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ICTD: A semi-supervised cell type identification and deconvolution method for multi-omics data

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/s00262-018-2150-zopenalex-snapshot

Quantifying tumor-infiltrating immune cells from transcriptomics data

inferredcites →https://doi.org/10.1007/s40484-018-0131-zopenalex-snapshot

MRHCA: a nonparametric statistics based method for hub and co‐expression module identification in large gene co‐expression network

inferredcites →https://doi.org/10.1016/j.celrep.2018.03.086openalex-snapshot

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

inferredcites →https://doi.org/10.1038/nmeth.3337openalex-snapshot

Robust enumeration of cell subsets from tissue expression profiles

inferredcites →https://doi.org/10.1038/nrg.2016.67openalex-snapshot

Computational genomics tools for dissecting tumour–immune cell interactions

inferredcites →https://doi.org/10.1038/nri2506openalex-snapshot

Myeloid-derived suppressor cells as regulators of the immune system

inferredcites →https://doi.org/10.1038/s41467-018-07242-6openalex-snapshot

Leveraging heterogeneity across multiple datasets increases cell-mixture deconvolution accuracy and reduces biological and technical biases

inferredcites →https://doi.org/10.1038/s41467-018-08023-xopenalex-snapshot

Bulk tissue cell type deconvolution with multi-subject single-cell expression reference

inferredcites →https://doi.org/10.1038/s41587-019-0114-2openalex-snapshot

Determining cell type abundance and expression from bulk tissues with digital cytometry

inferredcites →https://doi.org/10.1038/s41591-018-0136-1openalex-snapshot

Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response

inferredcites →https://doi.org/10.1038/s41592-018-0229-2openalex-snapshot

Deep generative modeling for single-cell transcriptomics

inferredcites →https://doi.org/10.1038/s41592-019-0355-5openalex-snapshot

Cell composition analysis of bulk genomics using single-cell data

inferredcites →https://doi.org/10.1038/sj.gene.6364173openalex-snapshot

Immune response in silico (IRIS): immune-specific genes identified from a compendium of microarray expression data

inferredcites →https://doi.org/10.1093/biostatistics/kxj037openalex-snapshot

Adjusting batch effects in microarray expression data using empirical Bayes methods

inferredcites →https://doi.org/10.1093/jmcb/mjv031openalex-snapshot

Elucidation of drivers of high-level production of lactates throughout a cancer development

inferredcites →https://doi.org/10.1109/tsp.2013.2285514openalex-snapshot

Non-Negative Matrix Factorization Revisited: Uniqueness and Algorithm for Symmetric Decomposition

inferredcites →https://doi.org/10.1111/j.1600-0587.2012.07348.xopenalex-snapshot

Collinearity: a review of methods to deal with it and a simulation study evaluating their performance

inferredcites →https://doi.org/10.1126/science.1091903openalex-snapshot

MicroRNAs Modulate Hematopoietic Lineage Differentiation

inferredcites →https://doi.org/10.1126/science.aad0501openalex-snapshot

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

inferredcites →https://doi.org/10.1126/science.aai8478openalex-snapshot

Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq

inferredcites →https://doi.org/10.1158/0008-5472.can-16-2490openalex-snapshot

Systematic Pan-Cancer Analysis Reveals Immune Cell Interactions in the Tumor Microenvironment

inferredcites →https://doi.org/10.1158/2326-6074.tumimm17-b24openalex-snapshot

Abstract B24: Digital signatures of T cell dysfunction predict immunotherapy response

inferredcites →https://doi.org/10.1186/1471-2105-9-559openalex-snapshot

WGCNA: an R package for weighted correlation network analysis

inferredcites →https://doi.org/10.1186/s13059-015-0844-5openalex-snapshot

MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data

inferredcites →https://doi.org/10.1186/s13059-016-1028-7openalex-snapshot

Comprehensive analyses of tumor immunity: implications for cancer immunotherapy

inferredcites →https://doi.org/10.1186/s13059-017-1256-5openalex-snapshot

Revisit linear regression-based deconvolution methods for tumor gene expression data

inferredcites →https://doi.org/10.1186/s13059-019-1778-0openalex-snapshot

TOAST: improving reference-free cell composition estimation by cross-cell type differential analysis

inferredcites →https://doi.org/10.1371/journal.pone.0006098openalex-snapshot

Deconvolution of Blood Microarray Data Identifies Cellular Activation Patterns in Systemic Lupus Erythematosus

inferredcites →https://doi.org/10.3389/fimmu.2017.00892openalex-snapshot

CD56 in the Immune System: More Than a Marker for Cytotoxicity?

inferredcites →https://doi.org/10.7554/elife.26476openalex-snapshot

Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Inhibition of Glutamate‐to‐Glutathione Flux Promotes Tumor Antigen Presentation in Colorectal Cancer Cells

inferred← citeshttps://doi.org/10.1016/j.gpb.2022.06.003openalex-snapshot

Acid–Base Homeostasis and Implications to the Phenotypic Behaviors of Cancer

inferred← citeshttps://doi.org/10.1016/j.patter.2022.100440openalex-snapshot

DAISM-DNNXMBD: Highly accurate cell type proportion estimation with in silico data augmentation and deep neural networks

inferred← citeshttps://doi.org/10.1038/s41467-023-40611-4openalex-snapshot

Whole genome deconvolution unveils Alzheimer’s resilient epigenetic signature

inferred← citeshttps://doi.org/10.1093/bib/bbaa307openalex-snapshot

SSMD: a semi-supervised approach for a robust cell type identification and deconvolution of mouse transcriptomics data

inferred← citeshttps://doi.org/10.1172/jci140837openalex-snapshot

MAL2 drives immune evasion in breast cancer by suppressing tumor antigen presentation

inferred← citeshttps://doi.org/10.1186/s40001-025-03013-4openalex-snapshot

Deferoxamine addresses metabolic dysregulation and urinary tract infections in weight-associated gestational diabetes mellitus

inferred← citeshttps://doi.org/10.3390/biom11101501openalex-snapshot

Effects of Molecular Iodine/Chemotherapy in the Immune Component of Breast Cancer Tumoral Microenvironment

inferred← citeshttps://doi.org/10.70675/52e5031azbec1z427azadafzf0cbf809a35eopenalex-snapshot

Application of Multivariate Gaussian Convolution and Mixture Models for Identifying Key Biomarkers Underlying Variability in Transcriptomic Profiles and the Diversity of Therapeutic Responses

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