Publications 2024

Federico L, Malone B, Tennøe S, Chaban V, Osen JR, Gainullin M, Smorodina E, Kared H, Akbar R, Greiff V, Stratford R, Clancy T, Munthe LA (2024)
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

Gainullin M, Federico L, Røkke Osen J, Chaban V, Kared H, Alirezaylavasani A, Lund-Johansen F, Wildendahl G, Jacobsen JA, Sarwar Anjum H, Stratford R, Tennøe S, Malone B, Clancy T, Vaage JT, Henriksen K, Wüsthoff L, Munthe LA (2024)
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

Netskar H, Pfefferle A, Goodridge JP, Sohlberg E, Dufva O, Teichmann SA, Brownlie D, Michaëlsson J, Marquardt N, Clancy T, Horowitz A, Malmberg KJ (2024)
Pan-cancer profiling of tumor-infiltrating natural killer cells through transcriptional reference mapping
Nat Immunol, 25 (8), 1445-1459
DOI 10.1038/s41590-024-01884-z, PubMed 38956379

Sugita Y, Muraoka D, Demachi-Okamura A, Komuro H, Masago K, Sasaki E, Fukushima Y, Matsui T, Shinohara S, Takahashi Y, Nishida R, Takashima C, Yamaguchi T, Horio Y, Hashimoto K, Tanaka I, Hamana H, Kishi H, Miura D, Tanaka Y, Onoue K, Onoguchi K, Yamashita Y, Stratford R, Clancy T et al. (2024)
Candidate tumor-specific CD8⁺ T cell subsets identified in the malignant pleural effusion of advanced lung cancer patients by single-cell analysis
Oncoimmunology, 13 (1), 2371556
DOI 10.1080/2162402X.2024.2371556, PubMed 38952674

Sverchkova A, Burkholz S, Rubsamen R, Stratford R, Clancy T (2024)
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

Vardaxis I, Simovski B, Anzar I, Stratford R, Clancy T (2024)
Deep learning of antibody epitopes using positional permutation vectors
Comput Struct Biotechnol J, 23, 2695-2707
DOI 10.1016/j.csbj.2024.06.005, PubMed 39035832

Publications 2023

Anzar I, Malone B, Samarakoon P, Vardaxis I, Simovski B, Fontenelle H, Meza-Zepeda LA, Stratford R, Keung EZ, Burgess M, Tawbi HA, Myklebost O, Clancy T (2023)
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

Chen Z, Zhang B, Guo H, Emani P, Clancy T, Jiang C, Gerstein M, Ning X, Cheng C, Min MR (2023)
Binding peptide generation for MHC Class I proteins with deep reinforcement learning
Bioinformatics, 39 (2)
DOI 10.1093/bioinformatics/btad055, PubMed 36692135

Ellingsen EB, O'Day S, Mezheyeuski A, Gromadka A, Clancy T, Kristedja TS, Milhem M, Zakharia Y (2023)
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

Federico L, Malone B, Tennøe S, Chaban V, Osen JR, Gainullin M, Smorodina E, Kared H, Akbar R, Greiff V, Stratford R, Clancy T, Munthe LA (2023)
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

Federico L, Tvedt THA, Gainullin M, Osen JR, Chaban V, Lund KP, Tietze L, Tran TT, Lund-Johansen F, Kared H, Lind A, Vaage JT, Stratford R, Tennøe S, Malone B, Clancy T, Myhre AEL, Gedde-Dahl T, Munthe LA (2023)
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

Komuro H, Shinohara S, Fukushima Y, Demachi-Okamura A, Muraoka D, Masago K, Matsui T, Sugita Y, Takahashi Y, Nishida R, Takashima C, Ohki T, Shigematsu Y, Watanabe F, Adachi K, Fukuyama T, Hamana H, Kishi H, Miura D, Tanaka Y, Onoue K, Onoguchi K, Yamashita Y, Stratford R, Clancy T et al. (2023)
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

Nielsen M, Monberg T, Sundvold V, Albieri B, Hovgaard D, Petersen MM, Krarup-Hansen A, Met Ö, Camilio K, Clancy T, Stratford R, Sveinbjornsson B, Rekdal Ø, Junker N, Svane IM (2023)
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

Publications 2022

Anzar I, Sverchkova A, Samarakoon P, Ellingsen EB, Gaudernack G, Stratford R, Clancy T (2022)
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

Ellingsen EB, Bounova G, Kerzeli I, Anzar I, Simnica D, Aamdal E, Guren T, Clancy T, Mezheyeuski A, Inderberg EM, Mangsbo SM, Binder M, Hovig E, Gaudernack G (2022)
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

Tennøe S, Gheorghe M, Stratford R, Clancy T (2022)
The T Cell Epitope Landscape of SARS-CoV-2 Variants of Concern
Vaccines (Basel), 10 (7)
DOI 10.3390/vaccines10071123, PubMed 35891287

Publications 2020

Malone B, Simovski B, Moliné C, Cheng J, Gheorghe M, Fontenelle H, Vardaxis I, Tennøe S, Malmberg JA, Stratford R, Clancy T (2020)
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

Publications 2019

Anzar I, Sverchkova A, Stratford R, Clancy T (2019)
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

Goodridge JP, Jacobs B, Saetersmoen ML, Clement D, Hammer Q, Clancy T, Skarpen E, Brech A, Landskron J, Grimm C, Pfefferle A, Meza-Zepeda L, Lorenz S, Wiiger MT, Louch WE, Ask EH, Liu LL, Oei VYS, Kjällquist U, Linnarsson S, Patel S, Taskén K, Stenmark H, Malmberg KJ (2019)
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

Pfefferle A, Jacobs B, Netskar H, Ask EH, Lorenz S, Clancy T, Goodridge JP, Sohlberg E, Malmberg KJ (2019)
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

Sverchkova A, Anzar I, Stratford R, Clancy T (2019)
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

Publications 2018

Björklund AT, Carlsten M, Sohlberg E, Liu LL, Clancy T, Karimi M, Cooley S, Miller JS, Klimkowska M, Schaffer M, Watz E, Wikström K, Blomberg P, Wahlin BE, Palma M, Hansson L, Ljungman P, Hellström-Lindberg E, Ljunggren HG, Malmberg KJ (2018)
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

Tutturen AEV, Dørum S, Clancy T, Reims HM, Christophersen A, Lundin KEA, Sollid LM, de Souza GA, Stamnaes J (2018)
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

Publications 2017

Clancy T, Dannenfelser R, Troyanskaya O, Malmberg KJ, Hovig E, Kristensen V (2017)
Bioinformatics Approaches to Profile the Tumor Microenvironment for Immunotherapeutic Discovery
Curr Pharm Des, 23 (32), 4716-4725
DOI 10.2174/1381612823666170710154936, PubMed 28699527

Publications 2016

Björklund AT, Clancy T, Goodridge JP, Béziat V, Schaffer M, Hovig E, Ljunggren HG, Ljungman PT, Malmberg KJ (2016)
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

Clancy T, Hovig E (2016)
Profiling networks of distinct immune-cells in tumors
BMC Bioinformatics, 17 (1), 263
DOI 10.1186/s12859-016-1141-3, PubMed 27377892

Jonsson M, Ragnum HB, Julin CH, Yeramian A, Clancy T, Frikstad KM, Seierstad T, Stokke T, Matias-Guiu X, Ree AH, Flatmark K, Lyng H (2016)
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

Publications 2014

Clancy T, Hovig E (2014)
From proteomes to complexomes in the era of systems biology
Proteomics, 14 (1), 24-41
DOI 10.1002/pmic.201300230, PubMed 24243660

Clancy T, Hovig E (2014)
Differential protein network analysis of the immune cell lineage
Biomed Res Int, 2014, 363408
DOI 10.1155/2014/363408, PubMed 25309909

Nygård S, Reitan T, Clancy T, Nygaard V, Bjørnstad J, Skrbic B, Tønnessen T, Christensen G, Hovig E (2014)
Identifying pathogenic processes by integrating microarray data with prior knowledge
BMC Bioinformatics, 15, 115
DOI 10.1186/1471-2105-15-115, PubMed 24758699

Nygaard V, Prasmickaite L, Vasiliauskaite K, Clancy T, Hovig E (2014)
Melanoma brain colonization involves the emergence of a brain-adaptive phenotype
Oncoscience, 1 (1), 82-94
DOI 10.18632/oncoscience.11, PubMed 25593989

Publications 2013

Bettum IJ, Vasiliauskaite K, Nygaard V, Clancy T, Pettersen SJ, Tenstad E, Mælandsmo GM, Prasmickaite L (2013)
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

Clancy T, Rødland EA, Nygard S, Hovig E (2013)
Predicting physical interactions between protein complexes
Mol Cell Proteomics, 12 (6), 1723-34
DOI 10.1074/mcp.O112.019828, PubMed 23438732

Lando M, Wilting SM, Snipstad K, Clancy T, Bierkens M, Aarnes EK, Holden M, Stokke T, Sundfør K, Holm R, Kristensen GB, Steenbergen RD, Lyng H (2013)
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

Lorvik KB, Haabeth OA, Clancy T, Bogen B, Corthay A (2013)
Molecular profiling of tumor-specific T_H1 cells activated in vivo
Oncoimmunology, 2 (5), e24383
DOI 10.4161/onci.24383, PubMed 23762808

Sandve GK, Gundersen S, Johansen M, Glad IK, Gunathasan K, Holden L, Holden M, Liestøl K, Nygård S, Nygaard V, Paulsen J, Rydbeck H, Trengereid K, Clancy T, Drabløs F, Ferkingstad E, Kalas M, Lien T, Rye MB, Frigessi A, Hovig E (2013)
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

Publications 2011

Clancy T, Pedicini M, Castiglione F, Santoni D, Nygaard V, Lavelle TJ, Benson M, Hovig E (2011)
Immunological network signatures of cancer progression and survival
BMC Med Genomics, 4, 28
DOI 10.1186/1755-8794-4-28, PubMed 21453479

Halle C, Lando M, Svendsrud DH, Clancy T, Holden M, Sundfør K, Kristensen GB, Holm R, Lyng H (2011)
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

Sandve GK, Gundersen S, Rydbeck H, Glad IK, Holden L, Holden M, Liestøl K, Clancy T, Drabløs F, Ferkingstad E, Johansen M, Nygaard V, Tøstesen E, Frigessi A, Hovig E (2011)
The differential disease regulome
BMC Genomics, 12, 353
DOI 10.1186/1471-2164-12-353, PubMed 21736759

Ågesen TH, Berg M, Clancy T, Thiis-Evensen E, Cekaite L, Lind GE, Nesland JM, Bakka A, Mala T, Hauss HJ, Fetveit T, Vatn MH, Hovig E, Nesbakken A, Lothe RA, Skotheim RI (2011)
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

Publications 2010

Beck H, Nähse V, Larsen MS, Groth P, Clancy T, Lees M, Jørgensen M, Helleday T, Syljuåsen RG, Sørensen CS (2010)
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

Cekaite L, Clancy T, Sioud M (2010)
Increased miR-21 expression during human monocyte differentiation into DCs
Front Biosci (Elite Ed), 2 (3), 818-28
DOI 10.2741/e143, PubMed 20515755

Pedicini M, Barrenäs F, Clancy T, Castiglione F, Hovig E, Kanduri K, Santoni D, Benson M (2010)
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

Sandve GK, Gundersen S, Rydbeck H, Glad IK, Holden L, Holden M, Liestøl K, Clancy T, Ferkingstad E, Johansen M, Nygaard V, Tøstesen E, Frigessi A, Hovig E (2010)
The Genomic HyperBrowser: inferential genomics at the sequence level
Genome Biol, 11 (12), R121
DOI 10.1186/gb-2010-11-12-r121, PubMed 21182759

Publications 2007

Benson M, Steenhoff Hov DA, Clancy T, Hovig E, Rudemo M, Cardell LO (2007)
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