Spearheading future omics analyses using dyngen, a multi-modal simulator of single cells

Welcome to the tidyverse

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Scenic: single-cell regulatory network inference and clustering.

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Dynamic regulatory network controlling TH17 cell differentiation

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Alignment of single-cell trajectories to compare cellular expression dynamics

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Gold Standard Single-Cell -Omics Datasets For Comparing Trajectory Inference Methods

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RNA velocity unraveled

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

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Network inference with Granger causality ensembles on single-cell transcriptomics

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scDesign2: a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured

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Single-cell omics: experimental workflow, data analyses and applications

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

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Recent advances in trajectory inference from single-cell omics data

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Current Bioinformatics Tools in Precision Oncology

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Deconvolving Clinically Relevant Cellular Immune Cross-talk from Bulk Gene Expression Using CODEFACS and LIRICS Stratifies Patients with Melanoma to Anti–PD-1 Therapy

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Entropy sorting of single-cell RNA sequencing data reveals the inner cell mass in the human pre-implantation embryo

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Trajectory inference across multiple conditions with condiments

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Inference of high-resolution trajectories in single-cell RNA-seq data by using RNA velocity

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scMultiSim: simulation of single-cell multi-omics and spatial data guided by gene regulatory networks and cell–cell interactions

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The shaky foundations of simulating single-cell RNA sequencing data

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Inferring single-cell transcriptomic dynamics with structured latent gene expression dynamics

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A deep manifold-regularized learning model for improving phenotype prediction from multi-modal data

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Modeling bursty transcription and splicing with the chemical master equation

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Studying stochastic systems biology of the cell with single-cell genomics data

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Gene-level alignment of single-cell trajectories

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One model fits all: Combining inference and simulation of gene regulatory networks

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Single‐cell RNA sequencing integrated with bulk RNA sequencing analysis reveals the protective effects of lactate‐mediated lactylation of microglia‐related proteins on spinal cord injury

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VeTra: a tool for trajectory inference based on RNA velocity

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Joint trajectory inference for single-cell genomics using deep learning with a mixture prior

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Manifold Interpolating Optimal-Transport Flows for Trajectory Inference.

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dynDeepDRIM: a dynamic deep learning model to infer direct regulatory interactions using time-course single-cell gene expression data

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RegVelo: Gene-regulatory-informed dynamics of single cells

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Alignment of single-cell trajectory trees with CAPITAL

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GraphVelo allows for accurate inference of multimodal velocities and molecular mechanisms for single cells

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Branching topology of the human embryo transcriptome revealed by Entropy Sort Feature Weighting

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A multi-layered integrative analysis reveals a cholesterol metabolic program in outer radial glia with implications for human brain evolution

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

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Milo2.0 unlocks population genetic analyses of cell state abundance using a count-based mixed modelPreprint

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ONTraC characterizes spatially continuous variations of tissue microenvironment through niche trajectory analysis

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Characterization of cell-fate decision landscapes by estimating transcription factor dynamics

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Scalable identification of lineage-specific gene regulatory networks from metacells with NetID

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Joint Trajectory Inference for Single-cell Genomics Using Deep Learning with a Mixture PriorPreprint

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Deep neural network learning biological condition information refines gene-expression-based cell subtypes

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Inference of high-resolution trajectories in single cell RNA-Seq data from RNA velocityPreprint

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Inferring causal trajectories from spatial transcriptomics using CASCAT

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Exploring structured molecular landscape from single-cell multi-omics data by an explainable multimodal model

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Mathematical modeling suggests heterogeneous replication of Mycobacterium tuberculosis in rabbits

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VeTra: a tool for trajectory inference based on RNA velocityPreprint

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scMomentum: Inference of Cell-Type-Specific Regulatory Networks and Energy LandscapesPreprint

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GAN-Based Training of Semi-Interpretable Generators for Biological Data Interpolation and Augmentation

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Integrative genome-wide association studies, proteome-wide Mendelian randomization, and single-cell RNA sequencing identify interleukin-6 receptor protein as a therapeutic target in aortic aneurysm

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MLBKFD: Probabilistic Model Methods to Infer Pseudo Trajectories from Single-cell Data

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Inferring Gene Regulatory Networks from Single-Cell Time-Course Data Based on Temporal Convolutional Networks

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Ezh2‐dependent methylation in oral epithelia promotes secondary palatogenesis

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SuperGLUE facilitates an explainable training framework for multi-modal data analysis

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Comprehensive benchmarking of RNA velocity methods across single-cell datasets

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Effects of migration rates and vaccination on the spread of yellow fever in Latin American communities

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

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Inferring virtual cell environments using multi-agent reinforcement learningPreprint

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ESCHR: a hyperparameter-randomized ensemble approach for robust clustering across diverse datasets

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Efficient Stochastic Simulation of Gene Regulatory Networks Using Hybrid Models of Transcriptional Bursting

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Graph-Embedded Deep Generative Clustering for Single-Cell Multi-Omics Data Integration

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eSPRESSO: topological clustering of single-cell transcriptomics data to reveal informative genes for spatio–temporal architectures of cells

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Fuzzy-Based Identification of Transition Cells to Infer Cell Trajectory for Single-Cell Transcriptomics

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Mathematical modeling suggests heterogeneous replication of Mycobacterium tuberculosis in rabbitsPreprint

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GillespieSSA2: Gillespie's Stochastic Simulation Algorithm for Impatient People

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scMoE: single-cell Multi-Modal Multi-Task Learning via Sparse Mixture-of-ExpertsPreprint

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Totem: a user-friendly tool for clustering-based inference of tree-shaped trajectories from single-cell dataPreprint

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VData: Temporally annotated data manipulation and storagePreprint

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Additional file 7 of eSPRESSO: topological clustering of single-cell transcriptomics data to reveal informative genes for spatio–temporal architectures of cells

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Additional file 10 of eSPRESSO: topological clustering of single-cell transcriptomics data to reveal informative genes for spatio–temporal architectures of cells

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VeloSim: Simulating single cell gene-expression and RNA velocityPreprint

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scMultiSim: simulation of multi-modality single cell data guided by cell-cell interactions and gene regulatory networksPreprint

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