The peptide woods are lovely, dark and deep: Hunting for novel cancer antigens

Versatile RNA : Overlooked gems of the transcriptome

(2023) Murat Erdem et al.   FEBS Journal

TCR-engineered T cell therapy in solid tumors: State of the art and perspectives

(2023) Estelle Baulu et al.   Science Advances

Navigating Critical Challenges Associated with Immunopeptidomics-Based Detection of Proteasomal Spliced Peptide Candidates

(2022) Cheryl F. Lichti et al.   Cancer Immunology Research

PBRM1 Inactivation Promotes Upregulation of Human Endogenous Retroviruses in a HIF-Dependent Manner

(2022) Mi Zhou et al.   Cancer Immunology Research

Alternative Splicing, Epigenetic Modifications and Cancer: A Dangerous Triangle, or a Hopeful One?

(2022) Francisco Gimeno-Valiente et al.   Cancers

Reliability analysis of exonic-breakpoint fusions identified by DNA sequencing for predicting the efficacy of targeted therapy in non-small cell lung cancer

(2022) Weihua Li et al.   BMC Medicine

Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation

(2022) Andreas‐David Brunner et al.   Molecular Systems Biology

Accurate detection of tumor-specific gene fusions reveals strongly immunogenic personal neo-antigens

(2022) David Weber et al.   NATURE BIOTECHNOLOGY

SCAPE: a mixture model revealing single-cell polyadenylation diversity and cellular dynamics during cell differentiation and reprogramming

(2022) Ran Zhou et al.   NUCLEIC ACIDS RESEARCH

Improved transcriptome assembly using a hybrid of long and short reads with StringTie

(2022) Alaina Shumate et al.   PLoS Computational Biology

Alternative Splicing in Cancer and Immune Cells

(2022) Antoine Bernard et al.   Cancers

FFPE-Based NGS Approaches into Clinical Practice: The Limits of Glory from a Pathologist Viewpoint

(2022) Filippo Cappello et al.   Journal of Personalized Medicine

Dark genome, bright ideas: Recent approaches to harness transposable elements in immunotherapies

(2022) Ashley Reid Cahn et al.   CANCER CELL

TransMeta simultaneously assembles multisample RNA-seq reads

(2022) Ting Yu et al.   GENOME RESEARCH

MS2Rescore: Data-Driven Rescoring Dramatically Boosts Immunopeptide Identification Rates

(2022) Arthur Declercq et al.   MOLECULAR & CELLULAR PROTEOMICS

Alternative splicing as a source of phenotypic diversity

(2022) Charlotte J. Wright et al.   NATURE REVIEWS GENETICS

Proteogenomics and Differential Ion Mobility Enable the Exploration of the Mutational Landscape in Colon Cancer Cells

(2022) Zhaoguan Wu et al.   ANALYTICAL CHEMISTRY

ABEILLE: a novel method for ABerrant Expression Identification empLoying machine LEarning from RNA-sequencing data

(2022) Justine Labory et al.   BIOINFORMATICS

Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactions

(2022) Lian Narunsky-Haziza et al.   CELL

Seq2Neo: A Comprehensive Pipeline for Cancer Neoantigen Immunogenicity Prediction

(2022) Kaixuan Diao et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Alternative cleavage and polyadenylation generates downstream uncapped RNA isoforms with translation potential

(2022) Yuval Malka et al.   MOLECULAR CELL

The tumor-specific antigen landscape of acute myeloid leukemia

(2022) Grégory Ehx et al.   MOLECULAR IMMUNOLOGY

Post-translational modifications reshape the antigenic landscape of the MHC I immunopeptidome in tumors

(2022) Assaf Kacen et al.   NATURE BIOTECHNOLOGY

Performance evaluation of differential splicing analysis methods and splicing analytics platform construction

(2022) Kuokuo Li et al.   NUCLEIC ACIDS RESEARCH

The A to I editing landscape in melanoma and its relation to clinical outcome

(2022) Austeja Amweg et al.   RNA Biology

A Survey on Methods for Predicting Polyadenylation Sites from DNA Sequences, Bulk RNA-seq, and Single-cell RNA-seq

(2022) Wenbin Ye et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

T cells of colorectal cancer patients’ stimulated by neoantigenic and cryptic peptides better recognize autologous tumor cells

(2022) Sandra Schwarz et al.   Journal for ImmunoTherapy of Cancer

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

(2021) Zhuting Hu et al.   NATURE MEDICINE

Advances in the development of personalized neoantigen-based therapeutic cancer vaccines

(2021) Eryn Blass et al.   Nature Reviews Clinical Oncology

Detection of aberrant splicing events in RNA-seq data using FRASER

(2021) Christian Mertes et al.   Nature Communications

Detection of gene fusions using targeted next-generation sequencing: a comparative evaluation

(2021) Carina Heydt et al.   BMC Medical Genomics

Noncanonical open reading frames encode functional proteins essential for cancer cell survival

(2021) John R. Prensner et al.   NATURE BIOTECHNOLOGY

Deep learning the collisional cross sections of the peptide universe from a million experimental values

(2021) Florian Meier et al.   Nature Communications

Immune Therapy Resistance and Immune Escape of Tumors

(2021) Barbara Seliger et al.   Cancers

A-to-I RNA Editing in Cancer: From Evaluating the Editing Level to Exploring the Editing Effects

(2021) Heming Wang et al.   Frontiers in Oncology

Atypical acute myeloid leukemia-specific transcripts generate shared and immunogenic MHC class-I-associated epitopes

(2021) Grégory Ehx et al.   IMMUNITY

Are there indeed spliced peptides in the immunopeptidome?

(2021) Arie Admon   MOLECULAR & CELLULAR PROTEOMICS

Identification of bacteria-derived HLA-bound peptides in melanoma

(2021) Shelly Kalaora et al.   NATURE

Epigenetic silencing by SETDB1 suppresses tumour intrinsic immunogenicity

(2021) Gabriel K. Griffin et al.   NATURE

Splicing patterns in SF3B1 mutated uveal melanoma generate shared immunogenic tumor-specific neo-epitopes

(2021) Jeremy Bigot et al.   Cancer Discovery

HLA Ligand Atlas: a benign reference of HLA-presented peptides to improve T-cell-based cancer immunotherapy

(2021) Ana Marcu et al.   Journal for ImmunoTherapy of Cancer

Increased expression of peptides from non-coding genes in cancer proteomics datasets suggests potential tumor neoantigens

(2021) Rong Xiang et al.   Communications Biology

Comparative evaluation of full-length isoform quantification from RNA-Seq

(2021) Dimitra Sarantopoulou et al.   BMC BIOINFORMATICS

Cancer-associated dynamics and potential regulators of intronic polyadenylation revealed by IPAFinder using standard RNA-seq data

(2021) Zhaozhao Zhao et al.   GENOME RESEARCH

Diagnostic Utility of Gene Fusion Panel to Detect Gene Fusions in Fresh and Formalin-Fixed, Paraffin-Embedded Cancer Specimens

(2021) Lisa Haley et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Comprehensive characterization of somatic variants associated with intronic polyadenylation in human cancers

(2021) Zhaozhao Zhao et al.   NUCLEIC ACIDS RESEARCH

scAPAdb: a comprehensive database of alternative polyadenylation at single-cell resolution

(2021) Sheng Zhu et al.   NUCLEIC ACIDS RESEARCH

Methods for actionable gene fusion detection in lung cancer: now and in the future

(2021) Pasquale Pisapia et al.   PHARMACOGENOMICS

Absolute quantification of tumor antigens using embedded MHC-I isotopologue calibrants

(2021) Lauren E. Stopfer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative study of bioinformatic tools for the identification of chimeric RNAs from RNA Sequencing

(2021) Sandeep Singh et al.   RNA Biology

Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics

(2021) Mathias Wilhelm et al.   Nature Communications

Improved methods for RNAseq-based alternative splicing analysis

(2021) Rebecca F. Halperin et al.   Scientific Reports

Tumor Infiltrating Lymphocytes Target HLA-I Phosphopeptides Derived From Cancer Signaling in Colorectal Cancer

(2021) Sarah A. Penny et al.   Frontiers in Immunology

Functional comparison of exome capture-based methods for transcriptomic profiling of formalin-fixed paraffin-embedded tumors

(2021) Kyrillus S. Shohdy et al.   npj Genomic Medicine

Oncogene-dependent sloppiness in mRNA translation

(2021) Julien Champagne et al.   MOLECULAR CELL

KDM5B promotes immune evasion by recruiting SETDB1 to silence retroelements

(2021) Shang-Min Zhang et al.   NATURE

Locus-specific expression of transposable elements in single cells with CELLO-seq

(2021) Rebecca V. Berrens et al.   NATURE BIOTECHNOLOGY

Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer

(2021) Tamara Ouspenskaia et al.   NATURE BIOTECHNOLOGY

DeepLC can predict retention times for peptides that carry as-yet unseen modifications

(2021) Robbin Bouwmeester et al.   NATURE METHODS

caAtlas: An immunopeptidome atlas of human cancer

(2021) Xinpei Yi et al.   iScience

Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: comparison of gene expression profiling approaches

(2020) Arran K. Turnbull et al.   BMC BIOINFORMATICS

Immunosurveillance and Immunoediting of Lung Cancer: Current Perspectives and Challenges

(2020) Kei Kunimasa et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Mutation position is an important determinant for predicting cancer neoantigens

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

Genomic basis for RNA alterations in cancer

(2020) Claudia Calabrese et al.   NATURE

Pan-cancer analysis of whole genomes

(2020)   NATURE

The landscape of viral associations in human cancers

(2020) Marc Zapatka et al.   NATURE GENETICS

Pervasive functional translation of noncanonical human open reading frames

(2020) Jin Chen et al.   SCIENCE

Comparison of Four Next Generation Sequencing Platforms for Fusion Detection: Oncomine by ThermoFisher, AmpliSeq by Illumina, FusionPlex by ArcherDX, and QIAseq by QIAGEN

(2020) Xiaoyu Qu et al.   Cancer Genetics

pVACtools: a computational toolkit to identify and visualize cancer neoantigens

(2020) Jasreet Hundal et al.   Cancer Immunology Research

Proteogenomics Uncovers a Vast Repertoire of Shared Tumor-Specific Antigens in Ovarian Cancer

(2020) Qingchuan Zhao et al.   Cancer Immunology Research

LeafCutterMD: an algorithm for outlier splicing detection in rare diseases

(2020) Garrett Jenkinson et al.   BIOINFORMATICS

Detection of somatic structural variants from short-read next-generation sequencing data

(2020) Tingting Gong et al.   BRIEFINGS IN BIOINFORMATICS

Single-cell RNA counting at allele and isoform resolution using Smart-seq3

(2020) Michael Hagemann-Jensen et al.   NATURE BIOTECHNOLOGY

PolyA-miner: accurate assessment of differential alternative poly-adenylation from 3′Seq data using vector projections and non-negative matrix factorization

(2020) Hari Krishna Yalamanchili et al.   NUCLEIC ACIDS RESEARCH

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

(2020) Chloe Chong et al.   Nature Communications

Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns

(2020) Alison D. Tang et al.   Nature Communications

Multiplexed relative and absolute quantitative immunopeptidomics reveals MHC I repertoire alterations induced by CDK4/6 inhibition

(2020) Lauren E. Stopfer et al.   Nature Communications

Extending the Comprehensiveness of Immunopeptidome Analyses Using Isobaric Peptide Labeling

(2020) Sibylle Pfammatter et al.   ANALYTICAL CHEMISTRY

Detection of leukemia gene fusions by targeted RNA-sequencing in routine diagnostics

(2020) Marie Engvall et al.   BMC Medical Genomics

Fusion transcript detection using spatial transcriptomics

(2020) Stefanie Friedrich et al.   BMC Medical Genomics

An RNA vaccine drives immunity in checkpoint-inhibitor-treated melanoma

(2020) Ugur Sahin et al.   NATURE

Towards new horizons: characterization, classification and implications of the tumour antigenic repertoire

(2020) Sebastian P. Haen et al.   Nature Reviews Clinical Oncology

Measuring and interpreting transposable element expression

(2020) Sophie Lanciano et al.   NATURE REVIEWS GENETICS

Identification of the Cryptic HLA-I Immunopeptidome

(2020) Florian Erhard et al.   Cancer Immunology Research

MHCflurry 2.0: Improved Pan-Allele Prediction of MHC Class I-Presented Peptides by Incorporating Antigen Processing

(2020) Timothy J. O’Donnell et al.   Cell Systems

DNA hypomethylation promotes transposable element expression and activation of immune signaling in renal cell cancer

(2020) Aguirre A. de Cubas et al.   JCI Insight

Next Generation Sequencing for Gene Fusion Analysis in Lung Cancer: A Literature Review

(2020) Rossella Bruno et al.   Diagnostics

Identifying and Targeting Human Tumor Antigens for T Cell-Based Immunotherapy of Solid Tumors

(2020) Vid Leko et al.   CANCER CELL

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

(2020) Daniel K. Wells et al.   CELL

Tolerance in the Age of Immunotherapy

(2020) Jeffrey A. Bluestone et al.   NEW ENGLAND JOURNAL OF MEDICINE

Spliced Peptides and Cytokine-Driven Changes in the Immunopeptidome of Melanoma

(2020) Pouya Faridi et al.   Cancer Immunology Research

Comprehensive targeted next‐generation sequencing approach in the molecular diagnosis of gastrointestinal stromal tumor

(2020) Isabelle Vanden Bempt et al.   GENES CHROMOSOMES & CANCER

Anti-tumour immunity induces aberrant peptide presentation in melanoma

(2020) Osnat Bartok et al.   NATURE

Integration of whole-exome and anchored PCR-based next generation sequencing significantly increases detection of actionable alterations in precision oncology

(2020) Shaham Beg et al.   Translational Oncology

Alternative Polyadenylation: a new frontier in post transcriptional regulation

(2020) Fanggang Ren et al.   Biomarker Research

Predicting Splicing from Primary Sequence with Deep Learning

(2019) Kishore Jaganathan et al.   CELL

Identification of candidate neoantigens produced by fusion transcripts in human osteosarcomas

(2019) Susan K. Rathe et al.   Scientific Reports

Cancer Vaccines: Steering T Cells Down the Right Path to Eradicate Tumors

(2019) Patrick A. Ott et al.   Cancer Discovery

Diagnosis of fusion genes using targeted RNA sequencing

(2019) Erin E. Heyer et al.   Nature Communications

Extraction-free whole transcriptome gene expression analysis of FFPE sections and histology-directed subareas of tissue

(2019) Christy L. Trejo et al.   PLoS One

Pre-fractionation Extends but also Creates a Bias in the Detectable HLA Class Ι Ligandome

(2019) Laura C. Demmers et al.   JOURNAL OF PROTEOME RESEARCH

Multiplexed Relative Quantitation with Isobaric Tagging Mass Spectrometry Reveals Class I Major Histocompatibility Complex Ligand Dynamics in Response to Doxorubicin

(2019) J. Patrick Murphy et al.   ANALYTICAL CHEMISTRY

Performance of Oncomine Fusion Transcript kit for formalin‐fixed, paraffin‐embedded lung cancer specimens

(2019) Kazuko Sakai et al.   CANCER SCIENCE

Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities

(2019) Suhas Vasaikar et al.   CELL

Immunogenic neoantigens derived from gene fusions stimulate T cell responses

(2019) Wei Yang et al.   NATURE MEDICINE

Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning

(2019) Siegfried Gessulat et al.   NATURE METHODS

Mass spectrometry–based identification of MHC-bound peptides for immunopeptidomics

(2019) Anthony W. Purcell et al.   Nature Protocols

Deep learning: new computational modelling techniques for genomics

(2019) Gökcen Eraslan et al.   NATURE REVIEWS GENETICS

Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma

(2019) Markus W. Löffler et al.   Genome Medicine

Alternative cleavage and polyadenylation in health and disease

(2019) Andreas J. Gruber et al.   NATURE REVIEWS GENETICS

RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues

(2019) Keren Yizhak et al.   SCIENCE

Paired-end mappability of transposable elements in the human genome

(2019) Corinne E. Sexton et al.   Mobile DNA

Defining HLA-II Ligand Processing and Binding Rules with Mass Spectrometry Enhances Cancer Epitope Prediction

(2019) Jennifer G. Abelin et al.   IMMUNITY

RNA editing in the forefront of epitranscriptomics and human health

(2019) Theodoulakis Christofi et al.   Journal of Translational Medicine

NTRK fusion detection across multiple assays and 33,997 cases: diagnostic implications and pitfalls

(2019) James P. Solomon et al.   MODERN PATHOLOGY

Targeting mRNA processing as an anticancer strategy

(2019) Joana Desterro et al.   NATURE REVIEWS DRUG DISCOVERY

Transcriptional Control by Premature Termination: A Forgotten Mechanism

(2019) Kinga Kamieniarz-Gdula et al.   TRENDS IN GENETICS

Fusion transcripts: Unexploited vulnerabilities in cancer?

(2019) Carla Neckles et al.   Wiley Interdisciplinary Reviews-RNA

Comment on “A subset of HLA-I peptides are not genomically templated: Evidence for cis- and trans-spliced peptide ligands”

(2019) Zach Rolfs et al.   Science Immunology

1670OADP-A2M4 (MAGE-A4) in patients with synovial sarcoma

(2019) B A Van Tine et al.   ANNALS OF ONCOLOGY

Fusion Transcripts of Adjacent Genes: New Insights into the World of Human Complex Transcripts in Cancer

(2019) Vincenza Barresi et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Developing neoantigen-targeted T cell–based treatments for solid tumors

(2019) Tori N. Yamamoto et al.   NATURE MEDICINE

Transposable element expression in tumors is associated with immune infiltration and increased antigenicity

(2019) Yu Kong et al.   Nature Communications

A multi-sample approach increases the accuracy of transcript assembly

(2019) Li Song et al.   Nature Communications

Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis

(2019) Jethro S. Johnson et al.   Nature Communications

Systematic evaluation of differential splicing tools for RNA-seq studies

(2019) Arfa Mehmood et al.   BRIEFINGS IN BIOINFORMATICS

Targeting cancers through TCR-peptide/MHC interactions

(2019) Qinghua He et al.   Journal of Hematology & Oncology

A large peptidome dataset improves HLA class I epitope prediction across most of the human population

(2019) Siranush Sarkizova et al.   NATURE BIOTECHNOLOGY

Accurate annotation of human protein-coding small open reading frames

(2019) Thomas F. Martinez et al.   Nature Chemical Biology

Mapping the HLA ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation

(2018) Markus W. Löffler et al.   CANCER RESEARCH

LSD1 Ablation Stimulates Anti-tumor Immunity and Enables Checkpoint Blockade

(2018) Wanqiang Sheng et al.   CELL

Improved Ribo-seq enables identification of cryptic translation events

(2018) Florian Erhard et al.   NATURE METHODS

DeTiN: overcoming tumor-in-normal contamination

(2018) Amaro Taylor-Weiner et al.   NATURE METHODS

De novo annotation and characterization of the translatome with ribosome profiling data

(2018) Zhengtao Xiao et al.   NUCLEIC ACIDS RESEARCH

Capturing the ‘ome’: the expanding molecular toolbox for RNA and DNA library construction

(2018) Morgane Boone et al.   NUCLEIC ACIDS RESEARCH

A Targeted LC-MS Strategy for Low-Abundant HLA Class-I-Presented Peptide Detection Identifies Novel Human Papillomavirus T-Cell Epitopes

(2018) Renata Blatnik et al.   PROTEOMICS

Personalized vaccines for cancer immunotherapy

(2018) Ugur Sahin et al.   SCIENCE

Widespread intronic polyadenylation diversifies immune cell transcriptomes

(2018) Irtisha Singh et al.   Nature Communications

Systematic Analysis of Splice-Site-Creating Mutations in Cancer

(2018) Reyka G. Jayasinghe et al.   Cell Reports

Improved Peptide Retention Time Prediction in Liquid Chromatography through Deep Learning

(2018) Chunwei Ma et al.   ANALYTICAL CHEMISTRY

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

(2018) André Kahles et al.   CANCER CELL

Widespread intronic polyadenylation inactivates tumour suppressor genes in leukaemia

(2018) Shih-Han Lee et al.   NATURE

Intron retention is a source of neoepitopes in cancer

(2018) Alicia C Smart et al.   NATURE BIOTECHNOLOGY

Terminal exon characterization with TECtool reveals an abundance of cell-specific isoforms

(2018) Andreas J. Gruber et al.   NATURE METHODS

JUM is a computational method for comprehensive annotation-free analysis of alternative pre-mRNA splicing patterns

(2018) Qingqing Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA editing derived epitopes function as cancer antigens to elicit immune responses

(2018) Minying Zhang et al.   Nature Communications

OUTRIDER: A Statistical Method for Detecting Aberrantly Expressed Genes in RNA Sequencing Data

(2018) Felix Brechtmann et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The HLA ligandome landscape of chronic myeloid leukemia delineates novel T-cell epitopes for immunotherapy

(2018) Tatjana Bilich et al.   BLOOD

ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events

(2018) Luca Denti et al.   BMC BIOINFORMATICS

Endogenous retroviral signatures predict immunotherapy response in clear cell renal cell carcinoma

(2018) Christof C. Smith et al.   JOURNAL OF CLINICAL INVESTIGATION

Online Parallel Accumulation–Serial Fragmentation (PASEF) with a Novel Trapped Ion Mobility Mass Spectrometer

(2018) Florian Meier et al.   MOLECULAR & CELLULAR PROTEOMICS

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

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

ERVmap analysis reveals genome-wide transcription of human endogenous retroviruses

(2018) Maria Tokuyama et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Sequence Determinants for Nuclear Retention and Cytoplasmic Export of mRNAs and lncRNAs

(2018) Alexander F. Palazzo et al.   Frontiers in Genetics

The Role of RNA Editing in Cancer Development and Metabolic Disorders

(2018) Che-Pei Kung et al.   Frontiers in Endocrinology

Deep intronic mutations and human disease

(2017) Rita Vaz-Drago et al.   HUMAN GENETICS

Mass Spectrometry Profiling of HLA-Associated Peptidomes in Mono-allelic Cells Enables More Accurate Epitope Prediction

(2017) Jennifer G. Abelin et al.   IMMUNITY

Treatment of Patients With Metastatic Cancer Using a Major Histocompatibility Complex Class II–Restricted T-Cell Receptor Targeting the Cancer Germline Antigen MAGE-A3

(2017) Yong-Chen Lu et al.   JOURNAL OF CLINICAL ONCOLOGY

Unveiling the Peptide Motifs of HLA-C and HLA-G from Naturally Presented Peptides and Generation of Binding Prediction Matrices

(2017) Moreno Di Marco et al.   JOURNAL OF IMMUNOLOGY

Detection of Proteome Diversity Resulted from Alternative Splicing is Limited by Trypsin Cleavage Specificity

(2017) Xiaojing Wang et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2017) Ugur Sahin 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

Accurate assembly of transcripts through phase-preserving graph decomposition

(2017) Mingfu Shao et al.   NATURE BIOTECHNOLOGY

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics

(2017) Andy T Kong et al.   NATURE METHODS

PolyA_DB 3 catalogs cleavage and polyadenylation sites identified by deep sequencing in multiple genomes

(2017) Ruijia Wang et al.   NUCLEIC ACIDS RESEARCH

Poly(A)-ClickSeq: click-chemistry for next-generation 3΄-end sequencing without RNA enrichment or fragmentation

(2017) Andrew Routh et al.   NUCLEIC ACIDS RESEARCH

The immunopeptidomic landscape of ovarian carcinomas

(2017) Heiko Schuster et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

De novo peptide sequencing by deep learning

(2017) Ngoc Hieu Tran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive analysis of normal adjacent to tumor transcriptomes

(2017) Dvir Aran et al.   Nature Communications

Alternative Polyadenylation: Methods, Findings, and Impacts

(2017) Wei Chen et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

A trichostatin A expression signature identified by TempO-Seq targeted whole transcriptome profiling

(2017) Joanne M. Yeakley et al.   PLoS One

Improved Identification and Analysis of Small Open Reading Frame Encoded Polypeptides

(2016) Jiao Ma et al.   ANALYTICAL CHEMISTRY

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

(2016) André Kahles et al.   BIOINFORMATICS

Inhibiting DNA Methylation Causes an Interferon Response in Cancer via dsRNA Including Endogenous Retroviruses

(2016) Katherine B. Chiappinelli et al.   CELL

Kallikrein-related peptidases (KLKs) as emerging therapeutic targets: focus on prostate cancer and skin pathologies

(2016) Margaritis Avgeris et al.   EXPERT OPINION ON THERAPEUTIC TARGETS

Unsupervised HLA Peptidome Deconvolution Improves Ligand Prediction Accuracy and Predicts Cooperative Effects in Peptide–HLA Interactions

(2016) Michal Bassani-Sternberg et al.   JOURNAL OF IMMUNOLOGY

Arginine (Di)methylated Human Leukocyte Antigen Class I Peptides Are Favorably Presented by HLA-B*07

(2016) Fabio Marino et al.   JOURNAL OF PROTEOME RESEARCH

Human Leukocyte Antigen (HLA) Peptides Derived from Tumor Antigens Induced by Inhibition of DNA Methylation for Development of Drug-facilitated Immunotherapy

(2016) Bracha Shraibman et al.   MOLECULAR & CELLULAR PROTEOMICS

A Molecular Basis for the Presentation of Phosphorylated Peptides by HLA-B Antigens

(2016) Adán Alpízar et al.   MOLECULAR & CELLULAR PROTEOMICS

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

TACO produces robust multisample transcriptome assemblies from RNA-seq

(2016) Yashar S Niknafs et al.   NATURE METHODS

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

(2016) N. McGranahan et al.   SCIENCE

A large fraction of HLA class I ligands are proteasome-generated spliced peptides

(2016) Juliane Liepe et al.   SCIENCE

Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry

(2016) Michal Bassani-Sternberg et al.   Nature Communications

Robust detection of immune transcripts in FFPE samples using targeted RNA sequencing

(2016) Benjamin E. Paluch et al.   Oncotarget

Use of HLA peptidomics and whole exome sequencing to identify human immunogenic neo-antigens

(2016) Shelly Kalaora et al.   Oncotarget

RNA-Seq methods for transcriptome analysis

(2016) Radmila Hrdlickova et al.   Wiley Interdisciplinary Reviews-RNA

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

(2016) Jorge Vaquero-Garcia et al.   eLife

Global burden of cancers attributable to infections in 2012: a synthetic analysis

(2016) Martyn Plummer et al.   Lancet Global Health

Mechanisms and Regulation of Alternative Pre-mRNA Splicing

(2015) Yeon Lee et al.   Annual Review of Biochemistry

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications

(2015) Xiaoyu Chen et al.   BIOINFORMATICS

Comparison of stranded and non-stranded RNA-seq transcriptome profiling and investigation of gene overlap

(2015) Shanrong Zhao et al.   BMC GENOMICS

DNA-Demethylating Agents Target Colorectal Cancer Cells by Inducing Viral Mimicry by Endogenous Transcripts

(2015) David Roulois et al.   CELL

Circadian clocks, epigenetics, and cancer

(2015) Selma Masri et al.   CURRENT OPINION IN ONCOLOGY

The use of exome capture RNA-seq for highly degraded RNA with application to clinical cancer sequencing

(2015) Marcin Cieslik et al.   GENOME RESEARCH

Extended O-GlcNAc on HLA Class-I-Bound Peptides

(2015) Fabio Marino et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Novor: Real-Time Peptide de Novo Sequencing Software

(2015) Bin Ma   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

A mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides

(2015) Joel M Chick et al.   NATURE BIOTECHNOLOGY

Glycolysis controls the induction of human regulatory T cells by modulating the expression of FOXP3 exon 2 splicing variants

(2015) Veronica De Rosa et al.   NATURE IMMUNOLOGY

Complementary IMAC enrichment methods for HLA-associated phosphopeptide identification by mass spectrometry

(2015) Jennifer G Abelin et al.   Nature Protocols

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

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Distinguishing the immunostimulatory properties of noncoding RNAs expressed in cancer cells

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