Topic 175

samples seq sample methods rna genomics profiles method technical transcriptome differential tissues data types sequencing tissue different estimates profile datasets single biological cell cancer scrna such type analysis protocol transcriptomic differences inference heterogeneity variation applied snrna expression profiling bioinformatics relevant whole reference breast large developed performance specific replicates microglia cells cohorts gene apply batch multiple detect frozen computational issues existing normalization subjects highlighted analyses changes systematic bulk four when each mixtures address aberrations reveals from protocols systems atlas across integrative fixed disease detecting profiled sensitivity identify biologically paraffin nuclei including deconvolution formalin compared derived reproducibility pathways tumor informed comparison techniques

46 items. Top items listed below.

Comprehensive evaluation of human brain gene expression deconvolution methods 175 43 9 4

Bayesian estimation of cell-type-specific gene expression per bulk sample with prior derived from single-cell data 175 43 9 4

Establishment of a simplified preparation method for single-nucleus RNA-sequencing and its application to long-term frozen tumor tissues 175 43 4

A Comprehensive Multi-Center Cross-platform Benchmarking Study of Single-cell RNA Sequencing Using Reference Samples 175 43 4

Efficient Representations of Tumor Diversity with Paired DNA-RNA Anomalies 175 9 4

Nabo - a framework to define leukemia-initiating cells and differentiation in single-cell RNA-sequencing data 175 43 4

Effect of methanol fixation on single-cell RNA sequencing data 175 43 4

Integrative transcriptomic analysis of SLE reveals IFN-driven cross-talk between immune cells 175 120 9

Differential Transcript Usage Analysis Incorporating Quantification Uncertainty Via Compositional Measurement Error Regression Modeling 175 123 83 4

An approach for normalization and quality control for NanoString RNA expression data 175 4

A novel single-cell based method for breast cancer prognosis 43 26 4

A single-cell and single-nucleus RNA-seq toolbox for fresh and frozen human tumors 175 43 14 9 4

RNA-Sieve: A likelihood-based deconvolution of bulk gene expression data using single-cell references 175 43 4

Unexpected variability of allelic imbalance estimates from RNA sequencing 175 125 4

Single nucleus sequencing fails to detect microglial activation 175 120 43 9

Cell Type Aware analysis of RNA-seq data(CARseq) reveals difference and similarities ofthe molecular mechanisms of Schizophrenia andAutism 175 43 9

A highly scalable method for joint whole genome sequencing and gene expression profiling of single cells 175 43 9 4

Reference-free deconvolution of complex DNA methylation data - a systematic protocol 175 43 14 9 4

Expression-Based Inference of Cancer Metabolic Flux Differences 175 9

Variance-adjusted Mahalanobis (VAM): a fast and accurate method for cell-specific gene set scoring 43 4

Probabilistic gene expression signatures identify cell-types from single cell RNA-seq data 43 4

A Multi-center Cross-platform Single-cell RNA Sequencing Reference Dataset 43 4

Global computational alignment of tumor and cell line transcriptional profiles 43 14 9 4

Impact of between-tissue differences on pan-cancer predictions of drug sensitivity 175 9 4

Alignment of single-cell RNA-seq samples without over-correction using kernel density matching 147 43 13 4

On the discovery of population-specific state transitions from multi-sample multi-condition single-cell RNA sequencing data 43 4

Use of relevancy and complementary information for discriminatory gene selection from high-dimensional cancer data 175 112 4

Charting extracellular transcriptomes in The Human Biofluid RNA Atlas 175 9

Probabilistic index models for testing differential expression in single cell RNA sequencing data 43 4

Detecting cell-type-specific allelic expression imbalance by integrative analysis of bulk and single-cell RNA sequencing data 43 4

Generating Ensembles of Gene Regulatory Networks to Assess Robustness of Disease Modules 175 112 4

Removing unwanted variation between samples in Hi-C experiments 175 4

Improving gene-network inference with graph-wavelets and making insights about ageing associated regulatory changes in lungs 175 112 9 4

Reference genome and transcriptome informed by the sex chromosome complement of the sample increases ability to detect sex differences in gene expression from RNA-Seq data 175 25 9

A Systematic Evaluation of Single-cell RNA-sequencing Imputation Methods 43 4

Proteogenomic single cell analysis of skeletal muscle myocytes 175 43 9

AutoGeneS: Automatic gene selection using multi-objective optimization for RNA-seq deconvolution 147 43 13 4

Proteogenomic Analysis of Pancreatic Cancer Subtypes 175 9 4

Single-cell RNA-seq reveals early heterogeneity during ageing in yeast 175 120 43 9 3

Highly sensitive in situ proteomics with cleavable fluorescent tyramide reveals human neuronal heterogeneity 175 18 4

CASB: A concanavalin A-based sample barcoding strategy for single-cell sequencing 175 43 9 4

Comprehensive gene expression analysis detects global reduction of proteasome subunits in schizophrenia 175 9

Design and power analysis for multi-sample single cell genomics experiments 43 4

Estimating the rate of cell type degeneration from epigenetic sequencing of cell-free DNA 175 87 4

Comprehensive benchmarking of computational deconvolution of transcriptomics data 43 4

Deciphering cellular transcriptional alterations in Alzheimer's disease brains 32 9 4

Determining subpopulation methylation profiles from bisulfite sequencing data of heterogeneous samples using DXM 175 43 4

Cluster similarity spectrum integration of single-cell genomics data 147 43 4

Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis 43 9 4

A computational method for direct imputation of cell type-specific expression profiles and cellular compositions from bulk-tissue RNA-Seq in brain disorders 43 9 4

miRNA activity inferred from single cell mRNA expression 43 4

Lipidomics of human adipose tissue reveals diversity between body areas 175 45 15

Denoising large-scale biological data using network filters 26 4

Stable gene expression for normalisation and single-sample scoring 43 4

Intra-exon motif correlations as a proxy measure for mean per-tile sequence quality data in RNA-Seq 175 4

BayesSpace enables the robust characterization of spatial gene expression architecture in tissue sections at increased resolution 43 4

FIRM: Fast Integration of single-cell RNA-sequencing data across Multiple platforms 43 4

cFIT: Integration and transfer learning of single cell transcriptomes, illustrated by fetal brain cell development 43 4

CytoTalk: De novo construction of signal transduction networks using single-cell RNA-Seq data 43 9 4

Whole-organism mapping of the genetics of gene expression at cellular resolution 19 9 4

MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data 97 25 9 4

Multi-tissue transcriptome-wide association studies 19 4

Supervised Adversarial Alignment of scRNA-seq Data 147 43 26 4

Detection of differential RNA modifications from direct RNA sequencing of human cell lines 147 13 4

ICELLNET: a transcriptome-based framework to dissect intercellular communication 175 43 4

Robust decomposition of cell type mixtures in spatial transcriptomics 147 43 13 4

Accuracy and Reproducibility of Somatic Point Mutation Calling in Clinical-Type Targeted Sequencing Data 175 97 4

Probabilistic Harmonization and Annotation of Single-cell Transcriptomics Data with Deep Generative Models 43 4

Knowledge-based classification of fine-grained immune cell types in single-cell RNA-Seq data with ImmClassifier 43 26 4

Joint single cell DNA-Seq and RNA-Seq of gastric cancer reveals subclonal signatures of genomic instability and gene expression 43 9 4

BATMAN: fast and accurate integration of single-cell RNA-Seq datasets via minimum-weight matching 147 43 13 4

Enzymatic dissociation induces transcriptional and proteotype bias in brain cell populations 175 120 43 9

New gene association measures by joint network embedding of multiple gene expression datasets 43 4

Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts 120 9 3

Cryopreservation of human cancers conserves tumour heterogeneity for single-cell multi-omics analysis 43 9 4

Network-based imputation of dropouts in single-cell RNA sequencing data 147 43 13 4

Imputing missing RNA-seq data from DNA methylation by using transfer learning based-deep neural network 105 26 4

Computational approaches towards reducing contamination in single-cell RNA-seq data 43 4

Estimating RNA dynamics using one time point for one sample in a single-pulse metabolic experiment 83 4

Improving replicability in single-cell RNA-Seq cell type discovery with Dune 147 43 4

Mouse Aging Cell Atlas Analysis Reveals Global and Cell Type Specific Aging Signatures 120 43 9

Machine learning-based investigation of the cancer protein secretory pathway 112 14 9 4

Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling 43 9 4

Bayesian cell-type deconvolution and gene expression inference reveals tumor-microenvironment interactions 43 9 4

When DNA gets in the way in RNA-seq experiments, a sequel 175 4

Transcriptomic entropy benchmarks stem cell-derived cardiomyocyte maturation against endogenous tissue at single cell level 43 4

Latent Feature Representations for Human Gene Expression Data Improve Phenotypic Predictions 43 26 4

Novel Human Kidney Cell Subsets Identified by Mux-Seq 43 9 4

Mapping multicellular programs from single-cell profiles 43 9

Phenotype-guided subpopulation identification from single-cell sequencing data 147 43 4

Spatial analysis of ligand-receptor interactions in skin cancer at genome-wide and single-cell resolution 43 9 4

A validated strategy to infer protein biomarkers from RNA-Seq by combining multiple mRNA splice variants and time-delay 45 9 4

Subpopulation identification for single-cell RNA-sequencing data using functional data analysis 43 4

Iterative point set registration for aligning scRNA-seq data 43 26 4

Single-cell mapper (scMappR): using scRNA-seq to infer cell-type specificities of differentially expressed genes 43 4

RNAseq analysis of rodent spaceflight experiments is confounded by sample collection techniques 175 4

Comparison of High-Throughput Single-Cell RNA Sequencing Data Processing Pipelines 43 4

Multi-Objective Approach for Identifying Cancer Subnetwork Markers 112 26 4

MONET: Multi-omic patient module detection by omic selection 147 43 4

TISCH: a comprehensive web resource enabling interactive single-cell transcriptome visualization of tumor microenvironment 43 9 4