Original articles

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Review articles

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

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