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.   |   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.   |   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.   |   in press

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.   |   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.   |   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


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.  |   in press


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.  |   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. pii: canres.2320.2016   |   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.   |   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


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.   |   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   |  

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


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


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


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   |  



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


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


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


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


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


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


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


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


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


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


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