De novo prediction of cancer-associated T cell receptors for noninvasive cancer detection

Biophysicochemical motifs in T cell receptor sequences distinguish repertoires from tumor-infiltrating lymphocytes and adjacent healthy tissue

(2019) Jared Ostmeyer et al.   CANCER RESEARCH

Comprehensive Analysis of TCR-β Repertoire in Patients with Neurological Immune-mediated Disorders

(2019) Alessandra de Paula Alves Sousa et al.   Scientific Reports

Immunotherapy in hepatocellular carcinoma

(2019) Luigi Buonaguro et al.   Annals of Hepatology

Exploring the emerging role of the microbiome in cancer immunotherapy

(2019) Jessica Fessler et al.   Journal for ImmunoTherapy of Cancer

Longitudinal immunosequencing in healthy people reveals persistent T cell receptors rich in highly public receptors

(2019) Nathaniel D. Chu et al.   BMC IMMUNOLOGY

Clonal replacement of tumor-specific T cells following PD-1 blockade

(2019) Kathryn E. Yost et al.   NATURE MEDICINE

Deep single-cell RNA sequencing data of individual T cells from treatment-naïve colorectal cancer patients

(2019) Yuanyuan Zhang et al.   Scientific Data

Human CD4+CD103+ cutaneous resident memory T cells are found in the circulation of healthy individuals

(2019) Maria M. Klicznik et al.   Science Immunology

Compartmental analysis of T cell clonal dynamics as a function of pathologic response to neoadjuvant PD-1 blockade in resectable non-small cell lung cancer

(2019) Jiajia Zhang et al.   CLINICAL CANCER RESEARCH

High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants

(2019) Pedram Razavi et al.   NATURE MEDICINE

Investigation of Antigen-Specific T-Cell Receptor Clusters in Human Cancers

(2019) Hongyi Zhang et al.   CLINICAL CANCER RESEARCH

αβ T-cell receptors with a central CDR3 cysteine are enriched in CD8αα intraepithelial lymphocytes and their thymic precursors

(2018) Rushika C Wirasinha et al.   IMMUNOLOGY AND CELL BIOLOGY

A Diverse Lipid Antigen–Specific TCR Repertoire Is Clonally Expanded during Active Tuberculosis

(2018) William S. DeWitt et al.   JOURNAL OF IMMUNOLOGY

Detection and localization of surgically resectable cancers with a multi-analyte blood test

(2018) Joshua D. Cohen et al.   SCIENCE

Contraction of T cell richness in lung cancer brain metastases

(2018) Aaron S. Mansfield et al.   Scientific Reports

Symptom Signatures and Diagnostic Timeliness in Cancer Patients: A Review of Current Evidence

(2018) Minjoung M. Koo et al.   NEOPLASIA

DNA repair defects and implications for immunotherapy

(2018) Katherine M. Bever et al.   JOURNAL OF CLINICAL INVESTIGATION

Sensitive tumour detection and classification using plasma cell-free DNA methylomes

(2018) Shu Yi Shen et al.   NATURE

Evaluation of immune repertoire inference methods from RNA-seq data

(2018) Xihao Hu et al.   NATURE BIOTECHNOLOGY

High-throughput determination of the antigen specificities of T cell receptors in single cells

(2018) Shu-Qi Zhang et al.   NATURE BIOTECHNOLOGY

Low and variable tumor reactivity of the intratumoral TCR repertoire in human cancers

(2018) Wouter Scheper et al.   NATURE MEDICINE

Radiotherapy induces responses of lung cancer to CTLA-4 blockade

(2018) Silvia C. Formenti et al.   NATURE MEDICINE

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

Identification of unique neoantigen qualities in long-term survivors of pancreatic cancer

(2017) Vinod P. Balachandran et al.   NATURE

Ultrasensitive detection of TCR hypervariable-region sequences in solid-tissue RNA–seq data

(2017) Bo Li et al.   NATURE GENETICS

Immunosequencing identifies signatures of cytomegalovirus exposure history and HLA-mediated effects on the T cell repertoire

(2017) Ryan O Emerson et al.   NATURE GENETICS

T cell receptor sequencing of early-stage breast cancer tumors identifies altered clonal structure of the T cell repertoire

(2017) John F. Beausang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mismatch repair deficiency predicts response of solid tumors to PD-1 blockade

(2017) Dung T. Le et al.   SCIENCE

Somatic mutations in clonally expanded cytotoxic T lymphocytes in patients with newly diagnosed rheumatoid arthritis

(2017) P. Savola et al.   Nature Communications

Contribution of systemic and somatic factors to clinical response and resistance to PD-L1 blockade in urothelial cancer: An exploratory multi-omic analysis

(2017) Alexandra Snyder et al.   PLOS MEDICINE

T cell receptor repertoires of mice and humans are clustered in similarity networks around conserved public CDR3 sequences

(2017) Asaf Madi et al.   eLife

T-cell Localization, Activation, and Clonal Expansion in Human Pancreatic Ductal Adenocarcinoma

(2017) Ingunn M. Stromnes et al.   Cancer Immunology Research

Landscape of tumor-infiltrating T cell repertoire of human cancers

(2016) Bo Li et al.   NATURE GENETICS

Prospective identification of neoantigen-specific lymphocytes in the peripheral blood of melanoma patients

(2016) Alena Gros et al.   NATURE MEDICINE

Diversity and divergence of the glioma-infiltrating T-cell receptor repertoire

(2016) Jennifer S. Sims et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TCR Sequencing Can Identify and Track Glioma-Infiltrating T Cells after DC Vaccination

(2016) M. S. Hsu et al.   Cancer Immunology Research

Cytotoxic effects of chemotherapy on cancer and immune cells: how can it be modulated to generate novel therapeutic strategies?

(2015) Cédric Rébé et al.   Future Oncology

Complete Regression of Metastatic Cervical Cancer After Treatment With Human Papillomavirus–Targeted Tumor-Infiltrating T Cells

(2015) Sanja Stevanović et al.   JOURNAL OF CLINICAL ONCOLOGY

Dynamics of the Cytotoxic T Cell Response to a Model of Acute Viral Infection

(2015) William S. DeWitt et al.   JOURNAL OF VIROLOGY

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

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

(2015) Sachet A Shukla et al.   NATURE BIOTECHNOLOGY

Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

Estimating T-cell repertoire diversity: limitations of classical estimators and a new approach

(2015) Daniel J. Laydon et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

TCR contact residue hydrophobicity is a hallmark of immunogenic CD8+T cell epitopes

(2015) Diego Chowell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Review The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge

(2015) Katarzyna Tomczak et al.   Wspolczesna Onkologia-Contemporary Oncology

A bioinformatic framework for immune repertoire diversity profiling enables detection of immunological status

(2015) Victor Greiff et al.   Genome Medicine

CTLA4 Blockade Broadens the Peripheral T-Cell Receptor Repertoire

(2014) L. Robert et al.   CLINICAL CANCER RESEARCH

Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens

(2014) Matthew M. Gubin et al.   NATURE

PD-1 blockade induces responses by inhibiting adaptive immune resistance

(2014) Paul C. Tumeh et al.   NATURE

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

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

Morphological Differences between Circulating Tumor Cells from Prostate Cancer Patients and Cultured Prostate Cancer Cells

(2014) Sunyoung Park et al.   PLoS One

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

(2014) E. Tran et al.   SCIENCE

Immunosequencing: applications of immune repertoire deep sequencing

(2013) Harlan Robins   CURRENT OPINION IN IMMUNOLOGY

High-throughput sequencing of T-cell receptors reveals a homogeneous repertoire of tumour-infiltrating lymphocytes in ovarian cancer

(2013) Ryan O Emerson et al.   JOURNAL OF PATHOLOGY

Circulating Tumor Cells: Liquid Biopsy of Cancer

(2012) C. Alix-Panabieres et al.   CLINICAL CHEMISTRY

The Role of Naive T Cell Precursor Frequency and Recruitment in Dictating Immune Response Magnitude

(2012) M. K. Jenkins et al.   JOURNAL OF IMMUNOLOGY

Combination of neoadjuvant chemotherapy followed by surgical resection as a new strategy for WHO grade II gliomas: a study of cognitive status and quality of life

(2011) Marie Blonski et al.   JOURNAL OF NEURO-ONCOLOGY

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

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

Memory CD8+ T cell differentiation

(2010) Joshua J. Obar et al.   Annals of the New York Academy of Sciences

Positive predictive values of ≥5% in primary care for cancer: systematic review

(2010) Mark Shapley et al.   BRITISH JOURNAL OF GENERAL PRACTICE

Tumour hypoxia induces a metabolic shift causing acidosis: a common feature in cancer

(2010) Johanna Chiche et al.   JOURNAL OF CELLULAR AND MOLECULAR MEDICINE

Antibody recycling by engineered pH-dependent antigen binding improves the duration of antigen neutralization

(2010) Tomoyuki Igawa et al.   NATURE BIOTECHNOLOGY

High throughput sequencing reveals a complex pattern of dynamic interrelationships among human T cell subsets

(2010) C. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Review of cytomegalovirus seroprevalence and demographic characteristics associated with infection

(2010) Michael J. Cannon et al.   REVIEWS IN MEDICAL VIROLOGY

Structural Biology of the T-cell Receptor: Insights into Receptor Assembly, Ligand Recognition, and Initiation of Signaling

(2010) K. W. Wucherpfennig et al.   Cold Spring Harbor Perspectives in Biology

Tumor antigen-specific CD8 T cells infiltrating the tumor express high levels of PD-1 and are functionally impaired

(2009) M. Ahmadzadeh et al.   BLOOD

Evaluation of biomarker panels for early stage ovarian cancer detection and monitoring for disease recurrence

(2008) Laura J. Havrilesky et al.   GYNECOLOGIC ONCOLOGY

Imaging and cancer: A review

(2008) Leonard Fass   Molecular Oncology