Publications by Trevor Clancy
42 publications found
Original articles
Integrative HLA typing of tumor and adjacent normal tissue can reveal insights into the tumor immune response
BMC Med Genomics, 17 (1), 37
DOI 10.1186/s12920-024-01808-8, PubMed 38281021
People who use drugs show no increase in pre-existing T-cell cross-reactivity toward SARS-CoV-2 but develop a normal polyfunctional T-cell response after standard mRNA vaccination
Front Immunol, 14, 1235210
DOI 10.3389/fimmu.2023.1235210, PubMed 38299149
LTX-315 and adoptive cell therapy using tumor-infiltrating lymphocytes generate tumor specific T cells in patients with metastatic soft tissue sarcoma
Oncoimmunology, 13 (1), 2290900
DOI 10.1080/2162402X.2023.2290900, PubMed 38125722
Experimental validation of immunogenic SARS-CoV-2 T cell epitopes identified by artificial intelligence
Front Immunol, 14, 1265044
DOI 10.3389/fimmu.2023.1265044, PubMed 38045681
The interplay between neoantigens and immune cells in sarcomas treated with checkpoint inhibition
Front Immunol, 14, 1226445
DOI 10.3389/fimmu.2023.1226445, PubMed 37799721
Clinical Activity of Combined Telomerase Vaccination and Pembrolizumab in Advanced Melanoma: Results from a Phase I Trial
Clin Cancer Res, 29 (16), 3026-3036
DOI 10.1158/1078-0432.CCR-23-0416, PubMed 37378632
Single-cell sequencing on CD8+ TILs revealed the nature of exhausted T cells recognizing neoantigen and cancer/testis antigen in non-small cell lung cancer
J Immunother Cancer, 11 (8)
DOI 10.1136/jitc-2023-007180, PubMed 37544663
Robust spike-specific CD4+ and CD8+ T cell responses in SARS-CoV-2 vaccinated hematopoietic cell transplantation recipients: a prospective, cohort study
Front Immunol, 14, 1210899
DOI 10.3389/fimmu.2023.1210899, PubMed 37503339
Binding peptide generation for MHC Class I proteins with deep reinforcement learning
Bioinformatics, 39 (2)
DOI 10.1093/bioinformatics/btad055, PubMed 36692135
Characterization of the T cell receptor repertoire and melanoma tumor microenvironment upon combined treatment with ipilimumab and hTERT vaccination
J Transl Med, 20 (1), 419
DOI 10.1186/s12967-022-03624-z, PubMed 36089578
The T Cell Epitope Landscape of SARS-CoV-2 Variants of Concern
Vaccines (Basel), 10 (7)
DOI 10.3390/vaccines10071123, PubMed 35891287
Personalized HLA typing leads to the discovery of novel HLA alleles and tumor-specific HLA variants
HLA, 99 (4), 313-327
DOI 10.1111/tan.14562, PubMed 35073457
Artificial intelligence predicts the immunogenic landscape of SARS-CoV-2 leading to universal blueprints for vaccine designs
Sci Rep, 10 (1), 22375
DOI 10.1038/s41598-020-78758-5, PubMed 33361777
Intra-lineage Plasticity and Functional Reprogramming Maintain Natural Killer Cell Repertoire Diversity
Cell Rep, 29 (8), 2284-2294.e4
DOI 10.1016/j.celrep.2019.10.058, PubMed 31747601
Improved HLA typing of Class I and Class II alleles from next-generation sequencing data
HLA, 94 (6), 504-513
DOI 10.1111/tan.13685, PubMed 31496113
NeoMutate: an ensemble machine learning framework for the prediction of somatic mutations in cancer
BMC Med Genomics, 12 (1), 63
DOI 10.1186/s12920-019-0508-5, PubMed 31096972
Remodeling of secretory lysosomes during education tunes functional potential in NK cells
Nat Commun, 10 (1), 514
DOI 10.1038/s41467-019-08384-x, PubMed 30705279
Characterization of the Small Intestinal Lesion in Celiac Disease by Label-Free Quantitative Mass Spectrometry
Am J Pathol, 188 (7), 1563-1579
DOI 10.1016/j.ajpath.2018.03.017, PubMed 29684362
Complete Remission with Reduction of High-Risk Clones following Haploidentical NK-Cell Therapy against MDS and AML
Clin Cancer Res, 24 (8), 1834-1844
DOI 10.1158/1078-0432.CCR-17-3196, PubMed 29444931
Hypoxia-independent gene expression signature associated with radiosensitisation of prostate cancer cell lines by histone deacetylase inhibition
Br J Cancer, 115 (8), 929-939
DOI 10.1038/bjc.2016.278, PubMed 27599042
Profiling networks of distinct immune-cells in tumors
BMC Bioinformatics, 17 (1), 263
DOI 10.1186/s12859-016-1141-3, PubMed 27377892
Naive Donor NK Cell Repertoires Associated with Less Leukemia Relapse after Allogeneic Hematopoietic Stem Cell Transplantation
J Immunol, 196 (3), 1400-11
DOI 10.4049/jimmunol.1501434, PubMed 26746188
Identifying pathogenic processes by integrating microarray data with prior knowledge
BMC Bioinformatics, 15, 115
DOI 10.1186/1471-2105-15-115, PubMed 24758699
Melanoma brain colonization involves the emergence of a brain-adaptive phenotype
Oncoscience, 1 (1), 82-94
DOI 10.18632/oncoscience.11, PubMed 25593989
Differential protein network analysis of the immune cell lineage
Biomed Res Int, 2014, 363408
DOI 10.1155/2014/363408, PubMed 25309909
Metastasis-associated protein S100A4 induces a network of inflammatory cytokines that activate stromal cells to acquire pro-tumorigenic properties
Cancer Lett, 344 (1), 28-39
DOI 10.1016/j.canlet.2013.10.036, PubMed 24215866
Molecular profiling of tumor-specific TH1 cells activated in vivo
Oncoimmunology, 2 (5), e24383
DOI 10.4161/onci.24383, PubMed 23762808
The Genomic HyperBrowser: an analysis web server for genome-scale data
Nucleic Acids Res, 41 (Web Server issue), W133-41
DOI 10.1093/nar/gkt342, PubMed 23632163
Identification of eight candidate target genes of the recurrent 3p12-p14 loss in cervical cancer by integrative genomic profiling
J Pathol, 230 (1), 59-69
DOI 10.1002/path.4168, PubMed 23335387
Predicting physical interactions between protein complexes
Mol Cell Proteomics, 12 (6), 1723-34
DOI 10.1074/mcp.O112.019828, PubMed 23438732
The differential disease regulome
BMC Genomics, 12, 353
DOI 10.1186/1471-2164-12-353, PubMed 21736759
Membranous expression of ectodomain isoforms of the epidermal growth factor receptor predicts outcome after chemoradiotherapy of lymph node-negative cervical cancer
Clin Cancer Res, 17 (16), 5501-12
DOI 10.1158/1078-0432.CCR-11-0297, PubMed 21737508
CLC and IFNAR1 are differentially expressed and a global immunity score is distinct between early- and late-onset colorectal cancer
Genes Immun, 12 (8), 653-62
DOI 10.1038/gene.2011.43, PubMed 21716316
Immunological network signatures of cancer progression and survival
BMC Med Genomics, 4, 28
DOI 10.1186/1755-8794-4-28, PubMed 21453479
Combining network modeling and gene expression microarray analysis to explore the dynamics of Th1 and Th2 cell regulation
PLoS Comput Biol, 6 (12), e1001032
DOI 10.1371/journal.pcbi.1001032, PubMed 21187905
Increased miR-21 expression during human monocyte differentiation into DCs
Front Biosci (Elite Ed), 2 (3), 818-28
DOI 10.2741/e143, PubMed 20515755
Regulators of cyclin-dependent kinases are crucial for maintaining genome integrity in S phase
J Cell Biol, 188 (5), 629-38
DOI 10.1083/jcb.200905059, PubMed 20194642
The Genomic HyperBrowser: inferential genomics at the sequence level
Genome Biol, 11 (12), R121
DOI 10.1186/gb-2010-11-12-r121, PubMed 21182759
Connectivity can be used to identify key genes in DNA microarray data: a study based on gene expression in nasal polyps before and after treatment with glucocorticoids
Acta Otolaryngol, 127 (10), 1074-9
DOI 10.1080/00016480701200277, PubMed 17851899
Review articles
Bioinformatics Approaches to Profile the Tumor Microenvironment for Immunotherapeutic Discovery
Curr Pharm Des, 23 (32), 4716-4725
DOI 10.2174/1381612823666170710154936, PubMed 28699527
From proteomes to complexomes in the era of systems biology
Proteomics, 14 (1), 24-41
DOI 10.1002/pmic.201300230, PubMed 24243660
Other articles
Corrigendum: Experimental validation of immunogenic SARS-CoV-2 T cell epitopes identified by artificial intelligence
Front Immunol, 15, 1377041
DOI 10.3389/fimmu.2024.1377041, PubMed 38449865