mail address

AIT Austrian Institute of Technology GmbH
Muthgasse 11
1190 Vienna


I am a scientist in the Molecular Diagnostics Unit at the Austrian Institute of Technology.




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View Stephan Pabinger's profile on GitHub


Research Interests

(*) Analysis of high-throughput biological data - especially next-generation sequencing data

(*) Development of bioinformatics methods and tools (NGS, Assembly, QPCR, ...)

(*) Epigenetics

(*) Integration of heterogeneous high-throughput data

(*) Multivariate data analysis


Gencay M, Vermeulen M, Neofytos D, Westergaard G, Pabinger S, Kriegner A, Seffner A, Gohl P, Huebner K, Nauck M, Kaminski WE.
Substantial variation in the hepatitis B surface antigen (HBsAg) in hepatitis B virus (HBV)-positive patients from South Africa: Reliable detection of HBV by the Elecsys HBsAg II assay.
J Clin Virol. 2018 Jan 30;101:38-43. pubmed

Gencay M, Hübner K, Gohl P, Seffner A, Weizenegger M, Neofytos D, Batrla R, Woeste A, Kim HS, Westergaard G, Reinsch C, Brill E, Thu Thuy PT, Hoang BH, Sonderup M, Spearman CW, Pabinger S, Gautier J, Brancaccio G, Fasano M, Santantonio T, Gaeta GB, Nauck M, Kaminski WE.
Ultra-deep sequencing reveals high prevalence and broad structural diversity of hepatitis B surface antigen mutations in a global population.
PLoS One. 2017 May 4;12(5). pubmed

Pandey RV, Pabinger S, Kriegner A, Weinhäusel A.
DaMold: a data-mining platform for variant annotation and visualization in molecular diagnostics research.
Hum Mutat. 2017 Apr 11. pubmed

Pandey RV, Pulverer W, Kallmeyer R, Beikircher G, Pabinger S, Kriegner A, Weinhäusel A.
MSP-HTPrimer: a high-throughput primer design tool to improve assay design for DNA methylation analysis in epigenetics.
Clin Epigenetics. 2016 Sep 21;8. pubmed

Pabinger S, Ernst K, Pulverer W, Kallmeyer R, Valdes AM, Metrustry S, Katic D, Nuzzo A, Kriegner A, Vierlinger K, Weinhäusel A.
Analysis and Visualization Tool for Targeted Amplicon Bisulfite Sequencing on Ion Torrent Sequencers.
PLoS One. 2016 July 28;11(7). pubmed

Pandey RV, Pulverer W, Kallmeyer R, Beikircher G, Pabinger S, Kriegner A, Weinhäusel A.
MSRE-HTPrimer: a high-throughput and genome-wide primer design pipeline optimized for epigenetic research.
Clin Epigenetics. 2016 Mar 5;8:26. pubmed

Pandey RV, Pabinger S, Kriegner A, Weinhäusel A.
MutAid: Sanger and NGS Based Integrated Pipeline for Mutation Identification, Validation and Annotation in Human Molecular Genetics.
PLoS One. 2016 Feb 3;11(2). pubmed

Pandey RV, Pabinger S, Kriegner A, Weinhäusel A.
ClinQC: a tool for quality control and cleaning of Sanger and NGS data in clinical research.
BMC Bioinformatics. 2016 Feb 2;17(1):56. pubmed

Friedrich V, Pabinger S, Chen T, Messner P, Dewhirst FE, Schäffer C.
Draft Genome Sequence of Tannerella forsythia Type Strain ATCC 43037.
Genome Announc. 2015 Jun 11;3(3). pubmed

Friedrich V, Gruber C, Nimeth I, Pabinger S, Sekot G, Posch G, Altmann F, Messner P, Andrukhov O, Schäffer C.
Outer membrane vesicles of Tannerella forsythia: biogenesis, composition, and virulence.
Mol Oral Microbiol. 2015 May 8. pubmed

Maghuly F, Jankowicz-Cieslak J, Pabinger S, J. Till B, and Laimer M.
Geographic origin is not supported by the genetic variability found in a large living collection of Jatropha curcas with accessions from three continents.
Biotechnology Journal. 2014 Dec. pubmed

Pabinger S, Rödiger S, Kriegner A, Vierlinger K, Weinhäusel A.
A survey of tools for the analysis of quantitative PCR (qPCR).
Biomolecular Detection and Quantification. 2014 Sep 18;1:23-33. pubmed

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 Sep 18;15:306. pubmed

Schweiger D, Trajanoski Z, Pabinger S.
SPARQLGraph: a web-based platform for graphically querying biological Semantic Web databases.
BMC Bioinformatics. 2014 Aug 15;15(1):279. pubmed

Baldauf M, Dander A, Sperk M, Pabinger S, Trajanoski Z.
Integration of NGS Data and Images of Tissue Sections for Personalized Oncology.
UMIT - Lecture Notes in Biomedical Computer Science and Mechatronics. 2014:4. open access

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 (Oxford), 2014, bau004. pubmed

Dander A*, Pabinger S*, Sperk M, Fischer M, Stocker G, and Trajanoski Z.
SeqBench: Integrated solution for the management and analysis of exome sequencing data.
BMC Research Notes, 2014, 7:43. *These authors contributed equally to this work. pubmed

Pabinger S and Trajanoski Z.
MEMOSys: Platform for Genome-Scale Metabolic Models.
Encyclopedia of Metagenomics. 2014, pp 1-7. DOI: 10.1007/978-1-4614-6418-1_702-5

Dander A, Mueller L, Gallasch R, Pabinger S, Emmert-Streib F, Graber A, and Dehmer M.
[COMMODE] a large-scale database of molecular descriptors using compounds from pubchem.
Source Code for Biology and Medicine, 2013, 8:22. pubmed

Magoc T, Pabinger S, Canzar S, Liu X, Su Q, Puiu D, Tallon LJ, and Salzberg SL.
GAGE-B: An Evaluation of Genome Assemblers for Bacterial Organisms.
Bioinformatics, 2013 May 10. pubmed

Pabinger S, Dander A, Fischer M, Snajder R, Sperk M, Efremova M, Krabichler B, Speicher MR, Zschocke J, and Trajanoski Z.
A survey of tools for variant analysis of next-generation genome sequencing data.
Brief Bioinform, 2013 Jan 21. pubmed

Pabinger S and Trajanoski Z.
Genome-scale model management and comparison.
Methods Mol Biol, 2013;985:3-16. pubmed

Fischer M, Snajder R, Pabinger S, Dander A, Schossig A, Zschocke J, Trajanoski Z, and Stocker G.
SIMPLEX: cloud-enabled pipeline for the comprehensive analysis of exome sequencing data.
PLoS One, 2012;7(8). pubmed

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, and Zschocke J.
Mutations in ROGDI Cause Kohlschütter-Tönz Syndrome.
Am J Hum Genet, 2012 Apr 6;90(4):701-7. pubmed

Pabinger S, Rader R, Agren R, Nielsen J, and Trajanoski Z.
MEMOSys: Bioinformatics platform for genome-scale metabolic models.
BMC Syst Biol, 5:20, 2011. pubmed

Pabinger S, Thallinger GG, Snajder R, Eichhorn H, Rader R, and Trajanoski Z.
QPCR: Application for real-time PCR data management and analysis.
BMC Bioinformatics, 10:268, 2009. pubmed



web application to store and analyze data from qPCR experiments. More information here.


bioinformatics platform for the management and development of metabolic models.


cloud-enabled pipeline for the comprehensive analysis of exome sequencing data.


visual query builder for biological RDF databases. Winner of the EBI RDFApp competition.


analysis of targeted bisulfite sequencing data generated on an Ion Torrent PGM / Illumina MiSeq.


Data-mining platform for variant annotation and visualization.

PRINSEQ Parallel

parallelized, multithreading version of PRINSEQ.