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Items: 1 to 50 of 141

1.

Guadecitabine plus ipilimumab in unresectable melanoma: the NIBIT-M4 clinical trial.

Di Giacomo AM, Covre A, Finotello F, Rieder D, Danielli R, Sigalotti L, Giannarelli D, Petiprez F, Lacroix L, Valente M, Cutaia O, Fazio C, Amato G, Lazzeri A, Monterisi S, Miracco C, Coral S, Anichini A, Bock C, Nemc A, Oganesian A, Lowder JN, Azab M, Fridman WH, Sautes-Fridman C, Trajanoski Z, Maio M.

Clin Cancer Res. 2019 Sep 17. pii: clincanres.1335.2019. doi: 10.1158/1078-0432.CCR-19-1335. [Epub ahead of print]

PMID:
31530631
2.

Next-generation computational tools for interrogating cancer immunity.

Finotello F, Rieder D, Hackl H, Trajanoski Z.

Nat Rev Genet. 2019 Sep 12. doi: 10.1038/s41576-019-0166-7. [Epub ahead of print] Review.

PMID:
31515541
3.

LAMTOR/Ragulator regulates lipid metabolism in macrophages and foam cell differentiation.

Lamberti G, De Smet CH, Angelova M, Kremser L, Taub N, Herrmann C, Hess MW, Rainer J, Tancevski I, Schweigreiter R, Kofler R, Schmiedinger T, Vietor I, Trajanoski Z, Ejsing CS, Lindner HH, Huber LA, Stasyk T.

FEBS Lett. 2019 Aug 19. doi: 10.1002/1873-3468.13579. [Epub ahead of print]

PMID:
31423582
4.

Advancing cancer immunotherapy: a vision for the field.

de Miranda NFCC, Trajanoski Z.

Genome Med. 2019 Jul 29;11(1):51. doi: 10.1186/s13073-019-0662-6. No abstract available.

5.

Correction to: Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data.

Finotello F, Mayer C, Plattner C, Laschober G, Rieder D, Hackl H, Krogsdam A, Loncova Z, Posch W, Wilflingseder D, Sopper S, Ijsselsteijn M, Brouwer TP, Johnson D, Xu Y, Wang Y, Sanders ME, Estrada MV, Ericsson-Gonzalez P, Charoentong P, Balko J, da Cunha Carvalho de Miranda NF, Trajanoski Z.

Genome Med. 2019 Jul 29;11(1):50. doi: 10.1186/s13073-019-0655-5.

6.

Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data.

Finotello F, Mayer C, Plattner C, Laschober G, Rieder D, Hackl H, Krogsdam A, Loncova Z, Posch W, Wilflingseder D, Sopper S, Ijsselsteijn M, Brouwer TP, Johnson D, Xu Y, Wang Y, Sanders ME, Estrada MV, Ericsson-Gonzalez P, Charoentong P, Balko J, de Miranda NFDCC, Trajanoski Z.

Genome Med. 2019 May 24;11(1):34. doi: 10.1186/s13073-019-0638-6. Erratum in: Genome Med. 2019 Jul 29;11(1):50.

7.

Microbial Colonization in Adulthood Shapes the Intestinal Macrophage Compartment.

Schmidt F, Dahlke K, Batra A, Keye J, Wu H, Friedrich M, Glauben R, Ring C, Loh G, Schaubeck M, Hackl H, Trajanoski Z, Schumann M, Kühl AA, Blaut M, Siegmund B.

J Crohns Colitis. 2019 Sep 19;13(9):1173-1185. doi: 10.1093/ecco-jcc/jjz036.

PMID:
30938416
8.

A Variant of a Killer Cell Immunoglobulin-like Receptor Is Associated with Resistance to PD-1 Blockade in Lung Cancer.

Trefny MP, Rothschild SI, Uhlenbrock F, Rieder D, Kasenda B, Stanczak MA, Berner F, Kashyap AS, Kaiser M, Herzig P, Poechtrager S, Thommen DS, Geier F, Savic S, Jermann P, Alborelli I, Schaub S, Stenner F, Früh M, Trajanoski Z, Flatz L, Mertz KD, Zippelius A, Läubli H.

Clin Cancer Res. 2019 May 15;25(10):3026-3034. doi: 10.1158/1078-0432.CCR-18-3041. Epub 2019 Feb 14.

PMID:
30765392
9.

Mutational and Antigenic Landscape in Tumor Progression and Cancer Immunotherapy.

Vitale I, Sistigu A, Manic G, Rudqvist NP, Trajanoski Z, Galluzzi L.

Trends Cell Biol. 2019 May;29(5):396-416. doi: 10.1016/j.tcb.2019.01.003. Epub 2019 Feb 11. Review.

PMID:
30765144
10.

Addressing current challenges and future directions in immuno-oncology: expert perspectives from the 2017 NIBIT Foundation Think Tank, Siena, Italy.

Maio M, Coukos G, Ferrone S, Fox BA, Fridman WH, Garcia PL, Lahn M, Provendier O, Russo V, Rüttinger D, Shalabi A, Trajanoski Z, Viallet J, Wolchok JD, Ibrahim R.

Cancer Immunol Immunother. 2019 Jan;68(1):1-9. doi: 10.1007/s00262-018-2285-y. Epub 2018 Dec 18.

PMID:
30564889
11.

Adoptive T Cell Therapy: New Avenues Leading to Safe Targets and Powerful Allies.

Hammerl D, Rieder D, Martens JWM, Trajanoski Z, Debets R.

Trends Immunol. 2018 Nov;39(11):921-936. doi: 10.1016/j.it.2018.09.004. Epub 2018 Oct 9. Review.

PMID:
30309702
12.

Nuclear receptor NR2F6 inhibition potentiates responses to PD-L1/PD-1 cancer immune checkpoint blockade.

Klepsch V, Hermann-Kleiter N, Do-Dinh P, Jakic B, Offermann A, Efremova M, Sopper S, Rieder D, Krogsdam A, Gamerith G, Perner S, Tzankov A, Trajanoski Z, Wolf D, Baier G.

Nat Commun. 2018 Apr 18;9(1):1538. doi: 10.1038/s41467-018-04004-2.

13.

Quantifying tumor-infiltrating immune cells from transcriptomics data.

Finotello F, Trajanoski Z.

Cancer Immunol Immunother. 2018 Jul;67(7):1031-1040. doi: 10.1007/s00262-018-2150-z. Epub 2018 Mar 14. Review.

14.

3D-cultivation of NSCLC cell lines induce gene expression alterations of key cancer-associated pathways and mimic in-vivo conditions.

Gamerith G, Rainer J, Huber JM, Hackl H, Trajanoski Z, Koeck S, Lorenz E, Kern J, Kofler R, Kelm JM, Zwierzina H, Amann A.

Oncotarget. 2017 Nov 6;8(68):112647-112661. doi: 10.18632/oncotarget.22636. eCollection 2017 Dec 22.

15.

Targeting immune checkpoints potentiates immunoediting and changes the dynamics of tumor evolution.

Efremova M, Rieder D, Klepsch V, Charoentong P, Finotello F, Hackl H, Hermann-Kleiter N, Löwer M, Baier G, Krogsdam A, Trajanoski Z.

Nat Commun. 2018 Jan 2;9(1):32. doi: 10.1038/s41467-017-02424-0.

16.

Neoantigens Generated by Individual Mutations and Their Role in Cancer Immunity and Immunotherapy.

Efremova M, Finotello F, Rieder D, Trajanoski Z.

Front Immunol. 2017 Nov 28;8:1679. doi: 10.3389/fimmu.2017.01679. eCollection 2017. Review.

17.

Intratumoral HPV16-Specific T Cells Constitute a Type I-Oriented Tumor Microenvironment to Improve Survival in HPV16-Driven Oropharyngeal Cancer.

Welters MJP, Ma W, Santegoets SJAM, Goedemans R, Ehsan I, Jordanova ES, van Ham VJ, van Unen V, Koning F, van Egmond SI, Charoentong P, Trajanoski Z, van der Velden LA, van der Burg SH.

Clin Cancer Res. 2018 Feb 1;24(3):634-647. doi: 10.1158/1078-0432.CCR-17-2140. Epub 2017 Oct 10.

18.

TIminer: NGS data mining pipeline for cancer immunology and immunotherapy.

Tappeiner E, Finotello F, Charoentong P, Mayer C, Rieder D, Trajanoski Z.

Bioinformatics. 2017 Oct 1;33(19):3140-3141. doi: 10.1093/bioinformatics/btx377.

19.

New strategies for cancer immunotherapy: targeting regulatory T cells.

Finotello F, Trajanoski Z.

Genome Med. 2017 Jan 27;9(1):10. doi: 10.1186/s13073-017-0402-8.

20.

Reduced CD62L Expression on T Cells and Increased Soluble CD62L Levels Predict Molecular Response to Tyrosine Kinase Inhibitor Therapy in Early Chronic-Phase Chronic Myelogenous Leukemia.

Sopper S, Mustjoki S, White D, Hughes T, Valent P, Burchert A, Gjertsen BT, Gastl G, Baldauf M, Trajanoski Z, Giles F, Hochhaus A, Ernst T, Schenk T, Janssen JJ, Ossenkoppele GJ, Porkka K, Wolf D.

J Clin Oncol. 2017 Jan 10;35(2):175-184. Epub 2016 Nov 7.

PMID:
28056193
21.

Pan-cancer Immunogenomic Analyses Reveal Genotype-Immunophenotype Relationships and Predictors of Response to Checkpoint Blockade.

Charoentong P, Finotello F, Angelova M, Mayer C, Efremova M, Rieder D, Hackl H, Trajanoski Z.

Cell Rep. 2017 Jan 3;18(1):248-262. doi: 10.1016/j.celrep.2016.12.019.

22.

TIS7 induces transcriptional cascade of methylosome components required for muscle differentiation.

Lammirato A, Patsch K, Feiereisen F, Maly K, Nofziger C, Paulmichl M, Hackl H, Trajanoski Z, Valovka T, Huber LA, Vietor I.

BMC Biol. 2016 Oct 25;14(1):95.

23.

Differential cytokine sensitivities of STAT5-dependent enhancers rely on Stat5 autoregulation.

Willi M, Yoo KH, Wang C, Trajanoski Z, Hennighausen L.

Nucleic Acids Res. 2016 Dec 1;44(21):10277-10291. Epub 2016 Sep 30.

24.

Computational genomics tools for dissecting tumour-immune cell interactions.

Hackl H, Charoentong P, Finotello F, Trajanoski Z.

Nat Rev Genet. 2016 Jul 4;17(8):441-58. doi: 10.1038/nrg.2016.67. Review.

PMID:
27376489
25.

Loss of adipose triglyceride lipase is associated with human cancer and induces mouse pulmonary neoplasia.

Al-Zoughbi W, Pichler M, Gorkiewicz G, Guertl-Lackner B, Haybaeck J, Jahn SW, Lackner C, Liegl-Atzwanger B, Popper H, Schauer S, Nusshold E, Kindt AS, Trajanoski Z, Speicher MR, Haemmerle G, Zimmermann R, Zechner R, Vesely PW, Hoefler G.

Oncotarget. 2016 Jun 7;7(23):33832-40. doi: 10.18632/oncotarget.9418.

26.

Impact of the Chromatin Remodeling Factor CHD1 on Gut Microbiome Composition of Drosophila melanogaster.

Sebald J, Willi M, Schoberleitner I, Krogsdam A, Orth-Höller D, Trajanoski Z, Lusser A.

PLoS One. 2016 Apr 19;11(4):e0153476. doi: 10.1371/journal.pone.0153476. eCollection 2016.

27.

The colorectal cancer immune paradox revisited.

Angelova M, Charoentong P, Hackl H, Trajanoski Z.

Oncoimmunology. 2015 Aug 27;5(2):e1078058. eCollection 2016 Feb.

28.

Integrative Analyses of Colorectal Cancer Show Immunoscore Is a Stronger Predictor of Patient Survival Than Microsatellite Instability.

Mlecnik B, Bindea G, Angell HK, Maby P, Angelova M, Tougeron D, Church SE, Lafontaine L, Fischer M, Fredriksen T, Sasso M, Bilocq AM, Kirilovsky A, Obenauf AC, Hamieh M, Berger A, Bruneval P, Tuech JJ, Sabourin JC, Le Pessot F, Mauillon J, Rafii A, Laurent-Puig P, Speicher MR, Trajanoski Z, Michel P, Sesboüe R, Frebourg T, Pagès F, Valge-Archer V, Latouche JB, Galon J.

Immunity. 2016 Mar 15;44(3):698-711. doi: 10.1016/j.immuni.2016.02.025.

29.

Serum Autoantibodies in Chronic Prostate Inflammation in Prostate Cancer Patients.

Schlick B, Massoner P, Lueking A, Charoentong P, Blattner M, Schaefer G, Marquart K, Theek C, Amersdorfer P, Zielinski D, Kirchner M, Trajanoski Z, Rubin MA, Müllner S, Schulz-Knappe P, Klocker H.

PLoS One. 2016 Feb 10;11(2):e0147739. doi: 10.1371/journal.pone.0147739. eCollection 2016.

30.

meRanTK: methylated RNA analysis ToolKit.

Rieder D, Amort T, Kugler E, Lusser A, Trajanoski Z.

Bioinformatics. 2016 Mar 1;32(5):782-5. doi: 10.1093/bioinformatics/btv647. Epub 2015 Nov 4.

PMID:
26543174
31.

miR-22 and miR-29a Are Members of the Androgen Receptor Cistrome Modulating LAMC1 and Mcl-1 in Prostate Cancer.

Pasqualini L, Bu H, Puhr M, Narisu N, Rainer J, Schlick B, Schäfer G, Angelova M, Trajanoski Z, Börno ST, Schweiger MR, Fuchsberger C, Klocker H.

Mol Endocrinol. 2015 Jul;29(7):1037-54. doi: 10.1210/me.2014-1358. Epub 2015 Jun 8.

32.

The coordinated action of the MVB pathway and autophagy ensures cell survival during starvation.

Müller M, Schmidt O, Angelova M, Faserl K, Weys S, Kremser L, Pfaffenwimmer T, Dalik T, Kraft C, Trajanoski Z, Lindner H, Teis D.

Elife. 2015 Apr 22;4:e07736. doi: 10.7554/eLife.07736.

33.

Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy.

Angelova M, Charoentong P, Hackl H, Fischer ML, Snajder R, Krogsdam AM, Waldner MJ, Bindea G, Mlecnik B, Galon J, Trajanoski Z.

Genome Biol. 2015 Mar 31;16:64. doi: 10.1186/s13059-015-0620-6.

34.

Immediate T-Helper 17 Polarization Upon Triggering CD11b/c on HIV-Exposed Dendritic Cells.

Wilflingseder D, Schroll A, Hackl H, Gallasch R, Frampton D, Lass-Flörl C, Pancino G, Saez-Cirion A, Lambotte O, Weiss L, Kellam P, Trajanoski Z, Geijtenbeek T, Weiss G, Posch W.

J Infect Dis. 2015 Jul 1;212(1):44-56. doi: 10.1093/infdis/jiv014. Epub 2015 Jan 12.

PMID:
25583169
35.

Personalized Oncology Suite: integrating next-generation sequencing data and whole-slide bioimages.

Dander A, Baldauf M, Sperk M, Pabinger S, Hiltpolt B, Trajanoski Z.

BMC Bioinformatics. 2014 Sep 18;15:306. doi: 10.1186/1471-2105-15-306.

36.

3DSpectra: A 3-dimensional quantification algorithm for LC-MS labeled profile data.

Nasso S, Hartler J, Trajanoski Z, Di Camillo B, Mechtler K, Toffolo GM.

J Proteomics. 2015 Jan 1;112:156-65. doi: 10.1016/j.jprot.2014.08.017. Epub 2014 Sep 16.

PMID:
25218586
37.

Somatically mutated tumor antigens in the quest for a more efficacious patient-oriented immunotherapy of cancer.

Trajanoski Z, Maccalli C, Mennonna D, Casorati G, Parmiani G, Dellabona P.

Cancer Immunol Immunother. 2015 Jan;64(1):99-104. doi: 10.1007/s00262-014-1599-7. Epub 2014 Aug 28. Review.

PMID:
25164877
38.

SPARQLGraph: a web-based platform for graphically querying biological Semantic Web databases.

Schweiger D, Trajanoski Z, Pabinger S.

BMC Bioinformatics. 2014 Aug 15;15:279. doi: 10.1186/1471-2105-15-279.

39.

Molecular aspects of adipoepithelial transdifferentiation in mouse mammary gland.

Prokesch A, Smorlesi A, Perugini J, Manieri M, Ciarmela P, Mondini E, Trajanoski Z, Kristiansen K, Giordano A, Bogner-Strauss JG, Cinti S.

Stem Cells. 2014 Oct;32(10):2756-66. doi: 10.1002/stem.1756.

40.

High STAT1 mRNA levels but not its tyrosine phosphorylation are associated with macrophage infiltration and bad prognosis in breast cancer.

Tymoszuk P, Charoentong P, Hackl H, Spilka R, Müller-Holzner E, Trajanoski Z, Obrist P, Revillion F, Peyrat JP, Fiegl H, Doppler W.

BMC Cancer. 2014 Apr 12;14:257. doi: 10.1186/1471-2407-14-257.

41.

MEMOSys 2.0: an update of the bioinformatics database for genome-scale models and genomic data.

Pabinger S, Snajder R, Hardiman T, Willi M, Dander A, Trajanoski Z.

Database (Oxford). 2014 Feb 14;2014:bau004. doi: 10.1093/database/bau004. Print 2014.

42.

SeqBench: integrated solution for the management and analysis of exome sequencing data.

Dander A, Pabinger S, Sperk M, Fischer M, Stocker G, Trajanoski Z.

BMC Res Notes. 2014 Jan 20;7:43. doi: 10.1186/1756-0500-7-43.

43.

Mathematical models for translational and clinical oncology.

Gallasch R, Efremova M, Charoentong P, Hackl H, Trajanoski Z.

J Clin Bioinforma. 2013 Nov 7;3(1):23. doi: 10.1186/2043-9113-3-23.

44.

microRNAs in nociceptive circuits as predictors of future clinical applications.

Kress M, Hüttenhofer A, Landry M, Kuner R, Favereaux A, Greenberg D, Bednarik J, Heppenstall P, Kronenberg F, Malcangio M, Rittner H, Uçeyler N, Trajanoski Z, Mouritzen P, Birklein F, Sommer C, Soreq H.

Front Mol Neurosci. 2013 Oct 17;6:33. doi: 10.3389/fnmol.2013.00033. Review.

45.

Spatiotemporal dynamics of intratumoral immune cells reveal the immune landscape in human cancer.

Bindea G, Mlecnik B, Tosolini M, Kirilovsky A, Waldner M, Obenauf AC, Angell H, Fredriksen T, Lafontaine L, Berger A, Bruneval P, Fridman WH, Becker C, Pagès F, Speicher MR, Trajanoski Z, Galon J.

Immunity. 2013 Oct 17;39(4):782-95. doi: 10.1016/j.immuni.2013.10.003.

46.

Co-expressed genes prepositioned in spatial neighborhoods stochastically associate with SC35 speckles and RNA polymerase II factories.

Rieder D, Ploner C, Krogsdam AM, Stocker G, Fischer M, Scheideler M, Dani C, Amri EZ, Müller WG, McNally JG, Trajanoski Z.

Cell Mol Life Sci. 2014 May;71(9):1741-59. doi: 10.1007/s00018-013-1465-3. Epub 2013 Sep 12.

PMID:
24026398
47.

GPViz: dynamic visualization of genomic regions and variants affecting protein domains.

Snajder R, Trajanoski Z, Hackl H.

Bioinformatics. 2013 Sep 1;29(17):2195-6. doi: 10.1093/bioinformatics/btt354. Epub 2013 Jun 19.

PMID:
23782613
48.

Identification of microRNA-mRNA functional interactions in UVB-induced senescence of human diploid fibroblasts.

Greussing R, Hackl M, Charoentong P, Pauck A, Monteforte R, Cavinato M, Hofer E, Scheideler M, Neuhaus M, Micutkova L, Mueck C, Trajanoski Z, Grillari J, Jansen-Dürr P.

BMC Genomics. 2013 Apr 4;14:224. doi: 10.1186/1471-2164-14-224.

49.

Genome-scale model management and comparison.

Pabinger S, Trajanoski Z.

Methods Mol Biol. 2013;985:3-16. doi: 10.1007/978-1-62703-299-5_1.

PMID:
23417796
50.

A survey of tools for variant analysis of next-generation genome sequencing data.

Pabinger S, Dander A, Fischer M, Snajder R, Sperk M, Efremova M, Krabichler B, Speicher MR, Zschocke J, Trajanoski Z.

Brief Bioinform. 2014 Mar;15(2):256-78. doi: 10.1093/bib/bbs086. Epub 2013 Jan 21.

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