DeconRNASeq: a statistical framework for deconvolution of heterogeneous tissue samples based on mRNA-Seq data

No abstract is available for this paper.

• Publication year

  2013

• Venue

  Bioinform.

• Publication date

  2013-04-15

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1093/bioinformatics/btt090PMID 23428642
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• ContEst: estimating cross-contamination of human samples in next-generation sequencing data

  2011cited by this paper
• Population-specific expression analysis (PSEA) reveals molecular changes in diseased brain

  2011cited by this paper
• Efficiently identifying genome-wide changes with next-generation sequencing data

  2011cited by this paper
• Bayesian community-wide culture-independent microbial source tracking

  2011cited by this paper
• Optimal Deconvolution of Transcriptional Profiling Data Using Quadratic Programming with Application to Complex Clinical Blood Samples

  2011cited by this paper
• Gene expression deconvolution in clinical samples

  2010cited by this paper
• Advancing RNA-Seq analysis

  2010cited by this paper
• mRNA-Seq whole-transcriptome analysis of a single cell

  2009cited by this paper
• ISOLATE: a computational strategy for identifying the primary origin of cancers using high-throughput sequencing

  2009cited by this paper
• Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

  2008cited by this paper
• CHEMTAX - a program for estimating class abundances from chemical markers: application to HPLC measurements of phytoplankton

  1996cited by this paper
• Nonlinear Programming

  1995cited by this paper

• Protocol for a biomarker discovery study to identify correlates of risk for future tuberculosis disease progression in South African children (INTREPID)

  2026cites this paper
• A Pan‐Cancer Microenvironment Atlas Constructed by DECEPTICONx

  2026cites this paper
• Real-paired single-cell/bulk RNA-seq benchmark and a practical protocol for accurate cell-type deconvolution in human BAL samples

  2026cites this paper
• Comparative Transcriptomics of Human Breast Tissue Suggests Conserved Epithelial Secretory Programs and Tissue-Associated Regulatory Specialization

  2026cites this paper
• Transcriptomic analysis reveals the impact of concurrent, resistance, and endurance training on skeletal muscle

  2026cites this paper
• Estropausal gut microbiota transplant improves measures of ovarian function in adult mice.

  2026cites this paper
• AI-driven deciphering of cell niches with single-cell and spatial omics: a new perspective for traditional Chinese medicine research

  2026cites this paper
• Suppression of ERK signalling promotes pluripotent epiblast in the human blastocyst

  2025cites this paper
• NETSseq Reveals Inflammatory and Aging Mechanisms in Distinct Cell Types Driving Cerebellar Decline in Ataxia Telangiectasia

  2025cites this paper
• Estropausal gut microbiota transplant improves measures of ovarian function in adult mice

  2025cites this paper
• Automating Exploratory Multiomics Research via Language Models

  2025cites this paper
• Salivary Extracellular Vesicle RNA Profiling Reveals Biomarkers for Sjögren’s

  2025cites this paper
• Deep learning-based cell type profiles reveal signatures of Alzheimer’s disease resilience and resistance

  2025cites this paper
• Transcriptomic and proteomic profiling reveal immune and metabolic dysregulation in the colonic mucosa of people living with HIV with incomplete immune recovery

  2025cites this paper
• Comparative transcriptomics in serial organs uncovers early and pan-organ developmental changes associated with organ-specific morphological adaptation

  2025cites this paper
• Optimized RNA sequencing deconvolution illustrates the impact of obesity and weight loss on cell composition of human adipose tissue

  2025cites this paper
• Robustness and resilience of computational deconvolution methods for bulk RNA sequencing data

  2025cites this paper
• omnideconv: a unifying framework for using and benchmarking single-cell-informed deconvolution of bulk RNA-seq data

  2025cites this paper
• Single‐cell insights into the role of T cells in B‐cell malignancies

  2025cites this paper
• Physics-informed AI with chemical master equation dynamics for driver-gene subclone detection and risk labeling

  2025cites this paper
• A guide to transcriptomic deconvolution in cancer

  2025cites this paper
• Bioinformatics perspectives on transcriptomics: A comprehensive review of bulk and single‐cell RNA sequencing analyses

  2025cites this paper
• NETSseq reveals inflammatory and aging mechanisms in distinct cell types, driving cerebellar decline in ataxia telangiectasia

  2025cites this paper
• A robust workflow to benchmark deconvolution of multi-omic data

  2025cites this paper
• An improved reference library and method for accurate cell-type deconvolution of bulk-tissue miRNA data

  2025cites this paper
• Artificial Intelligence in Ocular Transcriptomics: Applications of Unsupervised and Supervised Learning

  2025cites this paper
• DECEPTICON: a correlation-based strategy for RNA-seq deconvolution inspired by a variation of the Anna Karenina principle

  2025cites this paper
• Deconer: An Evaluation Toolkit for Reference-based Deconvolution Methods Using Gene Expression Data

  2025cites this paper
• Identification of the body fluid donors from mixture stains using bulk transcriptomes data

  2025cites this paper
• An augmented GSNMF model for complete deconvolution of bulk RNA-seq data.

  2025cites this paper
• Comprehensive genomic and transcriptomic analyses reveal prognostic stratification for esophageal squamous cell carcinoma

  2025cites this paper
• xCell 2.0: robust algorithm for cell type proportion estimation predicts response to immune checkpoint blockade

  2024cites this paper
• Deconvolution from bulk gene expression by leveraging sample-wise and gene-wise similarities and single-cell RNA-seq data

  2024cites this paper
• Evaluating cell type deconvolution in FFPE breast tissue: application to benign breast disease

  2024cites this paper
• Benchmarking transcriptional deconvolution methods for estimating tissue- and cell type-specific extracellular vesicle abundances

  2024cites this paper
• Benchmarking transcriptome deconvolution methods for estimating tissue‐ and cell‐type‐specific extracellular vesicle abundances

  2024cites this paper
• Assessing transcriptomic heterogeneity of single-cell RNASeq data by bulk-level gene expression data

  2024cites this paper
• Altered Genome-Wide DNA Methylation in the Duodenum of Common Variable Immunodeficiency Patients

  2024cites this paper
• imply: improving cell-type deconvolution accuracy using personalized reference profiles

  2024cites this paper
• An optimized pipeline for high-throughput bulk RNA-Seq deconvolution illustrates the impact of obesity and weight loss on cell composition of human adipose tissue

  2024cites this paper
• Enhancing immuno-oncology investigations through multidimensional decoding of tumor microenvironment with IOBR 2.0

  2024cites this paper
• New generative methods for single-cell transcriptome data in bulk RNA sequence deconvolution

  2024cites this paper
• Unlocking biological insights from differentially expressed genes: Concepts, methods, and future perspectives

  2024cites this paper
• Next-generation deconvolution of transcriptomic data to investigate the tumor microenvironment.

  2024cites this paper
• Suppression of ERK signalling promotes pluripotent epiblast in the human blastocyst

  2024cites this paper
• spatialHeatmap: visualizing spatial bulk and single-cell assays in anatomical images

  2024cites this paper
• Inferring tumor purity using multi-omics data based on a uniform machine learning framework MoTP

  2024cites this paper
• Alleviating batch effects in cell type deconvolution with SCCAF-D

  2024cites this paper
• Missing cell types in single-cell references impact deconvolution of bulk data but are detectable

  2024cites this paper
• Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data

  2024cites this paper
• Integrating omics data for personalized medicine in treating psoriasis

  2024cites this paper
• lute: estimating the cell composition of heterogeneous tissue with varying cell sizes using gene expression

  2024cites this paper
• Fourteen years of cellular deconvolution: methodology, applications, technical evaluation and outstanding challenges

  2024cites this paper
• Identification of Circular RNAs associated with Ageing of the Dorsolateral Prefrontal Cortex across the Adult Lifespan

  2024cites this paper
• Multilayer Analysis of RNA Sequencing Data in Alzheimer's Disease to Unravel Molecular Mysteries.

  2024cites this paper
• IOBR2: Multidimensional Decoding Tumor Microenvironment for Immuno-Oncology Research

  2024cites this paper
• Single-cell transcriptomic-informed deconvolution of bulk data identifies immune checkpoint blockade resistance in urothelial cancer

  2024cites this paper
• STdGCN: spatial transcriptomic cell-type deconvolution using graph convolutional networks

  2024cites this paper
• Emerging Insights into Molecular Mechanisms of Inflammation in Myelodysplastic Syndromes

  2023cites this paper
• Unraveling the complexity: understanding the deconvolutions of RNA-seq data

  2023cites this paper
• DeCOOC Deconvoluted Hi‐C Map Characterizes the Chromatin Architecture of Cells in Physiologically Distinctive Tissues

  2023cites this paper
• Comparative Analysis of Cell Mixtures Deconvolution and Gene Signatures Generated for Blood, Immune and Cancer Cells

  2023cites this paper
• imply: improving cell-type deconvolution accuracy using personalized reference profiles

  2023cites this paper
• Highly Accurate Estimation of Cell Type Abundance in Bulk Tissues Based on Single‐Cell Reference and Domain Adaptive Matching

  2023cites this paper
• Linking environmental risk factors with epigenetic mechanisms in Parkinson’s disease

  2023cites this paper
• Challenges and opportunities to computationally deconvolve heterogeneous tissue with varying cell sizes using single cell RNA-sequencing datasets

  2023cites this paper
• Novel evaluation approach for molecular signature-based deconvolution methods

  2023cites this paper
• Phenotypic innovation in one tooth induced concerted developmental evolution in another

  2023influential citation
• InstaPrism: an R package for fast implementation of BayesPrism

  2023cites this paper
• PUREE: accurate pan-cancer tumor purity estimation from gene expression data

  2023cites this paper
• Leveraging inter-individual transcriptional correlation structure to infer discrete signaling mechanisms across metabolic tissues

  2023cites this paper
• Towards Artificial Intelligence to Multi-omics Characterization of Tumor Heterogeneity in Esophageal Cancer.

  2023cites this paper
• ELITE: Expression deconvoLution using lInear optimizaTion in bulk transcriptomics mixturEs

  2023cites this paper
• Interpretable and context-free deconvolution of multi-scale whole transcriptomic data with UniCell deconvolve

  2023cites this paper
• Expression quantitative trait locus studies in the era of single-cell omics

  2023cites this paper
• A novel Bayesian framework for harmonizing information across tissues and studies to increase cell type deconvolution accuracy

  2023cites this paper
• Molecular group and correlation guided structural learning for multi-phenotype prediction

  2023cites this paper
• Challenges and opportunities to computationally deconvolve heterogeneous tissue with varying cell sizes using single-cell RNA-sequencing datasets

  2023cites this paper
• Age, sex, and cell type-resolved hypothalamic gene expression across the pubertal transition in mice

  2023cites this paper
• Longitudinal single-cell data informs deterministic modelling of inflammatory bowel disease

  2023cites this paper
• Deconer: A comprehensive and systematic evaluation toolkit for reference-based cell type deconvolution algorithms using gene expression data

  2023cites this paper
• Spatial Transcriptomic Cell-type Deconvolution Using Graph Neural Networks

  2023cites this paper
• Pan-cancer Analysis of the Disulfidptosis-related Gene NCKAP1 and Its Prognostic Value for Lung Adenocarcinoma

  2023cites this paper
• Systems immunology spanning tumors, lymph nodes, and periphery

  2023cites this paper
• Robust and accurate estimation of cellular fraction from tissue omics data via ensemble deconvolution

  2022cites this paper
• Amniogenesis occurs in two independent waves in primates

  2022cites this paper
• CAMML with the Integration of Marker Proteins (ChIMP)

  2022cites this paper
• Developmental System Drift in One Tooth Facilitates the Adaptation of the Other

  2022cites this paper
• Comprehensive evaluation of deconvolution methods for human brain gene expression

  2022influential citation
• More accurate estimation of cell composition in bulk expression through robust integration of single-cell information

  2022cites this paper
• Decosus: An R Framework for Universal Integration of Cell Proportion Estimation Methods

  2022cites this paper
• GEOMETRIC STRUCTURE GUIDED MODEL AND ALGORITHMS FOR COMPLETE DECONVOLUTION OF GENE EXPRESSION DATA.

  2022cites this paper
• RNA-seq analysis of gene expression profiles in posttraumatic stress disorder, Parkinson’s disease and schizophrenia identifies roles for common and distinct biological pathways

  2022cites this paper
• Network biology and artificial intelligence drive the understanding of the multidrug resistance phenotype in cancer.

  2022cites this paper
• The Power of Single-Cell RNA Sequencing in eQTL Discovery

  2022cites this paper
• Tumor microenvironment: barrier or opportunity towards effective cancer therapy

  2022cites this paper
• Multiset multicover methods for discriminative marker selection

  2022cites this paper
• Dual scRNA-Seq analysis reveals rare and uncommon parasitized cell populations in chronic L. donovani infection

  2022cites this paper
• Metastatic triple negative breast cancer adapts its metabolism to destination tissues while retaining key metabolic signatures

  2022cites this paper
• Challenges and perspectives in computational deconvolution of genomics data

  2022cites this paper