Contact

email

stephan.pabinger@gmail.com

about

Former scientist in the Molecular Diagnostics Unit at the AIT.

Now working at the International Supply Chain Management group at HOFER KG

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Research interests

Software

A tool for multiplex oligonucleotide design. Publication.
Analysis of targeted bisulfite sequencing data generated on an Ion Torrent PGM / Illumina MiSeq.
Data-mining platform for variant annotation and visualization.
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.
Parallelized, multithreading version of PRINSEQ.

Publications

Gemmell NJ, Rutherford K, Prost S, Tollis M, Winter D, Macey JR, Adelson DL, Suh A, Bertozzi T, Grau JH, Organ C, Gardner PP, Muffato M, Patricio M, Billis K, Martin FJ, Flicek P, Petersen B, Kang L, Michalak P, Buckley TR, Wilson M, Cheng Y, Miller H, Schott RK, Jordan MD, Newcomb RD, Arroyo JI, Valenzuela N, Hore TA, Renart J, Peona V, Peart CR, Warmuth VM, Zeng L, Kortschak RD, Raison JM, Zapata VV, Wu Z, Santesmasses D, Mariotti M, Guigó R, Rupp SM, Twort VG, Dussex N, Taylor H, Abe H, Bond DM, Paterson JM, Mulcahy DG, Gonzalez VL, Barbieri CG, DeMeo DP, Pabinger S, Van Stijn T, Clarke S, Ryder O, Edwards SV, Salzberg SL, Anderson L, Nelson N, Stone C.
The tuatara genome reveals ancient features of amniote evolution.
Nature 2020. pubmed

Maghuly F, Deák T, Vierlinger K, Pabinger S, Tafer H, Laimer M.
Gene expression profiling identifies pathways involved in seed maturation of Jatropha curcas.
BMC Genomics 2020. pubmed

Wisnieski F, Santos LC, Calcagno DQ, Geraldis JC, Gigek CO, Anauate AC, Chen ES, Rasmussen LT, Payão SLM, Artigiani R, Demachki S, Assumpção PP, Lourenço LG, Arasaki CH, Pabinger S, Krainer J, Leal MF, Burbano RR, Arruda Cardoso Smith M.
The impact of DNA demethylation on the upregulation of the NRN1 and TNFAIP3 genes associated with advanced gastric cancer.
J. Mol. Med. 2020. pubmed

Conzemius R, Hendling M, Pabinger S, Barišić I.
PRIMEval: Optimization and screening of multiplex oligonucleotide assays.
Sci Rep 2019. pubmed

Ramme AP, Koenig L, Hasenberg T, Schwenk C, Magauer C, Faust D, Lorenz AK, Krebs AC, Drewell C, Schirrmann K, Vladetic A, Lin GC, Pabinger S, Neuhaus W, Bois F, Lauster R, Marx U, Dehne EM.
Autologous induced pluripotent stem cell-derived four-organ-chip.
Future Sci OA 2019. pubmed

Krainer J, Weinhäusel A, Hanak K, Pulverer W, Özen S, Vierlinger K, Pabinger S.
EPIC-TABSAT: analysis tool for targeted bisulfite sequencing experiments and array-based methylation studies.
Nucleic Acids Res. 2019. pubmed

Maghuly F, Pabinger S, Krainer J, Laimer M.
The Pattern and Distribution of Induced Mutations in J. curcas Using Reduced Representation Sequencing.
Front Plant Sci 2018. pubmed

Hendling M, Pabinger S, Peters K, Wolff N, Conzemius R, Barišic I.
Oli2go: an automated multiplex oligonucleotide design tool.
Nucleic Acids Res. 2018. pubmed

Gencay M, Seffner A, Pabinger S, Gautier J, Gohl P, Weizenegger M, Neofytos D, Batrla R, Woeste A, Kim HS, Westergaard G, Reinsch C, Brill E, Thuy PTT, Hoang BH, Sonderup M, Spearman CW, Brancaccio G, Fasano M, Gaeta GB, Santantonio T, Kaminski WE.
Detection of in vivo hepatitis B virus surface antigen mutations-A comparison of four routine screening assays.
J. Viral Hepat. 2018. pubmed

Kim HS, Chen X, Xu M, Yan C, Liu Y, Deng H, Hoang BH, Thuy PTT, Wang T, Yan Y, Zeng Z, Gencay M, Westergaard G, Pabinger S, Kriegner A, Nauck M, Seffner A, Gohl P, Hübner K, Kaminski WE.
Frequency of hepatitis B surface antigen variants (HBsAg) in hepatitis B virus genotype B and C infected East- and Southeast Asian patients: Detection by the Elecsys® HBsAg II assay.
J. Clin. Virol. 2018. pubmed

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. 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. 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. 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. pubmed

Pabinger S, Ernst K, Pulverer W, Kallmeyer R, Valdes AM, Metrustry S, Katic D, Nuzzo A, Kriegner A, Vierlinger K, Weinhaeusel A.
Analysis and Visualization Tool for Targeted Amplicon Bisulfite Sequencing on Ion Torrent Sequencers.
PLoS ONE 2016. 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. 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. 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. 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. 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. pubmed

Maghuly F, Jankowicz-Cieslak J, Pabinger S, Till BJ, 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.
Biotechnol J 2015. pubmed

Pabinger S, Rödiger S, Kriegner A, Vierlinger K, Weinhäusel A.
A survey of tools for the analysis of quantitative PCR (qPCR) data.
Biomol Detect Quantif 2014. 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. pubmed

Schweiger D, Trajanoski Z, Pabinger S.
SPARQLGraph: a web-based platform for graphically querying biological Semantic Web databases.
BMC Bioinformatics 2014. pubmed

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. pubmed

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. pubmed

Dander A, Mueller LA, 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. pubmed

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. pubmed

Pabinger S, Dander A, Fischer M, Snajder R, Sperk M, Efremova M, Krabichler B, Speicher MR, Zschocke J, Trajanoski Z.
A survey of tools for variant analysis of next-generation genome sequencing data.
Brief. Bioinformatics 2014. pubmed

Pabinger S, Trajanoski Z.
Genome-scale model management and comparison.
Methods Mol. Biol. 2013. pubmed

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. 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, Zschocke J.
Mutations in ROGDI Cause Kohlschütter-Tönz Syndrome.
Am. J. Hum. Genet. 2012. pubmed

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

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. pubmed