Next-generation computational tools for interrogating cancer immunity

Predicting peptide presentation by major histocompatibility complex class I: an improved machine learning approach to the immunopeptidome

(2019) Kevin Michael Boehm et al.   BMC BIOINFORMATICS

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage

(2019) Dvir Aran et al.   NATURE IMMUNOLOGY

Approaches to treat immune hot, altered and cold tumours with combination immunotherapies

(2019) Jérôme Galon et al.   NATURE REVIEWS DRUG DISCOVERY

Challenges in unsupervised clustering of single-cell RNA-seq data

(2019) Vladimir Yu Kiselev et al.   NATURE REVIEWS GENETICS

Why geneticists stole cancer research even though cancer is primarily a signaling disease

(2019) Michael B. Yaffe   Science Signaling

Revolutionizing Cancer Immunology: The Power of Next-Generation Sequencing Technologies

(2019) Meromit Singer et al.   Cancer Immunology Research

Performance evaluation of MHC class-I binding prediction tools based on an experimentally validated MHC-peptide binding dataset

(2019) Maria Bonsack et al.   Cancer Immunology Research

DeepSeqPan, a novel deep convolutional neural network model for pan-specific class I HLA-peptide binding affinity prediction

(2019) Zhonghao Liu et al.   Scientific Reports

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

(2019) Samuel G. Rodriques et al.   SCIENCE

Avelumab plus Axitinib versus Sunitinib for Advanced Renal-Cell Carcinoma

(2019) Robert J. Motzer et al.   NEW ENGLAND JOURNAL OF MEDICINE

Integrative single-cell analysis

(2019) Tim Stuart et al.   NATURE REVIEWS GENETICS

Cancer-associated fibroblasts in gastrointestinal cancer

(2019) Hiroki Kobayashi et al.   Nature Reviews Gastroenterology & Hepatology

Comparing and contrasting predictive biomarkers for immunotherapy and targeted therapy of NSCLC

(2019) D. Ross Camidge et al.   Nature Reviews Clinical Oncology

Landscape of B cell immunity and related immune evasion in human cancers

(2019) Xihao Hu et al.   NATURE GENETICS

Characterization of cell fate probabilities in single-cell data with Palantir

(2019) Manu Setty et al.   NATURE BIOTECHNOLOGY

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

(2019) Chee-Huat Linus Eng et al.   NATURE

HLA*LA—HLA typing from linearly projected graph alignments

(2019) Alexander T Dilthey et al.   BIOINFORMATICS

scMatch: a single-cell gene expression profile annotation tool using reference datasets

(2019) Rui Hou et al.   BIOINFORMATICS

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

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

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

Immunogenic neoantigens derived from gene fusions stimulate T cell responses

(2019) Wei Yang et al.   NATURE MEDICINE

Benchmarking single cell RNA-sequencing analysis pipelines using mixture control experiments

(2019) Luyi Tian et al.   NATURE METHODS

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

(2019) Francesca Finotello et al.   Genome Medicine

Decomposing Cell Identity for Transfer Learning across Cellular Measurements, Platforms, Tissues, and Species

(2019) Genevieve L. Stein-O’Brien et al.   Cell Systems

arcasHLA: high resolution HLA typing from RNAseq

(2019) R Orenbuch et al.   BIOINFORMATICS

Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology

(2019) Gregor Sturm et al.   BIOINFORMATICS

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Current best practices in single‐cell RNA‐seq analysis: a tutorial

(2019) Malte D Luecken et al.   Molecular Systems Biology

Complete deconvolution of cellular mixtures based on linearity of transcriptional signatures

(2019) Konstantin Zaitsev et al.   Nature Communications

Systems Immunology: Learning the Rules of the Immune System

(2018) Alexandra-Chloé Villani et al.   Annual Review of Immunology

B-cell receptor reconstruction from single-cell RNA-seq with VDJPuzzle

(2018) Simone Rizzetto et al.   BIOINFORMATICS

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

(2018) Kelly Street et al.   BMC GENOMICS

Quantifying tumor-infiltrating immune cells from transcriptomics data

(2018) Francesca Finotello et al.   CANCER IMMUNOLOGY IMMUNOTHERAPY

High-throughput screening of combinatorial immunotherapies with patient-specific in silico models of metastatic colorectal cancer

(2018) Jakob Nikolas Kather et al.   CANCER RESEARCH

Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment

(2018) Elham Azizi et al.   CELL

Single-Cell Genomics: A Stepping Stone for Future Immunology Discoveries

(2018) Amir Giladi et al.   CELL

Single-Cell Transcriptomics Meets Lineage Tracing

(2018) Lennart Kester et al.   Cell Stem Cell

Cell type discovery using single-cell transcriptomics: implications for ontological representation

(2018) Brian D Aevermann et al.   HUMAN MOLECULAR GENETICS

The Immune Landscape of Cancer

(2018) Vésteinn Thorsson et al.   IMMUNITY

Improved methods for predicting peptide binding affinity to MHC class II molecules

(2018) Kamilla Kjaergaard Jensen et al.   IMMUNOLOGY

Systematic Identification of Druggable Epithelial–Stromal Crosstalk Signaling Networks in Ovarian Cancer

(2018) Tsz-Lun Yeung et al.   JNCI-Journal of the National Cancer Institute

Immune-centric network of cytokines and cells in disease context identified by computational mining of PubMed

(2018) Ksenya Kveler et al.   NATURE BIOTECHNOLOGY

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing

(2018) Xinyi Guo et al.   NATURE MEDICINE

Phenotype molding of stromal cells in the lung tumor microenvironment

(2018) Diether Lambrechts et al.   NATURE MEDICINE

scmap: projection of single-cell RNA-seq data across data sets

(2018) Vladimir Yu Kiselev et al.   NATURE METHODS

BraCeR: B-cell-receptor reconstruction and clonality inference from single-cell RNA-seq

(2018) Ida Lindeman et al.   NATURE METHODS

FateID infers cell fate bias in multipotent progenitors from single-cell RNA-seq data

(2018) Josip S Herman et al.   NATURE METHODS

Best practices for analysing microbiomes

(2018) Rob Knight et al.   NATURE REVIEWS MICROBIOLOGY

CellAtlasSearch: a scalable search engine for single cells

(2018) Divyanshu Srivastava et al.   NUCLEIC ACIDS RESEARCH

Update on Tumor Neoantigens and Their Utility: Why It Is Good to Be Different

(2018) Chung-Han Lee et al.   TRENDS IN IMMUNOLOGY

Interpretable dimensionality reduction of single cell transcriptome data with deep generative models

(2018) Jiarui Ding et al.   Nature Communications

BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data

(2018) Amit A. Upadhyay et al.   Genome Medicine

Systematic Identification of Druggable Epithelial–Stromal Crosstalk Signaling Networks in Ovarian Cancer

(2018) Tsz-Lun Yeung et al.   JNCI-Journal of the National Cancer Institute

Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry

(2018) Daniel Schulz et al.   Cell Systems

MHCflurry: Open-Source Class I MHC Binding Affinity Prediction

(2018) Timothy J. O'Donnell et al.   Cell Systems

A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data

(2018) Chang Xu   Computational and Structural Biotechnology Journal

Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging

(2018) Yury Goltsev et al.   CELL

A Structured Tumor-Immune Microenvironment in Triple Negative Breast Cancer Revealed by Multiplexed Ion Beam Imaging

(2018) Leeat Keren et al.   CELL

A radiomics approach to assess tumour-infiltrating CD8 cells and response to anti-PD-1 or anti-PD-L1 immunotherapy: an imaging biomarker, retrospective multicohort study

(2018) Roger Sun et al.   LANCET ONCOLOGY

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response

(2018) Peng Jiang et al.   NATURE MEDICINE

Robust prediction of response to immune checkpoint blockade therapy in metastatic melanoma

(2018) Noam Auslander et al.   NATURE MEDICINE

The hallmarks of successful anticancer immunotherapy

(2018) Lorenzo Galluzzi et al.   Science Translational Medicine

Predicting Antigen Presentation—What Could We Learn From a Million Peptides?

(2018) David Gfeller et al.   Frontiers in Immunology

Cancer Neoantigens

(2018) Ton N. Schumacher et al.   Annual Review of Immunology

High-Dimensional Analysis Delineates Myeloid and Lymphoid Compartment Remodeling during Successful Immune-Checkpoint Cancer Therapy

(2018) Matthew M. Gubin et al.   CELL

The anatomy of single cell mass cytometry data

(2018) Lars R. Olsen et al.   CYTOMETRY PART A

The Cancer Immunogram: A Pledge for a Comprehensive Biomarker Approach for Personalized Immunotherapy in Urothelial Cancer

(2018) Haris Zahoor et al.   EUROPEAN UROLOGY

The Length Distribution and Multiple Specificity of Naturally Presented HLA-I Ligands

(2018) David Gfeller et al.   JOURNAL OF IMMUNOLOGY

Single-cell reconstruction of the early maternal–fetal interface in humans

(2018) Roser Vento-Tormo et al.   NATURE

Lineage tracking reveals dynamic relationships of T cells in colorectal cancer

(2018) Lei Zhang et al.   NATURE

Reply to "Evaluation of immune repertoire inference methods from RNA-seq data"

(2018) Dmitriy A Bolotin et al.   NATURE BIOTECHNOLOGY

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

Deep learning using tumor HLA peptide mass spectrometry datasets improves neoantigen identification

(2018) Brendan Bulik-Sullivan et al.   NATURE BIOTECHNOLOGY

Trial watch: The clinical trial landscape for PD1/PDL1 immune checkpoint inhibitors

(2018) Jun Tang et al.   NATURE REVIEWS DRUG DISCOVERY

Systematically benchmarking peptide-MHC binding predictors: From synthetic to naturally processed epitopes

(2018) Weilong Zhao et al.   PLoS Computational Biology

Multi-Omics Profiling of the Tumor Microenvironment: Paving the Way to Precision Immuno-Oncology

(2018) Francesca Finotello et al.   Frontiers in Oncology

HLA-HD: An accurate HLA typing algorithm for next-generation sequencing data

(2017) Shuji Kawaguchi et al.   HUMAN MUTATION

NetMHCpan-4.0: Improved Peptide–MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data

(2017) Vanessa Jurtz et al.   JOURNAL OF IMMUNOLOGY

Comparative Analysis of Single-Cell RNA Sequencing Methods

(2017) Christoph Ziegenhain et al.   MOLECULAR CELL

Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer

(2017) Ugur Sahin et al.   NATURE

Quantifiable predictive features define epitope-specific T cell receptor repertoires

(2017) Pradyot Dash et al.   NATURE

Identifying specificity groups in the T cell receptor repertoire

(2017) Jacob Glanville et al.   NATURE

A neoantigen fitness model predicts tumour response to checkpoint blockade immunotherapy

(2017) Marta Łuksza et al.   NATURE

An immunogenic personal neoantigen vaccine for patients with melanoma

(2017) Patrick A. Ott et al.   NATURE

Antigen receptor repertoire profiling from RNA-seq data

(2017) Dmitriy A Bolotin et al.   NATURE BIOTECHNOLOGY

The problem with neoantigen prediction

(2017)   NATURE BIOTECHNOLOGY

Multiplexed quantification of proteins and transcripts in single cells

(2017) Vanessa M Peterson et al.   NATURE BIOTECHNOLOGY

Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors

(2017) Huipeng Li et al.   NATURE GENETICS

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

histoCAT: analysis of cell phenotypes and interactions in multiplex image cytometry data

(2017) Denis Schapiro et al.   NATURE METHODS

Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning

(2017) Bo Wang et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

The immune contexture in cancer prognosis and treatment

(2017) Wolf H. Fridman et al.   Nature Reviews Clinical Oncology

Mechanobiology of YAP and TAZ in physiology and disease

(2017) Tito Panciera et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The SysteMHC Atlas project

(2017) Wenguang Shao et al.   NUCLEIC ACIDS RESEARCH

VDJdb: a curated database of T-cell receptor sequences with known antigen specificity

(2017) Mikhail Shugay et al.   NUCLEIC ACIDS RESEARCH

Targeted reconstruction of T cell receptor sequence from single cell RNA-seq links CDR3 length to T cell differentiation state

(2017) Shaked Afik et al.   NUCLEIC ACIDS RESEARCH

Fast and accurate HLA typing from short-read next-generation sequence data with xHLA

(2017) Chao Xie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors

(2017) Alexandra-Chloé Villani et al.   SCIENCE

Visual analysis of mass cytometry data by hierarchical stochastic neighbour embedding reveals rare cell types

(2017) Vincent van Unen et al.   Nature Communications

Massively parallel digital transcriptional profiling of single cells

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

Quantitative Multiplex Immunohistochemistry Reveals Myeloid-Inflamed Tumor-Immune Complexity Associated with Poor Prognosis

(2017) Takahiro Tsujikawa et al.   Cell Reports

Pan-cancer Immunogenomic Analyses Reveal Genotype-Immunophenotype Relationships and Predictors of Response to Checkpoint Blockade

(2017) Pornpimol Charoentong et al.   Cell Reports

Granatum: a graphical single-cell RNA-Seq analysis pipeline for genomics scientists

(2017) Xun Zhu et al.   Genome Medicine

HLAProfiler utilizes k-mer profiles to improve HLA calling accuracy for rare and common alleles in RNA-seq data

(2017) Martin L. Buchkovich et al.   Genome Medicine

Deciphering HLA-I motifs across HLA peptidomes improves neo-antigen predictions and identifies allostery regulating HLA specificity

(2017) Michal Bassani-Sternberg et al.   PLoS Computational Biology

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

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

(2017) Julien Racle et al.   eLife

Assembly-based inference of B-cell receptor repertoires from short read RNA sequencing data with V’DJer

(2016) Lisle E. Mose et al.   BIOINFORMATICS

CellProfiler Analyst: interactive data exploration, analysis and classification of large biological image sets

(2016) David Dao et al.   BIOINFORMATICS

Computational methods for trajectory inference from single-cell transcriptomics

(2016) Robrecht Cannoodt et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Linking the T cell receptor to the single cell transcriptome in antigen-specific human T cells

(2016) Auda A Eltahla et al.   IMMUNOLOGY AND CELL BIOLOGY

Pan-Specific Prediction of Peptide–MHC Class I Complex Stability, a Correlate of T Cell Immunogenicity

(2016) Michael Rasmussen et al.   JOURNAL OF IMMUNOLOGY

Mass-spectrometric exploration of proteome structure and function

(2016) Ruedi Aebersold et al.   NATURE

Landscape of tumor-infiltrating T cell repertoire of human cancers

(2016) Bo Li et al.   NATURE GENETICS

Automated mapping of phenotype space with single-cell data

(2016) Nikolay Samusik et al.   NATURE METHODS

T cell fate and clonality inference from single-cell transcriptomes

(2016) Michael J T Stubbington et al.   NATURE METHODS

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

Computational genomics tools for dissecting tumour–immune cell interactions

(2016) Hubert Hackl et al.   NATURE REVIEWS GENETICS

2016 update of the PRIDE database and its related tools

(2016) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

(2016) P. L. Stahl et al.   SCIENCE

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

(2016) I. Tirosh et al.   SCIENCE

Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq

(2016) David Redmond et al.   Genome Medicine

pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens

(2016) Jasreet Hundal et al.   Genome Medicine

Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments

(2016) David A. Van Valen et al.   PLoS Computational Biology

Gapped sequence alignment using artificial neural networks: application to the MHC class I system

(2015) Massimo Andreatta et al.   BIOINFORMATICS

Immunological Effects of Conventional Chemotherapy and Targeted Anticancer Agents

(2015) Lorenzo Galluzzi et al.   CANCER CELL

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

The first five years of single-cell cancer genomics and beyond

(2015) Nicholas E. Navin   GENOME RESEARCH

The Technology and Biology of Single-Cell RNA Sequencing

(2015) Aleksandra A. Kolodziejczyk et al.   MOLECULAR CELL

Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes

(2015) Sachet A Shukla et al.   NATURE BIOTECHNOLOGY

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

Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues

(2015) Je Hyuk Lee et al.   Nature Protocols

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

An interactive reference framework for modeling a dynamic immune system

(2015) M. H. Spitzer et al.   SCIENCE

Highly multiplexed imaging of single cells using a high-throughput cyclic immunofluorescence method

(2015) Jia-Ren Lin et al.   Nature Communications

Transcriptome Analysis of Individual Stromal Cell Populations Identifies Stroma-Tumor Crosstalk in Mouse Lung Cancer Model

(2015) Hyejin Choi et al.   Cell Reports

SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis

(2015) Minzhe Guo et al.   PLoS Computational Biology

Three-Dimensional Gradients of Cytokine Signaling between T Cells

(2015) Kevin Thurley et al.   PLoS Computational Biology

OptiType: precision HLA typing from next-generation sequencing data

(2014) András Szolek et al.   BIOINFORMATICS

Multiplexed immunohistochemistry, imaging, and quantitation: A review, with an assessment of Tyramide signal amplification, multispectral imaging and multiplex analysis

(2014) Edward C. Stack et al.   METHODS

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Multiplexed ion beam imaging of human breast tumors

(2014) Michael Angelo et al.   NATURE MEDICINE

Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry

(2014) Charlotte Giesen et al.   NATURE METHODS

Single-cell in situ RNA profiling by sequential hybridization

(2014) Eric Lubeck et al.   NATURE METHODS

Expanding the computational toolbox for mining cancer genomes

(2014) Li Ding et al.   NATURE REVIEWS GENETICS

The immune epitope database (IEDB) 3.0

(2014) Randi Vita et al.   NUCLEIC ACIDS RESEARCH

Automated identification of stratifying signatures in cellular subpopulations

(2014) Robert V. Bruggner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Oncology Meets Immunology: The Cancer-Immunity Cycle

(2013) Daniel S. Chen et al.   IMMUNITY

NetMHCstab- predicting stability of peptide-MHC-I complexes; impacts for cytotoxic T lymphocyte epitope discovery

(2013) Kasper W. Jørgensen et al.   IMMUNOLOGY

viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia

(2013) El-ad David Amir et al.   NATURE BIOTECHNOLOGY

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

Automatic Classification of Cellular Expression by Nonlinear Stochastic Embedding (ACCENSE)

(2013) K. Shekhar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Highly multiplexed single-cell analysis of formalin-fixed, paraffin-embedded cancer tissue

(2013) M. J. Gerdes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multispectral Imaging

(2013) J. R. Mansfield   VETERINARY PATHOLOGY

From single cells to deep phenotypes in cancer

(2012) Sean C Bendall et al.   NATURE BIOTECHNOLOGY

Protein interaction data curation: the International Molecular Exchange (IMEx) consortium

(2012) Sandra Orchard et al.   NATURE METHODS

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

HLA typing from RNA-Seq sequence reads

(2012) Sebastian Boegel et al.   Genome Medicine

A Race between Tumor Immunoescape and Genome Maintenance Selects for Optimum Levels of (epi)genetic Instability

(2012) Shingo Iwami et al.   PLoS Computational Biology

Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE

(2011) Peng Qiu et al.   NATURE BIOTECHNOLOGY