Computational genomics tools for dissecting tumour–immune cell interactions

Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation

(2016) Jernej Godec et al.   IMMUNITY

T cell fate and clonality inference from single-cell transcriptomes

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

Single-cell genome sequencing: current state of the science

(2016) Charles Gawad et al.   NATURE REVIEWS GENETICS

Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade

(2016) N. McGranahan et al.   SCIENCE

NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets

(2016) Morten Nielsen et al.   Genome Medicine

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

(2016) Jasreet Hundal et al.   Genome Medicine

IMSEQ—a fast and error aware approach to immunogenetic sequence analysis

(2015) Leon Kuchenbecker et al.   BIOINFORMATICS

Automated benchmarking of peptide-MHC class I binding predictions

(2015) Thomas Trolle et al.   BIOINFORMATICS

EpiToolKit—a web-based workbench for vaccine design

(2015) Benjamin Schubert et al.   BIOINFORMATICS

Cell-composition effects in the analysis of DNA methylation array data: a mathematical perspective

(2015) E Andres Houseman et al.   BMC BIOINFORMATICS

HLA-VBSeq: accurate HLA typing at full resolution from whole-genome sequencing data

(2015) Naoki Nariai et al.   BMC GENOMICS

Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline

(2015) Yasir Rahmatallah et al.   BRIEFINGS IN BIOINFORMATICS

Personalized cancer immunotherapy using Systems Medicine approaches

(2015) Shailendra K. Gupta et al.   BRIEFINGS IN BIOINFORMATICS

Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity

(2015) Jellert T. Gaublomme et al.   CELL

PD-1 Blockers

(2015) Jedd D. Wolchok   CELL

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

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

(2015) Jacob H. Levine et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Immune Checkpoint Targeting in Cancer Therapy: Toward Combination Strategies with Curative Potential

(2015) Padmanee Sharma et al.   CELL

Oncotator: Cancer Variant Annotation Tool

(2015) Alex H. Ramos et al.   HUMAN MUTATION

Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification

(2015) Massimo Andreatta et al.   IMMUNOGENETICS

Pooled Analysis of Long-Term Survival Data From Phase II and Phase III Trials of Ipilimumab in Unresectable or Metastatic Melanoma

(2015) Dirk Schadendorf et al.   JOURNAL OF CLINICAL ONCOLOGY

Methods for discovery and characterization of cell subsets in high dimensional mass cytometry data

(2015) Kirsten E. Diggins et al.   METHODS

Mutant MHC class II epitopes drive therapeutic immune responses to cancer

(2015) Sebastian Kreiter et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

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

(2015) Sachet A Shukla et al.   NATURE BIOTECHNOLOGY

Therapeutic genome editing: prospects and challenges

(2015) David Benjamin Turitz Cox et al.   NATURE MEDICINE

TransVar: a multilevel variant annotator for precision genomics

(2015) Wanding Zhou et al.   NATURE METHODS

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

LymAnalyzer: a tool for comprehensive analysis of next generation sequencing data of T cell receptors and immunoglobulins

(2015) Yaxuan Yu et al.   NUCLEIC ACIDS RESEARCH

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

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

Neoantigens in cancer immunotherapy

(2015) T. N. Schumacher et al.   SCIENCE

Immunogenicity of somatic mutations in human gastrointestinal cancers

(2015) E. Tran et al.   SCIENCE

Combinatorial labeling of single cells for gene expression cytometry

(2015) H. C. Fan et al.   SCIENCE

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

Single-Cell Analysis in Cancer Genomics

(2015) Assieh Saadatpour et al.   TRENDS IN GENETICS

Bioinformatic and Statistical Analysis of Adaptive Immune Repertoires

(2015) Victor Greiff et al.   TRENDS IN IMMUNOLOGY

Immunoinformatics and epitope prediction in the age of genomic medicine

(2015) Linus Backert et al.   Genome Medicine

Profiling tissue-resident T cell repertoires by RNA sequencing

(2015) Scott D. Brown et al.   Genome Medicine

HLAreporter: a tool for HLA typing from next generation sequencing data

(2015) Yazhi Huang et al.   Genome Medicine

Practical guidelines for B-cell receptor repertoire sequencing analysis

(2015) Gur Yaari et al.   Genome Medicine

Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy

(2015) Mihaela Angelova et al.   GENOME BIOLOGY

OptiType: precision HLA typing from next-generation sequencing data

(2014) András Szolek et al.   BIOINFORMATICS

Inference of high resolution HLA types using genome-wide RNA or DNA sequencing reads

(2014) Yu Bai et al.   BMC GENOMICS

NetTepi: an integrated method for the prediction of T cell epitopes

(2014) Thomas Trolle et al.   IMMUNOGENETICS

ImmPort: disseminating data to the public for the future of immunology

(2014) Sanchita Bhattacharya et al.   IMMUNOLOGIC RESEARCH

TCRklass: A New K-String–Based Algorithm for Human and Mouse TCR Repertoire Characterization

(2014) Xi Yang et al.   JOURNAL OF IMMUNOLOGY

PD-1 blockade induces responses by inhibiting adaptive immune resistance

(2014) Paul C. Tumeh et al.   NATURE

Linking T-cell receptor sequence to functional phenotype at the single-cell level

(2014) Arnold Han et al.   NATURE BIOTECHNOLOGY

Unifying immunology with informatics and multiscale biology

(2014) Brian A Kidd et al.   NATURE IMMUNOLOGY

Single-cell technologies for monitoring immune systems

(2014) Pratip K Chattopadhyay et al.   NATURE IMMUNOLOGY

PyClone: statistical inference of clonal population structure in cancer

(2014) Andrew Roth et al.   NATURE METHODS

Towards error-free profiling of immune repertoires

(2014) Mikhail Shugay et al.   NATURE METHODS

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

(2014) Charlotte Giesen et al.   NATURE METHODS

Epigenome-wide association studies without the need for cell-type composition

(2014) James Zou et al.   NATURE METHODS

Expanding the computational toolbox for mining cancer genomes

(2014) Li Ding et al.   NATURE REVIEWS GENETICS

COSMIC: exploring the world's knowledge of somatic mutations in human cancer

(2014) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

svaseq: removing batch effects and other unwanted noise from sequencing data

(2014) Jeffrey T. Leek   NUCLEIC ACIDS RESEARCH

IMGT®, the international ImMunoGeneTics information system® 25 years on

(2014) Marie-Paule Lefranc et al.   NUCLEIC ACIDS RESEARCH

The immune epitope database (IEDB) 3.0

(2014) Randi Vita et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Cancer Immunotherapy Based on Mutation-Specific CD4+ T Cells in a Patient with Epithelial Cancer

(2014) E. Tran et al.   SCIENCE

Characterizing immune repertoires by high throughput sequencing: strategies and applications

(2014) Jorg J.A. Calis et al.   TRENDS IN IMMUNOLOGY

Choice of transcripts and software has a large effect on variant annotation

(2014) Davis J McCarthy et al.   Genome Medicine

Quantitative reconstruction of leukocyte subsets using DNA methylation

(2014) William P Accomando et al.   GENOME BIOLOGY

Unintended Consequences of Expensive Cancer Therapeutics—The Pursuit of Marginal Indications and a Me-Too Mentality That Stifles Innovation and Creativity

(2014) Tito Fojo et al.   JAMA Otolaryngology-Head & Neck Surgery

A catalog of HLA type, HLA expression, and neo-epitope candidates in human cancer cell lines

(2014) Sebastian Boegel et al.   OncoImmunology

Decombinator: a tool for fast, efficient gene assignment in T-cell receptor sequences using a finite state machine

(2013) N. Thomas et al.   BIOINFORMATICS

MMAD: microarray microdissection with analysis of differences is a computational tool for deconvoluting cell type-specific contributions from tissue samples

(2013) David A. Liebner et al.   BIOINFORMATICS

CellMix: a comprehensive toolbox for gene expression deconvolution

(2013) R. Gaujoux et al.   BIOINFORMATICS

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

(2013) Ting Gong et al.   BIOINFORMATICS

A survey of tools for variant analysis of next-generation genome sequencing data

(2013) S. Pabinger et al.   BRIEFINGS IN BIOINFORMATICS

Computational deconvolution: extracting cell type-specific information from heterogeneous samples

(2013) Shai S Shen-Orr et al.   CURRENT OPINION IN IMMUNOLOGY

Cancer immunotherapy strategies based on overcoming barriers within the tumor microenvironment

(2013) Thomas F Gajewski et al.   CURRENT OPINION IN IMMUNOLOGY

Blood-based profiles of DNA methylation predict the underlying distribution of cell types

(2013) Devin C Koestler et al.   Epigenetics

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

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

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

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

MiTCR: software for T-cell receptor sequencing data analysis

(2013) Dmitriy A Bolotin et al.   NATURE METHODS

IntOGen-mutations identifies cancer drivers across tumor types

(2013) Abel Gonzalez-Perez et al.   NATURE METHODS

ATHLATES: accurate typing of human leukocyte antigen through exome sequencing

(2013) Chang Liu et al.   NUCLEIC ACIDS RESEARCH

An empirical Bayesian framework for somatic mutation detection from cancer genome sequencing data

(2013) Yuichi Shiraishi et al.   NUCLEIC ACIDS RESEARCH

IgBLAST: an immunoglobulin variable domain sequence analysis tool

(2013) Jian Ye et al.   NUCLEIC ACIDS RESEARCH

HLA Haplotyping from RNA-seq Data Using Hierarchical Read Weighting

(2013) Hyunsung John Kim et al.   PLoS One

Connecting Genomic Alterations to Cancer Biology with Proteomics: The NCI Clinical Proteomic Tumor Analysis Consortium

(2013) M. J. Ellis et al.   Cancer Discovery

Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers

(2013) Qingguo Wang et al.   Genome Medicine

Properties of MHC Class I Presented Peptides That Enhance Immunogenicity

(2013) Jorg J. A. Calis et al.   PLoS Computational Biology

Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

Tools for mapping high-throughput sequencing data

(2012) Nuno A. Fonseca et al.   BIOINFORMATICS

DNA methylation arrays as surrogate measures of cell mixture distribution

(2012) Eugene Houseman et al.   BMC BIOINFORMATICS

Next generation sequencing for TCR repertoire profiling: Platform-specific features and correction algorithms

(2012) Dmitry A. Bolotin et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

From single cells to deep phenotypes in cancer

(2012) Sean C Bendall et al.   NATURE BIOTECHNOLOGY

Absolute quantification of somatic DNA alterations in human cancer

(2012) Scott L Carter et al.   NATURE BIOTECHNOLOGY

Multipeptide immune response to cancer vaccine IMA901 after single-dose cyclophosphamide associates with longer patient survival

(2012) Steffen Walter et al.   NATURE MEDICINE

Analysing and interpreting DNA methylation data

(2012) Christoph Bock   NATURE REVIEWS GENETICS

The UCSC Cancer Genomics Browser: update 2013

(2012) Mary Goldman et al.   NUCLEIC ACIDS RESEARCH

The IMGT/HLA database

(2012) James Robinson et al.   NUCLEIC ACIDS RESEARCH

InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation

(2012) Karin Breuer et al.   NUCLEIC ACIDS RESEARCH

Quantitative Image Analysis of Cellular Heterogeneity in Breast Tumors Complements Genomic Profiling

(2012) Y. Yuan et al.   Science Translational Medicine

The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data: Figure 1.

(2012) Ethan Cerami et al.   Cancer Discovery

CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

(2012) Tamar Hashimshony et al.   Cell Reports

HLA typing from RNA-Seq sequence reads

(2012) Sebastian Boegel et al.   Genome Medicine

Derivation of HLA types from shotgun sequence datasets

(2012) René L Warren et al.   Genome Medicine

PERT: A Method for Expression Deconvolution of Human Blood Samples from Varied Microenvironmental and Developmental Conditions

(2012) Wenlian Qiao et al.   PLoS Computational Biology

SomaticSniper: identification of somatic point mutations in whole genome sequencing data

(2011) David E. Larson et al.   BIOINFORMATICS

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

POPISK: T-cell reactivity prediction using support vector machines and string kernels

(2011) Chun-Wei Tung et al.   BMC BIOINFORMATICS

Cell subset prediction for blood genomic studies

(2011) Christopher R Bolen et al.   BMC BIOINFORMATICS

NetMHCcons: a consensus method for the major histocompatibility complex class I predictions

(2011) Edita Karosiene et al.   IMMUNOGENETICS

Dana-Farber repository for machine learning in immunology

(2011) Guang Lan Zhang et al.   JOURNAL OF IMMUNOLOGICAL METHODS

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

(2011) Peng Qiu et al.   NATURE BIOTECHNOLOGY

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

(2011) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2012

(2011) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

Cancer Immunoediting: Integrating Immunity's Roles in Cancer Suppression and Promotion

(2011) R. D. Schreiber et al.   SCIENCE

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

(2010) William McLaren et al.   BIOINFORMATICS

Biomarker discovery in heterogeneous tissue samples -taking the in-silico deconfounding approach

(2010) Dirk Repsilber et al.   BMC BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

NetCTLpan: pan-specific MHC class I pathway epitope predictions

(2010) Thomas Stranzl et al.   IMMUNOGENETICS

International network of cancer genome projects

(2010) Thomas J. Hudson (Chairperson) et al.   NATURE

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: application to MHC-peptide binding

(2009) Hao Zhang et al.   BIOINFORMATICS

A HaemAtlas: characterizing gene expression in differentiated human blood cells

(2009) Nicholas A. Watkins et al.   BLOOD

NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction

(2009) Morten Nielsen et al.   BMC BIOINFORMATICS

Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1

(2009) David A. Barbie et al.   NATURE

NetMHCpan, a method for MHC class I binding prediction beyond humans

(2008) Ilka Hoof et al.   IMMUNOGENETICS

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE

The Immunological Genome Project: networks of gene expression in immune cells

(2008) Tracy S P Heng et al.   NATURE IMMUNOLOGY

NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8–11

(2008) Claus Lundegaard et al.   NUCLEIC ACIDS RESEARCH

CTdatabase: a knowledge-base of high-throughput and curated data on cancer-testis antigens

(2008) L. G. Almeida et al.   NUCLEIC ACIDS RESEARCH

A Systematic Assessment of MHC Class II Peptide Binding Predictions and Evaluation of a Consensus Approach

(2008) Peng Wang et al.   PLoS Computational Biology