downstream analyses to prevent suboptimal method selection and unintended bias.

CZI Cell Science Program, Abdulla S, Aevermann B, Assis P, Badajoz S, Bell SM, Bezzi E, Cakir B, Chaffer J, Chambers S, Cherry J, Chi T, Chien J, Dorman L, Garcia-Nieto P, Gloria N, Hastie M, Hegeman D, Hilton J, Huang T, Infeld A, Istrate AM, Jelic I, Katsuya K, Kim YJ, Liang K, Lin M, Lombardo M, Marshall B, Martin B, McDade F, Megill C, Patel N, Predeus A, Raymor B, Robatmili B, Rogers D, Rutherford E, Sadgat D, Shin A, Small C, Smith T, Sridharan P, Tarashansky A, Tavares N, Thomas H, Tolopko A, Urisko M, Yan J, Yeretssian G, Zamanian J, Mani A, Cool J, Carr A. CZ CELLxGENE Discover: a single-cell data platform for scalable exploration, analysis and modeling of aggregated data

Hundreds of millions of single cells have been analyzed using high-throughput transcriptomic methods. The cumulative knowledge within these datasets provides an exciting opportunity for unlocking insights into health and disease at the level of single cells. Meta-analyses that span diverse datasets building on recent advances in large language models and other machine-learning approaches pose exciting new directions to model and extract insight from single-cell data. Despite the promise of these and emerging analytical tools for analyzing large amounts of data, the sheer number of datasets, data models and accessibility remains a challenge. Here, we present CZ CELLxGENE Discover (cellxgene.cziscience.com), a data platform that provides curated and interoperable single-cell data. Available via a free-to-use online data portal, CZ CELLxGENE hosts a growing corpus of community-contributed data of over 93 million unique cells. Curated, standardized and associated with consistent cell-level metadata, this collection of single-cell transcriptomic data is the largest of its kind and growing rapidly via community contributions. A suite of tools and features enables accessibility and reusability of the data via both computational and visual interfaces to allow researchers to explore individual datasets, perform cross-corpus analysis, and run meta-analyses of tens of millions of cells across studies and tissues at the resolution of single cells.

Interpretable single-cell factor decomposition using sciRED

Single-cell RNA sequencing (scRNA-seq) maps gene expression heterogeneity within a tissue. However, identifying biological signals in this data is challenging due to confounding technical factors, sparsity, and high dimensionality. Data factorization methods address this by separating and identifying signals in the data, such as gene expression programs, but the resulting factors must be manually interpreted. We developed Single-Cell Interpretable REsidual Decomposition (sciRED) to improve the interpretation of scRNA-seq factor analysis. sciRED removes known confounding effects, uses rotations to improve factor interpretability, maps factors to known covariates, identifies unexplained factors that may capture hidden biological phenomena and determines the genes and biological processes represented by the resulting factors. We apply sciRED to multiple scRNA-seq datasets and identify sex-specific variation in a kidney map, discern strong and weak immune stimulation signals in a PBMC dataset, reduce ambient RNA contamination in a rat liver atlas to help identify strain variation, and reveal rare cell type signatures and anatomical zonation gene programs in a healthy human liver map. These demonstrate that sciRED is useful in characterizing diverse biological signals within scRNA-seq data.

Inferring Cell-Type-Specific Co-Expressed Genes from Single Cell Data

Background

Cell-type-specific gene co-expression networks are widely used to characterize gene relationships. Although many methods have been developed to infer such co-expression networks from single-cell data, the lack of consideration of false positive control in many evaluations may lead to incorrect conclusions because higher reproducibility, higher functional coherence, and a larger overlap with known biological networks may not imply better performance if the false positives are not well controlled.

Results

In this study, we have developed an efficient and effective simulation tool to derive empirical p-values in co-expression inference to appropriately control false positives in assessing method performance. We studied the power of the p-value-based approach in inferring cell-type-specific co-expressions from single-cell data using both simulated and real data. We also highlight the need to adjust for random overlaps between the inferred and known networks when the number of selected correlated gene pairs varies substantially across different methods. We further illustrate the expression level bias in known biological networks and the impact of such bias in method assessment.

Conclusion

Our study indicates the importance of controlling false positives in the inference of co-expressed genes to achieve more reliable results and proposes a simulation-based p-value method to achieve this.

Mcadet: A feature selection method for fine-resolution single-cell RNA-seq data based on multiple correspondence analysis and community detection

Single-cell RNA sequencing (scRNA-seq) data analysis faces numerous challenges, including high sparsity, a high-dimensional feature space, and biological noise. These challenges hinder downstream analysis, necessitating the use of feature selection methods to identify informative genes, and reduce data dimensionality. However, existing methods for selecting highly variable genes (HVGs) exhibit limited overlap and inconsistent clustering performance across benchmark datasets. Moreover, these methods often struggle to accurately select HVGs from fine-resolution scRNA-seq datasets and minority cell types, which are more difficult to distinguish, raising concerns about the reliability of their results. To overcome these limitations, we propose a novel feature selection framework for scRNA-seq data called Mcadet. Mcadet integrates Multiple Correspondence Analysis (MCA), graph-based community detection, and a novel statistical testing approach. To assess the effectiveness of Mcadet, we conducted extensive evaluations using both simulated and real-world data, employing unbiased metrics for comparison. Our results demonstrate the superior performance of Mcadet in the selection of HVGs in scenarios involving fine-resolution scRNA-seq datasets and datasets containing minority cell populations. Overall, we demonstrate that Mcadet enhances the reliability of selected HVGs, although the impact of HVG selection on various downstream analyses varies and needs to be further investigated.

scNODE : generative model for temporal single cell transcriptomic data prediction

SUMMARY

Measurement of single-cell gene expression at different timepoints enables the study of cell development. However, due to the resource constraints and technical challenges associated with the single-cell experiments, researchers can only profile gene expression at discrete and sparsely sampled timepoints. This missing timepoint information impedes downstream cell developmental analyses. We propose scNODE, an end-to-end deep learning model that can predict in silico single-cell gene expression at unobserved timepoints. scNODE integrates a variational autoencoder with neural ordinary differential equations to predict gene expression using a continuous and nonlinear latent space. Importantly, we incorporate a dynamic regularization term to learn a latent space that is robust against distribution shifts when predicting single-cell gene expression at unobserved timepoints. Our evaluations on three real-world scRNA-seq datasets show that scNODE achieves higher predictive performance than state-of-the-art methods. We further demonstrate that scNODE's predictions help cell trajectory inference under the missing timepoint paradigm and the learned latent space is useful for in silico perturbation analysis of relevant genes along a developmental cell path.

AVAILABILITY AND IMPLEMENTATION

The data and code are publicly available at https://github.com/rsinghlab/scNODE.

GeneSPIDER2: large scale GRN simulation and benchmarking with perturbed single-cell data

Single-cell data is increasingly used for gene regulatory network (GRN) inference, and benchmarks for this have been developed based on simulated data. However, existing single-cell simulators cannot model the effects of gene perturbations. A further challenge lies in generating large-scale GRNs that often struggle with computational and stability issues. We present GeneSPIDER2, an update of the GeneSPIDER MATLAB toolbox for GRN benchmarking, inference, and analysis. Several software modules have improved capabilities and performance, and new functionalities have been added. A major improvement is the ability to generate large GRNs with biologically realistic topological properties in terms of scale-free degree distribution and modularity. Another major addition is a simulation of single-cell data, which is becoming increasingly popular as input for GRN inference. Specifically, we introduced the unique feature to generate single-cell data based on genetic perturbations. Finally, the simulated single-cell data was compared to real single-cell Perturb-seq data from two cell lines, showing that the synthetic and real data exhibit similar properties.

Interpretable single-cell factor decomposition using sciRED

Single-cell RNA sequencing (scRNA-seq) maps gene expression heterogeneity within a tissue. However, identifying biological signals in this data is challenging due to confounding technical factors, sparsity, and high dimensionality. Data factorization methods address this by separating and identifying signals in the data, such as gene expression programs, but the resulting factors must be manually interpreted. We developed Single-Cell Interpretable Residual Decomposition (sciRED) to improve the interpretation of scRNA-seq factor analysis. sciRED removes known confounding effects, uses rotations to improve factor interpretability, maps factors to known covariates, identifies unexplained factors that may capture hidden biological phenomena and determines the genes and biological processes represented by the resulting factors. We apply sciRED to multiple scRNA-seq datasets and identify sex-specific variation in a kidney map, discern strong and weak immune stimulation signals in a PBMC dataset, reduce ambient RNA contamination in a rat liver atlas to help identify strain variation, and reveal rare cell type signatures and anatomical zonation gene programs in a healthy human liver map. These demonstrate that sciRED is useful in characterizing diverse biological signals within scRNA-seq data.

Feature selection followed by a novel residuals-based normalization that includes variance stabilization simplifies and improves single-cell gene expression analysis

Normalization is a crucial step in the analysis of single-cell RNA-sequencing (scRNA-seq) counts data. Its principal objectives are reduction of systematic biases primarily introduced through technical sources and transformation of counts to make them more amenable for the application of established statistical frameworks. In the standard workflows, normalization is followed by feature selection to identify highly variable genes (HVGs) that capture most of the biologically meaningful variation across the cells. Here, we make the case for a revised workflow by proposing a simple feature selection method and showing that we can perform feature selection before normalization by relying on observed counts. We highlight that the feature selection step can be used to not only select HVGs but to also identify stable genes. We further propose a novel variance stabilization transformation inclusive residuals-based normalization method that in fact relies on the stable genes to inform the reduction of systematic biases. We demonstrate significant improvements in downstream clustering analyses through the application of our proposed methods on biological truth-known as well as simulated counts datasets. We have implemented this novel workflow for analyzing high-throughput scRNA-seq data in an R package called Piccolo.

Bayesian-frequentist hybrid inference framework for single cell RNA-seq analyses

BACKGROUND

Single cell RNA sequencing technology (scRNA-seq) has been proven useful in understanding cell-specific disease mechanisms. However, identifying genes of interest remains a key challenge. Pseudo-bulk methods that pool scRNA-seq counts in the same biological replicates have been commonly used to identify differentially expressed genes. However, such methods may lack power due to the limited sample size of scRNA-seq datasets, which can be prohibitively expensive.

RESULTS

Motivated by this, we proposed to use the Bayesian-frequentist hybrid (BFH) framework to increase the power and we showed in simulated scenario, the proposed BFH would be an optimal method when compared with other popular single cell differential expression methods if both FDR and power were considered. As an example, the method was applied to an idiopathic pulmonary fibrosis (IPF) case study.

CONCLUSION

In our IPF example, we demonstrated that with a proper informative prior, the BFH approach identified more genes of interest. Furthermore, these genes were reasonable based on the current knowledge of IPF. Thus, the BFH offers a unique and flexible framework for future scRNA-seq analyses.

Systematic evaluation with practical guidelines for single-cell and spatially resolved transcriptomics data simulation under multiple scenarios

BACKGROUND

Single-cell RNA sequencing (scRNA-seq) and spatially resolved transcriptomics (SRT) have led to groundbreaking advancements in life sciences. To develop bioinformatics tools for scRNA-seq and SRT data and perform unbiased benchmarks, data simulation has been widely adopted by providing explicit ground truth and generating customized datasets. However, the performance of simulation methods under multiple scenarios has not been comprehensively assessed, making it challenging to choose suitable methods without practical guidelines.

RESULTS

We systematically evaluated 49 simulation methods developed for scRNA-seq and/or SRT data in terms of accuracy, functionality, scalability, and usability using 152 reference datasets derived from 24 platforms. SRTsim, scDesign3, ZINB-WaVE, and scDesign2 have the best accuracy performance across various platforms. Unexpectedly, some methods tailored to scRNA-seq data have potential compatibility for simulating SRT data. Lun, SPARSim, and scDesign3-tree outperform other methods under corresponding simulation scenarios. Phenopath, Lun, Simple, and MFA yield high scalability scores but they cannot generate realistic simulated data. Users should consider the trade-offs between method accuracy and scalability (or functionality) when making decisions. Additionally, execution errors are mainly caused by failed parameter estimations and appearance of missing or infinite values in calculations. We provide practical guidelines for method selection, a standard pipeline Simpipe ( https://github.com/duohongrui/simpipe ; https://doi.org/10.5281/zenodo.11178409 ), and an online tool Simsite ( https://www.ciblab.net/software/simshiny/ ) for data simulation.

CONCLUSIONS

No method performs best on all criteria, thus a good-yet-not-the-best method is recommended if it solves problems effectively and reasonably. Our comprehensive work provides crucial insights for developers on modeling gene expression data and fosters the simulation process for users.

Challenges and best practices in omics benchmarking

Technological advances enabling massively parallel measurement of biological features - such as microarrays, high-throughput sequencing and mass spectrometry - have ushered in the omics era, now in its third decade. The resulting complex landscape of analytical methods has naturally fostered the growth of an omics benchmarking industry. Benchmarking refers to the process of objectively comparing and evaluating the performance of different computational or analytical techniques when processing and analysing large-scale biological data sets, such as transcriptomics, proteomics and metabolomics. With thousands of omics benchmarking studies published over the past 25 years, the field has matured to the point where the foundations of benchmarking have been established and well described. However, generating meaningful benchmarking data and properly evaluating performance in this complex domain remains challenging. In this Review, we highlight some common oversights and pitfalls in omics benchmarking. We also establish a methodology to bring the issues that can be addressed into focus and to be transparent about those that cannot: this takes the form of a spreadsheet template of guidelines for comprehensive reporting, intended to accompany publications. In addition, a survey of recent developments in benchmarking is provided as well as specific guidance for commonly encountered difficulties.

MESBC: A novel mutually exclusive spectral biclustering method for cancer subtyping

Many soft biclustering algorithms have been developed and applied to various biological and biomedical data analyses. However, few mutually exclusive (hard) biclustering algorithms have been proposed, which could better identify disease or molecular subtypes with survival significance based on genomic or transcriptomic data. In this study, we developed a novel mutually exclusive spectral biclustering (MESBC) algorithm based on spectral method to detect mutually exclusive biclusters. MESBC simultaneously detects relevant features (genes) and corresponding conditions (patients) subgroups and, therefore, automatically uses the signature features for each subtype to perform the clustering. Extensive simulations revealed that MESBC provided superior accuracy in detecting pre-specified biclusters compared with the non-negative matrix factorization (NMF) and Dhillon's algorithm, particularly in very noisy data. Further analysis of the algorithm on real datasets obtained from the TCGA database showed that MESBC provided more accurate (i.e., smaller p-value) overall survival prediction in patients with lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) cancers when compared to the existing, gold-standard subtypes for lung cancers (integrative clustering). Furthermore, MESBC detected several genes with significant prognostic value in both LUAD and LUSC patients. External validation on an independent, unseen GEO dataset of LUAD showed that MESBC-derived clusters based on TCGA data still exhibited clear biclustering patterns and consistent, outstanding prognostic predictability, demonstrating robust generalizability of MESBC. Therefore, MESBC could potentially be used as a risk stratification tool to optimize the treatment for the patient, improve the selection of patients for clinical trials, and contribute to the development of novel therapeutic agents.

DELVE: feature selection for preserving biological trajectories in single-cell data

Single-cell technologies can measure the expression of thousands of molecular features in individual cells undergoing dynamic biological processes. While examining cells along a computationally-ordered pseudotime trajectory can reveal how changes in gene or protein expression impact cell fate, identifying such dynamic features is challenging due to the inherent noise in single-cell data. Here, we present DELVE, an unsupervised feature selection method for identifying a representative subset of molecular features which robustly recapitulate cellular trajectories. In contrast to previous work, DELVE uses a bottom-up approach to mitigate the effects of confounding sources of variation, and instead models cell states from dynamic gene or protein modules based on core regulatory complexes. Using simulations, single-cell RNA sequencing, and iterative immunofluorescence imaging data in the context of cell cycle and cellular differentiation, we demonstrate how DELVE selects features that better define cell-types and cell-type transitions. DELVE is available as an open-source python package: https://github.com/jranek/delve .

BEERS2: RNA-Seq simulation through high fidelity in silico modeling

Simulation of RNA-seq reads is critical in the assessment, comparison, benchmarking and development of bioinformatics tools. Yet the field of RNA-seq simulators has progressed little in the last decade. To address this need we have developed BEERS2, which combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline. BEERS2 takes input transcripts (typically fully length messenger RNA transcripts with polyA tails) from either customizable input or from CAMPAREE simulated RNA samples. It produces realistic reads of these transcripts as FASTQ, SAM or BAM formats with the SAM or BAM formats containing the true alignment to the reference genome. It also produces true transcript-level quantification values. BEERS2 combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline and is designed to include the effects of polyA selection and RiboZero for ribosomal depletion, hexamer priming sequence biases, GC-content biases in polymerase chain reaction (PCR) amplification, barcode read errors and errors during PCR amplification. These characteristics combine to make BEERS2 the most complete simulation of RNA-seq to date. Finally, we demonstrate the use of BEERS2 by measuring the effect of several settings on the popular Salmon pseudoalignment algorithm.

Challenges and perspectives in computational deconvolution of genomics data

Deciphering cell-type heterogeneity is crucial for systematically understanding tissue homeostasis and its dysregulation in diseases. Computational deconvolution is an efficient approach for estimating cell-type abundances from a variety of omics data. Despite substantial methodological progress in computational deconvolution in recent years, challenges are still outstanding. Here we enlist four important challenges related to computational deconvolution: the quality of the reference data, generation of ground truth data, limitations of computational methodologies, and benchmarking design and implementation. Finally, we make recommendations on reference data generation, new directions of computational methodologies, and strategies to promote rigorous benchmarking.

scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics

We present a statistical simulator, scDesign3, to generate realistic single-cell and spatial omics data, including various cell states, experimental designs and feature modalities, by learning interpretable parameters from real data. Using a unified probabilistic model for single-cell and spatial omics data, scDesign3 infers biologically meaningful parameters; assesses the goodness-of-fit of inferred cell clusters, trajectories and spatial locations; and generates in silico negative and positive controls for benchmarking computational tools.

BIDCell: Biologically-informed self-supervised learning for segmentation of subcellular spatial transcriptomics data

Recent advances in subcellular imaging transcriptomics platforms have enabled high-resolution spatial mapping of gene expression, while also introducing significant analytical challenges in accurately identifying cells and assigning transcripts. Existing methods grapple with cell segmentation, frequently leading to fragmented cells or oversized cells that capture contaminated expression. To this end, we present BIDCell, a self-supervised deep learning-based framework with biologically-informed loss functions that learn relationships between spatially resolved gene expression and cell morphology. BIDCell incorporates cell-type data, including single-cell transcriptomics data from public repositories, with cell morphology information. Using a comprehensive evaluation framework consisting of metrics in five complementary categories for cell segmentation performance, we demonstrate that BIDCell outperforms other state-of-the-art methods according to many metrics across a variety of tissue types and technology platforms. Our findings underscore the potential of BIDCell to significantly enhance single-cell spatial expression analyses, enabling great potential in biological discovery.

Geometric constraint-triggered collagen expression mediates bacterial-host adhesion

Cells living in geometrically confined microenvironments are ubiquitous in various physiological processes, e.g., wound closure. However, it remains unclear whether and how spatially geometric constraints on host cells regulate bacteria-host interactions. Here, we reveal that interactions between bacteria and spatially constrained cell monolayers exhibit strong spatial heterogeneity, and that bacteria tend to adhere to these cells near the outer edges of confined monolayers. The bacterial adhesion force near the edges of the micropatterned monolayers is up to 75 nN, which is ~3 times higher than that at the centers, depending on the underlying substrate rigidities. Single-cell RNA sequencing experiments indicate that spatially heterogeneous expression of collagen IV with significant edge effects is responsible for the location-dependent bacterial adhesion. Finally, we show that collagen IV inhibitors can potentially be utilized as adjuvants to reduce bacterial adhesion and thus markedly enhance the efficacy of antibiotics, as demonstrated in animal experiments.

Cytomulate: accurate and efficient simulation of CyTOF data

Recently, many analysis tools have been devised to offer insights into data generated via cytometry by time-of-flight (CyTOF). However, objective evaluations of these methods remain absent as most evaluations are conducted against real data where the ground truth is generally unknown. In this paper, we develop Cytomulate, a reproducible and accurate simulation algorithm of CyTOF data, which could serve as a foundation for future method development and evaluation. We demonstrate that Cytomulate can capture various characteristics of CyTOF data and is superior in learning overall data distributions than single-cell RNA-seq-oriented methods such as scDesign2, Splatter, and generative models like LAMBDA.

simCAS: an embedding-based method for simulating single-cell chromatin accessibility sequencing data

MOTIVATION

Single-cell chromatin accessibility sequencing (scCAS) technology provides an epigenomic perspective to characterize gene regulatory mechanisms at single-cell resolution. With an increasing number of computational methods proposed for analyzing scCAS data, a powerful simulation framework is desirable for evaluation and validation of these methods. However, existing simulators generate synthetic data by sampling reads from real data or mimicking existing cell states, which is inadequate to provide credible ground-truth labels for method evaluation.

RESULTS

We present simCAS, an embedding-based simulator, for generating high-fidelity scCAS data from both cell- and peak-wise embeddings. We demonstrate simCAS outperforms existing simulators in resembling real data and show that simCAS can generate cells of different states with user-defined cell populations and differentiation trajectories. Additionally, simCAS can simulate data from different batches and encode user-specified interactions of chromatin regions in the synthetic data, which provides ground-truth labels more than cell states. We systematically demonstrate that simCAS facilitates the benchmarking of four core tasks in downstream analysis: cell clustering, trajectory inference, data integration, and cis-regulatory interaction inference. We anticipate simCAS will be a reliable and flexible simulator for evaluating the ongoing computational methods applied on scCAS data.

AVAILABILITY AND IMPLEMENTATION

simCAS is freely available at https://github.com/Chen-Li-17/simCAS.

Optimal adjustment sets for causal query estimation in partially observed biomolecular networks

Causal query estimation in biomolecular networks commonly selects a 'valid adjustment set', i.e. a subset of network variables that eliminates the bias of the estimator. A same query may have multiple valid adjustment sets, each with a different variance. When networks are partially observed, current methods use graph-based criteria to find an adjustment set that minimizes asymptotic variance. Unfortunately, many models that share the same graph topology, and therefore same functional dependencies, may differ in the processes that generate the observational data. In these cases, the topology-based criteria fail to distinguish the variances of the adjustment sets. This deficiency can lead to sub-optimal adjustment sets, and to miss-characterization of the effect of the intervention. We propose an approach for deriving 'optimal adjustment sets' that takes into account the nature of the data, bias and finite-sample variance of the estimator, and cost. It empirically learns the data generating processes from historical experimental data, and characterizes the properties of the estimators by simulation. We demonstrate the utility of the proposed approach in four biomolecular Case studies with different topologies and different data generation processes. The implementation and reproducible Case studies are at https://github.com/srtaheri/OptimalAdjustmentSet.

scRAA: the development of a robust and automatic annotation procedure for single-cell RNA sequencing data

A critical task in single-cell RNA sequencing (scRNA-Seq) data analysis is to identify cell types from heterogeneous tissues. While the majority of classification methods demonstrated high performance in scRNA-Seq annotation problems, a robust and accurate solution is desired to generate reliable outcomes for downstream analyses, for instance, marker genes identification, differentially expressed genes, and pathway analysis. It is hard to establish a universally good metric. Thus, a universally good classification method for all kinds of scenarios does not exist. In addition, reference and query data in cell classification are usually from different experimental batches, and failure to consider batch effects may result in misleading conclusions. To overcome this bottleneck, we propose a robust ensemble approach to classify cells and utilize a batch correction method between reference and query data. We simulated four scenarios that comprise simple to complex batch effect and account for varying cell-type proportions. We further tested our approach on both lung and pancreas data. We found improved prediction accuracy and robust performance across simulation scenarios and real data. The incorporation of batch effect correction between reference and query, and the ensemble approach improve cell-type prediction accuracy while maintaining robustness. We demonstrated these through simulated and real scRNA-Seq data.

Multi-task learning from multimodal single-cell omics with Matilda

Multimodal single-cell omics technologies enable multiple molecular programs to be simultaneously profiled at a global scale in individual cells, creating opportunities to study biological systems at a resolution that was previously inaccessible. However, the analysis of multimodal single-cell omics data is challenging due to the lack of methods that can integrate across multiple data modalities generated from such technologies. Here, we present Matilda, a multi-task learning method for integrative analysis of multimodal single-cell omics data. By leveraging the interrelationship among tasks, Matilda learns to perform data simulation, dimension reduction, cell type classification, and feature selection in a single unified framework. We compare Matilda with other state-of-the-art methods on datasets generated from some of the most popular multimodal single-cell omics technologies. Our results demonstrate the utility of Matilda for addressing multiple key tasks on integrative multimodal single-cell omics data analysis. Matilda is implemented in Pytorch and is freely available from https://github.com/PYangLab/Matilda.

SimCH: simulation of single-cell RNA sequencing data by modeling cellular heterogeneity at gene expression level

Single-cell ribonucleic acid (RNA) sequencing (scRNA-seq) has been a powerful technology for transcriptome analysis. However, the systematic validation of diverse computational tools used in scRNA-seq analysis remains challenging. Here, we propose a novel simulation tool, termed as Simulation of Cellular Heterogeneity (SimCH), for the flexible and comprehensive assessment of scRNA-seq computational methods. The Gaussian Copula framework is recruited to retain gene coexpression of experimental data shown to be associated with cellular heterogeneity. The synthetic count matrices generated by suitable SimCH modes closely match experimental data originating from either homogeneous or heterogeneous cell populations and either unique molecular identifier (UMI)-based or non-UMI-based techniques. We demonstrate how SimCH can benchmark several types of computational methods, including cell clustering, discovery of differentially expressed genes, trajectory inference, batch correction and imputation. Moreover, we show how SimCH can be used to conduct power evaluation of cell clustering methods. Given these merits, we believe that SimCH can accelerate single-cell research.

A Framework for Comparison and Assessment of Synthetic RNA-Seq Data

The ever-growing number of methods for the generation of synthetic bulk and single cell RNA-seq data have multiple and diverse applications. They are often aimed at benchmarking bioinformatics algorithms for purposes such as sample classification, differential expression analysis, correlation and network studies and the optimization of data integration and normalization techniques. Here, we propose a general framework to compare synthetically generated RNA-seq data and select a data-generating tool that is suitable for a set of specific study goals. As there are multiple methods for synthetic RNA-seq data generation, researchers can use the proposed framework to make an informed choice of an RNA-seq data simulation algorithm and software that are best suited for their specific scientific questions of interest.

Unconstrained generation of synthetic antibody-antigen structures to guide machine learning methodology for antibody specificity prediction

Machine learning (ML) is a key technology for accurate prediction of antibody-antigen binding. Two orthogonal problems hinder the application of ML to antibody-specificity prediction and the benchmarking thereof: the lack of a unified ML formalization of immunological antibody-specificity prediction problems and the unavailability of large-scale synthetic datasets to benchmark real-world relevant ML methods and dataset design. Here we developed the Absolut! software suite that enables parameter-based unconstrained generation of synthetic lattice-based three-dimensional antibody-antigen-binding structures with ground-truth access to conformational paratope, epitope and affinity. We formalized common immunological antibody-specificity prediction problems as ML tasks and confirmed that for both sequence- and structure-based tasks, accuracy-based rankings of ML methods trained on experimental data hold for ML methods trained on Absolut!-generated data. The Absolut! framework has the potential to enable real-world relevant development and benchmarking of ML strategies for biotherapeutics design.

splatPop: simulating population scale single-cell RNA sequencing data

Population-scale single-cell RNA sequencing (scRNA-seq) is now viable, enabling finer resolution functional genomics studies and leading to a rush to adapt bulk methods and develop new single-cell-specific methods to perform these studies. Simulations are useful for developing, testing, and benchmarking methods but current scRNA-seq simulation frameworks do not simulate population-scale data with genetic effects. Here, we present splatPop, a model for flexible, reproducible, and well-documented simulation of population-scale scRNA-seq data with known expression quantitative trait loci. splatPop can also simulate complex batch, cell group, and conditional effects between individuals from different cohorts as well as genetically-driven co-expression.