Publications
2026
Marteau V*, Nemati N*, Handler K*, Raju D, Kirchmair A, Rieder D, Kvalem Soto E, Fotakis G, De Lange G, Carollo S, Boeck N, Rossi A, Daum S, Scheiber A, Amann A, Seeber A, Gasser E, Ormanns S, Günther M, Martowicz A, Loncova Z, Lamberti G, Krogsdam AM, Carlet M, Horvath L, Eling MT, Fazilaty H, Valenta T, Sturm G, Sopper S, Pircher A, Stoitzner P, Wild PJ, Welker P, May PJ, Ziegler P, Tschurtschenthaler M, Neureiter D, Huemer F, Greil R, Weiss L, Ijsselsteijn M, de Miranda NFCC, Wolf D*, Arnold IC*, Salcher S*, Trajanoski Z*. Single-cell integration and multi-modal profiling reveals phenotypes and spatial organization of neutrophils in colorectal cancer. Cancer Cell. 2026. 44:146-165. https://doi.org/10.1016/j.ccell.2025.12.003
2025
Boeck N, Grubwieser P, Glueckert R, Soto EK, Sonnweber T, Hoffmann A, Hilbe R, Dichtl S, Posch W, Nairz M, Theurl I, Trajanoski Z, Weiss G. The role of ciliary function in airway epithelial defense against Pseudomonas aeruginosa. Med Microbiol Immunol. 2025. 215:3. https://doi.org/10.1007/s00430-025-00865-9
Dingfelder J, Pereyra D, Riha M, Becker N, Rauter L, Hackl H, Müller JF, Hammer-Purgstall F, Aiad M, Eichelter J, Starlinger P, Silberhumer GR, Salat A, Berlakovich GA, Györi G, Soliman T. HTK is a viable UW alternative for hypothermic oxygenated machine perfusion of liver grafts supporting a single-solution protocol. J Clin Med. 2026. 15:112. https://doi.org/10.3390/jcm15010112
Damisch E, Brunner E, Nommensen L, Neumann L, Fotakis G, Trajanoski Z, Sopper S, Schäfer G, Puhr M, Heidegger I, Kruithof-de Julio M, Sampson N. Optimised dissociation and multimodal profiling of prostate cancer stroma reveal fibromuscular cell heterogeneity with clinical correlates. Front Cell Dev Biol. 2025. 13:1653780. https://doi.org/10.3389/fcell.2025.1653780
Brunner E, Damisch E, Groninger ME, Baschieri F, Tyckaert F, Nommensen L, Neumann L, Fotakis G, Trajanoski Z, Schäfer G, Puhr M, Heidegger I, Ausserlechner MJ, Ploner C, Karkampouna S, Bonollo F, Julio MK, Sampson N. Unraveling the YAP1-TGFβ1 axis: a key driver of androgen receptor loss in prostate cancer-associated fibroblasts. J Exp Clin Cancer Res. 2025. https://doi.org/10.1186/s13046-025-03578-2
Steger K, Fiegl H, Rungger K, Leitner K, Tsibulak I, Feroz B, Ebner C, Marth C, Hackl H*, Zeimet AG*. The role of plasmacytoid dendritic cells in the immune contexture of TP53-mutated high-grade serous ovarian cancer. Cancers. 2025. 17:3877. https://doi.org/10.3390/cancers17233877
Amor M, Diaz M, Fürlinger A, Svecla M, Bianco V, Dobrijević A, Akhmetshina A, Vujić N, Schooltink L, Korbelius M, Hirtl M, Bürger M, Pirchheim A, Schwarz B, Rainer S, Schauer S, Beretta G, Goessler W, Kolb D, Hoefler G, Hackl H, Madreiter-Sokolowski C, Abdellatif M, Norata GN, Kratky D. Deletion of MMP12 improves energy metabolism and brown adipose tissue function in mice prone to cardiometabolic diseases. J Lipid Res. 2025. https://doi.org/10.1016/j.jlr.2025.100951
Nemati N, Böck N, Trajanoski Z. Patient-derived models of tumor-immune cell interactions. Methods Cell Biol. 2025. https://doi.org/10.1016/bs.mcb.2025.10.001
Meyer M*, Grabherr F*, Plattner C*, Hadjihannas MV, Rao Z, Marteau V, López-Agudelo VA, Schwärzler J, Mayr L, Jukic A, Scheffauer L, Zundel L, Enrich B, Pfister A, Simonini A, Grander C, Hilbe R, Haschka D, Zollner A, Vouk K, Moser P, Hess MW, Nemati N, Rieder D, Sommer F, Rosenstiel P, Ran Q, Blumberg RS, Kaser A, Rieder F, Koeberle A, Becker C, Atreya A, Kühl AA, Siegmund B, Franke A, The IBDome consortium, Tilg H, Trajanoski Z*, Adolph TE*. Metabolic stress sensing by epithelial RXRα links Westernization of diet with Crohn’s disease. Cell Metab. 2025. https://doi.org/10.1016/j.cmet.2025.11.008
Loncova Z, Trajanoski Z, Rieder D. Analysis of the tumor microenvironment using imaging mass cytometry data. Methods Cell Biol. 2025. 199:63-90 https://doi.org/10.1016/bs.mcb.2025.03.00641106942
Danklmaier S, Vijver SV, Pipperger L, Floriani G, Perro L, Konrad V, Hofer T, Hackl H, Das K, Wollmann G. Newly identified oncolytic VSV-GP-specific CD8+ T cell epitopes for monitoring of anti-viral immune responses in the BALB/c mouse model. Mol Ther Oncol. 2025. 33:201072. https://doi.org/10.1016/j.omton.2025.201072
Schindlmaier K, Haitzmann T, Bubalo V, Konrad B, Jelwan J, Bluemel G, Rittchen S, Jäger V, Dengler MA, Brcic L, Lindenmann J, Marsh LM, Eichmann TO, Kirchmair A, Trajanoski Z, Kargl J, Muñoz-Pinedo C, Leithner K. Metabolic Adaptation of Glucose-Deprived Macrophages Involves Partial Gluconeogenesis. Proc Natl Acad Sci U S A. 2025. in press
Ausserhofer M, Rieder D, Finotello F. Comprehensive prediction of tumor neoantigens with nextNEOpi. Methods Cell Biol. 2025. 196:113-137. https://doi.org/10.1016/bs.mcb.2025.01.007
Mayr L, Schwärzler J, Scheffauer L, Rao Z, Rieder D, Grabherr F, Meyer M, Scheler J, Jukic A, Zundel L, Wieser V, Zollner A, Simonini A, Auer S, Amann L, Philipp M, Leierer J, Hilbe R, Weiss G, Moser P, Rosenstiel P, Ran Q, Blumberg RS, Kaser A, Koeberle A, Trajanoski Z, Tilg H, Adolph TE. Chronic enteritis triggered by diet Westernization is driven by epithelial ATG16L1-mediated autophagy. Autophagy. 2025. https://doi.org/10.1080/15548627.2025.2600906
Delazer I, Bauer I, Rummel T, Nykiel K, Rieder D, Fickl M, Tumler V, Razkova A, Schaefer M, Scheed T, Erlacher M, Erhard F, Micura R, Lusser A. mRNA turnover dynamics is affected by cell differentiation and loss of the cytosine methyltransferase Nsun2. Nucleic Acids Res. 2025. in press
Rumpf B, Santol J, Kern AE, Ammann M, Probst J, Baumgartner R, Jankoschek AS, Podrascanin V, Lehner F, Huber FX, Pereyra D, Ortmayr G, Dong Y, Petschnak S, Wolf B, Assinger A, Hackl H, Gilg S, Gruenberger T, Starlinger P. PNPLA3 polymorphism worsens chemotherapy associated liver injury and affects overall survival in colorectal cancer patients with liver metastasis undergoing hepatic resection. EBioMedicine. 2025. 120:105928. https://doi.org/10.1016/j.ebiom.2025.105928
Jukic A, Hilbe R, Zundel L, Willeit P, Faserl K, Plattner C, Zollner A, Meyer M, Siegmund K, Klepsch V, Marteau V, Vila AV, Schwärzler J, Vouk K, Kozsar A, Rieder D, Weichberger A, Sarg B, Grabherr F, Mayr L, Moser P, Nemati N, Scholl-Bürgi S, Karall D, Vogel GF, Welz L, Aldrian D, Koch R, Pfister A, Ran Q, Kaser A, Blumberg RS, Tancevski I, Sommer F, Bacher P, Rosenstiel P, Aden K, Baier G, Bakiri L, Müller T, Weiss G, The IBDome Consortium, Weersma RK, Trajanoski Z, Wagner EF, Tilg H, Adolph TE. Fecal detection of calprotectin dimers links IBD activity with chronicity of intestinal inflammation. Gastroenterology. 2025. in press
Ausserhofer M, Rieder D, Facciolla M, Gronauer R, Lamberti G, Lisandrelli R, Pellegatta S, Trajanoski Z, Finotello F. NovumRNA: accurate prediction of non-canonical tumor antigens from RNA sequencing data. iScience. 2025. in press
Heregger R, Huemer F, Greil R, Canadas-Ortega M, Posselt G, Ijsselsteijn ME, Plattner C, Rieder D, Trajanoski Z, Krogsdam A, Klieser E, Neureiter D, Wessler S, Weiss L. Impact of Fusobacterium nucleatum on Immune Cell Interactions and Gene Expression in Colorectal Cancer: A Retrospective Cohort Study. Front Immunol. 2025. 16:1629014. https://doi.org/10.3389/fimmu.2025.1629014
Meyer M, Gruber P, Plattner C, Enrich B, Zollner A, Jukic A, Effenberger M, Grander C, Tilg H, Grabherr F. Hepatic expression of ACBP is a prognostic marker for weight loss after bariatric surgery. Biomolecules. 2025. 15:1173. https://doi.org/10.3390/biom15081173
Trebo M, Maurer T, Krendl FJ, Salcher S, Martowicz A, Hautz T, Sopper S, Amann A, Cardini B, Poelsler LH, Mair A, Hofmann J, Meszaros AT, Hermann M, Günther M, Ormanns S, Trajanoski Z, Schneeberger S, Wolf D, Oberhuber R, Pircher A. Ex vivo modeling of human colorectal cancer liver metastasis by normotheric machine perfusion. Mol Cancer. 2025. in press
Bauer M, Vaxevanis C, Jaekel N, Hackl H, Wilfer A, Zoellig C, Haemmerle M, Müller-Tidow C, Al-Ali HK, Seliger B, Wickenhauser C. Association of the composition of the bone marrow tumor microenvironment in BCR::ABL1-negative myeloproliferative neoplasms with IFN-g signaling and driver mutations. Leukemia. 2025. 39. 2391–2405. https://doi.org/10.1038/s41375-025-02706-3
Dong Y, Gregory LA, Podrascanin V, Santol J, Ammann M, Pereyra D, Hackl H, Li Z, Truty MJ, Warner SG, Smoot RL, Gruenberger T, Nagorney DM, Starlinger PP. Preoperative von Willebrand Factor is an independent predictive biomarker for posthepatectomy liver failure – a multivariable model with APRI+ALBI. Liver Transpl. 2025. https://doi.org/10.1097/lvt.0000000000000676
Cineus R, Luo Y, Saliutina M, Manna S, Cancino CA, Velasco Blázquez L, Wang L, Bösel D, Abdelrahman A, Klementowicz JE, Scherl A, Hainbuch S, Bréart B, Kwon G, Konopka A, Guerra GM, von Coburg E, Gerbeth L, Roels J, Heinrich F, Müller N, Durek P, Deigendesch N, Ziai J, Hung J, Conrad T; TRR241 IBDome Consortium; Kühl AA, Wirtz S, Löhning M, Keir M, Diefenbach A, Mashreghi MF, Siegmund B, Schumann M, Romagnani C, West NR, Hegazy AN. The IL-22-oncostatin M axis promotes intestinal inflammation and tumorigenesis. Nat Immunol. 2025. 26:837–853. https://doi.org/10.1038/s41590-025-02149-z
Petroni G, Galassi C, Gouin KH, Chen HH, Buque A, Bloy N, Yamazaki T, Sato A, Beltrán-Visiedo, Campia G, Jiménez-Cortegana C, Shah A, Kirchmair A, Massa C, Wickenhauser C, de Andrea CE, Navarro-Rubio B, Serrano-Mendioroz I, Navarro Manzano E, Satty AM, Rippon B, Finotello F, Trajanoski Z, Kathy Zhou X, Scandura JM, García-Martínez E, Ayala de la Peña F, Rodríguez-Ruiz ME, Seliger B, Sánchez-Margalet V, de la Cruz-Merino L, Basho RK, Shiao SL, McArthur HL, Formenti SC, Knott SRV, Galluzzi L. IL17A-secreting γδ T cells promote resistance to CDK4/6 inhibitors in HR+HER2-breast cancer via CX3CR1+ macrophages. Nat Cancer. 2025. 6:1656–1675. https://doi.org/10.1038/s43018-025-01007-z
Erkert L, Kabisch M, Gamez-Belmonte R, Gonzalez-Acera M, Patankar JV, Schödel L, Hofmann K, Wagner Y, Plattner C, Spath EM, Distler U, Tenzer S, TRR241 IBDome Consortium, Neufert C, Neurath MF, Becker C. Pharmacological inhibitors of the gamma-secretase enzyme complex disrupt epithelial cell function triggering colitis in mice. J Crohn Colitis. 2025. 19:jjaf096. https://doi.org/10.1093/ecco-jcc/jjaf096
Mehic D, Pirabe A, Schrottmaier W, Schmuckenschlager A, Fruehwirth S, Hackl H, Tolios A, Ay C, Gebhart J, Pabinger I, Asssinger A. Impaired surface receptor expression on immature platelets in bleeding patients with abnormal light transmission aggregometry. J Thromb Haemost. 2025. 23:2982-2989. https://doi.org/10.1016/j.jtha.2025.05.011
Lisandrelli R, Winler M, Trajanoski Z, Lamberti G. Studying immunogenic cell death in human colorectal cancer organoids. Onco Targets Ther. 2025. 18:705-715. https://doi.org/10.2147/ott.s521346
Forster PM, Jakob MO, Yusuf D, Bubeck M, Limberger H, Luo Y, Thieme P, Polici A, Sterczyk N, Boulekou S, Bartel L, Cosovanu C, Witkowski M, González-Acera M, Kühl AA, Weidinger C; TRR241 IBDome Consortium; Backofen R, Hegazy AN, Patankar JV, Klose CSN. A transcriptional atlas of gut-innervating neurons reveals activation of interferon signaling and ferroptosis during intestinal inflammation. Neuron. 2025. 113:1333-1351. https://doi.org/10.1016/j.neuron.2025.02.018
Ranches G, Hackl H, Zaderer V, Ploner M, Posch W, Wilflingseder D, Kummer K, Hüttenhofer A*. Differentially expressed ncRNAs as key regulators in infection of human bronchial epithelial cells by the SARS-CoV-2 Delta variant. Mol Ther Nucleic Acids. 2025. 36:102559. https://doi.org/10.1016/j.omtn.2025.102559
Guerrero-Navarro L, Monfort-Lanzas P, Krichbaumer V, De Araújo MEG, Monfregola J, Huber LA, Ballabio A, Jansen-Dürr P, Cavinato M. TFEB Orchestrates Stress Recovery and Paves the Way for Senescence Induction in Human Dermal Fibroblasts. Aging Cell. 2025. 24:e70083. https://doi.org/10.1111/acel.70083
Hussein S, Kühl AA, Golusda L, Plattner C, Heinze N, Sturm G, Freise C, Traub H, Schannor M, Trajanoski Z, Taupitz M, Siegmund B, Paclik D. Phenotype and function of human monocytes remain mainly unaffected by very small superparamagnetic iron oxide particles. Front Nanotechnol. 2025. in press
Hecker J, Plattner C, Cancino CA, Löscher B-S, Saurenbach J, Letizia M, Rieder D, TRR241 IBDome Consortium, Freise I, Koop K, Neufert C, Kunkel D, Al Khatim Z, Schaafs L-A, Schütz A, Becker C, Atreya R, Trajanoski Z, Franke A, Sonnenberg E, Hegazy AN, Siegmund B, Weidinger C. IL-36 signaling as a drug target in Crohn’s disease patients with IL36RN mutations. EMBO Mol Med. 2025. 17:1539-1555. https://doi.org/10.1038/s44321-025-00245-z
González-Acera M, Patankar JV, Erkert L, Cineus R, Gámez-Belmonte R, Leupold T, Bubeck M, Bao L-L, Dinkel M, Wang R, Schickedanz L, Limberger H, Stolzer I, Gerlach K, Diemand L, Mascia F, Gupta P, Naschberger E, Koop K, Plattner C, Sturm G, Weigmann B, Günther C, Wirtz S, Stürzl M, Hildner K, Kühl AA, Siegmund B, Gießl A, Atreya R, The IBDome Consortium, Hegazy AN, Trajanoski Z, Neurath MF, Becker C. Integrated multi-model analysis of intestinal inflammation exposes key molecular features of preclinical and clinical IBD. Gut. 2025. 74:1602–1615. https://doi.org/10.1136/gutjnl-2024-333729
Rusu EC, Clavero-Mestres H, Sánchez-Álvarez M, Veciana-Molins M, Bertran L, Monfort-Lanzas P, Aguilar C, Camaron J, Auguet T. Uncovering hepatic transcriptomic and circulating proteomic signatures in MASH: A meta-analysis and machine learning-based biomarker discovery. Comput Biol Med. 2025. 191:110170. https://doi.org/10.1016/j.compbiomed.2025.110170
Krauß D, Moreno-Viedma V, Adachi-Fernandez E, de Sá Fernandes C, Genger J-W, Fari O, Blauensteiner B, Kirchhofer D, Bradaric N, Gushchina V, Fotakis G, Mohr T, Abramovich I, Mor I, Holcmann M, Bergthaler A, Haschemi A, Trajanoski Z, Winkler J, Gottlieb E, Sibilia M. EGFR controls transcriptional and metabolic rewiring in KRASG12D colorectal cancer. EMBO Mol Med. 2025. 17:1355-1392. https://doi.org/10.1038/s44321-025-00240-4
Monfort-Lanzas P, Gostner JM, Hackl H. Modeling omics dose-response at the pathway level with DoseRider. Comput Struct Biotechnol J. 2025. 27:1440-1448. https://doi.org/10.1016/bs.mcb.2025.03.007
Plattner C, Sturm G, Rieder D. Analysis of single-cell TCR repertoires and gene expression from multi-modal scRNA-seq data. Methods Mol Biol. 2025. 199:191-220.
Hofer S, Jenny M, Klein A, Becker K, Parráková L, Überall F, Ganzera M, Fuchs D, Hackl H, Monfort-Lanzas P, Gostner JM. Myrobalan fruit extracts modulate immunobiochemical pathways in vitro. Antioxidants. 2025. 14:350. https://doi.org/10.3390/antiox14030350
Monfort-Lanzas P, Rungger K, Madersbacher L, Hackl H. Machine learning to dissect perturbations in complex cellular systems. Comput Struct Biotechnol J. 2025. 27:832-842. https://doi.org/10.1016/j.csbj.2025.02.028
Steger K, Fiegl H, Feroz B, Leitner K, Marth C, Hackl H, Zeimet AG. Differences in immunogenicity of TP53-mutated cancers with low tumor mutational burden (TMB) – A study on TP53mut endometrial-, ovarian- and triple negative breast cancer. Eur J Cancer. 2025. 219:115320. https://doi.org/10.1016/j.ejca.2025.115320
Müller TM, Liu LJ, Wiesinger M; TRR241 IBDome Consortium; Neurath MF, Voskens CJ, Zundler S. Engineering Therapeutic Regulatory T Cells to Overexpress G Protein-Coupled Receptor 15 Improves Functional Fitness for In Vivo Gut Homing. Gastroenterology. 2025. 168:389-392. https://doi.org/10.1053/j.gastro.2024.10.003
Graber M, Gollmann-Tepeköylü C, Schweiger V, Hirsch J, Pölzl L, Nägele F, Hackl H, Sopper, S, Kirchmair E, Mair S, Voelkl J, Plattner C, Eichin F, Trajanoski Z, Krogsdam A, Eder J, Fiegl M, Hau D, Tancevski I, Grimm M, Cooke JP, Holfeld J. Modulation of cell fate by shock wave therapy in ischemic heart disease. Eur Heart J Open. 2025. 5:oeaf011. https://doi.org/10.1093/ehjopen/oeaf011
Erkert L, Ruder B, Kabisch M, Gamez Belmonte R, Patankar JV, Gonzalez Acera M, Schödel L, Chiriac MT, Cineus R, Gnafakis S, Leupold T, Thoma OM, Stolzer I, Taut A, Thonn V, Zundler S, Günther C, Diefenbach A, Kühl AA, Hegazy AN, Waldner M, Basic M, Bleich A, Neurath MF, Wirtz S, Becker C; TRR241 IBDome Consortium. TIFA renders intestinal epithelial cells responsive to microbial ADP-heptose and drives colonic inflammation in mice. Mucosal Immunol. 2025. 18:453-466. https://doi.org/10.1016/j.mucimm.2025.01.003
Rendo V, Schubert M, Khuu N, Suarez Peredo Rodriguez MF, Whyte D, Ling X, van den Brink A, Huang K, Swift M, He Y, Zerbib J, Smith R, Raaijmakers J, Bandopadhayay P, Guenther LM, Hwang JH, Iniguez A, Moody S, Seo JH, Stover EH, Garraway L, Hahn WC, Stegmaier K, Medema RH, Chowdhury D, Colomé-Tatché M, Ben-David U, Beroukhim R, Foijer F. A compendium of Amplification-Related Gain Of Sensitivity genes in human cancer. Nat Commun. 2025. 16:1077. https://doi.org/10.1186/s12943-024-02221-6
Daum S, Decristoforo L, Mousa M, Salcher S, Plattner C, Hosseinkhani B, Trajanoski Z, Wolf D, Carmeliet P, Pircher A. Unveiling the immunomodulatory dance: endothelial cells’ function and their role in non-small cell lung cancer. Mol Cancer. 2025. 24:21. https://doi.org/10.1186/s12943-024-02221-6
Jonas JP, Müller PC, Linecker M, Hackl H, Santol J, Eshmuminov D, Rössler F, Ammann M, Ignatavicius P, Guidetto C, Sander S, Ardiles V, Wen Z, Romic I, Fronek J, Kysela M, Truant S, Oldhafer K, Reese T, Rauchfuss F, Ulmer TF, Wahba R, Hahn O, Di Benedetto F, Fernandez-Placencia R, Robles-Campos R, Lopez Lopez V, Sparrelid E, Petrowsky H, Clavien PA, Starlinger P. Optimization of ALPPS stage II timing with the APR/ALBI score – an international, multicenter cohort study. Hepatobiliary Surg Nutr. 2025. 14:742-754. https://doi.org/10.21037/hbsn-24-617
2024
Bao LL, Yu YQ, González-Acera M, Patankar JV, Giessl A, Sturm G, Kühl AA, Atreya R, Erkert L, Gámez-Belmonte R, Krug SM, Schmid B, Tripal P, Chiriac MT, Hildner K, Siegmund B, Wirtz S, Stürzl M, Abdou MM, Trajanoski Z, TRR241 IBDome Consortium, Neurath MF, Zorzano A, Becker C. Epithelial OPA1 links mitochondrial fusion to inflammatory bowel disease. Sci Transl Med. 2025. 17:eadn8699. https://doi.org/10.1126/scitranslmed.adn8699
Melero I, de Miguel Luken MJ, de Velasco G, Garralda E, Martin-Liberal J, Joerger M, Alonso G, Goebeler ME, Schuler M, König D, Dummer R, Reig M, Rodriguez-Ruiz M,Calvo E, Esteban-Villarrubia J, Oberoi A, Sàbat P, Soto-Castillo JJ, Koster KL, Saavedra O, Sayehli C, Gromke T, Läubli H, Ramelyte E, Fortuny M, Landa-Magdalena A, Moreno I, Torres-Jiménez J, Hernando-Calvo A, Hess D, Racca F, Richly H, Schmitt A, Eggenschwiler C, Sanduzzi-Zamparelli M, Vilalta-Lacarra A, Trojan J, Koch C, Galle P, Foester F, Trajanoski Z, Hackl H, Gogolla F, Koll F, Wild P, Chun FK, Reis H, Lloyd P, Machacek M, Gajewski TF, Fridman W, Eggermont A, Bargou R, Schöniger S, Rüschoff J, Tereshchenko A, Zink C, de Silva A, Lichtenegger F, Akdemir J, Rüdiger M, L’Huillier P, Dutta A, Haake M, Wischhusen J, Auckenthaler A, Gjorgjioska A, Rössler B, Hermann F, Liebig M, Reichhardt D, Schuberth-Wagner C, Fettes P, Auer M, Klar K, Leo E. Neutralizing GDF-15 can overcome anti-PD-1 and anti-PD-L1 resistance in solid tumours. Nature. 2025. 637:1218-1227. https://doi.org/10.1038/s41586-024-08305-z
Steinacher C, Nishio S, Usami S, Dudas J, Rieder D, Rask-Andersen H, Crespo B, Moreno N, Konschake M, Seifharth C, Glueckert R. Expression of neurotrophins and its receptors during fetal development in the human cochlea. Int J Mol Sci. 2024. 25:13007. https://doi.org/10.3390/ijms252313007
Pirabe A, Mehic D, Hackl H, Frühwirth S, Schmuckenschlager A, Beck S, Gebhart J, Gleixner K, Sperr W, Schrottmaier WC, Assinger A. Impaired hemostatic and immune functions of platelets after acute thrombocytopenia. J Thromb Haemost. 2024. 23:1052-1065. https://doi.org/10.1016/j.jtha.2024.11.029
Ammann M, Adjei Antwi SK, Gudmundsdottir H, Hackl H, Santol J, Guillot BE, Pappalettera G, Thiels CA, Warner SG, Trury MJ, Kendrick ML, Smoot RL, Nagorney DM, Cleary SP, Halfdanarson TR, Starlinger P. Surgical and oncologic outcomes for liver resections of cystic neuroendocrine tumor liver metastasis. Eur J Surg Oncol. 2025. 51:109464. https://doi.org/10.1016/j.ejso.2024.109464
Gossner L, Rieder D, Müller T, Janecke AR. The recurrent E-cadherin (CDH1) mutation c.760G>A causes orofacial clefts but does not predispose to hereditary cancer. Genes. 2024. 15:1475. https://doi.org/10.3390/genes15111475
Gronauer R, Madersbacher L, Monfort-Lanzas P, Floriani G, Sprung S, Zeimet AG, Marth C, Fiegl H, Hackl H. Integrated immuno-genomic analyses of high-grade serous ovarian cancer reveal vulnerability to combination immunotherapy. Front Immunol. 2024. 15:1489235. https://doi.org/10.3389/fimmu.2024.1489235
Ammann M, Jonas JP, Pereyra D, Santol J, Hackl H, Kalchbrenner T, Laengle J, Podrascanin V, Lehner F, Viragos-Toth IL, Hulla W, Ruso V, Smoot RL, Gruenberger T, Assinger A, Starlinger P. Plasma GLP-1 and metabolic dynamics during human liver regeneration and their association with posthepatectomy liver failure. Hepatobiliary Surg Nutr. 2025. 14:49-65. https://doi.org/10.21037/hbsn-24-464
Grubwieser P, Boeck N, Kvalem Soto E, Hilbe R, Moser P, Seifert M, Dichtl S, Govrins MA, Posch W, Sonnweber T, Nairz M, Theurl I, Trajanoski Z, Weiss G. Human Airway Epithelium Controls Pseudomonas aeruginosa Infection via inducible Nitric Oxide Synthase. Front Immunol. 2024. 15:1508727. https://doi.org/10.3389/fimmu.2024.1508727
Breithofer J, Bulfon D, Fawzy N, Tischitz M, Zitta C, Hartig L, Grabner GF, Pirchheim A, Hackl H, Taschler U, Lass A, Tam-Amersdorfer C, Strobl H, Kratky D, Zimmermann R. Phospholipase A2 group IVD mediates the transacylation of glycerophospholipids and acylglycerols. J Lipid Res. 2024. 65:100685. https://doi.org/10.1016/j.jlr.2024.100685
Resch U, Hackl H, Pereyra D, Santol J, Brunnthaler L, Probst J, Jankoschek AS, Aiad M, Nolte H, Krueger M, Starlinger P, Assinger A. SILAC-based characterization of plasma-derived extracellular vesicles in patients undergoing partial hepatectomy. Int J Mol Sci. 2024. 25:10685. https://doi.org/10.3390/ijms251910685
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Wieser V, Tsibulak I, Reimer D, Zeimet AG, Fiegl H, Hackl H, Marth C. An angiogenic tumor phenotype predicts poor prognosis in ovarian cancer. Gynecol Oncol. 2023. 170:290-299. https://doi.org/10.1016/j.ygyno.2023.01.034
Starlinger P, Brunnthaler L, McCabe C, Pereyra D, Santol J, Steadman J, Hackl M, Skalicky S, Hackl H, Gronauer R, O’Brien D, Kain R, Hirsova P, Gores GJ, Wang C, Gruenberger T, Smoot RL, Assinger A. The transcriptomic landscapes of effective and failed liver regeneration in humans. JHEP Rep. 2023. 5:100683. https://doi.org/10.1016/j.jhepr.2023.100683
Vijver SV, Danklmaier S, Pipperger L, Gronauer R, Floriani G, Hackl H, Das K, Wollmann G. Prediction and validation of murine MHC class I epitopes of the recombinant virus VSV-GP. Front Immunol. 2023. 13:1100730. https://doi.org/10.3389/fimmu.2022.1100730
2022
Cesaro G, Milia M, Baruzzo G, Finco G, Morandini F, Lazzarini A, Alotto P, da Cunha Carvalho de Miranda NF, Trajanoski Z, Finotello F, Di Camillo B. MAST: a hybrid Multi-Agent Spatio-Temporal model of tumor microenvironment informed using a data-driven approach. Bioinf Adv. 2022. 2:vbac092. https://doi.org/10.1093/bioadv/vbac092
Salcher S, Sturm G, Horvath L, Untergasser G, Kuempers C, Fotakis G, Panizzolo E, Martowicz A, Trebo M, Pall G, Gamerith G, Sykora M, Augustin F, Schmitz K, Finotello F, Rieder D, Perner S, Sopper S, Wolf D, Pircher A, Trajanoski Z*. High-resolution single-cell atlas reveals diversity and plasticity of tissue-resident neutrophils in non-small cell lung cancer. Cancer Cell. 2022. 40:1503-1520. https://doi.org/10.1016/j.ccell.2022.10.008
Moreno S, Fickl M, Bauer I, Brunner M, Rázková A, Rieder D, Delazer I, Micura R, Lusser A. 6-Thioguanosine monophosphate prodrugs display enhanced performance against thiopurine-resistant leukemia and breast cancer cells. J Med Chem. 2022. 65:15165-15173. https://doi.org/10.1021/acs.jmedchem.2c01010
Dietrich A, Sturm G, Merotto L, Marini F, Finotello F, List M. SimBu: bias-aware simulation of bulk RNA-seq data with variable cell-type composition. Bioinformatics. 2022. 38:ii141-ii147. https://doi.org/10.1093/bioinformatics/btac499
Ranches G, Zeidler M, Kessler R, Hoelzl M, Hess MW, Vosper J, Perco P, Schramek H, Kummer KK, Kress M, Krogsdam A, Rudnicki M, Mayer G, Huettenhofer A. Exosomal mitochondrial tRNAs and miRNAs as potential predictors of inflammation in renal proximal tubular epithelial cells. Mol Ther Nucleic Acids. 2022. 28:794-813. https://doi.org/10.1016/j.omtn.2022.04.035
Monfort-Lanzas P, Gronauer R, Madersbacher L, Schatz C, Rieder D, Hackl H. MIO: MicroRNA target analysis system for Immuno-Oncology. Bioinformatics. 2022. 38:3665-3667. https://doi.org/10.1093/bioinformatics/btac499
Grubwieser P, Hoffmann A, Hilbe R, Seifert M, Sonnweber T, Böck N, Theurl I, Weiss G, Nairz M. Airway epithelial cells differentially adapt their iron metabolism to infection with Klebsiella pneumoniae and Escherichia coli in vitro. Front Cell Infect Microbiol. 2022. 12:875543. https://doi.org/10.3389/fcimb.2022.875543
Heidegger IM, Fotakis G, Offermann A, Goveia J, Noureen A, Daum S, Salcher S, Bosscha HT, Schäfer G, Walenkamp A, Beatovic A, Moisse M, Perner S, Plattner C, Krogsdam A, Haybäck J, Sopper S, Thaler S, Keller M, Klocker H, Trajanoski Z, Wolf D, Pircher A. Comprehensive characterization of the prostate tumor microenvironment identifies CXCR4/CXCL12 crosstalk as a novel antiangiogenic therapeutic target in prostate cancer. Mol Cancer. 2022. 21:132. https://doi.org/10.1186/s12943-022-01597-7
Effenberger M, Widjaja AA, Grabherr F, Schaefer B, Grander C, Mayr L, Schwaerzler J, Enrich B, Moser P, Fink J, Pedrini A, Jaschke N, Kirchmair A, Pfister A, Hausmann B, Bale R, Putzer D, Zoller H, Schafer S, Pjevac P, Trajanoski Z, Oberhuber G, Adolph T, Cook S, Tilg H. Interleukin-11 drives human and mouse alcohol-related liver disease. Gut. 2023. 72:168-179. https://doi.org/10.1136/gutjnl-2021-326076
Atreya R, Bojarski C, Kühl AA, Trajanoski Z, Neurath MF, Siegmund B. Ileal and colonic Crohn’s disease: Does location makes a difference in therapy efficacy? Curr Res Pharmacol Drug Discov. 2022. 3:100097. https://doi.org/10.1016/j.crphar.2022.100097
Ingruber J, Dudás J, Savic D, Schweigl G, Steinbichler TB, Greier MDC, Santer M, Carollo S, Trajanoski Z, Riechelmann H. EMT-related transcription factors and protein stabilization mechanisms involvement in cadherin switch of head and neck squamous cell carcinoma. Exp Cell Res. 2022. 414:113084. https://doi.org/10.1016/j.yexcr.2022.113084
Moreno S, Brunner M, Delazer I, Rieder D, Lusser A, Micura R. Synthesis of 4-thiouridines with prodrug functionalization for RNA metabolic labeling. RCS Chemical Biology. 2022. 3:447-455. https://doi.org/10.1039/D2CB00001F
De la Cruz-Ku G, Aizpuru M, Hackl H, Ubl DS, Habermann E, Pery R, Driedger M, Assinger A, Nagorney D, Cleary S, Smoot R, Starlinger P. Hepatocellular carcinoma as predominant cancer subgroup accounting for sex differences in post-hepatectomy liver failure, morbidity and mortality. HPB. 2022. 24:1453-1463. https://doi.org/10.1016/j.hpb.2022.02.009
Abdulrahman Z, Santegoets SJ, Sturm G, Charoentong P, Ijsselsteijn ME, Somarakis A, Höllt T, Finotello F, Trajanoski Z, van Egmond SL, Mustafa DM, Welters MJP, de Miranda NF, van der Burg SH. Tumor specific T cells support chemokine-driven spatial organization of intratumoral immune microaggregates needed for long survival. J Immunother Cancer. 2022. 10:e004346. https://doi.org/10.1136/jitc-2021-004346
Schrottmaier WC, Pirabe A, Pereyra D, Heber S, Hackl H, Schmuckenschlager A, Brunnthaler L, Santol J, Kammerer K, Oosterlee J, Pawelka E, Treiber SM, Khan AO, Pugh M, Traugott MT, Schoergenhofer C, Seitz T, Karolyi M, Jilma B, Rayes J, Zoufaly A, Assinger A. Platelets and anti-platelet medication in COVID-19 related thrombotic complications. Front Cardiovasc Med. 2022. 8:802566. http://dx.doi.org/10.3389/fcvm.2021.802566
Duurland CL, Santegoets SJ, Abdulrahman Z, Loof NM, Sturm G, Wesselink TH, Arens R, Boekestijn S, Ehsan I, van Poelgeest MIE, Finotello F, Hackl H, Trajanoski Z, ten Dijke P, Braud VM, Welters MJP, van der Burg SH. CD161 expression and regulation defines rapidly responding effector CD4+ T cells associated with improved survival in HPV16-associated tumors. J Immunother Cancer. 2022. 10:e003995. http://dx.doi.org/10.1136/jitc-2021-003995
Seeber A, Battaglin F, Zimmer K, Spizzo G, Xiu J, Novotny-Diermayr V, Kocher F, Rieder D, Puccini A, Swensen J, Ellis M, Goldberg RM, Grothey A, Shields AF, Marshall JL, Weinberg BA, Sackstein PE, Lim KH, Tan GS, Nabhan C, Korn WM, Amann A, Trajanoski T, Berger MD, Lou E, Wolf D, Lenz H-J. Comprehensive analysis of R-spondin fusions and RNF43 mutations implicate novel therapeutic options in colorectal cancer. Clin Cancer Res. 2022. 28:1863-1870. https://doi.org/10.1158/1078-0432.ccr-21-3018
2021
Schrottmaier WC, Pirabe A, Pereyra D, Heber S, Hackl H, Schmuckenschlager A, Brunnthaler L, Santol J, Kammerer K, Oosterlee J, Pawelka E, Treiber SM, Khan AO, Pugh M, Traugott MT, Schoergenhofer C, Seitz T, Karolyi M, Jilma B, Rayes J, Zoufaly A, Assinger A. Adverse outcome in COVID-19 is associated with an aggravating hypo-responsive platelet phenotype. Front Cardiovasc Med. 2021. 8:795624. https://doi.org/10.3389/fcvm.2021.795624
Fotakis G, Trajanoski Z, Rieder D. Computational cancer neoantigen prediction: current status and recent advances. Immunooncol Technol. 2021. 12:100052. https://doi.org/10.1016/j.iotech.2021.100052
Karbon G, Haschka M, Hackl H, Rocamora-Reverte L, Parson W, Fiegl H, Soratroi C, Villunger A. The BH3-only protein NOXA serves as an independent predictor of breast cancer patient survival and defines susceptibility to microtubule targeting agents. Cell Death Dis. 2021. 12:1151. https://doi.org/10.1038/s41419-021-04415-y
Rieder D, Fotakis G, Ausserhofer M, Geyeregger R, Paster W, Trajanoski Z, Finotello F. nextNEOpi: a comprehensive pipeline for computational neoantigen prediction. Bioinformatics. 2021. 38:1131–1132. https://doi.org/10.1093/bioinformatics/btab759
Borst L, Sluijter M, Sturm G, Charoentong P, Santegoets SAM, van Gulijk M, van Elsas MJ, Groeneveldt C, van Montfoort N, Finotello F, Trajanoski Z, Kielbasa SM, van der Burg SH, van Hall T. Immune checkpoint NKG2A marks repeatedly stimulated CD8 T cells whereas PD-1 is indicative for recent activation. Int J Cancer. 2021. 150:688-704. https://doi.org/10.1002/ijc.33859
Welz L, Kakavand N, Hang X, Laue G, Ito G, Gomes Silva M, Plattner C, Mishra N, Tengen F, Ogris C, Jesinghaus M, Wottawa F, Arndold P, Kaikkonen L, Stengel S, Tran, F, Das S, Kaser A, Trajanoski Z, Blumberg R, Roecken C, Saur D, Tschurscthenthaller M, Schreiber S, Rosenstiel P, Aden K. Epithelial XBP1 coordinates p53-driven DNA damage responses and suppression of intestinal carcinogenesis. Gastroenterology. 2021. 162:223-237. https://doi.org/10.1053/j.gastro.2021.09.057
Maio M, Lahn M, Di Giacomo AM, Covre A, Calabrò L, Ibrahim R, Fox B; Siena Think Tank. A vision of immuno-oncology: the Siena think tank of the Italian network for tumor biotherapy (NIBIT) foundation. J Exp Clin Cancer Res. 2021. 40:240. https://doi.org/10.1186/s13046-021-02023-4
Posch W, Bermejo-Jambrina M, Steger M, Witting C, Diem G, Hörtnagl P, Hackl H, Lass-Floerl C, Huber LA, Geijtenbeek T, Wilflingseder D. Complement potentiates immune sensing of HIV-1 and early type I IFN responses. mBio. 2021. 12:e0240821. https://doi.org/10.1128/mbio.02408-21
Matschinske J, Alcaraz N, Benis A, Golebiewski M, Grimm DG, Heumos L, Kacprowski T, Lazareva O, List M, Louadi Z, Pauling JK, Pfeifer N, Röttger R, Schwämmle V, Sturm G, Traverso A, Van Steen K, de Freitas MV, Villalba Silva GC, Wee L, Wenke NK, Zanin M, Zolotareva O, Baumbach J, Blumenthal DB. The AIMe registry for artificial intelligence in biomedical research. Nat Methods. 2021. 18:1128-1131. https://doi.org/10.1038/s41592-021-01241-0
Sturm G, List M, Zhang JD. Tissue heterogeneity is prevalent in gene expression studies. NAR Genom Bioinform. 2021. 3:lqab077. https://doi.org/10.1093/nargab/lqab077
Niederwieser T, Braunwarth E, Dasari BVM, Pufal K, Szatmary P, Hackl H, Haselmann C, Connolly CE, Cardini B, Öfner D, Roberts K, Malik H, Stättner S, Primavesi F. Arterial lactate concentrations early after liver resection stratify risk of post-hepatectomy liver failure and associated other complications. Brit J Surg. 2021. 108:1360-1370. https://doi.org/10.1093/bjs/znab338
Schoberleitner I, Bauer I, Huang A, Andreyeva EN, Sebald J, Pascher K, Rieder D, Brunner M, Podhraski V, Oemer G, Cázarez García D, Rieder L, Keller MA, Winkler R, Fyodorov DF, Lusser A. CHD1 controls H3.3 incorporation in adult brain chromatin to maintain metabolic homeostasis and normal lifespan. Cell Rep. 2021. 37:109769. https://doi.org/10.1016/j.celrep.2021.109769
Rufo N, Korovesis D, Van Eygen S, Derua R, Garg AD, Finotello F, Vara-Perez M, Rožanc J, Dewaele M, de Witte PA, Alexopoulos LG, Janssens S, Sinkkonen L, Sauter T, Verhelst SHL, Agostinis P. Stress-induced inflammation evoked by immunogenic cell death is blunted by the IRE1a kinase inhibitor KIRA6 through HSP60 targeting. Cell Death Diff. 2021. 29:230-245. https://doi.org/10.1016/j.celrep.2021.109769
Bergmann CB, Hammock BD, Wan D, Gogolla F, Goetzman H, Caldwell CC, Supp DM. TPPU treatment of burned mice dampens inflammation and generation of bioactive DHET which impairs neutrophil function. Sci Rep. 2021. 11:16555. https://doi.org/10.1038/s41598-021-96014-2
Gonzalez Acera M, Bubeck M, Masica F, Diemand L, Sturm G, Kühl AA, Atreya R, Lie DC, Neurath MF, Schumann M, Klose C, Trajanoski Z, Becker C, Patankar JV. Dynamic, transient, and robust increase in the innervation of the inflamed mucosa in inflammatory bowel diseases. Cells. 2021. 10:2253. https://doi.org/10.3390/cells10092253
Lapuente-Sanatana O, van Genderen M, Hilbers PAJ, Finotello F, Eduati F. Interpretable systems biomarkers predict response to immune-checkpoint inhibitors. Patterns. 2021. 2:100293. https://doi.org/10.1016/j.patter.2021.100293
Resch T, Hackl H, Esser H, Guenther J, Schwelberger H, Ritschl P, Ebner S, Maglione M, Mellitzer V, Biebl M, Oellinger R, Zoller H, Schneeberger S, Kotsch K. Expression of MICA in zero hour biopsies predicts graft survival after liver transplantation. Front Immunol. 2021. 12:606146. https://doi.org/10.3389/fimmu.2021.606146
Jonas JP, Hackl H, Pereyra D, Santol J, Ortmayr G, Rumpf B, Najarnia S, Schauer D, Brostjan C, Gruenberger T, Starlinger P. Circulating metabolites as a concept beyond tumor biology determining disease recurrence after resection of colorectal liver metastasis. HPB. 2021. 24:116-129. https://doi.org/10.1016/j.hpb.2021.06.415
Ghadge SK, Messner M, Seiringer H, Maurer T, Staggl S, Zeller T, Möller C, Börnigen D, Wolfgang J. Weninger WJ, Stefan H. Geyer SH, Sopper S, Krogsdam A, Pölzl G, Bauer A, Zaruba MM. Smooth Muscle Specific Ablation of CXCL12 in Mice Downregulates CXCR7 Associated with Defective Coronary Arteries and Cardiac Hypertrophy. Int J Mol Sci. 2021. 22:5908. https://doi.org/10.3390/ijms22115908
Starlinger P, Ahn J, Mullan A, Gyoeri G, Pereyra D, Alva-Ruiz R, Hackl H, Reiberger T, Trauner M, Santol J, Simbrunner B, Mandorfer M, Berlakovich GA, Kamath PS, Heimbach J. The addition of C-reactive protein and von Willebrand factor to MELD-Na improves prediction of waitlist mortality. Hepatology. 2021. 74:1533-1545. https://doi.org/10.1002/hep.31838
Puhr M, Eigentler A, Handle F, Hackl H, Ploner C, Heidegger I, Schaefer G, Brandt M, Hoefer J, van der Pluijm G, Klocker H. Targeting the glucocorticoid receptor signature gene Mono Amine Oxidase-A enhances the efficacy of chemo- and anti-androgen therapy in advanced prostate cancer. Oncogene. 2021. 40:3087-3100. https://doi.org/10.1038/s41388-021-01754-0
Grandits A, Nguyen C, Schlerka A, Hackl H, Sill H, Etzler J, Heyes E, Stoiber D, Grebien F, Heller G, Wieser R. Down-regulation of MTSS1 in acute myeloid leukemia is associated with a poor prognosis, chemotherapy resistance, and disease aggressiveness. Leukemia. 2021. 35:2827-2839. https://doi.org/10.1038/s41375-021-01224-2
Messner F, Etra JW, Shores JT, Thoburn CJ, Hackl H, Lozano MI, Fidder SAJ, Guo Y, Kambarashvili K, Alagol K, Kalsi R, Cooney C, Furtmüller GJ, Krapf J, Oh BC, Brandacher G. Non-invasive evaluation of intragraft immune responses in upper extremity transplantation. Transpl Int. 2021. 34:894-905. https://doi.org/10.1111/tri.13854
Furlan T, Kirchmair A, Sampson N, Puhr M, Gruber M, Trajanoski Z, Santer FB, Parson W, Culig Z. MYC-mediated ribosomal gene expression sensitizes enzalutamide-resistant prostate cancer cells to EP300/CREBBP inhibitors. Am J Pathol. 2021. 191:1094-1107. https://doi.org/10.1016/j.ajpath.2021.02.017
Prokopi A, Tripp CH, Timmers B, Hornsteiner F, Spoeck S, Crawford JC, Clements DR, Efremova R, Hutter K, Bellmann K, Cappelano G, Cadilha BL, Kobold S, Boon I, Ortner D, Trajanoski Z, de Gruijl TD, Idoyaga J, Green DR, Stoitzner P. Skin dendritic cells in melanoma are key for successful checkpoint blockade therapy. J Immunother Cancer. 2021. 9:e000832. https://doi.org/10.1136/jitc-2020-000832
Starlinger P, Ubl DS, Hackl H, Starlinger J, Nagorney DM, Smoot RL, Habermann EB, Cleary SP. The combined APRI/ALBI score to predict mortality after hepatic resection. BJS open. 2021. 5:zraa043. https://doi.org/10.1093/bjsopen/zraa043
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Binenbaum I, Atamni HA, Fotakis G, Kontogianni G, Koutsandreas T, Pilalis E, Mott R, Himmelbauer H, Iraqi FA, Chatziioannou AA. Container-aided integrative QTL and RNA-seq analysis of Collaborative Cross mice supports distinct sex-oriented molecular modes of response in obesity. BMC Genomics. 2020. 21:761. https://doi.org/10.1186/s12864-020-07173-x
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Tsibulak I, Wieser V, Welponer H, Leitner K, Hackl H, Marth C, Fiegl H, Zeimet AG. Clinical impact of BRCA2 mRNA expression in high-grade serous ovarian cancer: Validation using the TCGA cohort. Acta Oncol. 2020. 60:187-190. https://doi.org/10.1080/0284186x.2020.1841288
Finotello F, Calura E, Risso D, Hautaniemi S, Romualdi C. Editorial: Multi-omic Data Integration in Oncology. Front Oncol. 2020. 10:1768. https://doi.org/10.3389/fonc.2020.01768
Starlinger P, Pereyra D, Hackl H, Orthmayer G, Braunwarth E, Santol J, Najarnia S, Driedger M, Gregory L, Alva-Rui R, Glasgow A, Assinger A, Nagorney D, Habermann E, Staetttner S, Cleary S, Smoot R, Gruenberger T. Consequences of perioperative serotonin reuptake inhibitor treatment during hepatic surgery. Hepatology. 2021. 73:1956-1966. https://doi.org/10.1002/hep.31601
Huemer F, Piringer G, Schlintl V, Hackl H, Rinnerthaler G, Thaler J, Greil R, Weiss L. Hospitalizations and clinical outcome in metastatic colorectal cancer during regorafenib or TAS-102 therapy. Cancers. 2020. 12:2812. https://doi.org/10.3390/cancers12102812
Hautz T, Messner F, Weissenbacher A, Hackl H, Kumnig M, Ninkovic M, Berchtold V, Krapf J, Zelger BG, Zelger B, Wolfram D, Pierer G, Löscher W, Zimmermann R, Gabl M, Arora R, Brandacher G, Öfner D, Schneeberger S. Long-term outcome after hand and forearm transplantation. Transpl Int. 2020. 33:1762-1778. https://doi.org/10.1111/tri.13752
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Kortekaas K, Santegoets S, Sturm G, Ehsan I, van Egmond S, Finotello F, Trajanoski Z, Welters M, Poelgeest M, van der Burg S. CD39 identifies the CD4-positive tumor-specific T cell population in human cancer. Cancer Immunol Res. 2020. 8:1311-1321. https://doi.org/10.1158/2326-6066.cir-20-0270
Gollmann-Tepeköylü C, Nägele F, Graber M, Pölzl L, Lobenwein D, Hirsch J, An A, Irschick R, Roehrs BT, Kremser C, Hackl H, Huber R, Venezia S, Hercher D, Fritsch H, Bonaros N, Stefanova N, Tancevski I, Meyer D, Grimm M, Holfeld J. Shock waves promote spinal cord repair via TLR3. JCI insight. 2020. 5:134552. https://doi.org/10.1172/jci.insight.134552
Sturm G, Fotakis G, Haider M, Rieder D, Trajanoski Z, Finotello F. Scirpy: A Scanpy extension for analyzing single-cell T-cell receptor sequencing data. Bioinformatics. 2020. 36:4817-4818. https://doi.org/10.1093/bioinformatics/btaa611
Yamazaki T, Kirchmair A, Sato A, Buqué A, Rybstein M, Petroni G, Bloy N, Finotello F, Stafford L, Manzano EN, de la Peña FA, García-Martínez E, Formenti SC, Trajanoski Z, Galluzzi L. Mitochondrial DNA drives abscopal responses to radiation that are inhibited by autophagy. Nat Immunol. 2020. 21:1160-1171. https://doi.org/10.1038/s41590-020-0751-0
Rinnerthaler G, Gampenrieder SP, Hackl H, Steiner M, Monzo-Fuentes C, Melchardt T, Magnes T, Huemer F, Westphal T, Hufnagl C, Hauser-Kronberger C, Egle A, Greil R. Low expression of miR-20a-5p predicts benefit to bevacizumab in metastatic breast cancer patients treated within the TANIA phase III trial. J Clin Med. 2020. 9:E1663. https://doi.org/10.3390/jcm9061663
Moosbrugger-Martinz V, Hackl H, Gruber R, Pilecky M, Knabl L, Orth-Höller D, Dubrac S. First evidences of distinguishable bacterial and fungal dysbiosis in the skin of patients with Atopic Dermatitis or Netherton Syndrome. J Invest Dermatol. 2021. 141:114-123. https://doi.org/10.1016/j.jid.2020.05.102
De Mattos-Arruda L, Vazquez M, Finotello F, Lepore R, Porta E, Hundal J, Amengual-Rigo P, Ng CKY, Valencia A, Carrillo J, Chan TA, Guallar V, McGranahan N, Blanco J, Griffith M. Neoantigen prediction and computational perspectives towards clinical benefit: Recommendations from the ESMO Precision Medicine Working Group. Ann Oncol. 2020. 31:978-990. https://doi.org/10.1016/j.annonc.2020.05.008
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Wieser V, Azim SA, Sprung S, Knoll K, Kögl J, Hackl H, Marth C, Zeimet AG, Fiegl H. TNF signalling predicts poor prognosis of patients with endometrial cancer. Carcinogenesis. 2020. 41:1065-1073. https://doi.org/10.1093/carcin/bgaa034
Plattner C, Finotello F, Rieder D. Deconvoluting tumor-infiltrating immune cells from RNA-seq data using quanTIseq. Methods Enzymol. 2020. 636:261-285. https://doi.org/10.1016/bs.mie.2019.05.056
Troyanskaya O, Trajanoski Z, Carpenter A, Thrun S, Razavian N, Oliver N. Artificial intelligence and cancer. Nature Cancer. 2020. 1:149-152. https://doi.org/10.1038/s43018-020-0034-6
Sturm G, Finotello F, List M. Immunedeconv: An R Package for Unified Access to Computational Methods for Estimating Immune Cell Fractions from Bulk RNA-Sequencing Data. Methods Mol Biol. 2020. 2120:191-211. https://doi.org/10.1007/978-1-0716-0327-7_16
Sturm G, Finotello F, List M. In Silico Cell-Type Deconvolution Methods in Cancer Immunotherapy. Methods Mol Biol. 2020. 2120:213-222. https://doi.org/10.1007/978-1-0716-0327-7_15
Kirchmair A, Finotello F. In Silico Prediction of Tumor Neoantigens with TIminer. Methods Mol Biol. 2020. 2120:129-145. https://doi.org/10.1007/978-1-0716-0327-7_9
Gasser C, Delazer I, Neuner E, Pascher K, Brillet K, Klotz S, Trixl L, Himmelstoß M, Ennifar E, Rieder D, Lusser A, Micura R. Thioguanosine conversion enables mRNA life-time evaluation by RNA sequencing via double metabolic labeling. Angew Chem Int Ed. 2020. 59:6881-6886. https://doi.org/10.1002/anie.201916272
de Boo L, Cimono Mathews A, Lubeck Y, Daletzakis A, Opdam M, Sanders J, van Rossum A, Loncova Z, Rieder D, Trajanoski Z, Vollebergh M, Sobral-Leite M, Broeks A, van der Wiel R, van Tinteren H, Linn S, Horlings HM, Kok M. Tumour-infiltrating lymphocytes (TILs) and BRCA-like status in stage III breast cancer patients randomized to adjuvant intensified platinum-based chemotherapy versus conventional chemotherapy. Eur J Cancer. 2020. 127:240-250. https://doi.org/10.1016/j.ejca.2019.12.003
Gollmann-Tepeköylü C, Graber M, Pölzl L, Nägele F, Moling R, Esser H, Summerer B, Mellitzer V, Ebner S, Hirsch J, Schäfer G, Hackl H, Cardini B, Oberhuber R, Primavesi F, Öfner D, Bonaros N, Troppmair J, Grimm M, Schneeberger S, Holfeld J*, Resch *. Toll-like receptor 3 mediates ischaemia/reperfusion injury after cardiac transplantation. Eur J Cardiothorac Surg. 2020. 57:826-835. https://doi.org/10.1093/ejcts/ezz383
Lusser A, Gasser C, Trixl L, Piatti P, Delazer I, Rieder D, Bashin J, Riml C, Amort T, Micura R. Thiouridine-to-Cytidine Conversion Sequencing (TUC-Seq) to Measure mRNA Transcription and Degradation Rates. Methods Mol Biol. 2020. 2062:191-211. https://doi.org/10.1007/978-1-4939-9822-7_10
Welponer H, Tsibulak I, Wieser V, Degasper C, Shivalingaiah G, Wenzel S, Sprung S, Marth C, Hackl H, Fiegl H, Zeimet AG. The miR-34 family and its clinical significance in ovarian cancer. J Cancer. 2020. 11:1446-1456. https://doi.org/10.7150/jca.33831
Zeidner JF, Knaus HA, Zeidan AM, Blackford AL, Montiel-Esparza R, Hackl H, Prince GT, Gondek LP, Ghiaur G, Showel MM, DeZern AE, Pratz KW, Smith BD, Levis MJ, Gore S, Coombs CC, Foster MC, Streicher H, Karp JE, Luznik L, Gojo I. Immunomodulation with pomalidomide at early lymphocyte recovery after induction chemotherapy in newly diagnosed AML and high-risk MDS. Leukemia. 2020. 34:1563-1576. https://doi.org/10.1038/s41375-019-0693-4
2019
Nguyen CH, Bauer K, Hackl H, Schlerka A, Koller E, Hladik A, Stoiber D, Zuber J, Staber PB, Hoelbl-Kovacic A, Purton LE, Grebien F, Wieser R. All-trans retinoic acid enhances, and a pan-RAR antagonist counteracts, the stem cell promoting activity of EVI1 in acute myeloid leukemia. Cell Death Dis. 2019. 10:944. https://doi.org/10.1038/s41419-019-2172-2
Fotakis G, Rieder D, Haider M, Trajanoski Z, Finotello F. NeoFuse: predicting fusion neoantigens from RNA sequencing data. Bioinformatics. 2019. 36:2260-2261. https://doi.org/10.1093/bioinformatics/btz879
Glüxam T, Grandits AM, Schlerka B, Nguyen CH, Etzler J, Finkes T, Fuchs M, Scheid C, Heller G, Hackl H, Harrer N, Sill H, Koller E, Stoiber D, Sommergruber W, Wieser R. CGRP signaling via CALCRL increases chemotherapy resistance and stem cell properties in acute myeloid leukemia. Int J Mol Sci. 2019. 20:5826. https://doi.org/10.3390/ijms20235826
Györi GP, Pereyra D, Rumpf B, Hackl H, Köditz C, Fuxsteiner J, Ortmayr G, Reiberger T, Trauner M, Berlakovich GA, Starlinger P. Von Willebrand factor facilitates MELD-independent risk stratification on the waiting list for liver transplantation. Hepatology. 2020. 72:584-594. https://doi.org/10.1002/hep.31047
Finotello F, Rieder D, Hackl H, Trajanoski Z. Next-generation computational tools for interrogating cancer immunity. Nat Rev Genet. 2019. 20:724-746. https://doi.org/10.1038/s41576-019-0166-7
Messner F, Etra JW, Haugen CE, Bösmüller C, Maglione M, Hackl H, Riedmann M, Oberhuber R, Cardini B, Resch T, Scheidl S, Margreiter R, Öfner D, Schneeberger S, Margreiter C. Sex matching does not impact the outcome after simultaneous pancreas kidney transplantation. Clin Transplant. 2019. 33:e13717. https://doi.org/10.1111/ctr.13717
Leopold B, Strutz J, Weiß E, Gindlhuber J, Birner-Gruenberger R, Hackl H, Appel HM, Cvitic S, Hiden U. Outgrowth, proliferation, viability, angiogenesis and phenotype of primary human endothelial cells in different purchasable endothelial culture media: Feed wisely. Histochem Cell Biol. 2019. 152:377-390. https://doi.org/10.1007/s00418-019-01815-2
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 J, Azab M, Fridman W, Sautes-Fridman C, Trajanoski Z, Maio M. Epigenetic remodelling and CTLA-4 blockade in melanoma: the NIBIT-M4 clinical trial. Clin Cancer Res. 2019. 25:7351-7362. https://doi.org/10.1158/1078-0432.CCR-19-1335
Tepeköylü C, Pölzl L, Graber M, Hirsch J, Nägele, Lobenwein D, Hess MW, Blumer MJ, Kirchmair E, Zipperle J, Hromada C, Hackl H, Hermann M, Al Khamisi H, Förster M, Lichtenauer M, Mittermayr R, Paulus P, Fritsch H, Bonaros N, Kirchmair R, Sluijter JPG, Davidson S, Grimm M, Holfeld J. miR-19a-3p containing exosomes improve function of ischemic myocardium upon shock wave therapy. Cardiovasc Res. 2019. 116:1226-1236. https://doi.org/10.1093/cvr/cvz209
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. LAMTOR/Ragulator regulates lipid metabolism in macrophages and foam cell differentiation. FEBS Lett. 2019. 594:31-42. https://doi.org/10.1002/1873-3468.13579
de Miranda NFCC, Trajanoski Z. Advancing cancer immunotherapy: a vision for the field. Genome Med. 2019. 11:51. https://doi.org/10.1186/s13073-019-0662-6
Fischer P, Chen H, Pacho F, Rieder D, Kimmel RA, Meyer D. FoxH1 represses miR-430 during early embryonic development of zebrafish via non-canonical regulation. BMC Biol. 2019. 17:61. https://doi.org/10.1186/s12915-019-0683-z
Sturm G, Finotello F, Petitprez F, Zhang JD, Baumbach J, Fridman WH, List M, Aneichyk T. Comprehensive evaluation of computational cell-type quantification methods for immuno-oncology. Bioinformatics. 2019. 14:i436-445. https://doi.org/10.1093/bioinformatics/btz363
Huemer F, Lang D, Westphal T, Gampenrieder SP, Hutarew G, Weiss L, Hackl H, Lamprecht B, Rinnerthaler G, Greil R. Baseline absolute lymphocyte count and ECOG performance score are associated with survival in advanced non-small cell lung cancer undergoing PD-1/PD-L1 blockade. J Clin Med. 2019. 8:1014. https://doi.org/10.3390/jcm8071014
Nguyen CH, Glüxam T, Schlerka A, Bauer K, Grandits AM, Hackl H, Dovey O, Zöchbauer-Müller S, Cooper JL, Vassiliou GS, Stoiber D, Wieser R, Heller G. SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness. Sci Rep. 2019. 9:9139. https://doi.org/10.1038/s41598-019-45579-0
Wieser V, Sprung S, Tsibulak I, Haybaeck J, Hackl H, Fiegl H, Marth C, Zeimet AG. Clinical impact of RANK signalling in ovarian cancer. Cancers. 2019. 11:791. https://doi.org/10.3390/cancers11060791
Huemer F, Schlintl V, Hecht S, Hackl H, Melchardt T, Rinnerthaler G, Greil R, Weiss L. Regorafenib is associated with increased skeletal muscle loss compared to TAS-102 in metastatic colorectal cancer. Clin Colorectal Cancer. 2019. 18:159-166. https://doi.org/10.1016/j.clcc.2019.04.003
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 N, Trajanoski Z. Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data. Genome Med. 2019. 11:34. https://doi.org/10.1186/s13073-019-0638-6
Plattner C, Hackl H. Modeling therapy resistance via the EGFR signaling pathway. FEBS J. 2019. 286:1284-1286. https://doi.org/10.1111/febs.14809
Vitale I, Sistigu A, Manic G, Rudqvist NP, Trajanoski Z, Galluzzi L. Mutational and Antigenic Landscape in Tumor Progression and Cancer Immunotherapy. Trends Cell Biol. 2019. 29:396-416. https://doi.org/10.1016/j.tcb.2019.01.003
Starlinger P, Hackl H, Pereyra D, Skalicky S, Geiger E, Finsterbusch M, Tamandl D, Brostjan C, Grünberger T, Hackl M, Assinger A. Predicting Postoperative Liver Dysfunction Based on Blood Derived MicroRNA Signatures. Hepatology. 2019. 69:2636-2651. https://doi.org/10.1002/hep.30572
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. Microbial colonization in adulthood shapes the intestinal macrophage compartment. J Crohns Colitis. 2019. 13:1173-1185. https://doi.org/10.1093/ecco-jcc/jjz036
Huemer F, Rinnerthaler G, Lang D, Hackl H, Lamprecht B, Greil R. Association between antibiotics use and outcome in patients with NSCLC treated with immunotherapeutics. Ann Oncol. 2019. 30:652-653. https://doi.org/10.1093/annonc/mdz021
Trefny M, Rothschild S, Uhlenbrock F, Rieder D, Kasenda B, Stanczak M, Berner F, Kashyap A, Kaiser M, Herzig P, Poechtrager S, Thommen D, Geier F, Savic S, Jermann P, Alborelli I, Schaub S, Stenner-Liewen F, Früh M, Trajanoski Z, Flatz L, Mertz K, Zippelius A, Laubli H. A variant of a killer cell immunoglobulin-like receptor is associated with resistance to PD-1 blockade in lung cancer. Clin Cancer Res. 2019. 25:3026-3034. https://doi.org/10.1158/1078-0432.ccr-18-3041
Trixl L, Rieder D, Amort T, Lusser A. Bisulfite sequencing of RNA for transcriptome-wide detection of 5-methylcytosine. Methods Mol Biol. 2019. 1870:1-21. https://doi.org/10.1007/978-1-4939-8808-2_1
2018
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. Addressing current challenges and future directions in immuno-oncology: expert perspectives from the 2017 NIBIT Foundation Think Tank, Siena, Italy. Cancer Immunol Immunother. 2019. 68:1-9. https://doi.org/10.1007/s00262-018-2285-y
Schubert M, Hackl H, Gassner FJ, Greil R, Geisberger R. Investigating epigenetic effects of activation-induced deaminase in chronic lymphocytic leukemia. PLoS One. 2018. 13:e0208753. https://doi.org/10.1371/journal.pone.0208753
Strutz J, Cvitic S, Hackl H, Kashofer K, Appel HM, Thüringer A, Desoye G, Koolwijk P, Hiden U. Gestational diabetes alters microRNA signatures in human feto-placental endothelial cells depending on fetal sex. Clin Sci. 2018. 132:2437-2449. https://doi.org/10.1042/cs20180825
Sambo F, Finotello F, Lavezzo E, Baruzzo G, Masi G, Peta E, Falda M, Toppo S, Barzon L, Di Camillo B. Optimizing PCR primers targeting the bacterial 16S. BMC Bioinformatics. 2018. 19:343. https://doi.org/10.1186/s12859-018-2360-6
Finotello F, Eduati F. Multi-omics profiling of the tumor microenvironment: paving the way to precision immuno-oncology. Front Oncol. 2018. 8:430. https://doi.org/10.3389/fonc.2018.00430
Hammerl D, Rieder D, Martens JWM, Trajanoski Z, Debets R. Adoptive T cell treatment: new avenues leading to safe targets and powerful allies. Trends Immunol. 2018. 39:921-936. https://doi.org/10.1016/j.it.2018.09.004
Knaus HA, Berglund S, Hackl H, Blackford AL, Zeidner JF, Montiel-Esparza R, Mukhopadhyay R, Vanura K, Blazar BR, Karp JE, Luznik L, Gojo I. Signatures of CD8+ T-cell dysfunction in AML patients and their reversibility with response to chemotherapy. JCI Insight. 2018. 3:120974. https://doi.org/10.1172/jci.insight.120974
Jakic B, Carlsson M, Buszko M, Cappellano G, Ploner C, Onestingel E, Foti M, Hackl H, Demetz E, Dietrich H, Wick C, Wick G. The effects of endurance exercise and diet on atherosclerosis in young and aged ApoE-/- and WT mice. Gerontology. 2019. 65:45-56. https://doi.org/10.1159/000492571
Whitton L, Apostolova G, Rieder D, Dechant G, Rea S, Donohoe G, Morris DW. Genes regulated by SATB2 during neurodevelopment contribute to schizophrenia and educational attainment PLoS Genet. 2018. 14:e1007515. https://doi.org/10.1371/journal.pgen.1007515
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. Nuclear receptor NR2F6 inhibition potentiates responses to PD-L1/PD-1 cancer immune checkpoint blockade. Nat Commun. 2018. 9:1538. https://doi.org/10.1038/s41467-018-04004-2
Xia W, Pessentheiner AR, Hofer D, Amor M, Schreiber R, Schoiswohl G, Eichmann TO, Valenta E, Itariu B, Prager G, Hackl H, Stulnig T, Kratky D, Rülicke R, Bogner-Strauss JG. Loss of Abhd15 impairs the anti-lipolytic action of insulin by altering PDE3B stability and contributes to insulin resistance. Cell Rep. 2018. 23:1948-1961. https://doi.org/10.1016/j.celrep.2018.04.055
Finotello F, Trajanoski Z. Quantifying tumor-infiltrating immune cells from transcriptomics data. Cancer Immunol Immunother. 2018. 67:1031-1040. https://doi.org/10.1007/s00262-018-2150-z
Rohr-Udilova N, Klinglmüller F, Schulte-Hermann R, Stift J, Herac M, Salzmann M, Finotello F, Timelthaler G, Oberhuber G, Pinter M, Reiberger T, Jensen-Jarolim E, Eferl R, Trauner M. Deviations of the immune cell landscape between healthy liver and hepatocellular carcinoma. Sci Rep. 2018. 8:6220. https://doi.org/10.1038/s41598-018-24437-5
Huemer F, Rinnerthaler G, Westphal T, Hackl H, Hutarew G, Gampenrieder SP, Weiss L, Greil R. Impact of antibiotic treatment on immune-checkpoint blockade efficacy in advanced non-squamous non-small cell lung cancer. Oncotarget. 2018. 9:16512-16520. https://doi.org/10.18632/oncotarget.24751
Efremova M, Rieder D, Klepsch V, Charoentong P, Finotello F, Hackl H, Hermann-Kleiter N, Löwer M, Baier G, Krogsdam AM, Trajanoski Z. Targeting immune checkpoints potentiates immunoediting and changes the dynamics of tumor evolution. Nat Commun. 2018. 9:32. https://doi.org/10.1038/s41467-017-02424-0
Huemer F, Thaler J, Piringer G, Hackl H, Pleyer L, Hufnagl C, Weiss L, Greil R. Sidedness and TP53 mutations impact OS in anti-EGFR but not anti-VEGF treated mCRC – an analysis of the KRAS registry of the AGMT (Arbeitsgemeinschaft Medikamentöse Tumortherapie). BMC Cancer. 2018. 18:11. https://doi.org/10.1186/s12885-017-3955-4
Gampenrieder SP, Rinnerthaler G, Hackl H, Pulverer W, Weinhaeusel A, Ilic S, Hufnagl C, Hauser-Kronberger C, Egle A, Risch A, Greil R. DNA methylation signatures predicting bevacizumab efficacy in metastatic breast cancer. Theranostics. 2018. 8:2278-2288. https://doi.org/10.7150/thno.23544
2017
Efremova M, Finotello F, Rieder D, Trajanoski Z. Neoantigens generated by individual mutations and their role in cancer immunity and immunotherapy. Front Immunol. 2017. 8:1679. https://doi.org/10.3389/fimmu.2017.01679
Gamerith G, Rainer J, Huber JM, Hackl H, Trajanoski Z, Koeck S, Lorenz E, Kern J, Kofler R, Kelm JM, Zwierzina H, Amann A. 3D – cultivation of NSCLC cell lines induce gene expression alterations of key cancer-associated pathways and mimic in-vivo conditions. Oncotarget. 2017. 8:112647-112661. https://doi.org/10.18632/oncotarget.22636
Welters MJP, Ma W, Santegoets SJ, Goedemans R, Ehsan I, Jordanova K, van Ham V, van Unen V, Koning F, van Egmond S, Charoentong P, Trajanoski Z, van der Velden VA, van der Burg S. Intratumoral HPV16-specific T-cells constitute a type 1 oriented tumor microenvironment to improve survival in HPV16-driven oropharyngeal cancer. Clin Cancer Res. 2017. https://doi.org/10.1158/1078-0432.CCR-17-2140
Rammer M, Webersinke G, Haitchi-Petnehazy S, Maier E, Hackl H, Charoentong P, Malli T, Steinmair M, Petzer AL, Rumpold H. MicroRNAs and their Role for T stage Determination and Lymph Node Metastasis in Early Colon Carcinoma. Clin Exp Metastasis. 2017. 34:431-440. https://doi.org/10.1007/s10585-017-9863-9
Blunder S, Kõks S, Kõks G, Reimann E, Hackl H, Gruber R, Moosbrugger-Martinz V, Schmuth M, Dubrac S. Enhanced expression of genes related to xenobiotic metabolism in the skin of patients with atopic dermatitis but not with ichthyosis vulgaris. J Invest Dermatol. 2017. 138:98-108. https://doi.org/10.1016/j.jid.2017.08.036
Riml C, Amort T, Rieder D, Gasser C, Lusser A, Micura R*. Osmium-mediated 4sU-to-C transformation as key to study RNA dynamics by sequencing (TUC-seq). Angew Chem Int Ed. 2017. 56:13479-13483. https://doi.org/10.1002/anie.201707465
Willi M, Yoo KH, Reinisch F, Kuhns TM, Lee HK, Wang C, Hennighausen L. Facultative CTCF sites moderate mammary super-enhancer activity and regulate juxtaposed gene in non-mammary cells. Nat Commun. 2017. 8:16069. https://doi.org/10.1038/ncomms16069
Tappeiner E, Finotello F, Charoentong P, Mayer C, Rieder D, Trajanoski Z. NGS data mining pipeline for cancer immunology and immunotherapy. Bioinformatics. 2017. 33:3140-3141. https://doi.org/10.1093/bioinformatics/btx377
Thöni V, Pfister A, Melmer A, Enrich B, Salzmann K, Kaser S, Lamina C, Ebenbichler CF, Hackl H, Tilg H, Moschen AR. Dynamics of bile acid profiles, GLP-1 and FGF19 after laparoscopic gastric banding. J Clin Endocrinol Metab. 2017. 102:2974-2984. https://doi.org/10.1210/jc.2017-00235
Lee HK, Willi M, Wang C, Yang CM,Smith HE, Liu C, Hennighausen L. Functional assessment of CTCF sites at cytokine-sensing mammary enhancers using CRISPR/Cas9 gene editing in mice. Nucleic Acids Res. 2017. 45:4606-4618. https://doi.org/10.1093/nar/gkx185
Weiss L, Melchardt T, Egle A, Hopfinger G, Hackl H, Greil R, Barth J, Rummel M. Influence of body mass index on survival in indolent and mantle cell lymphomas: analysis of the StiL NHL1 trial. Ann Hematol. 2017. 96:1155-1162. https://doi.org/10.1007/s00277-017-3003-0
Rieder D, Finotello F. Analysis of high-throughput RNA bisulfite sequencing data. Methods Mol Biol. 2017. 1562:143-154. https://doi.org/10.1007/978-1-4939-6807-7_10
Deutsch AJ, Rinner B, Pichler M, Troppan K, Pansy K, Bischof M, Fechter K,Hatzl S, Feichtinger J, Wenzl K, Frisch MT, Stiegelbauer V, Prokesch A, Krogsdam AM, Sill H, Thallinger GG, Greinix HT, Wang C, Beham-Schmid C, Neumeister P. NR4A3 suppresses lymphomagenesis through induction of pro-apoptotic genes. Cancer Res. 2017. 77:2375-2386. https://doi.org/10.1158/0008-5472.can-16-2320
Hackl H, Astania K, Wieser R. Molecular and genetic alterations associated with therapy resistance and relapse of acute myeloid leukemia. J Hematol Oncol. 2017. 10:51. https://doi.org/10.1186/s13045-017-0416-0
Finotello F, Trajanoski Z. New strategies for cancer immunotherapy: targeting regulatory T cells. Genome Med. 2017. 9:10. https://doi.org/10.1186/s13073-017-0402-8
Günther J, Resch T, Hackl H, Sattler A, Ebner S, Ritschl PV, Biebl M, Öllinger R, Schneeberger S, Brandacher G, Schwelberger H, Zelger B, Stauch D, Pascher A, Pratschke J, Kotsch K. Identification of NKG2D as senescence marker in zero-hour kidney biopsies is indicative for clinical outcome. Kidney Int. 2017. 91:1447-1463. https://doi.org/10.1016/j.kint.2016.12.018
Amort T, Rieder D, Wille A, Khokhlova-Cubberley D, Riml C, Trixl L, Jia XY, Micura R, Lusser A. Distinct 5-methylcytosine profiles in poly(A)RNA from mouse embryonic stem cells and the brain. Genome Biol. 2017. 18:1. https://doi.org/10.1186/s13059-016-1139-1
Charoentong P, Finotello F, Angelova M*, Mayer C, Efremova M, Rieder D, Hackl H, Trajanoski Z. Pan-cancer immunogenomic analyses reveal genotype-immunophenotype relationships and predictors of response to checkpoint blockade. Cell Rep. 2017. 18:248-262. https://doi.org/10.1016/j.celrep.2016.12.019
Sopper S, Mustjoki S, White D, Hughes T, Valent P, Burchert A, Gjertsen BT, Gastl G, Baldauf M, Trajanoski Z, Giles FJ, Hochhaus A, Ernst T, Schenk T, Janssen J, Ossenkoppele GJ, Porkka K, Wolf D. Reduced CD62L expression on T cells and increased soluble CD62L levels predict molecular response to tyrosine kinase inhibitor (TKI) therapy in early Chronic Phase Chronic Myelogenous Leukemia (CML-CP). J Clin Oncol. 2017. 10:175-184. https://doi.org/10.1200/jco.2016.67.0893
2016
Finotello F, Mastrorilli E, Di Camillo B. Measuring the diversity of the human microbiota with targeted next-generation sequencing. Brief Bioinform. 2016. pii: bbw119. https://doi.org/10.1093/bib/bbw119
Zeng X, Willi M, Shin HY, Hennighausen L, Wang C. Lineage-specific and non-specific cytokine-sensing genes respond differentially to the master regulator STAT5. Cell Rep. 2016. 17:3333-3346. https://doi.org/10.1016/j.celrep.2016.11.079
Jaitner C, Reddy C, Abentung A, Whittle N, Rieder D, Delekate A, Korte M, Jain G, Fischer A, Sananbenesi F, Cera I, Singewald N, Dechant G, Apostolova G. Satb2 determines miRNA expression and long-term memory in the adult central nervous system. Elife. 2016. pii:e17361. https://doi.org/10.7554/elife.17361
Kammerer S, Sokolowski A, Hackl H, Platzer D, Jahn SW, El-Heliebi A, Schwarzenbacher D, Stiegelbauer V, Pichler M, Rezania S, Fiegl H, Peintinger F, Regitnig P, Hoefler G, Schreibmayer W, Bauernhofer T. KCNJ3 is a new independent prognostic marker for estrogen receptor positive breast cancer patients. Oncotarget. 2016. 7:84705-84717. https://doi.org/10.18632/oncotarget.13224
Wolf B, Goebel G, Hackl H, Fiegl H. Reduced mRNA expression levels of NFE2L2 are associated with poor outcome in breast cancer patients. BMC Cancer. 2016. 16:821. https://doi.org/10.1186/s12885-016-2840-x
Willi M, Yoo KH, Wang C, Trajanoski Z, Hennighausen L. Differential cytokine sensitivities of STAT5 enhancers depend on Stat5 autoregulation. Nucleic Acids Res. 2016. 44:10277-10291. https://doi.org/10.1093/nar/gkw844
Lammirato A, Patsch K, Feiereisen F, Maly K, Nofziger C, Paulmichl M, Hackl H, Trajanoski Z, Valovka T, Huber LA, Vietor I. TIS7 induces transcriptional cascade of methylosome components required for muscle differentiation. BMC Biology. 2016. 14:95. https://doi.org/10.1186/s12915-016-0318-6
Rezania S, Kammerer S, Li C, Steinecker-Frohnwieser B, Gorischek A, DeVaney T, Verheyen S, Passegger CA, Tabrizi-Wiszy NG, Hackl H, Platzer D, Zarnani AM, Jahn SW, Malle E, Bauernhofer T, Schreibmayer W. Overexpression of KCNJ3 gene splice variants affects vital parameters of the malignant breast cancer cell line MCF-7 in an opposing manner. BMC Cancer. 2016. 16:628. https://doi.org/10.1186/s12885-016-2664-8
Shin HY, Willi M, Yoo KH, Zeng X, Wang C, Metser G, Henninghausen L. Hierarchy within the mammary STAT-5-driven Wap super-enhancer. Nat Genet. 2016. 48:904-911. https://doi.org/10.1038/ng.3606
Hackl H, Charoentong P, Finotello F, Trajanoski Z. Computational genomics tools for dissecting tumor-immune cell interactions. Nat Rev Genet. 2016. 17:441-458. https://doi.org/10.1038/nrg.2016.67
Melchardt T, Hufnagl C, Weinstock DM, Kopp N, Neureiter D, Tränkenschuh W, Hackl H, Weiss L, Rinnerthaler G, Hartmann TN, Greil R, Weigert O, Egle A. Clonal evolution in relapsed and refractory diffuse large B-cell lymphoma is characterized by high dynamics of subclones. Oncotarget. 2016. 7:51494-51502. https://doi.org/10.18632/oncotarget.9860
Pichrtová M, Arc E, Stöggl W, Kranner I, Hájek T, Hackl H, Holzinger A. Formation of lipid bodies and fatty acid composition changes upon pre-akinete formation in arctic and antarctic Zygnema (Sygnematophyceae, Streptophyta) strains. FEMS Microbiol Ecol. 2016. 92:fiw096. https://doi.org/10.1093/femsec/fiw096
Phan L, Hsu J, Tri LQM, Willi M, Mansour T, Kai Y, Garner J, Lopez J, Busby B. dbVar structural variant cluster set for data analysis and variant comparison. F1000Res. 2016. 5:673. https://doi.org/10.12688/f1000research.8290.2
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 Z, Vesely PW, Hoefler G. An unrevealed role of adipose triglyceride lipase in cancer. Oncotarget. 2016. 7:33832-33840. https://doi.org/10.18632/oncotarget.9418
Sebald J, Willi M, Schoberleitner I*, Krogsdam A, Orth-Höller D, Trajanoski Z, Lusser A.Intestinal microbiome composition and longevity is affected by the chromatin remodeling factor CHD1 in D. melanogaster. PLoS One. 2016. 11:e0153476. https://doi.org/10.1371/journal.pone.0153476
Mlecnik B, Bindea G, Angell, HK, Maby P, Angelova M, Tougeron D, Church S, 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. Integrative Analyses of Colorectal Cancer Show Immunoscore Is a Stronger Predictor of Patient Survival Than Microsatellite Instability. Immunity. 2016. 44:698-711. https://doi.org/10.1016/j.immuni.2016.02.025
Moschen AR, Gerner RR, Wang J*, Klepsch V, Adolph TE, Reider SJ, Hackl H, Pfister A, Schilling J, Moser PL, Kempster SL, Swidsinski A, Orth-Höller D, Weiss G, Baines JF, Kaser A, Tilg H. Lipocalin 2 protects from inflammation and tumorigenesis associated with gut microbiota alterations. Cell Host Microbe. 2016. 19:455-469. https://doi.org/10.1016/j.chom.2016.03.007
Gampenrieder SP, Hufnagl C, Brechelmacher S, Huemer F, Hackl H, Rinnerthaler G, Romeder F, Monzo Fuentes C, Morre P, Hauser-Kronberger C, Mlineritsch B, Greil R. Endothelin-1 genetic polymorphism as predictive marker for bevacizumab in metastatic breast cancer. Pharmacogenomics J. 2016. 17:344–350. https://doi.org/10.1038/tpj.2016.25
Schafferer S, Khurana R, Refolo V, Venezia S, Sturm E, Piatti P, Hechenberger C, Hackl H, Kessler R, Willi M, Gstir R, Krogsdam A, Lusser A, Poewe W, Wenning GK, Hüttenhofer A, Stefanova N. Changes in the miRNA-mRNA regulatory network precede motor symptoms in a mouse model of multiple system atrophy: clinical implications. PLoS One. 2016. 11:e0150705. https://doi.org/10.1371/journal.pone.0150705
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. Serum Autoantibodies in Chronic Prostate Inflammation in Prostate Cancer Patients. PLoS One. 2016. 11:e0147739. https://doi.org/10.1371/journal.pone.0147739
Rinnerthaler G, Hackl H, Gampenrieder SP, Hamacher F, Hufnagl C, Hauser-Kronberger C, Zehentmayr F, Fastner G, Sedlmayer F, Mlineritsch B, Greil R. MiR-16-5p is a stably-expressed housekeeping microRNA in breast cancer tissues from primary and metastatic sites. Int J Mol Sci. 2016. 17:156. https://doi.org/10.3390/ijms17020156
Bhatia M, McGrath KL, Di Trapani G, Charoentong P, Shah F, King MM, Clarke FM, Tonissen KF. The thioredoxin system in breast cancer cell invasion and migration. Redox Biol. 2016. 8:68-78. https://doi.org/10.1016/j.redox.2015.12.004
Rieder D, Amort T, Kugler E, Lusser A, Trajanoski Z. meRanTK: methylated RNA analysis ToolKit. Bioinformatics. 2016. 32:782-785. https://doi.org/10.1093/bioinformatics/btv647
Angelova M, Charoentong P, Hackl H, Trajanoski Z. The colorectal cancer immune paradox revisited. Oncoimmunology. 2016. 5:e1078058. https://doi.org/10.1080/2162402x.2015.1078058
2015
Wille A, Maurer V, Piatti P, Whittle N, Rieder D, Singewald N, Lusser A. Impaired contextual fear extinction learning is associated with aberrant regulation of CHD-type chromatin remodeling factors. Front Behav Neurosci. 2015. 9:313. https://doi.org/10.3389/fnbeh.2015.00313
Posch W, Steger M, Knackmuss U, Blatzer M, Baldauf HM, Doppler W, White TE, Hörtnagl P, Diaz-Griffero F, Lass-Flörl C, Hackl H, Moris A, Keppler OT, Wilflingseder D. Complement-opsonized HIV-1 overcomes restriction in dendritic cells. PLoS Pathog. 2015. 11:e1005005. https://doi.org/10.1371/journal.ppat.1005005
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. miR-22 and miR-29a as members of the androgen receptor transcriptome and modulators of LAMC1 and MCL1 proteins in prostate cancer. Mol Endocrinol. 2015. 29:1037-1054. https://doi.org/10.1210/me.2014-1358
Blatzer M, Jukic E, Posch W, Schöpf B, Binder U, Steger M, Blum G, Hackl H, Gnaiger E, Lass-Flörl C, Wilflingseder D. Amphotericin B resistance in Aspergillus terreus is overpowered by co-application of pro-oxidants. Antioxid Redox Signal. 2015. 23:1424-1438. https://doi.org/10.1089/ars.2014.6220
Müller M, Schmidt O, Angelova M, Faserl K, Weys S, Kremser L, Pfaffenwimmer T, Dalik T, Kraft C, Trajanoski Z, Lindner H, Teis D. The coordinated action of the MVB pathway and autophagy ensures cell survival during starvation. eLife. 2015. 4:e07736. https://doi.org/10.7554/elife.07736
Wolfram D, Hackl H, Eberhart N, Hautz T, Starzl R, Thuille N, Wachter T, Zelger B, Pierer G, Schneeberger S. Differentiation between vascularized composite allograft acute skin rejection and delayed type hypersensitivity reactions based on cytokine analysis. VCA. 2015. 2:9-16. https://doi.org/10.1080/23723505.2015.1044636
Angelova M, Charoentong P, Hackl H, Fischer M, Snajder R, Krogsdam AM, Waldner MJ, Bindea G, Mlecnik B, Galon J, Trajanoski Z. Characterization of the immunophenotypes and the antigenomes reveal distinct tumor escape mechanisms and novel targets for immunotherapy of colorectal cancers. Genome Biol. 2015. 16:64. https://doi.org/10.1186/s13059-015-0620-6
Heller G, Rommer A, Steinleitner K, Etzler J, Hackl H, Heffeter P, Tomasich E, Filipits M, Steinmetz B, Topakian T, Klingenbrunner S, Ziegler B, Spittler A, Zöchbauer-Müller S, Berger W, Wieser R. EVI1 promotes tumor growth via transcriptional repression of MS4A3. J Hematol Oncol. 2015. 8:28. https://doi.org/10.1186/s13045-015-0124-6
Li C, Rezania S, Kammerer S, Sokolowski A, Devaney T, Gorischek A, Jahn S, Hackl H, Groschner K, Windpassinger C, Malle E, Bauernhofer T, Schreibmayer W. Piezo1 forms mechanosensitive ion channels in the human MCF7 human breast cancer cell line. Sci Rep. 2015. 5:8364. https://doi.org/10.1038/srep08364
Perkhofer S, Zenzmaier C, Frealle E, Blatzer M, Hackl H, Sartori B, Lass-Flörl C. Differential gene expression in Aspergillus fumigatus induced by human platelets in vitro. Int J Med Microbiol. 2015. 305:327-338. https://doi.org/10.1016/j.ijmm.2015.01.002
Wolfram D, Morandi EM, Eberhart N, Hautz T, Hackl H, Zelger B, Riede G, Wachter T, Dubrac S, Ploner C, Pierer G, Schneeberger S. Differentiation between acute skin rejection in allotransplantation and Tcell mediated skin inflammation based on gene expression analysis. Biomed Res Int. 2015. 2015:259160. https://doi.org/10.1155/2015/259160
Wilflingseder D, Schroll A, Hackl H, Gallasch R, Frampton D, Pancino G, Sáez-Cirián A, Kellam P, Trajanoski Z, Geijtenbeek TB, Weiss G, Lass-Flörl C, Lambotte O, Weiss L, Posch W. Triggering CD11b/c on HIV-exposed DCs promotes immediate Th17 polarization. J Infect Dis. 2015. 212:44-56. https://doi.org/10.1093/infdis/jiv014
2014
Hautz T, Wolfram D, Eberhart N, Hackl H, Messner F, Weissenbacher A, Kimelman M, Zelger BG, Zelger B, Schneeberger S. The impact of skin type and area on skin rejection in limb transplantation. VCA. 2014. 1:42-49. https://doi.org/10.4161/23723505.2014.973795
Dander A, Baldauf M, Sperk M, Pabinger S, Hiltpolt B, Trajanoski Z. Personalized Oncology Suite: Integrating next-generation sequencing data and whole-slide bioimages. BMC Bioinformatics. 2014. 15:306. https://doi.org/10.1186/1471-2105-15-306
Koller D, Hackl H, Bogner-Strauss JG, Hermetter A. Effects of oxidized phospholipids on gene expression in RAW 264.7 macrophages: A microarray study. PLoS One. 2014. 9:e110486. https://doi.org/10.1371/journal.pone.0110486
Trajanoski Z, Maccalli C, Mennonna D, Casorati G, Parmiani G, Dellabona P. Somatically mutated tumor antigens in the quest for a more efficacious patient-oriented immunotherapy of cancer. Cancer Immunol Immunother. 2014. 64:99-104. https://doi.org/10.1007/s00262-014-1599-7
Nasso S, Hartler J, Di Camillo B, Mechtler K, Trajanoski Z, Toffolo G. 3DSpectra: A 3-Dimensional Quantification Algorithm For LC-MS Labeled Profile Data. J Proteomics. 2014. 112C:156-165. https://doi.org/10.1016/j.jprot.2014.08.017
Schweiger D, Trajanoski Z, Pabinger S. SPARQLGraph: a web-based platform for graphically querying biological Semantic Web databases. BMC Bioinformatics. 2014. 15:279. https://doi.org/10.1186/1471-2105-15-279
Hackl H, Steinleitner K, Lind K, Hofer S, Tosic N, Pavlovic S, Suvajdzic N, Sill H, Wieser R. A gene expression profile associated with relapse of cytogenetically normal acute myeloid leukemia is enriched for leukemia stem cell genes. Leuk Lymphoma. 2015. 56:1126-1128. https://doi.org/10.3109/10428194.2014.944523
Melchardt T, Troppan K, Weiss L, Hufnagl C, Neureiter D, Tränkenschuh W, Hopfinger G, Magnes T, Deutsch A, Neumeister P, Hackl H, Greil R, Pichler M, Egle A. A modified scoring of the NCCN-IPI is more accurate in the elderly and is improved by albumin and β2-microglobulin. Br J Haematol. 2014. 168:239-45. https://doi.org/10.1111/bjh.13116
Steinmetz B, Hackl H, Slabáková E, Schwarzinger I, Smejová M, Spittler A, Arbesu I, Shehata M, Souček K, Wieser R. The oncogene EVI1 enhances transcriptional and biological responses of human myeloid cells to all-trans retinoic acid. Cell Cycle. 2014. 13:2931-2943. https://doi.org/10.4161/15384101.2014.946869
Prokesch A, Smorlesi A, Perugini J, Manieri M, Ciarmela P, Mondini E, Trajanoski Z, Kristiansen K, Giordano A, Bogner-Strauss JG, Cinti S. Molecular aspects of adipo-epithelial transdifferentiation in mouse mammary gland. Stem Cells. 2014. 32:2756–2766. https://doi.org/10.1002/stem.1756
Wolfram D, Starzl R, Hackl H, Barclay D, Hautz T, Zelger B, Brandacher G, Lee WPA, Eberhart N, Vodovotz Y, Pratschke J, Pierer G, Schneeberger S. Insights from Computational Modeling in Inflammation and Acute Rejection in Limb Transplantation. PLoS One. 2014. 9:e99926. https://doi.org/10.1371/journal.pone.0099926
Tymoszuk P, Charoentong P, Hackl H, Spilka R, Müller-Holzner E, Trajanoski Z, Obrist P, Revillion F, Fiegl H, Doppler W. High STAT1 mRNA levels but not its tyrosine phosphorylation are associated with macrophage infiltration and bad prognosis in breast cancer. BMC Cancer. 2014. 14:257. https://doi.org/10.1186/1471-2407-14-257
Deutsch A, Rinner B, Wenzl K, Pichler M, Troppan K, Steinbauer E, Schwarzenbacher D, Reitter S, Feichtinger J, Tierling S, Prokesch A, Scheideler M, Krogsdam AM, Thallinger G, Schaider H, Beham-Schmid C, Neumeister P. NR4A1-mediated apoptosis suprresses lymphomagenesis and is associated with a favorable cancer specific survival in patients with aggressive B-cell lymphomas. Blood. 2014. 123:2367-77. https://doi.org/10.1182/blood-2013-08-518878
Dander A, Pabinger S, Sperk M, Fischer M, Stocker G, Trajanoski Z. SeqBench: Integrated solution for the management and analysis of exome sequencing data. BMC Res Notes. 2014. 7:43. https://doi.org/10.1186/1756-0500-7-43
Pabinger S, Snajder R, Hardiman T, Willi M, Dander A, Trajanoski Z. MEMOSys 2.0: an update of the bioinformatics database for genome-scale models and genomic data. Database. 2014. 2014:bau004. https://doi.org/10.1093/database/bau004
2013
Dander A, Mueller L Gallasch R, Pabinger S, Emmert-Streib F, Graber A, Dehmer M. [COMMODE] A Large-Scale Database of Molecular Descriptors using compounds from PubChem. Source Code Biol Med. 2013. 8:22. https://doi.org/10.1186/1751-0473-8-22
Gallasch R, Efremova M, Charoentong P, Hackl H, Trajanoski Z. Mathematical models for translational and clinical oncology. J Clin Bioinforma. 2013. 3:23. https://doi.org/10.1186/2043-9113-3-23
Pessentheiner AR, Pelzmann HJ, Walenta E, Schweiger M, Groschner LN, Graier WF, Kolb D, Uno K, Miyazaki T, Nitta A, Rieder D, Prokesch A, Bogner-Strauss JG. N-acetyltransferase 8-like accelerates lipid turnover and increases energy expenditure in brown adipocytes. J Biol Chem. 2013. 288:36040-36051. https://doi.org/10.1074/jbc.m113.491324
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. microRNAs in nociceptive circuits as predictors of future clinical applications. Front Mol Neurosci. 2013. 6:33. https://doi.org/10.3389/fnmol.2013.00033
Cvitic S, Longtine MS, Hackl H, Wagner K, Nelson MD, Desoye G, Hiden U. The human placental sexome differs between trophoblast epithelium and villous vessel endothelium. PLoS One. 2013. 8:e79233. https://doi.org/10.1371/journal.pone.0079233
Walenta E, Pessentheiner AR, Pelzmann HJ, Deutsch A, Goeritzer M, Kratky D, Hackl H, Oh DY, Prokesch A, Bogner-Strauss JG. α/β-hydrolase domain containing protein 15 (Abhd15): an adipogenic gene protecting from apoptosis. PLoS One. 2013. 8:e79134. https://doi.org/10.1371/journal.pone.0079134
Rieder D, Ploner C, Krogsdam AM, Stocker G, Fischer M, Scheideler M, Dani C, Amri EZ, Müller WG, McNally JG, Trajanoski Z. Co-expressed genes prepositioned in spatial neighborhoods stochastically associate with SC35 speckles and RNA polymerase II factories. Cell Mol Life Sci. 2013. 71:1741-59. https://doi.org/10.1007/s00018-013-1465-3
Bindea G, Mlecnik B, Tosolini M, Kirilovsky A, Waldner M, Obenauf AC, Angell H, Frederiksen T, Lafontaine L, Berger A, Bruneval P, Fridman WH, Becker C, Speicher MR, Trajanoski Z, Galon J. Spatio-temporal dynamics of intratumoral cells reveal the immune landscape in human cancer. Immunity. 2013. 39:782-795. https://doi.org/10.1016/j.immuni.2013.10.003
Rommer A, Steinleitner K, Hackl H, Schneckenleithner C, Engelmann M, Scheideler M, Vlatkovic I, Vanura K, Kralovics R, Cerny-Reiterer S, Valent P, Sill H, Wieser R. Overexpression of primary microRNA 221/222 in acute myeloid leukemia. BMC Cancer. 2013. 13:364. https://doi.org/10.1186/1471-2407-13-364
Snajder R, Trajanoski Z, Hackl H. GPViz: dynamic visualization of genomic regions and variants affecting protein domains. Bioinformatics. 2013. 29:2195-2196. https://doi.org/10.1093/bioinformatics/btt354
Magoc T, Pabinger S, Canzar S, Liu X, Su Q, Puiu D, Tallon LJ, Salzberg SL. GAGE-B: an evaluation of genome assemblers for bacterial organisms. Bioinformatics. 2013. 29:1718-1725. https://doi.org/10.1093/bioinformatics/btt273
Kienesberger PC, Pulinilkunnil T, Nagendran J, Young ME, Bogner-Strauss JG, Hackl H, Khadour R, Heydari E, Haemmerle G, Zechner R, Kershaw EE, Dyck JRB. Early structural and metabolic cardiac remodelling in response to inducible adipose triglyceride lipase ablation. Cardiovasc Res. 2013. 99:442-451. https://doi.org/10.1093/cvr/cvt124
Greussing R, Hackl M, Charoentong P, Pauck A, Monteforte R, Hofer E, Scheideler M, Neuhaus M, Micutkova L, Mueck C, Trajanoski Z, Grillari J, Jansen-Dürr P. Identification of microRNA-mRNA functional interactions in UVB-induced senescence of human diploid fibroblasts. BMC Genomics. 2013. 14:224. https://doi.org/10.1186/1471-2164-14-224
Prodan R, Sperk M. Scientific computing with Google App Engine. Future Generation Computer Systems. 2013. 29:1851-1859. https://doi.org/10.1016/j.future.2012.12.018
Pabinger S, Trajanoski Z. Genome-scale model management and comparison. Methods Mol Biol. 2013. 985:3-16. https://doi.org/10.1007/978-1-62703-299-5_1
Rommer A, Steinmetz B, Herbst F, Hackl H, Heffeter P, Heilos D, Filipits M, Steinleitner K, Hemmati S, Herbacek I, Schwarzinger I, Hartl K, Rondou P, Glimm H, Karakaya K, Krämer A, Berger W, Wieser R. EVI1 inhibits apoptosis induced by antileukemic drugs via upregulation of CDKN1A/p21/WAF in human myeloid cells. PLoS One. 2013. 8:e56308. https://doi.org/10.1371/journal.pone.0056308
Pabinger S, Dander A, Fischer M, Snajder R, Efremova M, Sperk M, Krabichler B, Speicher MR, Zschocke J, Trajanoski Z. A survey of tools for variant analysis of next-generation genome sequencing data. Brief Bioinf. 2013. 15:256-78. https://doi.org/10.1093/bib/bbs086
Duszka K, Bogner-Strauss JG, Hackl H, Rieder D, Neuhold C, Prokesch A, Trajanoski Z, Krogsdam AM. Nr4a1 is required for fasting-induced Pparg2 down regulation in white adipose. Mol Endocrinol. 2013. 27:135-149. https://doi.org/10.1210/me.2012-1248
2012
Rieder D, Trajanoski Z, McNally J. Transcription factories. Front Genet. 2012. 3:221. https://doi.org/10.3389/fgene.2012.00221
Villar D, Ortiz-Barahona A, Gómez-Maldonado L, Pescador N, Sánchez-Cabo F, Hackl H, Rodriguez BA, Trajanoski Z, Dopazo A, Huang TH, Yan PS, Del Peso L. Cooperativity of Stress-Responsive Transcription Factors in Core Hypoxia-Inducible Factor Binding Regions. PLoS One. 2012. 7:e45708. https://doi.org/10.1371/journal.pone.0045708
Charoentong P, Angelova M, Efremova M, Gallasch R, Hackl H, Galon J, Trajanoski Z. Bioinformatics for Cancer Immunology and Immunotherapy. Cancer Immunol Immunother. 2012. 61:1885-903. https://doi.org/10.1007/s00262-012-1354-x
Fischer M, Snajder R, Pabinger S, Dander A, Schossig A, Zschocke J, Trajanoski Z, Stocker G. SIMPLEX: cloud-enabled pipeline for the comprehensive analysis of exome sequencing data. PLoS One. 2012. 7:e41948. https://doi.org/10.1371/journal.pone.0041948
Schossig A, Wolf NI, Fischer C, Fischer M, Stocker G, Pabinger S, Dander A, Steiner B, Tönz O, Kotzot D, Haberlandt E, Amberger A, Burwinkel B, Wimmer K, Fauth C, Grond-Ginsbach C, Koch MJ, Deichmann A, von Kalle C, Bartram CR, Kohlschütter A, Trajanoski Z, Zschocke J. Mutations in ROGDI cause epileptic encephalopathy and amelogenesis imperfecta (Kohlschütter-Tönz syndrome). Am J Hum Genet. 2012. 90:701-707. https://doi.org/10.1016/j.ajhg.2012.02.012
Lassance L, Miedl H, Konya V, Heinemann A, Ebner B, Hackl H, Desoye G, Hiden U. Differential response of arterial and venous endothelial cells to extracellular matrix is modulated by oxygen. Histochem Cell Biol. 2012. 137:641-655. https://doi.org/10.1007/s00418-012-0917-4
Thallinger GG, Obermayr E, Charoentong P, Tong D, Trajanoski Z, Zeilinger R. A Sequence Based Validation of Gene Expression Microarray Data. Am J Bioinform. 2012. 1:1-9. https://doi.org/10.3844/ajbsp.2012.1.9
2011
Dander A, Handler M, Netzer M, Pfeifer B, Seger M, Baumgartner C. [KD3] A Workflow-Based Application for Exploration of Biomedical Data Sets. LNCS. 2011. 6990. https://doi.org/10.1007/978-3-642-23740-9_7
Augsten M, Hackl H, Ebner B, Chemelli A, Glatter O, Marsche G, Lang U, Desoye G, Wadsack C. Fetal HDL/apoE: A novel regulator of gene expression in human placental endothelial cells. Physiol Genomics. 2011. 43:1255-1262. https://doi.org/10.1152/physiolgenomics.00109.2011
Hakim-Weber R, Krogsdam AM, Jørgensen C, Fischer M, Prokesch A, Bogner-Strauss JG, Bornstein SR, Hansen JB, Madsen L, Kristiansen K, Trajanoski Z, Hackl H. Transcriptional regulatory program in wild-type and retinoblastoma gene-deficient mouse embryonic fibroblasts during adipocyte differentiation. BMC Res Notes. 2011. 4:157. https://doi.org/10.1186/1756-0500-4-157
Hofer E, Laschober G, Hackl M, Thallinger GG, Lepperdinger G, Grillari J, Jansen-Dürr P, Trajanoski Z. GiSAO.db: a database for ageing research. BMC Genomics. 2011. 12:262. https://doi.org/10.1186/1471-2164-12-262
Pinent M, Prokesch A, Hackl H, Voshol PJ, Klatzer A, Walenta E, Panzenböck U, Kenner L, Trajanoski Z, Höfler G, Bogner-Strauss JG. Adipose triglyceride lipase and hormone-sensitive lipase are involved in fat loss in JunB-deficient mice. Endocrinology. 2011. 152:2678-2689. https://doi.org/10.1210/en.2010-1477
Sanchez-Cabo F, Rainer J, Dopazo A, Trajanoski Z, Hackl H. Insights into global mechanisms and disease by gene expression profiling. Methods Mol Biol. 2011. 719:269-98. https://doi.org/10.1007/978-1-61779-027-0_13
Pabinger S, Rader R, Agren R, Nielsen J, Trajanoski Z. MEMOSys: Bioinformatics platform for genome-scale metabolic models. BMC Syst Biol. 2011. 5:20. https://doi.org/10.1186/1752-0509-5-20
Mlecnik B, Tosolini M, Kirilovsky A, Berger A, Bindea G, Meatchi T, Bruneval P, Trajanoski Z, Fridman W-H, Pages F, Galon J. Histopathological-based prognostic factors of colorectal cancers are associated with the state of the local immune reaction. J Clin Oncol. 2011. 29:610-618. https://doi.org/10.1200/jco.2010.30.5425
Mueller LA, Kugler KG, Dander A, Graber A, Dehmer M. QuACN: an R package for analyzing complex biological networks quantitatively. Bioinformatics. 2011. 27:140-141. https://doi.org/10.1093/bioinformatics/btq606
Aleksic K, Lackner C, Geigl JB, Auer M, Ulz P, Fischer M, Trajanoski Z, Otte M, Speicher MR. Evolution of genomic instability in the DEN mouse hepatocelluar carcinoma model. Hepatology. 2011. 53:895-904. https://doi.org/10.1002/hep.24133
Bennett KL, Funk M, Tschernutter M, Breitwieser FP, Planyavsky M, Ubaida Mohien C, Müller A, Trajanoski Z, Colinge J, Superti-Furga G. Proteomic Analysis of Human Cataract Aqueous Humour: Comparison of One-1 dimensional Gel LCMS with Two-dimensional LCMS of Unlabelled and iTRAQ®-labelled Specimens. J Proteomics. 2011. 74:151-166. https://doi.org/10.1016/j.jprot.2010.10.002
Prokesch A, Bogner-Strauss JG, Hackl H, Rieder D, Neuhold C, Walenta E, Krogsdam A, Scheideler M, Papak C, Wong WC, Vinson C, Eisenhaber F, Trajanoski Z. Arxes: Retrotransposed genes required for adipogenesis. Nucl Acids Res. 2011. 39:3224-3239. https://doi.org/10.1093/nar/gkq1289
2010
Laschober G, Ruli D, Hofer E, Carmona-Gutierrez D, Ring J, Hutter E, Muck C, Ruckenstuhl C, Micutkova L, Brunauer R, Jamnig A, Trimmel D, Herndler-Brandstetter D, Sampson N, Breitenbach M, Fröhlich K-U, Grubeck-Loebenstein B, Berger P, Wieser M, Grillari-Voglauer R, Thallinger G, Grillari J, Trajanoski Z, Madeo F, Lepperdinger G, Jansen-Dürr P. Identification of evolutionarily conserved genetic regulators of cellular aging. Aging Cell. 2010. 9:1084-1097. https://doi.org/10.1111/j.1474-9726.2010.00637.x
Hackl H, Stocker G, Pornpimol C, Mlecnik B, Bindea G, Galon J, Trajanoski Z. Information technology solutions for integration of biomolecular and clinical data in the identification of new cancer biomarkers and targets for therapy. Pharmacol Ther. 2010. 128:488-498. https://doi.org/10.1016/j.pharmthera.2010.08.012
Hackl H, Rommer A, Konrad TA, Nassimbeni C, Wieser R. Tetracycline regulator expression alters the transcriptional program of mammalian cells. PLoS One. 2010. 5:e13013. https://doi.org/10.1371/journal.pone.0013013
Merkel O, Hamacher F, Laimer D, Sifft E, Trajanoski Z, Scheideler M, Egger G, Hassler M, Thallinger C, Schmatz A, Turner S, Greil R, Kenner L. Identification of differential and functionally active miRNAs in both ALK+ and ALK- anaplastic large cell lymphoma. Proc Natl Acad Sci U S A. 2010. 107:16228-16233. https://doi.org/10.1073/pnas.1009719107
Bogner-Strauss JG, Prokesch A, Sanchez-Cabo F, Rieder D, Hackl H, Duszka K, Krogsdam A, Di Camillo B, Walenta E, Klatzer A, Lass A, Pinent M, Wong WC, Eisenhaber F, Trajanoski Z. Reconstruction of gene association network reveals a transmembrane protein required for adipogenesis and targeted by PPARg. Cell Mol Life Sci. 2010. 67:4049-4064. https://doi.org/10.1007/s00018-010-0424-5
Zaragosi LE, Wdziekonski B, Villageois P, Keophiphath M, Maumus M, Tchkonia T, Bourlier V, Mohsen-Kanson T, Ladoux A, Elabd C, Scheideler M, Trajanoski Z, Takashima Y, Amri EZ, Lacasa D, Sengenes C, Ailhaud G, Clément, K, Bouloumie A, Kirkland, JL, Dani C. Activin A plays a critical role in proliferation and differentiation of human adipose progenitors. Diabetes. 2010. 59:2513-2521. https://doi.org/10.2337/db10-0013
Ubaida Mohien C, Hartler J, Breitwieser F, Rix U, Remsing Rix L, Winter GE, Thallinger GG, Bennett KL, Superti-Furga G, Trajanoski Z, Colinge J. MASPECTRAS 2: An Integration and Analysis Platform for Proteomic Data. Proteomics. 2010. 10:2719-2722. https://doi.org/10.1002/pmic.201000075
Nusshold C, Kollroser M, Koefeler H, Rechberger G, Reicher H, Uellen A, Bernhart E, Waltl S, Kratzer I, Hermetter A, Hackl H, Trajanoski Z, Hrzenjak A, Malle E, Sattler W. Hypochlorite-modification of sphingomyelin generates chlorinated lipid species that induce apoptosis and proteome alterations in dopaminergic PC12 neurons in vitro. Free Radic Biol Med. 2010. 48:1588-1600. https://doi.org/10.1016/j.freeradbiomed.2010.02.037
Mlecnik B, Sanchez-Cabo F, Charoentong P, Bindea G, Pages F, Berger A, Galon J, Trajanoski Z. Data integration and exploration for the identification of molecular mechanisms in tumor-immune cells interaction. BMC Genomics. 2010. 11 Suppl 1:S7. https://doi.org/10.1186/1471-2164-11-s1-s7
Hackl M, Brunner S, Fortschegger K, Schreiner C, Micutkova L, Mück C, Laschober GT, Lepperdinger G, Sampson N, Berger P, Herndler-Brandstätter D, Wieser M, Kühnel H, Strasser A, Rinnerthaler M, Breitenbach M, Mildner M, Eckhart L, Tschachler E, Trost A, Bauer JW, Papak C, Trajanoski Z, Scheideler M, Grillari-Voglauer R, Grubeck-Loebenstein B, Jansen-Dürr P, Grillari J. miR-17, miR-19b, miR-20a and miR-106a are down-regulated in human aging. Aging Cell. 2010. 9:291-296. https://doi.org/10.1111/j.1474-9726.2010.00549.x
Mlecnik B, Tosolini M, Charoentong P, Kirilovsky A, Bindea G, Berger A, Camus M, Gillard M, Bruneval P, Fridman WH, Pages F, Trajanoski Z, Galon J. Biomolecular network reconstruction identifies T cell homing factors associated with survival in colorectal cancer. Gastroenterology. 2010. 138:1429-1440. https://doi.org/10.1053/j.gastro.2009.10.057
Wieser R, Scheideler M, Hackl H, Engelmann M, Schneckenleithner C, Hiden K, Papak C, Trajanoski Z, Sil H, Fonatsch C. microRNAs in acute myeloid leukemia: expression patterns, correlations with genetic and clinical parameters, and prognostic significance. Genes Chromosomes Cancer. 2010. 49:193-203. https://doi.org/10.1002/gcc.20740