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Publications


2025 

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.   |   in press
 
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.   |   in press
 
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.   |   in press
 
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.   |   in press
 
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   |  
 
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.   |   in press
 
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.   |   in press
 
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   |   PMID:40103613
 
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   |   PMID:3998602
 
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   |   PMID:39389186
 
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   |   PMID:40201592
 
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.   |   PMID: 39842611
 
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   |   PMID: 39870664
 
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   |   PMID: 39819502
 
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.   |   in press
 

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   |   PMID: 39813315
 
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   |   PMID:39663448
 
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   |   PMID:39684722
 
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.   |   PMID: 39675567
 
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   |   PMID: 39580261
 
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.
Gene. 2024. 15:1475   |   PMID:39596675
 
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   |   PMID:39669575
 
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   |   PMID:39925909
 
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.   |   PMID:39691712
 
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   |   PMID:39490928
 
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   |   PMID:39409015
 
Horn V, Cancino CA, Steinheuer LM, Obermayer B, Fritz K, Nguyen AL, Juhran KS, Plattner C, Bösel D, Oldenburg L, Burns M, Schulz AR, Saliutina M, Mantzivi E, Lissner D, Conrad T, Mashreghi MF, Zundler S, Sonnenberg E, Schumann M, Haag LM, Beule D, Flatz L; TRR241 IBDome Consortium; Trjanoski Z, D'Haens G, Weidinger C, Mei HE, Siegmund B, Thurley K, Hegazy AN. Multimodal profiling of peripheral blood identifies proliferating circulating effector CD4+ T cells as predictors for response to integrin α4β7-blocking therapy in inflammatory bowel disease.
Gastroenterology. 2024. 168:327-343   |   PMID:39343250
 
zur Nedden S, Safari MS, Weber D, Kuenkel L, Garmsiri C, Lang L, Orset C, Freret T, Haelewyn B, Motze M, Kwiatkowski M, Sarg B, Faserl K, Savic D, Skvortsova I, Krogsdam A, Carollo S, Trajanoski Z, Oberacher H, Zlotek D, Ostermaier F, Cameron A, Baier G, Baier-Bitterlich G. Protein kinase N1 deficiency results in upregulation of cerebral energy metabolism and is highly protective in in vivo and in vitro stroke models.
Metabolism. 2024. 161:156039   |   PMID:39332493
 
Mildner FO*, Sykora MM*, Hackl H, Amann A, Zelger B, Sprung S, Buch ML, Nocera F, Moser P, Maier H, Augustin F, Manzl C, Kocher F, Pircher A, Lindenmannm J, Mykoliuk I, Raftopoulou S, Kargl J, Wolf D, Sopper S, Gamerith G. Soluble PD-L1 shows no association to relapse and overall survival in early stage non-small cell lung cancer (NSCLC).
Lung Cancer. 2024. 196:107955   |   PMID:39306924
 
Lehmann M, Weixler B, Elezkurtaj S, Loddenkemper C; TRR241 IBDome Consortium; Kühl AA, Siegmund B. Spatial Single Cell Profiling Using Imaging Mass Cytometry: Inflammatory Versus Penetrating Crohn's Disease.
J Crohns Colitis. 2024. 18:1305-1318   |   PMID:38465390
 
Hautz T, Hackl H, Gottschling H, Gronauer R, Hofmann J, Salcher S, Zelger B, Oberhuber R, Cardini B, Weissenbacher A, Resch T, Troppmair J, Schneeberger S. Transcriptomic signatures during normothermic liver machine perfusion correspond with graft quality and predict the early graft function.
EBioMedicine. 2024. 108:105330   |   PMID:39299005
 
Amor M*, Diaz M*, Bianco V, Svecla M, Schwarz B, Rainer S, Pirchheim A, Schooltink L, Mukherjee S, Grabner G, Beretta G, Lamina C, Norata GD, Hackl H, Kratky D. Identification of regulatory networks and crosstalk factors in brown adipose tissue and liver of cold-exposed cardiometabolic mouse model.
Cardiovasc Diabetol. 2024. 23:298   |   PMID: 39143620
 
Hargitai R, Parráková L, Szatmári T, Monfort-Lanzas P, Galbiati V, Audouze K, Jornod F, Staal Y, Burla S, Chary A, Gutleb A, Lumniczky K, Vandebriel R, Gostner JM. Chemical respiratory sensitization - Current status of mechanistic understanding, knowledge gaps and possible identification methods of sensitizers.
Front Toxicol. 2024. 6:1331803   |   PMID:39135743
 
Brandt MP, Vakhrusheva O, Hackl H, Daher T, Tagscherer K, Roth W, Tsaur I, Handle F, Eigentler A, Culig Z, Thomas C, Erb HH, Haferkamp A, Jüngel E, Puhr M. Inhibition of the sterol regulatory element binding protein (SREB-P) SREBF-1 overcomes docetaxel resistance in advanced prostate cancer.
Am J Pathol. 2024.   |   PMID:39168364
 
Bauer M, Monecke A, Hackl H, Wilfer A, Jäkel N, Bläker H, Al-Ali H, Seliger B, Wickenhauser. Association of immune evasion in myeloid sarcomas with disease manifestation and patients' survival.
Front Immunol. 2024. 15:1396187   |   PMID:39170623
 
Lapuenta-Santana O, Sturm G, Kant J, Ausserhofer M, Zackl C, Zopoglou M, McGranahan N, Rieder D, Trajanoski Z, da Cunha Carvalho de Miranda NF, Eduati F, Finotello F. Multimodal analysis unveils tumor microenvironment heterogenity linked to immune activity and evasion.
iScience. 2024. 27:110529   |   PMID:39161957
 
Brunnthaler L, Hammond T, Pereyra D, Santol J, Probst J, Laferl V, Resch U, Aiad M, Janoschek AS, Gruenberger T, Hackl H, Starlinger P, Assinger A. HMGB1-mediated cell death - a crucial element in post-hepatectomy liver failure.
Int J Mol Sci. 2024. 25:7150   |   PMID:39000266
 
Monfort-Lanzas P, Rusu CE, Parrakova L, Karg CA, Kernbichler DE, Rieder D, Lackner P, Hackl H, Gostner JM. ExonSurfer: A web-tool to design primers at exon-exon junctions.
BMC Genomics. 2024. 25:594   |   PMID:38867172
 
Heidegger I*, Frantzi M*, Salcher S*, Tymoszuk P, Martowicz A, Gomez-Gomez E, Blanca A, Lendinez Cano G, Latosinska A, Mischak H, Vlahou A, Langer C, Aigner F, Puhr M, Trajanoski Z, WolfD, Pircher A. Alterations of collagen-related transcriptome, proteome and urinome hallmark clinically significant prostate cancer.
Eur Urol Oncol. 2024.   |   PMID:38851995
 
Ammann M, Gudmundsdottir H, Hackl H, Antwi SKA, Santol J, Habermann EB, Thiels CA, Warner SG, Truty MJ, Kendrick ML, Smoot RL, Nagorney DM, Cleary SP, Halfdanarson TR, Starlinger PP. Neuroendocrine Tumors of Unknown Primary in the Setting of Cytoreductive Hepatectomy.
Ann Surg Oncol. 2024. 31:4931-4941   |   PMID:38717544
 
Feroz B*, Pan TL*, Leitner K, Ebner C, Steger K, Kildal W, Kristensen GB, Zeimet AG, Hackl H, Fiegl H, Marth C, Wieser V. Tumoral PD1 expression in endometrial carcinoma is a prognostic marker for patient outcome.
Int J Gynecol Cancer. 2024.   |   PMID: 38969503
 
Rusu EC, Monfort-Lanzas P, Bertran L, Barrientos-Riosalido A, Solé E, Mahmoudian R, Aguilar C, Briansó S, Mohamed F, Garcia S, Camaron J, Auguet T. Towards understanding post-COVID-19 condition: a systematic meta-analysis of transcriptomic alterations with sex-specific insights
Comput Biol Med. 2024. 175:108507   |   PMID:38657468
 
Erkert L, Gamez Belmonte R, Kabisch M, Schödel L, Patankar JV, Gonzalez Acera M, Mahapatro M, Bao L-L, Plattner C, Kühl AA, Shen J, Serneels L, De Strooper B, TRR241 IBDome Consortium, Neurath MF, Wirtz S, Becker C. Alzheimer's disease-related presenilins are key to intestinal epithelial cell function and gut immune homeostasis.
Gut. 2024.   |   PMID:38684238
 
Spathopoulou A, Fenkart G, Marteau V, Podlesnic M, Kruszewski K, Koskuvi M, Réthelyi J, Apáti Á, Conti L, Ku M, Koal T, Müller U, Talmazan R, Ojansuu I, Vaurio O, Lähteenvuo M, Lehtonen Š, Mertens J, Günther K, Tiihonen J, Koistinaho J, Trajanoski Z, Lindlbauer T, Kipura T, Hotze M, Gabassi E, Kwiatkowski M, Edenhofer F. Integrative metabolomics-genomics analysis identifies key networks in a stem cell-based model of schizophrenia.
Mol Psychiatry. 2024.   |   PMID:38684795
 
Hornsteiner F, Vierthaler J, Strandt H, Resag A, Fu Z, Ausserhofer M, Tripp CH, Dieckmann S, Kanduth M, Farrand K, Bregar S, Nemati N, Hermann-Kleiter N, Seretis A, Morla S, Mullins DW, Finotello F, Trajanoski Z, Wollmann G, Ronchese F, Schmitz M, Hermans IF, Stoitzner. Tumor-targeted therapy with BRAF-inhibitor recruits activated dendritic cells to promote tumor immunity in melanoma.
J Immunother Cancer. 2024. 12:e008606   |   PMID:38631706
 
Vogel GF, Podpeskar A, Rieder D, Salzer H, Garczarczyk-Asim D, Wang L, Abuduxikuer K, Wang JS, Scharrer A, Faqeih EI, Aseeri AT, Vodopiutz J, Heilos A, Pichler J, Huber WD, Müller T, Knisely AS, Janecke AR. Kinesin family member 12-related hepatopathy: A generally indolent disorder with elevated gamma-glutamyl-transferase activity.
Clin Genet. 2024. 106:224-233   |   PMID:38553872
 
Salcher S, Heidegger I, Untergasser G, Fotakis G, Scheiber A, Martowicz A, Noureen A, Krogsdam A, Schatz C, Schäfer G, Trajanoski Z, Wolf D, Sopper S, Pircher A. Comparative analysis of 10X Chromium vs. BD Rhapsody whole transcriptome single-cell sequencing technologies in complex human tissues.
Heliyon. 2024. 10:e28358   |   PMID:38689972
 
Mazziotta F, Biavati L, Cataquiz Rimando J, Rutella S, Borcherding N, Parbhoo S, Mukhopadhyay R, Knaus HA, Valent P, Hackl H, Borrello I, Blazar BR, Hatzi K, Gojo I, Luznik L. CD8+ T-cell differentiation and dysfunction inform treatment response in acute myeolid leukemia.
Blood. 2024.   |   PMID:38776511
 
Jaylet T, Coustillet T, Smith NM, Viviani B, Lindeman B, Vergauwen L, Myhre O, Yarar N, Gostner JM, Monfort-Lanzas P, Jornod F, Holbech H, Coumoul X, Sarigiannis DA, Antczak P, Bal-Price A, Fritsche E, Kuchovska E, Stratidakis AK, Barouki R, Kim MJ, Taboureau O, Wojewodzic MW, Knapen D, Audouze K. Comprehensive mapping of the AOP-Wiki database: identifying biological an disease gaps.
Front Toxicol. 2024. 6:1285768   |   PMID:38523647
 
Steinacher C, Rieder D, Turner JE, Solanky N, Nishio S, Usami S, Hausott B, Schrott-Fischer A, Dudas J. Validation of RNA extraction methods and suitable reference genes for gene expression studies in developing foetal human inner ear tissue.
Int J Mol Sci. 2024. 25:2907   |   PMID:38474154
 
Nemati N, Böck N, Lamberti G, Lisandrelli R, Trajanoski Z. Protocol for functional profiling of patient-derived organoids for precision oncology.
STAR Protoc. 2024. 5:102887   |   PMID:38367233
 
Stegmann J, Kalanithy J, Dworschak G, Ishorst N, Mingardo E, Lopes F, Ho YM, Grote P, Lindenberg T, Yilmaz Ö, Channab K, Seltzsam S, Shril S, Hildebrandt F, Boschann F, Heinen A, Jolly A, Myers K, McBride K, Bekheirnia MR, Bekheirnia N, Scala M, Morleo M, Nigro V, Torella A, Pinelli M, Capra V, Accogli A, Maitz S, Spano A, Olson R, Klee E, Lanpher B, Jang SS, Chae JH, Steinbauer P, Rieder D, Janecke A, Vodopiutz J, Vogel I, Friis J, Cohen J, Riley K, Klee V, Walsh L, Begemann M, Elbracht M, Eggermann T, Stoppe A, Stuurman K, van Slegtenhorst M, Barakat TS, Mulhern M, Sands T, Cytrynbaum C, Weksberg R, Isidori F, Pippucci T, Severi G, Montanari F, Kruer M, Bakhtiari S, Darvish H, Reutter H, Hagelueken G, Geyer M, Woolf A, Posey J, Lupski J, Odermatt B, Hilger A. Bi-allelic variants in CELSR3 are implicated in central nervous system and urinary tract anomalies.
NPJ Genom Med. 2024. 9:18   |   PMID:38429302
 
Horvath L, Puschmann C, Scheiber A, Martowicz A, Sturm G, Trajanoski Z, Wolf D, Pircher A, Salcher S. Beyond binary: Bridging neutrophil diversity to new therapeutic approaches in NSCLC.
Trends Cancer. 2024. 10:457-474   |   PMID:38360439
 
Schulz-Kuhnt A, Rühle K, Javidmehr A, Döbrönti M, Biwank J, Knittel S, Neidlinger P, Leupold J, Liu LJ, Dedden M, Taudte RV, Gessner A, Fromm MF, Mielenz D, Kreiss L, Waldner M, Schürmann S, Friedrich O, Dietel B, López-Posadas R, Plattner C, TRR241 IBDome Consortium, Zundler S, Becker C, Atreya R, Neurath MF, Atreya I. ATP Citrate Lyase (ACLY)-dependent immunometabolism in mucosal T cells drives experimental colitis in vivo.
Gut. 2024. 73:601-612   |   PMID:38176897
 
Seidl-Philipp M, Veyt N, Schnaiter S, Krogsdam S, Schwendinger S, Maertens O, Schmuth M, Zschocke J, Legiu E, Wimmer K, Brems H. Gonadal and gonadosomatic mosaicism in NF1 detected by multiple affected children.
J Dtsch Dermatol Ges. 2024. 22:426-428   |   PMID:38185792
 
Chiriac MT, Hracsko Z, Günther C, Gonzalez-Acera M, Atreya R, Stolzer I, Wittner L, Dressel A, Schickedanz L, Gamez-Belmonte R, Hundorfean G, Zundler S, Rath T, Vetrano S, Danese S, Sturm G, Trajanoski Z, Kuühl AA, Siegmund B, Hartmann A, Wirtz S, Siebler J, Finotto S, Becker C, Neurath MF. The cytokine IL-20 controls resolution of experimental colitis by regulating epithelial IFN/STAT2 signalling.
Gut. 2024. 73:282-297   |   PMID:37884352
 

2023 

Taenzer M, Löffler-Ragg J, Schroll A, Monfort-Lanzas P, Engl S, Weiss G, Brigo N, Kurz K. Urine Metabolite Analysis to Identify Pathomechanisms of Long COVID: A Pilot Study.
Int J Tryptophan Res. 2023. 16:11786469231220781   |   PMID:38144169
 
Eigentler A, Handle F, Schanung S, Degen A, Hackl H, Erb HH, Fotakis G, Hoefer J, Ploner C, Jöhrer K, Heidgger I, Pircher A, Klotz W, Herold M, Schaefer G, Culig Z, Puhr M. Glucocorticoid treatment influences prostate cancer cell growth and the tumor microenvironment via altered glucocorticoid receptor signaling in prostate fibroblasts.
Oncogene. 2023. 43:235-247   |   PMID:38017134
 
Böck N, Trajanoski Z, Galuzzi L. Bacterial antigens unleash tumor-targeting immunity.
Cell Host Microbe. 2023. 31:1945-1947   |   PMID:38096784
 
Koeck S, Amann A, Kern J, Zwierzina M, Lorenz E, Sopper S, Zwierzina H, Mildner F, Sykora M, Sprung S, Hackl H, Pircher A, Pall G, Wolf D, Gamerith G. Whole stromal fibroblast signature is linked to specific chemokine and immune infiltration patterns and to improved survival in NSCLC.
Oncoimmunology. 2023. 12:2274130   |   PMID:38126028
 
Plattner C, Lamberti G, Blattmann P, Kirchmair A, Rieder D, Loncova Z, Sturm G, Scheidl S, Ijsselsteijn M, Fotakis G, Noureen A, Lisandrelli R, Böck N, Nemati N, Krogsdam A, Daum S, Finotello F, Somarakis A, Schäfer A, Wilflingseder D, Gonzalez Acera M, Öfner D, Huber LA, Clevers H, Becker C, Farin HF, Greten FR, Abersold R, da Cunha Carvalho de Miranda NF, Trajanoski Z. Functional and spatial proteomics profiling reveals intra- and intercellular signaling crosstalk in colorectal cancer.
iScience. 2023. 26:108399   |   PMID:38047086
 
Santol J, Kim S, Gregory LA, Baumgartner R, Murtha-Lemekhova A, Birgin E, Gloor S, Braunwarth E, Ammann M, Starlinger J, Pereyra D, Ammon D, Ninkovic M, Kern AE, Rumpf B, Ortmayr G, Herrmann Y, Dong Y, Huber FX, Weninger J, Thiels CA, Warner SG, Smoot RL, Truty MJ, Kendrick ML, Nagorney DN, Cleary SP, Beldi G, Rahbari NN, Hoffmann K, Gilg S, Assinger A, Gruenberger T, Hackl H, Starlinger P. An APRI+ALBI based multivariable model as preoperative predictor for posthepatectomy liver failure.
Ann Surg. 2023.   |   PMID:37860868
 
Pirabe A, Frühwirth S, Brunnthaler L, Hackl H, Schmuckenschlager A, Schrottmaier WC, Assinger A. Age dependent surface receptor expression pattern in immature versus mature platelets in mouse models of regenerative thrombocytopenia.
Cells. 2023. 12:2419   |   PMID:37830633
 
Kirchmair A, Nemati N, Lamberti G, Trefny M, Krogsdam A, Siller A, Hörtnagl P, Schumacher P, Sopper S, Sandbichler A, Zippelius A, Ghesquiere B, Trajanoski Z. 13 C tracer analysis reveals the landscape of metabolic checkpoints in human CD8 + T cell differentiation and exhaustion.
Front Immunol. 2023. 14:1267816   |   PMID:37928527
 
Sahanic S, Hilbe R, Dünser C, Tymoszuk P, Löffler-Ragg J, Rieder D, Trajanoski Z, Krogsdam A, Demetz E, Yurchenko M, Fischer C, Schirmer M, Theurl M, Lener D, Hirsch J, Holfeld J, Gollmann-Tepeköylü C, Zinner C, Tzankov A, Zhang SY, Casanova JL, Posch W, Wilflingseder D, Weiss G, Tancevski I. SARS-CoV-2 activates the TLR4/MyD88 pathway in human macrophages: a possible correlation with strong pro-inflammatory responses in severe COVID-19
Heliyon. 2023. 14:1267816   |   PMID:38034686
 
García-Mulero S*, Fornelino R*, Punta M, Lise S, Varela M, del Carpio LP, Moreno R, Costa-Garcia M, Rieder D, Trajanoski Z, Gros A, Alemany R, Piulats JM, Sanz-Pamplona R. Driver mutations in GNAQ and GNA11 genes as potential targets for precision immunotherapy in uveal melanoma patients.
Oncoimmunology. 2023. 12:2261278   |   PMID:38126027
 
Haake M, Haack B, Schäfer T, Harter PN, Mattavelli G, Eiring P, Vashist N, Wedekink F, Genssler S, Fischer B, Dahlhoff J, Mokhtari F, Kuznika A, Welters MJP, Benz TM, Sorger L, Thiemann V, Almanzar G, Selle M, Thein K, Späth J, Gonzalez MC, Reitinger C, Ipsen-Escobedo A, Wistuba-Hamprecht K, Eichler K, Filipski K, Zeiner PS, Beschorner R, Goedemans R, Gogolla FH, Hackl H, Rooswinkel RW, Thiem A, Romer Roche P, Joshi H, Pühringer D, Wöckel A, Diessner JE, Rüdiger M, Leo E, Cheng PF, Levesque MP, Goebeler M, Sauer M, Nimmerjahn F, Schuberth-Wagner C, von Felten S, Mittelbronn M, Mehling M, Beilhack A, van der Burg SH, Riedel A, Weide B, Dummer R, Wischhusen J. Tumor-derived GDF-15 blocks LFA-1 dependent T cell recruitment and suppresses responses to anti-PD-1 treatment.
Nat Commun. 2023. 14:4253   |   PMID:37474523
 
Seitter H, Obkircher J, Grabher P, Hartl J, Zanetti L, Lux UT, Fotakis G, Fernández-Quintero ML, Kaserer T, Koschak A. A novel calcium channel Cavβ2 splice variant with unique properties predominates in the retina.
J Biol Chem. 2023. 299:102972   |   PMID:36738788
 
Farin HF, Mosa MH, Ndreshkjana B, Ritter B, Grebbin B, Menche C, Kennel KB, Ziegler PK, Szabo L, Bollrath J, Rieder D, Michels BE, Kress A, Bozlar M, Darvishi T, Stier S, Kur IM, Bankov K, Kesselring R, Fichtner-Feigl S, Brüne B, Goetze TO, Al-Batran SE, Brandts CH, Bechstein WO, Wild PJ, Weigert A, Müller S, Knapp S, Trajanoski Z, Greten FR. Colorectal cancer organoid-stroma biobank allows subtype-specific assessment of individualized therapy responses.
Cancer Discov. 2023. 13:2192-2211   |   PMID:37489084
 
Pichler R, Diem G, Hackl H, Koutnik J, Mertens LS, D'Andrea D, Pradere B, Soria F, Mari A, Laukhtina, Krajewski W, Teoh J, Del Giudice F, Moschini M, Thurnher M, Posch W. Intravesical BCG in bladder cancer induces innate immune responses against SARS-CoV-2.
Front Immunol. 2023. 14:1202157   |   PMID:37520557
 
Effenberger M, Waschina S, Bronowski C, Sturm G, Tassiello O, Sommer F, Zollner A, Watschinger C, Grabherr F, Gstir R, Grander C, Enrich B, Bale R, Putzer D, Djanani A, Moschen AR, Zoller H, Rupp J, Schreiber S, Burcelin R, Lass-Flörl C, Trajanoski Z, Oberhuber G, Rosenstiel P, Adolph TE, Aden K, Tilg H. A gut bacterial signature in blood and liver tissue characterizes cirrhosis and hepatocellular carcinoma.
Hepatol Commun. 2023. 7:e00182   |   PMID:37314752
 
Obermoser K, Brigo N, Schroll A, Monfort-Lanzas P, Gostner JM, Engl S, Geisler S, Knoll M, Schennach H, Weiss G, Fuchs D, Bellmann-Weiler R, Kurz K. Positive effects of probiotic therapy in patients with post-infectious fatigue.
Metabolites. 2023. 13:639   |   PMID:3752055
 
Rieder D, Trajanoski Z. Checking immunotoxicity risks of checkpoint blockade.
Nat Cancer. 2023. 4:779-780   |   PMID:37308677
 
Koop K, Enderle K, Hillmann M, Ruspeckhofer L, Vieth M, Sturm G, Trajanoski Z, Kühl AA, Atreya R, Leppkes M, Baum P, Roy J, Martin A, Neurath M, Neufert C. Interleukin 36 receptor-inducible matrix metalloproteinase 13 mediates intestinal fibrosis.
Front Immunol. 2023. 14:1163198   |   PMID:37207229
 
Wittner L, Wagener L, Wiese JJ, Stolzer I, Krug SM, Naschberger E, Jackstadt R, Beyaert R, Atreya R, Kühl AA, Sturm G, Gonzalez Acera M, Patankar JV, Becker C, Siegmund B, Trajanoski Z, Winner B, Neurath MF, Schumann M, Günther C. Proteolytic activity of the paracaspase MALT1 is involved in epithelial restitution and mucosal healing.
Int J Mol Sci. 2023. 24:7402 |   PMID:37108564
 
Indelicato E, Kirchmair A, Amprosi M, Steixner S, Wahl N, Dechant G, Krogsdam A, Nachbauer W, Eigentler A, Schneider R, Wanschitz J, Trajanoski Z, Boesch S. Skeletal muscle transcriptomics underpins a double hit in the pathogenesis of Friedreich's Ataxia.
Hum Mol Genet. 2023. 32:2241-2250   |   PMID:37027192
 
Gollmann-Tepeköylü C, Graber M, Hirsch J, Mair S, Naschberger A, Pölzl L, Nägele F, Kirchmair E, Degenhart G, Demetz E, Hilbe R, Chen HY, Engert JC, Böhm A, Franz N, Lobenwein D, Lener D, Fuchs C, Weihs A, Töchterle S, Vogel GF, Schweiger V, Eder J, Pietschmann P, Seifert M, Kronenberg F, Coassin S, Blumer M, Hackl H, Meyer D, Feuchtner G, Kirchmair R, Troppmair J, Krane M, Weiss G, Tsimikas S, Thanassoulis G, Grimm M, Rupp B, Huber LA, Zhang SY, Casanova JL, Tancevski I*, Holfeld J*. Toll-like receptor 3 mediates aortic stenosis via a conserved mechanism of calcification.
Circulation. 2023. 147:1518-1533   |   PMID:37013819
 
Huang A, Riepler L, Rieder D, Kimpel J, Lusser A.No evidence for epitranscriptomic m5C modification of SARS-CoV-2, HIV and MLV viral RNA.
RNA. 2023. 29:756-763   |   PMID:36889928
 
Virshup I, Bredikhin D, Heumos L, Palla G, Sturm G, Gayoso A, Kats I, Koutrouli M, Scverse Community, Berger B, Pe′er D, Regev A, Teichmann SA, Finotello F, Wolf FA, Yosef N, Stegle O, Theis FJ. scverse: foundational tools for single-cell omics data analysis.
Nat Biotechnol. 2023. 41:604-606   |   PMID:37037904
 
Hautz T, Salcher S, Fodor M, Sturm G, Ebner S, Mair A, Trebo M, Untergasser G, Sopper S, Cardini B, Martovicz A, Hofmann J, Daum S, Kalb M, Resch T, Krendl F, Weissenbacher A, Otarashvili G, Obrist P, Zelger B, Öfner D, Trajanoski Z, Troppmair J,Oberhuber R, Pircher A, Wolf D, Schneeberger S. Immune cell dynamics deconvoluted by single-cell RNA sequencing in normothermic machine perfusion of the liver.
Nat Commun. 2023. 14:2285   |   PMID:37085477
 
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   |   PMID:36758419
 
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   |   PMID:36950091
 
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   |   PMID:36741416
 

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   |   PMID:36699399
 
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   |   PMID:36368318
 
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   |   PMID:36374020
 
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   |   PMID:36124800
 
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   |   PMID:35664695
 
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   |   PMID:35642895
 
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   |   PMID:35663465
 
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   |   PMID:35717322
 
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   |   PMID:35365572
 
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   |   PMID:35345820
 
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   |   PMID:35219646
 
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   |   PMID:35441143
 
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   |   PMID:35293321
 
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   |   PMID:35217577
 
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  |   PMID:35141292
 
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   |   PMID:35039463
 
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   |   PMID:35254413
 

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   |   PMID:34957266
 
Fotakis G, Trajanoski Z, Rieder D. Computational cancer neoantigen prediction: current status and recent advances.
Immunooncol Technol. 2021. 12:100052   |   PMID:35755950
 
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   |   PMID:34903710
 
Rieder D, Fotakis G, Ausserhofer M, Geyeregger R, Paster W, Trajanoski Z, Finotello F. nextNEOpi: a comprehensive pipeline for computational neoantigen prediction.
Bioinformatics. 2021.   |   PMID:34788790
 
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   |   PMID:34716584
 
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   |   PMID:34599932
 
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   |   PMID:34301276
 
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   |   PMID:34634939
 
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  |   PMID:34433960
 
Sturm G, List M, Zhang JD. Tissue heterogeneity is prevalent in gene expression studies.
NAR Genom Bioinform. 2021. 3:lqab077   |   PMID:34514392
 
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   |   PMID:34694377
 
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   |   PMID:34610319
 
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   |   PMID:34453119
 
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   |   PMID:34400718
 
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   |   PMID:34571902
 
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   |   PMID:34400718
 
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   |   PMID:34354697
 
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.   |   PMID:34257019
 
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   |   PMID:34072818
 
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   |   PMID:33786862
 
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.  |   PMID:33795839
 
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   |   PMID:33782537
 
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   |   PMID:33626223
 
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   |   PMID:33705753
 
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   |   PMID:33408092
 
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   |   PMID:33609383
 

2020 

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   |   PMID:33143653
 
Alkan HF, Vesely PW, Hackl H, Foßelteder J, Schmidt DR, Vander Heiden MG, Pichler M, Hoefler G, Bogner-Strauss JG. Deficiency of malate-aspartate shuttle component SLC25A12 induces pulmonary metastasis.
Cancer Metab. 2020. 8:26   |   PMID:33292758
 
Sonnweber T, Sahanic S, Pizzini A, Luger A, Schwabl C, Sonnweber B, Kurz K, Koppelstätter S, Haschka D, Petzer V, Boehm A, Aichner M, Tymoszuk P, Lehner D, Theurl M, Lorsbach-Köhler A, Tancevski A, Schaffl A, Schaber M, Hilbe R, Nairz M, Puchner B, Hüttenberger D, Tschurtschenthaler C, Asshoff M, Peer A, Hartig F, Bellmann R, Joannidis M, Gollmann-Tepeköylü C, Holfeld J, Feuchtner G, Egger A, Hoermann G, Schroll A, Fritsche G, Wildner S, Bellmann-Weiler R, Kirchmair R, Helbok R, Prosch H, Rieder D, Trajanoski Z, Kronenberg F, Wöll E, Weiss G, Widmann G, Löffler-Ragg J, Tancevski I. Cardiopulmonary recovery after COVID-19 - an observational prospective multi-center trial.
Eur Respir J. 2021. 57:2003481  |   PMID:33303539
 
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   |   PMID:33147104
 
Finotello F, Calura E, Risso D, Hautaniemi S, Romualdi C. Editorial: Multi-omic Data Integration in Oncology.
Front Oncol. 2020. 10:1768   |   PMID:33042824
 
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   |   PMID:33078426
 
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   |   PMID:33007814
 
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   |   PMID:32970891
 
Schlick K, Hohla F, Hamacher F, Hackl H, Hufnagl C, Magnes T, Gampenrieder SP, Melchardt T, Stättner S, Hauser-Kronberger C, Greil R, Rinnerthaler G. Overcoming negative predictions of microRNA expressions with FOLFIRINOX in advanced pancreatic cancer patients.
Future Sci OA. 2020. 7:FSO644   |   PMID:33437513
 
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   |   PMID:32759363
 
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   |   PMID:32759498
 
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   |   PMID:32614448
 
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   |   PMID:32747819
 
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   |   PMID:32492882
 
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   |   PMID:32553662
 
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   |   PMID:32610166
 
Pflügler S, Svinka J, Scharf I, Crncec I, Filipits M, Charoentong P, Tschurtschenthaler M, Kenner L, Awad M, Stift J, Glitzner E, Moll HP, Casanova E, Timelthaler G, Sibilia M, Gnant M, Lax S, Thaler J, Müller M, Strobl B, Mohr T, Kaser A, Trajanoski Z, Heller G, Eferl R. Ido1+ Paneth cells promote immune escape of colorectal cancer.
Commun Biol. 2020. 3:252   |   PMID:32444775
 
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   |   PMID:32301486
 
Plattner C, Finotello F, Rieder D. Deconvoluting tumor-infiltrating immune cells from RNA-seq data using quanTIseq.
Methods Enzymol. 2020. 636:261-285   |   PMID:32178821
 
Troyanskaya O, Trajanoski Z, Carpenter A, Thrun S, Razavian N, Oliver N. Artificial intelligence and cancer
Nature Cancer. 2020. 1:149-152   |  
 
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   |   PMID:32124323
 
Sturm G, Finotello F, List M. In Silico Cell-Type Deconvolution Methods in Cancer Immunotherapy.
Methods Mol Biol. 2020. 2120:213-222   |   PMID:32124322
 
Kirchmair A, Finotello F. In Silico Prediction of Tumor Neoantigens with TIminer.
Methods Mol Biol. 2020. 2120:129-145   |   PMID:32124316
 
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  |   PMID:31999864
 
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   |   PMID:31956037
 
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   |   PMID:32040169
 
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   |   PMID:31768978
 
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   |   PMID:32047551
 
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   |   PMID:31900407
 

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   |   PMID:31822659
 
Fotakis G, Rieder D, Haider M, Trajanoski Z, Finotello F. NeoFuse: predicting fusion neoantigens from RNA sequencing data.
Bioinformatics. 2019. 36:2260-2261   |   PMID:31755900
 
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   |   PMID:31756985
 
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   |   PMID:31773739
 
Finotello F, Rieder D, Hackl H, Trajanoski Z. Next-generation computational tools for interrogating cancer immunity.
Nat Rev Genet. 2019. 20:724-746   |   PMID:31515541
 
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   |   PMID:31545525
 
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   |   PMID:31541300
 
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   |   PMID:31530631
 
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   |   PMID:31410448
 
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   |   PMID:31423582
 
de Miranda NFCC, Trajanoski Z. Advancing cancer immunotherapy: a vision for the field.
Genome Med. 2019. 11:51   |   PMID:31358048
 
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   |   PMID:31362746
 
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   |   PMID:31510660
 
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   |   PMID:31295966
 
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   |   PMID:31235852
 
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   |   PMID:31181781
 
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   |   PMID:31060856
 
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   |   PMID:31126321
 
Plattner C, Hackl H. Modeling therapy resistance via the EGFR signaling pathway.
FEBS J. 2019. 286:1284-1286   |   PMID:30892828
 
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   |   PMID:30765144
 
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   |   PMID:30779441
 
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   |   PMID:30938416
 
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   |   PMID:30689705
 
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   |   PMID:30765392
 
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   |   PMID:30539543
 

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   |   PMID:30564889
 
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   |   PMID:30571766
 
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   |   PMID:30389858
 
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   |   PMID:30268091
 
Finotello F, Eduati F. Multi-omics profiling of the tumor microenvironment: paving the way to precision immuno-oncology.
Front Oncol. 2018. 8:430   |   PMID:30345255
 
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  |   PMID:30309702
 
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   |   PMID:30385732
 
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   |   PMID:30165362
 
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   |   PMID:30040823
 
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   |   PMID:29670099
 
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   |   PMID:29768196
 
Finotello F, Trajanoski Z. Quantifying tumor-infiltrating immune cells from transcriptomics data
Cancer Immunol Immunother. 2018. 67:1031-1040   |   PMID:29541787
 
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   |   PMID:29670256
 
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   |   PMID:29662663
 
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   |   PMID:29296022
 
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   |   PMID:29298682
 
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   |   PMID:29721079
 

2017 

Reimer D*, Boesch M*, Wolf D, Marth C, Sopper S, Hatina J, Altevogt P, Parson W, Hackl H, Zeimet AG. Truncated isoform Vav3.1 is highly expressed in ovarian cancer stem cells and clinically relevant in predicting prognosis and platinum-response.
Int J Cancer. 2017. 142:1640-1651   |   PMID:29194596
 
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   |   PMID:29234329
 
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   |   PMID:29348853
 
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.   |   PMID:29018052
 
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   |   PMID:29134398
 
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   |   PMID:28899689
 
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   |   PMID:28817234
 
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  |   PMID:28714474
 
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   |   PMID:28633385
 
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   |   PMID:28591793
 
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   |   PMID:28334928
 
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   |   PMID:28456850
 
Rieder D, Finotello F. Analysis of high-throughput RNA bisulfite sequencing data.
Methods Mol Biol. 2017. 1562:143-154  |   PMID:28349459
 
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   |   PMID:28249906
 
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   |   PMID:28219393
 
Finotello F, Trajanoski Z. New strategies for cancer immunotherapy: targeting regulatory T cells.
Genome Med. 2017. 9:10   |   PMID:28129791
 
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   |   PMID:28233611
 
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   |   PMID:28077169
 
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   |   PMID:28052254
 
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  |   PMID:28056193
 

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   |   PMID:28025179
 
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   |   PMID:28009300
 
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   |   PMID:27897969
 
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   |   PMID:27835900
 
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   |   PMID:27770790
 
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   |   PMID:27694626
 
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  |   PMID:27782840
 
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  |   PMID:27519272
 
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  |   PMID:27376239
 
Hackl H*, Charoentong P*, Finotello F*, Trajanoski Z. Computational genomics tools for dissecting tumor-immune cell interactions.
Nat Rev Genet. 2016. 17:441-458  |   PMID:27376489
 
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   |   PMID:27285986
 
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  |   PMID:27170362
 
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   |     |   PMID:27835900
 
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  |   PMID:27213586
 
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   |   PMID:27093431
 
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   |   PMID:26982367
 
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.   |   PMID:27078067
 
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.   |   PMID:27139155
 
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   |   PMID:26962858
 
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   |   PMID:26863016
 
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  |   PMID:26821018
 
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   |   PMID:26760912
 
Rieder D, Amort T, Kugler E, Lusser A, Trajanoski Z. meRanTK: methylated RNA analysis ToolKit.
Bioinformatics. 2016. 32:782-785.   |   PMID:26543174
 
Angelova M, Charoentong P, Hackl H, Trajanoski Z. The colorectal cancer immune paradox revisited.
Oncoimmunology. 2016. 5:e1078058  |   PMID:27057454
 

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.   |   PMID:26635563
 
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  |   PMID:26121641
 
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  |   PMID:26052614
 
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  |   PMID:26054424
 
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  |   PMID:25902403
 
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  |  
 
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  |   PMID:25853550
 
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  |   PMID:25886616
 
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.   |   PMID:25666479
 
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.   |   PMID:25661519
 
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  |   PMID:25756043
 
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  |   PMID:25583169
 

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
 
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   |   PMID:25230706
 
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  |   PMID:25333283 
 
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.   |   PMID:25164877 
 
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  |   PMID:25218586
 
Schweiger D, Trajanoski Z, Pabinger S. SPARQLGraph: a web-based platform for graphically querying biological Semantic Web databases.
BMC Bioinformatics. 2014. 15:279  |   PMID:25127889
 
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  |   PMID:25030037
 
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  |   PMID:25236324
 
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  |   PMID:25486480
 
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.   |   PMID:24898182
 
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  |   PMID:24926998
 
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   |   PMID:24725474
 
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   |   PMID:24553175
 
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   |   PMID:24444368
 
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  |   PMID:24532766
 

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  |   PMID:24225386
 
Gallasch R, Efremova M, Charoentong P, Hackl H, Trajanoski Z. Mathematical models for translational and clinical oncology.
J Clin Bioinforma. 2013. 3:23  |   PMID:24195863
 
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  |   PMID:24155240
 
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   |   PMID:24151455
 
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  |   PMID:24205377
 
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  |   PMID:24236098
 
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   |   PMID:24026398
 
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  |   PMID:24138885
 
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   |   PMID:23895238
 
Snajder R, Trajanoski Z, Hackl H. GPViz: dynamic visualization of genomic regions and variants affecting protein domains.
Bioinformatics. 2013. 29:2195-2196  |   PMID:23782613
 
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   |   PMID:23665771
 
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   |   PMID:23708736
 
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   |   PMID:23557329
 
Prodan R, Sperk M. Scientific computing with Google App Engine.
Future Generation Computer Systems. 2013. 29:1851-1859  |   DOI: 10.1016/j.future.2012.12.018
 
Pabinger S, Trajanoski Z. Genome-scale model management and comparison.
Methods Mol Biol. 2013. 985:3-16   |   PMID:23417796
 
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  |   PMID:23457546
 
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   |   PMID:23341494
 
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   |   PMID:23250487
 

2012

Rieder D, Trajanoski Z, McNally J. Transcription factories.
Front Genet . 2012. 3:221 |   PMID: 23109938
 
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   |   PMID: 23029193
 
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   |   PMID: 22986455
 
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   |   PMID: 22870267
 
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  |   PMID: 22424600
 
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   |   PMID: 22294260
 
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
 

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. Vol. 6990  |   TLDKS
 
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  |   PMID: 21954452
 
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   |   PMID: 21615920
 
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  |   PMID: 21609420
 
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   |   PMID: 21540289
 
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   |   PMID: 21370089
 
Pabinger S, Rader R, Agren R, Nielsen J, Trajanoski Z. MEMOSys: Bioinformatics platform for genome-scale metabolic models
BMC Syst Biol.. 2011. 5:20   |   PMID: 21276275
 
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  |   PMID: 21245428
 
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   |   PMID: 21075747
 
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   |   PMID: 21374661
 
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   |   PMID: 20940065
 
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   |   PMID: 21177646
 

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  |   PMID: 20883526
 
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   |   PMID: 20832425
 
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   |   PMID: 20886048
 
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   |   PMID: 20805506
 
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  |   PMID: 20552250
 
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  |   PMID: 20530742
 
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  |   PMID: 20455215
 
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   |   PMID: 20226853
 
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   |   PMID: 20158878
 
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  |   PMID: 20089119
 
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   |  PMID: 19909745
 
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  |  PMID: 20013895
 

2009

Stocker G, Fischer M, Rieder D, Bindea G, Kainz S, Oberstolz M, McNally JG, Trajanoski Z. iLAP: a workflow-driven software for experimental protocol development, data acquisition and analysis.
BMC Bioinformatics. 2009. 10:390  |  PMID: 19941647
 
Pabinger S, Thallinger GG, Snajder R, Eichhorn H, Rader R, Trajanoski Z. QPCR: Application for real-time PCR data management and analysis.
BMC Bioinformatics. 2009. 10:268  |  PMID: 19712446
 
Konrad TA, Karger A, Hackl H, Schwarzinger I, Herbacek I, Wieser R. Inducible expression of EVI1 in human myeloid cells causes phenotypes consistent with its role in myelodysplastic syndromes.
J Leukoc Biol. 2009. 86:813-822  |  PMID: 19605700
 
Geigl J, Obenauf A, Waldspuehl-Geigl J, Hoffmann E, Auer M, Hörmann M, Fischer M, Trajanoski Z, Schenk M, Bambusch L, Speicher M. Identification of small gains and losses in single cells after whole genome amplification on tiling oligo arrays.
Nucl Acids Res. 2009. 37:e105  |  PMID: 19541849
 
Prokesch A*, Hackl H*, Hakim-Weber R, Bornstein SR, Trajanoski Z. Novel insights into adipogenesis from omics data.
Curr Med Chem. 2009. 16:2952-2964  |  PMID: 19689276
 
Pages F, Kirilovsky A, Mlecnik B, Tosolini M, Bindea G, Lagorce C, Wind P, Marliot F, Bruneval P, Zatloukal K, Trajanoski Z, Berger A, Fridman W-H, Galon J. The in situ cytotoxic and memory T cells predict outcome in early-stage colorectal cancer patients.
J Clin Oncol. 2009. 27:5944-5951  |  PMID: 19858404
 
Bindea G*, Mlecnik B*, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman W-H, Pages F, Trajanoski Z, Galon J. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks
Bioinformatics. 2009. 25:1091-1093  |   PMID: 19237447
 
Camus M, Tosolini M, Mlecnik B, Pagès F, Kirilovsky A, Berger A, Costes A, Bindea G, Charoentong P, Bruneval P, Trajanoski Z, Fridman W-H, Galon J. Coordination of intratumoral immune reaction and human colorectal cancer recurrence.
Cancer Res. 2009. 69:2685-2693  |  PMID: 19258510
 
Rainer J, Ploner C, Jesacher S, Ploner A, Eduardoff M, Mansha M, Wasim M, Renate Panzer-Grümayer R, Trajanoski Z, Niederegger H, Kofler R. Glucocorticoid-regulated microRNAs and mirtrons in acute lymphoblastic leukemia.
Leukemia. 2009. 23:746-752  |  PMID: 19148136
 

2008

Scheideler M, Elabd C*, Zaragosi LE*, Chiellini C, Hackl H, Sanchez-Cabo F, Yadav S, Duszka K, Friedl G, Papak C, Prokesch A, Windhager R, Ailhaud G, Dani C, Amri E-Z, Trajanoski Z. Comparative transcriptomics of human multipotent stem cells during adipogenesis and osteoblastogenesis.
BMC Genomics. 2008. 9:340  |  PMID: 18637193
 
Chiellini C, Grenningloh G, Cochet O, Scheideler M, Trajanoski Z, Ailhaud G, Dani C, E-Z Amri. Stathmin-like 2, a developmentally-associated neuronal marker, is expressed and modulated during osteogenesis of human mesenchymal stem cells.
Biochem Biophys Res Commun. 2008. 374:64-68  |  PMID: 18611392
 
Elabd C, Basillais A, Beaupied H Breil V, Wagner N, Scheideler M, Zaragosi LE, Massiera F, Lemichez E, Trajanoski Z, Carle GF, Euller-Ziegler L, Ailhaud G, Benhamou CL, Dani C, Amri EZ. Oxytocin controls differentiation of human mesenchymal stem cells and reverses osteoporosis.
Stem Cells. 2008. 26:2399-2407  |  PMID: 18583541
 
Pinent M*, Hackl H*, Burkard TR, Prokesch A, Scheideler M, Paar C, Hämmerle G, Zechner R, Trajanoski Z, Strauss JG. Differential transcriptional modulation of biological processes in adipocyte triglyceride lipase and hormone-sensitive lipase deficient mice.
Genomics. 2008. 92:26-32  |  PMID: 18572100
 
Merkel O, Heyder C, Asslaber D, Hamacher F, Holler C, Stöcher M, Scheideler M, Paar C, Prokesch A, Trajanoski Z, Tinhofer I, Greil R. Arsenic trioxide induces apoptosis preferentially in B-CLL cells of patients with unfavourable prognostic factors including del17p13.
J Mol Med. 2008. 86:541-552  |  PMID: 18297255
 

2007

Nebauer R, Schuiki I, Kulterer B, Trajanoski Z, Daum G. The phosphatidylethanolamine level of yeast mitochondria is affected by the mitochondrial components Oxa1p and Yme1p.
FEBS J. 2007. 274:6810-6190  |  PMID: 17976194
 
Hartler J, Thallinger GG, Stocker G, Sturn A, Burkard TR, Körner E, Rader R, Schmidt A, Mechtler K, Trajanoski Z. MASPECTRAS: a platform for management and analysis of proteomics LC-MS/MS data.
BMC Bioinformatics. 2007. 8:197  |  PMID: 17567892
 
Müller WG, Rieder D, Karpova TS, John S, Trajanoski Z, McNally JG. Organization of chromatin and histone modifications at a transcription site.
J Cell Biol. 2007. 177:957-967  |  PMID: 17576795
 
Kowalska A, Bozsaky E, Ramsauer T, Rieder D, Bindea G, Lorch T, Trajanoski Z, Ambros PF. A new platform linking chromosomal and sequence information.
Chromosome Res. 2007. 15:327-340  |  PMID: 17406992
 
Kulterer B, Friedl G, Jandrositz A, Sanchez-Cabo F, Prokesch A, Paar C, Scheideler M, Windhager R, Preisegger K-H, Trajanoski Z. Gene Expression Profiling of Human Mesenchymal Stem Cells derived from Bone Marrow during Expansion and Osteoblast Differentiation.
BMC Genomics. 2007. 8:70  |   PMID: 17352823
 
Thallinger GG, Baumgartner K, Pirklbauer M, Uray M, Pauritsch E, Mehes G, Buck CR, Zatloukal K, Trajanoski Z. TAMEE: data management and analysis for tissue microarrays.
BMC Bioinformatics. 2007. 8:81  |   PMID: 17343750
 

2006

Galon J, Costes A, Sanchez-Cabo F, Kirilovsky A, Mlecnik B, Lagorce C, Tosolini M, Camus M, Berger A, Wind P, Zinzindohoué F, Bruneval P, Cugnenc P-H, Trajanoski Z, Fridman W-H, Pagès F. Type, density, and location of immune cells within human colorectal tumors predicts clinical outcome.
Science. 2006. 313:1960-1964  |   PMID: 17008531
 
Tschernatsch MMO, Mlecnik B, Trajanoski Z, Zechner R, Zimmermann R. LPL-mediated lipolysis of VLDL induces an upregulation of AU-rich mRNAs and an activation of HuR in endothelial cells.
Atherosclerosis. 2006. 189:310-317  |   PMID: 16494882
 
Rainer J, Sanchez-Cabo F, Stocker G, Sturn A, Trajanoski Z. CARMAweb: comprehensive R- and BioConductor-based web service for microarray data analysis.
Nucleic Acids Res. 2006. 34:W498-W503  |   PMID: 16845058
 

2005

Hackl H*, Burkard TR*, Sturn A, Rubio R, Schleiffer A, Tian S, Quackenbush J, Eisenhaber F, Trajanoski Z. Molecular processes during fat cell development revealed by gene expression profiling and functional annotation.
Genome Biol. 2005. 6:R108  |   PMID: 16420668
 
Pages F, Berger A, Camus M, Sanchez-Cabo F, Costes A, Molidor R, Mlecnik B, Kirilovsky A, Nilsson M, Damotte D, Meatchi T, Bruneval P, Cugnenenc PH, Trajanoski Z, Fridman WH, Galon J. Effector memory T cells, early metastasis, and survival in colorectal cancer.
N Engl J Med. 2005. 353:2654-2666  |   PMID: 16371631
 
Di Camillo B, Sanchez-Cabo F, Toffolo G, Nair SK, Trajanoski Z, Cobelli C. A quantization method based on threshold optimization for microarray short time series.
BMC Bioinformatics. 2005. 6 Suppl 4: S11  |   PMID: 16351737
 
Sturn A, Maurer M, Molidor R, Trajanoski Z. Systems for the management of pharmacogenomic information.
Methods Mol Biol. 2005. 311:193-208  |   PMID: 16100409
 
Bernroider E, Brehm A, Krssak M, Anderwald C, Trajanoski Z, Cline G, Shulman GI, Roden M. The Role of Intramyocellular Lipids During Hypoglycemia in Patients With Intensively Treated Type 1 Diabetes.
J Clin Endocrinol Metab. 2005. 90:5559-5565  |  PMID: 15998784
 
Vogl C*, Sanchez Cabo F*, Stocker G, Hubbard S, Wolkenhauer O, Trajanoski Z. A fully Bayesian model to cluster gene expression profiles.
Bioinformatics. 2005. 21 Suppl 2: ii130-ii136  |  PMID: 16204092
 
Maurer M, Molidor R, Sturn A, Hartler J, Hackl H, Stocker G, Prokesch A, Scheideler M, Trajanoski Z. MARS: Microarray analysis, retrieval and storage system.
BMC Bioinformatics. 2005. 6:101  |  PMID: 15836795
 
Pinent M, Bladeacute; MC, Salvadó MC, Arola L, Hackl H, Quackenbush J, Trajanoski Z, Ardévol. A Grape-seed derived procyanidins interfere with adipogenesis of 3T3-L1 cells at the onset of differentiation.
Int J Obes. 2005. 29:934-941  |  PMID: 15917849
 
Mlecnik B, Scheideler M, Hackl H, Hartler J, Sanchez-Cabo F , Trajanoski Z. PathwayExplorer: web service for visualizing high-throughput expression data on biological pathways.
Nucleic Acids Res. 2005. 33: W633-W637  |  PMID: 15980551
 
Yu JS, Ongarello S, Fiedler R, Chen RW, Toffolo G, Cobelli C, Trajanoski Z. Ovarian Cancer Identification Based on Dimensionality Reduction for High-Throughput Mass Spectrometry Data.
Bioinformatics. 2005. 21:2200-2209  |  PMID: 15784749
 
Kals M, Natter K, Thallinger GG, Trajanoski Z, Kohlwein SD. YPL.db(2): the yeast protein localization database, version 2.0.
Yeast. 2005. 22:213-218  |  PMID: 15704222
 

2004

Hackl H, Maurer M, Mlecnik B, Hartler J, Stocker G, Miranda-Saavedra D, Trajanoski Z. GOLD.db: Genomics of lipid-asociated disorders database.
BMC Genomics. 2004. 5:93  |  PMID: 15588328
 
Müller WG, Rieder D, Kreth G, Cremer C, Trajanoski Z, McNally JG. Generic features of tertiary chromatin structure as detected in natural chromosomes.
Mol Cell Biol. 2004. 24:9359-9370  |  PMID: 15485905
 
Pieler R, Sanchez-Cabo F, Hackl H, Thallinger GG, Trajanoski Z. ArrayNorm: Comprehensive Normalization and Analysis of Microarray Data.
Bioinformatics. 2004. 20:1971-1973  |  PMID: 15073026
 
Stocker G, Rieder D, Trajanoski Z. ClusterControl: A Web Interface for Distributing and Monitoring Bioinformatics Applications on a Linux Cluster.
Bioinformatics 2004. 20:805-807  |  PMID: 14751976
 
Hackl H, Sanchez Cabo F, Sturn A, Wolkenhauer O, Trajanoski Z. Analysis of DNA Microarray Data.
Curr Top Med Chem. 2004. 4:1355-1368  |  PMID: 15379650
 

2003

Molidor R, Sturn A, Maurer M, Trajanoski Z. New Trends in Bioinformatics: From Genome Sequence to Personalized Medicine.
Experimental Gerontology 2003. 38:1031-1036  |  PMID: 14580855
 
Regittnig W, Ellmerer M, Fauler G, Sendlhofer G, Trajanoski Z, Leis HJ, Schaupp L, Wach P, Pieber TR. Assessment of transcapillary glucose exchange in human skeletal muscle and adipose tissue.
Am J Physiol Endocrinol Metab. 2003. 285:E241-E251  |  PMID: 12684220
 
Sturn A, Mlecnik B, Pieler R, Rainer J, Truskaller T, Trajanoski Z. Client-Server Environment for High-Performance Gene Expression Data Analysis.
Bioinformatics. 2003. 19:772-773  |  PMID: 12691990
 
Trost E, Hackl H, Maurer M, Trajanoski Z. Java Editor for Biological Pathways.
Bioinformatics. 2003. 19:786-787  |   PMID: 12691997
 

2002

Thallinger GG, Trajanoski S, Stocker G, Trajanoski Z. Information management systems for pharmacogenomics.
Pharmacogenomics. 2002. 3:651-667  |  PMID: 12223050
 
Habeler G, Natter K, Thallinger GG, Crawford ME, Kohlwein SD, Trajanoski Z: YPL.db: The yeast protein localization database.
Nucleic Acids Res. 2002. 30:80-83  |  PMID: 11752260
 
Sturn A, Quackenbush J, Trajanoski Z. Genesis: Cluster analysis of microarray data.
Bioinformatics. 2002. 18:207-208  |  PMID: 11836235
 
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