Precise reconstruction of the TME using bulk RNA-seq and a machine learning algorithm trained on artificial transcriptomes

The Gene Expression Deconvolution Interactive Tool (GEDIT): accurate cell type quantification from gene expression data

(2021) Brian B Nadel et al.   GigaScience

Single-cell Spatial Proteomic Revelations on the Multiparametric MRI Heterogeneity of Clinically Significant Prostate Cancer

(2021) Russell K. Pachynski et al.   CLINICAL CANCER RESEARCH

The single-cell pathology landscape of breast cancer

(2020) Hartland W. Jackson et al.   NATURE

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

Comprehensive T cell repertoire characterization of non-small cell lung cancer

(2020) Alexandre Reuben et al.   Nature Communications

Corrigendum: Digitaldlsorter: Deep-Learning on scRNA-Seq to Deconvolute Gene Expression Data

(2020) Carlos Torroja et al.   Frontiers in Genetics

Patient-reported outcomes in a phase 2 study comparing atezolizumab alone or with bevacizumab vs sunitinib in previously untreated metastatic renal cell carcinoma

(2020) Sumanta K. Pal et al.   BJU INTERNATIONAL

Therapeutic implications of PD-L1 expression in bladder cancer with squamous differentiation

(2020) Ronja Morsch et al.   BMC CANCER

Accurate estimation of cell composition in bulk expression through robust integration of single-cell information

(2020) Brandon Jew et al.   Nature Communications

Pancreatic Cancer Associated Fibroblasts (CAF): Under-Explored Target for Pancreatic Cancer Treatment

(2020) Jeffrey Norton et al.   Cancers

Dissecting intratumour heterogeneity of nodal B-cell lymphomas at the transcriptional, genetic and drug-response levels

(2020) Tobias Roider et al.   NATURE CELL BIOLOGY

A single-cell landscape of high-grade serous ovarian cancer

(2020) Benjamin Izar et al.   NATURE MEDICINE

Deep learning–based cell composition analysis from tissue expression profiles

(2020) Kevin Menden et al.   Science Advances

Large scale, robust, and accurate whole transcriptome profiling from clinical formalin-fixed paraffin-embedded samples

(2020) Yulia Newton et al.   Scientific Reports

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

(2019) Xuran Wang et al.   Nature Communications

Prognostic Value of Macrophage Phenotypes in Resectable Non–Small Cell Lung Cancer Assessed by Multiplex Immunohistochemistry

(2019) Mehrdad Rakaee et al.   NEOPLASIA

RNA-Seq Signatures Normalized by mRNA Abundance Allow Absolute Deconvolution of Human Immune Cell Types

(2019) Gianni Monaco et al.   Cell Reports

Distinct Immune Cell Populations Define Response to Anti-PD-1 Monotherapy and Anti-PD-1/Anti-CTLA-4 Combined Therapy

(2019) Tuba N. Gide et al.   CANCER CELL

The barcode, UMI, set format and BUStools

(2019) Páll Melsted et al.   BIOINFORMATICS

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

(2019) Aaron M. Newman et al.   NATURE BIOTECHNOLOGY

Transcriptome networks identify mechanisms of viral and nonviral asthma exacerbations in children

(2019) Matthew C. Altman et al.   NATURE IMMUNOLOGY

Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data

(2019) Francesca Finotello et al.   Genome Medicine

Fast and robust deconvolution of tumor infiltrating lymphocyte from expression profiles using least trimmed squares

(2019) Yuning Hao et al.   PLoS Computational Biology

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

An Integrative Model of Cellular States, Plasticity, and Genetics for Glioblastoma

(2019) Cyril Neftel et al.   CELL

Computational approaches for characterizing the tumor immune microenvironment

(2019) Candace C. Liu et al.   IMMUNOLOGY

The local immune landscape determines tumor PD-L1 heterogeneity and sensitivity to therapy

(2019) Yuan Wei et al.   JOURNAL OF CLINICAL INVESTIGATION

Complete deconvolution of cellular mixtures based on linearity of transcriptional signatures

(2019) Konstantin Zaitsev et al.   Nature Communications

Immune cell PD-L1 co-localizes with macrophages and is associated with outcome in PD-1 pathway blockade therapy

(2019) Yuting Liu et al.   CLINICAL CANCER RESEARCH

Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition)

(2019) Andrea Cossarizza et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

Integrative molecular and clinical modeling of clinical outcomes to PD1 blockade in patients with metastatic melanoma

(2019) David Liu et al.   NATURE MEDICINE

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Phenotype molding of stromal cells in the lung tumor microenvironment

(2018) Diether Lambrechts et al.   NATURE MEDICINE

Comprehensive molecular characterization of clinical responses to PD-1 inhibition in metastatic gastric cancer

(2018) Seung Tae Kim et al.   NATURE MEDICINE

Detection and removal of barcode swapping in single-cell RNA-seq data

(2018) Jonathan A. Griffiths et al.   Nature Communications

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

(2018) Joel Saltz et al.   Cell Reports

TGFβ attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells

(2018) Sanjeev Mariathasan et al.   NATURE

Fundamental Mechanisms of Immune Checkpoint Blockade Therapy

(2018) Spencer C. Wei et al.   Cancer Discovery

Explainable machine-learning predictions for the prevention of hypoxaemia during surgery

(2018) Scott M. Lundberg et al.   Nature Biomedical Engineering

ArrayExpress update – from bulk to single-cell expression data

(2018) Awais Athar et al.   NUCLEIC ACIDS RESEARCH

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

On Statistical Modeling of Sequencing Noise in High Depth Data to Assess Tumor Evolution

(2017) Raul Rabadan et al.   JOURNAL OF STATISTICAL PHYSICS

Toil enables reproducible, open source, big biomedical data analyses

(2017) John Vivian et al.   NATURE BIOTECHNOLOGY

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

Tumor Microenvironment and Differential Responses to Therapy

(2017) Eishu Hirata et al.   Cold Spring Harbor Perspectives in Medicine

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

(2017) Julien Racle et al.   eLife

Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma

(2016) Willy Hugo et al.   CELL

Dynamics of Individual T Cell Repertoires: From Cord Blood to Centenarians

(2016) Olga V. Britanova et al.   JOURNAL OF IMMUNOLOGY

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

System-Wide Associations between DNA-Methylation, Gene Expression, and Humoral Immune Response to Influenza Vaccination

(2016) Michael T. Zimmermann et al.   PLoS One

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

(2016) I. Tirosh et al.   SCIENCE

Somatic Mutations and Neoepitope Homology in Melanomas Treated with CTLA-4 Blockade

(2016) Tavi Nathanson et al.   Cancer Immunology Research

Normalization and noise reduction for single cell RNA-seq experiments

(2015) Bo Ding et al.   BIOINFORMATICS

Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis

(2015) Jacob H. Levine et al.   CELL

FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data

(2015) Sofie Van Gassen et al.   CYTOMETRY PART A

MiXCR: software for comprehensive adaptive immunity profiling

(2015) Dmitriy A Bolotin et al.   NATURE METHODS

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

Genomic correlates of response to CTLA-4 blockade in metastatic melanoma

(2015) E. M. Van Allen et al.   SCIENCE

Systematic pan-cancer analysis of tumour purity

(2015) Dvir Aran et al.   Nature Communications

A Cell-Based Systems Biology Assessment of Human Blood to Monitor Immune Responses after Influenza Vaccination

(2015) Kristen L. Hoek et al.   PLoS One

Age-Related Decrease in TCR Repertoire Diversity Measured with Deep and Normalized Sequence Profiling

(2014) O. V. Britanova et al.   JOURNAL OF IMMUNOLOGY

Variation in RNA-Seq Transcriptome Profiles of Peripheral Whole Blood from Healthy Individuals with and without Globin Depletion

(2014) Heesun Shin et al.   PLoS One

Copy Number Loss of the Interferon Gene Cluster in Melanomas Is Linked to Reduced T Cell Infiltrate and Poor Patient Prognosis

(2014) Peter S. Linsley et al.   PLoS One

The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository

(2013) Kenneth Clark et al.   JOURNAL OF DIGITAL IMAGING

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Human housekeeping genes, revisited

(2013) Eli Eisenberg et al.   TRENDS IN GENETICS

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples

(2012) Günter P. Wagner et al.   THEORY IN BIOSCIENCES

RNA-Seq gene expression estimation with read mapping uncertainty

(2009) Bo Li et al.   BIOINFORMATICS