Challenges in neoantigen-directed therapeutics

Corrigendum: Predicting T Cell Receptor Antigen Specificity From Structural Features Derived From Homology Models of Receptor-Peptide-Major Histocompatibility Complexes

(2022) Martina Milighetti et al.   Frontiers in Physiology

DeepMHCII: a novel binding core-aware deep interaction model for accurate MHC-II peptide binding affinity prediction

(2022) Ronghui You et al.   BIOINFORMATICS

ATM-TCR: TCR-Epitope Binding Affinity Prediction Using a Multi-Head Self-Attention Model

(2022) Michael Cai et al.   Frontiers in Immunology

A Highly Effective System for Predicting MHC-II Epitopes With Immunogenicity

(2022) Shi Xu et al.   Frontiers in Oncology

Accurate and efficient detection of gene fusions from RNA sequencing data

(2021) Sebastian Uhrig et al.   GENOME RESEARCH

Benchmarking HLA genotyping and clarifying HLA impact on survival in tumor immunotherapy

(2021) Xiangyong Li et al.   Molecular Oncology

Personal neoantigen vaccines induce persistent memory T cell responses and epitope spreading in patients with melanoma

(2021) Zhuting Hu et al.   NATURE MEDICINE

Boosting Detection of Low-Abundance Proteins in Thermal Proteome Profiling Experiments by Addition of an Isobaric Trigger Channel to TMT Multiplexes

(2021) Sarah A. Peck Justice et al.   ANALYTICAL CHEMISTRY

Benchmarking the Human Leukocyte Antigen Typing Performance of Three Assays and Seven Next-Generation Sequencing-Based Algorithms

(2021) Ping Liu et al.   Frontiers in Immunology

Contribution of T Cell Receptor Alpha and Beta CDR3, MHC Typing, V and J Genes to Peptide Binding Prediction

(2021) Ido Springer et al.   Frontiers in Immunology

SwarmTCR: a computational approach to predict the specificity of T cell receptors

(2021) Ryan Ehrlich et al.   BMC BIOINFORMATICS

IMpower010: Primary results of a phase III global study of atezolizumab versus best supportive care after adjuvant chemotherapy in resected stage IB-IIIA non-small cell lung cancer (NSCLC).

(2021) Heather A. Wakelee et al.   JOURNAL OF CLINICAL ONCOLOGY

NetTCR-2.0 enables accurate prediction of TCR-peptide binding by using paired TCRα and β sequence data

(2021) Alessandro Montemurro et al.   Communications Biology

nextNEOpi: a comprehensive pipeline for computational neoantigen prediction

(2021) Dietmar Rieder et al.   BIOINFORMATICS

A structural-based machine learning method to classify binding affinities between TCR and peptide-MHC complexes

(2021) Kalyani Dhusia et al.   MOLECULAR IMMUNOLOGY

High-Dimensional Single-Cell Transcriptomics in Melanoma and Cancer Immunotherapy

(2021) Camelia Quek et al.   Genes

A New Human Leukocyte Antigen Typing Algorithm Combined With Currently Available Genotyping Tools Based on Next-Generation Sequencing Data and Guidelines to Select the Most Likely Human Leukocyte Antigen Genotype

(2021) Miseon Lee et al.   Frontiers in Immunology

DeepSeqPanII: An Interpretable Recurrent Neural Network Model With Attention Mechanism for Peptide-HLA Class II Binding Prediction

(2021) Zhonghao Liu et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

neoANT-HILL: an integrated tool for identification of potential neoantigens

(2020) Ana Carolina M. F. Coelho et al.   BMC Medical Genomics

Mutation position is an important determinant for predicting cancer neoantigens

(2020) Aude-Hélène Capietto et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Inferring structural variant cancer cell fraction

(2020) Marek Cmero et al.   Nature Communications

CaSpER identifies and visualizes CNV events by integrative analysis of single-cell or bulk RNA-sequencing data

(2020) Akdes Serin Harmanci et al.   Nature Communications

pVACtools: a computational toolkit to identify and visualize cancer neoantigens

(2020) Jasreet Hundal et al.   Cancer Immunology Research

Combining Immune Checkpoint Inhibitors with Anti-Angiogenic Agents

(2020) Paola Ciciola et al.   Journal of Clinical Medicine

Advancing CAR T-Cell Therapy for Solid Tumors: Lessons Learned from Lymphoma Treatment

(2020) Aleksei Titov et al.   Cancers

Atezolizumab plus Bevacizumab in Unresectable Hepatocellular Carcinoma

(2020) Richard S. Finn et al.   NEW ENGLAND JOURNAL OF MEDICINE

NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data

(2020) Birkir Reynisson et al.   NUCLEIC ACIDS RESEARCH

Strong vaccine responses during chemotherapy are associated with prolonged cancer survival

(2020) Cornelis J. M. Melief et al.   Science Translational Medicine

Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes

(2020) Chloe Chong et al.   Nature Communications

Benchmarking predictions of MHC class I restricted T cell epitopes in a comprehensively studied model system

(2020) Sinu Paul et al.   PLoS Computational Biology

Low-dose interferon-alpha preconditioning and adoptive cell therapy in patients with metastatic melanoma refractory to standard (immune) therapies: a phase I/II study

(2020) Els Verdegaal et al.   Journal for ImmunoTherapy of Cancer

Review of Indications of FDA-Approved Immune Checkpoint Inhibitors per NCCN Guidelines with the Level of Evidence

(2020) Raju K. Vaddepally et al.   Cancers

Treatment-Related Adverse Events of Combination Immune Checkpoint Inhibitors: Systematic Review and Meta-Analysis

(2020) Robin Park et al.   Frontiers in Oncology

MHCAttnNet: predicting MHC-peptide bindings for MHC alleles classes I and II using an attention-based deep neural model

(2020) Gopalakrishnan Venkatesh et al.   BIOINFORMATICS

Investigations of sequencing data and sample type on HLA class Ia typing with different computational tools

(2020) Jian Yi et al.   BRIEFINGS IN BIOINFORMATICS

SETE: Sequence-based Ensemble learning approach for TCR Epitope binding prediction

(2020) Yao Tong et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

cDC1 prime and are licensed by CD4+ T cells to induce anti-tumour immunity

(2020) Stephen T. Ferris et al.   NATURE

A Pan-Specific GRU-Based Recurrent Neural Network for Predicting HLA-I-Binding Peptides

(2020) Yu Heng et al.   ACS Omega

Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction

(2020) Daniel K. Wells et al.   CELL

Combination of anti-angiogenic therapy and immune checkpoint blockade normalizes vascular-immune crosstalk to potentiate cancer immunity

(2020) Won Suk Lee et al.   EXPERIMENTAL AND MOLECULAR MEDICINE

Association of tumour mutational burden with outcomes in patients with advanced solid tumours treated with pembrolizumab: prospective biomarker analysis of the multicohort, open-label, phase 2 KEYNOTE-158 study

(2020) Aurélien Marabelle et al.   LANCET ONCOLOGY

CAR T Cell Therapy for Solid Tumors: Bright Future or Dark Reality?

(2020) Jessica Wagner et al.   MOLECULAR THERAPY

Prediction of Specific TCR-Peptide Binding From Large Dictionaries of TCR-Peptide Pairs

(2020) Ido Springer et al.   Frontiers in Immunology

Immunogenic Cell Death and Elimination of Immunosuppressive Cells: A Double-Edged Sword of Chemotherapy

(2020) Jean-David Fumet et al.   Cancers

TruNeo: an integrated pipeline improves personalized true tumor neoantigen identification

(2020) Yunxia Tang et al.   BMC BIOINFORMATICS

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

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

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

Pembrolizumab plus Axitinib versus Sunitinib for Advanced Renal-Cell Carcinoma

(2019) Brian I. Rini et al.   NEW ENGLAND JOURNAL OF MEDICINE

HLA*LA—HLA typing from linearly projected graph alignments

(2019) Alexander T Dilthey et al.   BIOINFORMATICS

Synergistic effect of immune checkpoint blockade and anti-angiogenesis in cancer treatment

(2019) Ming Yi et al.   Molecular Cancer

Immunogenic neoantigens derived from gene fusions stimulate T cell responses

(2019) Wei Yang et al.   NATURE MEDICINE

Induction of neoantigen-reactive T cells from healthy donors

(2019) Muhammad Ali et al.   Nature Protocols

Whole Exome Sequencing of Cell-Free DNA for Early Lung Cancer: A Pilot Study to Differentiate Benign From Malignant CT-Detected Pulmonary Lesions

(2019) Tina D. Tailor et al.   Frontiers in Oncology

arcasHLA: high resolution HLA typing from RNAseq

(2019) R Orenbuch et al.   BIOINFORMATICS

NeoPredPipe: high-throughput neoantigen prediction and recognition potential pipeline

(2019) Ryan O. Schenck et al.   BMC BIOINFORMATICS

MHCSeqNet: a deep neural network model for universal MHC binding prediction

(2019) Poomarin Phloyphisut et al.   BMC BIOINFORMATICS

PD-1 blockade in subprimed CD8 cells induces dysfunctional PD-1+CD38hi cells and anti-PD-1 resistance

(2019) Vivek Verma et al.   NATURE IMMUNOLOGY

Adenoviral vaccine targeting multiple neoantigens as strategy to eradicate large tumors combined with checkpoint blockade

(2019) Anna Morena D’Alise et al.   Nature Communications

A library of Neo Open Reading Frame peptides (NOPs) as a sustainable resource of common neoantigens in up to 50% of cancer patients

(2019) Jan Koster et al.   Scientific Reports

Quantitative Prediction of the Landscape of T Cell Epitope Immunogenicity in Sequence Space

(2019) Masato Ogishi et al.   Frontiers in Immunology

neoepiscope improves neoepitope prediction with multivariant phasing

(2019) Mary A Wood et al.   BIOINFORMATICS

Tumor neoantigens: from basic research to clinical applications

(2019) Tao Jiang et al.   Journal of Hematology & Oncology

Structure Based Prediction of Neoantigen Immunogenicity

(2019) Timothy P. Riley et al.   Frontiers in Immunology

Meltos: multi-sample tumor phylogeny reconstruction for structural variants

(2019) Camir Ricketts et al.   BIOINFORMATICS

NeoFuse: predicting fusion neoantigens from RNA sequencing data

(2019) Georgios Fotakis et al.   BIOINFORMATICS

AIDE: annotation-assisted isoform discovery with high precision

(2019) Wei Vivian Li et al.   GENOME RESEARCH

Predicting HLA class II antigen presentation through integrated deep learning

(2019) Binbin Chen et al.   NATURE BIOTECHNOLOGY

Robust prediction of HLA class II epitopes by deep motif deconvolution of immunopeptidomes

(2019) Julien Racle et al.   NATURE BIOTECHNOLOGY

TCRpMHCmodels: Structural modelling of TCR-pMHC class I complexes

(2019) Kamilla Kjærgaard Jensen et al.   Scientific Reports

Refinements of LC-MS/MS Spectral Counting Statistics Improve Quantification of Low Abundance Proteins

(2019) Ha Yun Lee et al.   Scientific Reports

pTuneos: prioritizing tumor neoantigens from next-generation sequencing data

(2019) Chi Zhou et al.   Genome Medicine

Engineered T Cell Therapy for Cancer in the Clinic

(2019) Lijun Zhao et al.   Frontiers in Immunology

Systematic evaluation of differential splicing tools for RNA-seq studies

(2019) Arfa Mehmood et al.   BRIEFINGS IN BIOINFORMATICS

Ginsenoside Rb1 exerts antiarrhythmic effects by inhibiting INa and ICaL in rabbit ventricular myocytes

(2019) Zhipei Liu et al.   Scientific Reports

High-Throughput Prediction of MHC Class I and II Neoantigens with MHCnuggets

(2019) Xiaoshan M. Shao et al.   Cancer Immunology Research

Neopepsee: accurate genome-level prediction of neoantigens by harnessing sequence and amino acid immunogenicity information

(2018) S Kim et al.   ANNALS OF ONCOLOGY

Deconvolution and phylogeny inference of structural variations in tumor genomic samples

(2018) Jesse Eaton et al.   BIOINFORMATICS

The perfect personalized cancer therapy: cancer vaccines against neoantigens

(2018) Luigi Aurisicchio et al.   JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH

Immune recognition of somatic mutations leading to complete durable regression in metastatic breast cancer

(2018) Nikolaos Zacharakis et al.   NATURE MEDICINE

Strelka2: fast and accurate calling of germline and somatic variants

(2018) Sangtae Kim et al.   NATURE METHODS

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers

(2018) Qingsong Gao et al.   Cell Reports

MHCflurry: Open-Source Class I MHC Binding Affinity Prediction

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

Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients

(2018) André Kahles et al.   CANCER CELL

Identification of non-mutated neoantigens presented by TAP-deficient tumors

(2018) Koen A. Marijt et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Intron retention is a source of neoepitopes in cancer

(2018) Alicia C Smart et al.   NATURE BIOTECHNOLOGY

Acquired cancer resistance to combination immunotherapy from transcriptional loss of class I HLA

(2018) K. G. Paulson et al.   Nature Communications

Cancer Neoantigens

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

Neoantigen vaccine generates intratumoral T cell responses in phase Ib glioblastoma trial

(2018) Derin B. Keskin et al.   NATURE

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

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

Noncoding regions are the main source of targetable tumor-specific antigens

(2018) Céline M. Laumont et al.   Science Translational Medicine

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

(2018) Weilong Zhao et al.   PLoS Computational Biology

GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly

(2017) Daniel L. Cameron et al.   GENOME RESEARCH

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

(2017) Shuji Kawaguchi et al.   HUMAN MUTATION

Recent advances in malignant melanoma

(2017) Victoria Atkinson   INTERNAL MEDICINE JOURNAL

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

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

Antigen presentation profiling reveals recognition of lymphoma immunoglobulin neoantigens

(2017) Michael S. Khodadoust et al.   NATURE

Elements of cancer immunity and the cancer–immune set point

(2017) Daniel S. Chen et al.   NATURE

An immunogenic personal neoantigen vaccine for patients with melanoma

(2017) Patrick A. Ott et al.   NATURE

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Tumour heterogeneity and resistance to cancer therapies

(2017) Ibiayi Dagogo-Jack et al.   Nature Reviews Clinical Oncology

Tumor Mutational Burden and Response Rate to PD-1 Inhibition

(2017) Mark Yarchoan et al.   NEW ENGLAND JOURNAL OF MEDICINE

NNAlign: a platform to construct and evaluate artificial neural network models of receptor–ligand interactions

(2017) Morten Nielsen 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

DynaDom: structure-based prediction of T cell receptor inter-domain and T cell receptor-peptide-MHC (class I) association angles

(2017) Thomas Hoffmann et al.   BMC STRUCTURAL BIOLOGY

GFusion: an Effective Algorithm to Identify Fusion Genes from Cancer RNA-Seq Data

(2017) Jian Zhao et al.   Scientific Reports

Identification of Glycopeptides as Posttranslationally Modified Neoantigens in Leukemia

(2017) Stacy A. Malaker et al.   Cancer Immunology Research

SplAdder: identification, quantification and testing of alternative splicing events from RNA-Seq data

(2016) André Kahles et al.   BIOINFORMATICS

Targeting the Heterogeneity of Cancer with Individualized Neoepitope Vaccines

(2016) O. Tu reci et al.   CLINICAL CANCER RESEARCH

The importance of correctly timing cancer immunotherapy

(2016) Elham Beyranvand Nejad et al.   EXPERT OPINION ON BIOLOGICAL THERAPY

Analyzing the effect of peptide-HLA-binding ability on the immunogenicity of potential CD8+ and CD4+ T cell epitopes in a large dataset

(2016) Shufeng Wang et al.   IMMUNOLOGIC RESEARCH

Comparison of exome-based HLA class I genotyping tools: identification of platform-specific genotyping errors

(2016) Kazuma Kiyotani et al.   JOURNAL OF HUMAN GENETICS

Neoantigen landscape dynamics during human melanoma–T cell interactions

(2016) Els M. E. Verdegaal et al.   NATURE

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Computational genomics tools for dissecting tumour–immune cell interactions

(2016) Hubert Hackl et al.   NATURE REVIEWS GENETICS

Nivolumab for Recurrent Squamous-Cell Carcinoma of the Head and Neck

(2016) Robert L. Ferris et al.   NEW ENGLAND JOURNAL OF MEDICINE

Global proteogenomic analysis of human MHC class I-associated peptides derived from non-canonical reading frames

(2016) Céline M. Laumont et al.   Nature Communications

High-Accuracy HLA Type Inference from Whole-Genome Sequencing Data Using Population Reference Graphs

(2016) Alexander T. Dilthey et al.   PLoS Computational Biology

A new view of transcriptome complexity and regulation through the lens of local splicing variations

(2016) Jorge Vaquero-Garcia et al.   eLife

Allele-Specific Quantification of Structural Variations in Cancer Genomes

(2016) Yang Li et al.   Cell Systems

Evaluation of Nine Somatic Variant Callers for Detection of Somatic Mutations in Exome and Targeted Deep Sequencing Data

(2016) Anne Bruun Krøigård et al.   PLoS One

In-depth comparison of somatic point mutation callers based on different tumor next-generation sequencing depth data

(2016) Lei Cai et al.   Scientific Reports

Evaluation of somatic copy number estimation tools for whole-exome sequencing data

(2015) Jae-Yong Nam et al.   BRIEFINGS IN BIOINFORMATICS

The Evolution of T-cell Therapies for Solid Malignancies

(2015) K. Fousek et al.   CLINICAL CANCER RESEARCH

The MAGE protein family and cancer

(2015) Jenny L Weon et al.   CURRENT OPINION IN CELL BIOLOGY

INTEGRATE: gene fusion discovery using whole genome and transcriptome data

(2015) Jin Zhang et al.   GENOME RESEARCH

Mass Spectrometry of Human Leukocyte Antigen Class I Peptidomes Reveals Strong Effects of Protein Abundance and Turnover on Antigen Presentation

(2015) Michal Bassani-Sternberg et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2015) Sachet A Shukla et al.   NATURE BIOTECHNOLOGY

PD-1 Blockade in Tumors with Mismatch-Repair Deficiency

(2015) Dung T. Le et al.   NEW ENGLAND JOURNAL OF MEDICINE

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

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

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

A dendritic cell vaccine increases the breadth and diversity of melanoma neoantigen-specific T cells

(2015) B. M. Carreno et al.   SCIENCE

Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer

(2015) N. A. Rizvi et al.   SCIENCE

JAFFA: High sensitivity transcriptome-focused fusion gene detection

(2015) Nadia M Davidson et al.   Genome Medicine

PhyloWGS: Reconstructing subclonal composition and evolution from whole-genome sequencing of tumors

(2015) Amit G Deshwar et al.   GENOME BIOLOGY

RNA-Seq Analysis of Differential Splice Junction Usage and Intron Retentions by DEXSeq

(2015) Yafang Li et al.   PLoS One

OptiType: precision HLA typing from next-generation sequencing data

(2014) András Szolek et al.   BIOINFORMATICS

Inferring clonal evolution of tumors from single nucleotide somatic mutations

(2014) Wei Jiao et al.   BMC BIOINFORMATICS

Using single cell sequencing data to model the evolutionary history of a tumor

(2014) Kyung Kim et al.   BMC BIOINFORMATICS

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

(2014) Yu Bai et al.   BMC GENOMICS

An assessment of computational methods for estimating purity and clonality using genomic data derived from heterogeneous tumor tissue samples

(2014) V. K. Yadav et al.   BRIEFINGS IN BIOINFORMATICS

TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data

(2014) Gavin Ha et al.   GENOME RESEARCH

Role of peptide processing predictions in T cell epitope identification: contribution of different prediction programs

(2014) Jorg J. A. Calis et al.   IMMUNOGENETICS

Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens

(2014) Matthew M. Gubin et al.   NATURE

Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms

(2014) Rob Patro et al.   NATURE BIOTECHNOLOGY

High-throughput epitope discovery reveals frequent recognition of neo-antigens by CD4+ T cells in human melanoma

(2014) Carsten Linnemann et al.   NATURE MEDICINE

PyClone: statistical inference of clonal population structure in cancer

(2014) Andrew Roth et al.   NATURE METHODS

rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data

(2014) Shihao Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-Definition Reconstruction of Clonal Composition in Cancer

(2014) Andrej Fischer et al.   Cell Reports

SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution

(2014) Christopher A. Miller et al.   PLoS Computational Biology

CD4 T-cell Subsets and Tumor Immunity: The Helpful and the Not-so-Helpful

(2014) H.-J. Kim et al.   Cancer Immunology Research

EXPANDS: expanding ploidy and allele frequency on nested subpopulations

(2013) Noemi Andor et al.   BIOINFORMATICS

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

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Mining exomic sequencing data to identify mutated antigens recognized by adoptively transferred tumor-reactive T cells

(2013) Paul F Robbins et al.   NATURE MEDICINE

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

HLA Haplotyping from RNA-seq Data Using Hierarchical Read Weighting

(2013) Hyunsung John Kim et al.   PLoS One

An Integrated Tool to Study MHC Region: Accurate SNV Detection and HLA Genes Typing in Human MHC Region Using Targeted High-Throughput Sequencing

(2013) Hongzhi Cao et al.   PLoS One

Association of the Autoimmune Disease Scleroderma with an Immunologic Response to Cancer

(2013) C. G. Joseph et al.   SCIENCE

MHC Class I-Associated Phosphopeptides Are the Targets of Memory-like Immunity in Leukemia

(2013) M. Cobbold et al.   Science Translational Medicine

Properties of MHC Class I Presented Peptides That Enhance Immunogenicity

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

THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data

(2013) Layla Oesper et al.   GENOME BIOLOGY

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

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Detecting differential usage of exons from RNA-seq data

(2012) S. Anders et al.   GENOME RESEARCH

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

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

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

(2012) Marco Gerlinger et al.   NEW ENGLAND JOURNAL OF MEDICINE

A flexible docking approach for prediction of T cell receptor-peptide-MHC complexes

(2012) Brian G. Pierce et al.   PROTEIN SCIENCE

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

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

(2011) David E. Larson et al.   BIOINFORMATICS

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

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Derivation of an amino acid similarity matrix for peptide:MHC binding and its application as a Bayesian prior

(2009) Yohan Kim et al.   BMC BIOINFORMATICS

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

(2009) Morten Nielsen et al.   BMC BIOINFORMATICS

Quantitative modeling of peptide binding to TAP using support vector machine

(2009) Carmen M. Diez-Rivero et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS