

Hansi Weißensteiner: Scalable data analysis of mitochondrial DNA in the era of high-throughput data generation. PhD thesis, University of Innsbruck, Department of Computer Science, 2017.
@PHDTHESIS {weißensteiner-diss, author = {Hansi Weißensteiner}, title = {{Scalable data analysis of mitochondrial DNA in the era of high-throughput data generation}}, school = {University of Innsbruck, Department of Computer Science}, year = {2017}, month = {oct} }
Stefan Coassin, Gertraud Erhart, Hansi Weißensteiner, Mariana Eca Guimaraes de Araujo, Claudia Lamina, Sebastian Schönherr, Lukas Forer, Margot Haun, Jamie Lee Losso, Anna Köttgen, Gerd Uterman, Annette Peters, Christian Gieger, Konstantin Strauch, Armin Finkenstedt, Reto Bale, Heinz Zoller, Bernhard Paulweber, Kai-Uwe Eckardt, Alexander Hüttenhofer, Lukas Huber and Florian Kronenberg: A novel but frequent variant in LPA KIV-2 is associated with a pronounced Lp(a) and cardiovascular risk reduction. In European Heart Journal - in press. Wiley Online Library, 2017
@Article{coassin, author = {Coassin, Stefan and Erhart, Gertraud and Weissensteiner, Hansi and Guimaraes de Araujo, Mariana Eca and Lamina, Claudia and Sch\"onherr, Sebastian and Forer, Lukas and Haun, Margot and Lee Losso, Jamie and K\"ottgen, Anna and Uterman, Gerd and Peters, Annette and Gieger, Christian and Strauch, Konstantin and Finkenstedt, Armin and Bale, Reto and Zoller, Heinz and Paulweber, Bernhard and Eckardt, Kai-Uwe and H\"uttenhofer, Alexander and Huber, Lukas and Kronenberg, Florian}, title = {A novel but frequent variant in LPA KIV-2 is associated with a pronounced Lp(a) and cardiovascular risk reduction}, journal = {European Heart Journal - in press}, year = {2017}, publisher = {Wiley Online Library}, }
Lukas Forer, Enis Afgan, Hansi Weißensteiner, Davor Davidovic, Günther Specht, Florian Kronenberg and Sebastian Schönherr: Cloudflow-Enabling Faster Biomedical Pipelines with MapReduce and Spark. In Scalable Computing: Practice and Experience, vol. 17, no. 2, pages 103-114. 2016
@article{forer2016cloudflow, title={Cloudflow-enabling faster biomedical pipelines with MapReduce and Spark}, author={Forer, Lukas and Afgan, Enis and Weissensteiner, Hansi and Davidovic, Davor and Specht, Guenther and Kronenberg, Florian and Schoenherr, Sebastian}, journal={Scalable Computing: Practice and Experience}, volume={17}, number={2}, pages={103--114}, year={2016} }
Hansi Weißensteiner, Dominic Pacher, Anita Kloss-Brandstätter, Lukas Forer, Günther Specht, Hans-Jürgen Bandelt, Florian Kronenberg, Antonio Salas and Sebastian Schönherr: HaploGrep 2: Mitochondrial Haplogroup Classification in the Era of High-Throughput Sequencing. In Nucleic Acids Research, vol. 44, no. W1, pages W58-W63. 2016
@article{doi:10.1093/nar/gkw233, author = {Weissensteiner, Hansi and Pacher, Dominic and Kloss-Brandstätter, Anita and Forer, Lukas and Specht, Günther and Bandelt, Hans-Jürgen and Kronenberg, Florian and Salas, Antonio and Schönherr, Sebastian}, title = {HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing}, journal = {Nucleic Acids Research}, volume = {44}, number = {W1}, pages = {W58--W63}, year = {2016}, doi = {10.1093/nar/gkw233}, URL = { + http://dx.doi.org/10.1093/nar/gkw233}, eprint = {/oup/backfile/Content_public/Journal/nar/44/W1/10.1093_nar_gkw233/3/gkw233.pdf} }
Hansi Weißensteiner, Lukas Forer, Christian Fuchsberger, Bernd Schöpf, Anita Kloss-Brandstätter, Günther Specht, Florian Kronenberg and Sebastian Schönherr: mtDNA-Server: Next-Generation Sequencing Data Analysis of Human Mitochondrial DNA in the Cloud. In Nucleic Acids Research, vol. 44, no. W1, pages W64-W69. 2016
@article{doi:10.1093/nar/gkw247, author = {Weissensteiner, Hansi and Forer, Lukas and Fuchsberger, Christian and Schöpf, Bernd and Kloss-Brandstätter, Anita and Specht, Günther and Kronenberg, Florian and Schönherr, Sebastian}, title = {mtDNA-Server: next-generation sequencing data analysis of human mitochondrial DNA in the cloud}, journal = {Nucleic Acids Research}, volume = {44}, number = {W1}, pages = {W64-W69}, year = {2016}, doi = {10.1093/nar/gkw247}, URL = { + http://dx.doi.org/10.1093/nar/gkw247}, eprint = {/oup/backfile/Content_public/Journal/nar/44/W1/10.1093_nar_gkw247/3/gkw247.pdf} }
Lukas Forer, Enis Afgan, Hansi Weißensteiner, Davor Davidović, Günther Specht, Florian Kronenberg and Sebastian Schönherr: Cloudflow - A Framework for MapReduce Pipeline Development in Biomedical Research. In 2015 38th International Convention on Information and Communication Technology, Electronics and Microelectronics (MIPRO), pages 172-177. 2015
@INPROCEEDINGS{7160259, author={L. Forer and E. Afgan and H. Weißensteiner and D. Davidović and G. Specht and F. Kronenberg and S. Schönherr}, booktitle={2015 38th International Convention on Information and Communication Technology, Electronics and Microelectronics (MIPRO)}, title={Cloudflow - A framework for MapReduce pipeline development in Biomedical Research}, year={2015}, pages={172-177}, abstract={The data-driven parallelization framework Hadoop MapReduce allows analysing large data sets in a scalable way. Since the development of MapReduce programs can be a time-intensive and challenging task, the application and usage of Hadoop in Biomedical Research is still limited. Here we present Cloudflow, a high-level framework to hide the implementation details of Hadoop and to provide a set of building blocks to create biomedical pipelines in a more intuitive way. We demonstrate the benefit of Cloudflow on three different genetic use cases. It will be shown how the framework can be combined with the Hadoop workflow system Cloudgene and the cloud orchestration platform CloudMan to provide Hadoop pipelines as a service to everyone.}, keywords={cloud computing;data handling;medical computing;parallel processing;CloudMan;Cloudflow;Cloudgene;Hadoop MapReduce;biomedical research;cloud orchestration platform;data-driven parallelization framework;genetic use cases;high-level framework;pipeline development;workflow system;Bioinformatics;Genomics;Information filters;Pipeline processing;Pipelines}, doi={10.1109/MIPRO.2015.7160259}, month={May},}
Julia Raschenberger, Barbara Kollerits, Stephanie Titze, Anna Köttgen, Barbara Bärthlein, Arif Ekici, Lukas Forer, Sebastian Schönherr, Hansi Weißensteiner, Margot Haun, Christoph Wanner, Kai-Uwe Eckardt and Florian Kronenberg: Do Telomeres have a Higher Plasticity than thought? Results from the German Chronic Kidney Disease (GCKD) Study as a High-Risk Population. In Experimental Gerontology, Vol. 72, pages 162-166. Pergamon, 2015
@article{raschenberger2015telomeres, title={Do telomeres have a higher plasticity than thought? Results from the German Chronic Kidney Disease (GCKD) study as a high-risk population}, author = {Raschenberger, Julia and Kollerits, Barbara and Titze, Stephanie and K{\"{o}}ttgen, Anna and B{\"{a}}rthlein, Barbara and Ekici, Arif B. and Forer, Lukas and Sch{\"{o}}nherr, Sebastian and Weissensteiner, Hansi and Haun, Margot and Wanner, Christoph and Eckardt, Kai-Uwe and Kronenberg, Florian}, journal={Experimental gerontology}, volume={72}, pages={162--166}, year={2015}, publisher={Pergamon} }
Anita Kloss-Brandstätter, Hansi Weißensteiner, Gertraud Erhart, Georg Schäfer, Lukas Forer, Sebastian Schönherr, Dominic Pacher, Christof Seifarth, Andrea Stöckl, Liane Fendt, Irma Sottsas, Helmut Klocker, Christian Huck, Michael Rasse, Florian Kronenberg and Frank Kloss: Validation of Next-Generation Sequencing of Entire Mitochondrial Genomes and the Diversity of Mitochondrial DNA Mutations in Oral Squamous Cell Carcinoma. In PloS one, vol. 10, no. 8, pages e0135643. Public Library of Science, 2015
@article{kloss2015validation, title={Validation of next-generation sequencing of entire mitochondrial genomes and the diversity of mitochondrial DNA mutations in oral squamous cell carcinoma}, author = {Kloss-Brandst{\"{a}}tter, Anita and Weissensteiner, Hansi and Erhart, Gertraud and Sch{\"{a}}fer, Georg and Forer, Lukas and Sch{\"{o}}nherr, Sebastian and Pacher, Dominic and Seifarth, Christof and St{\"{o}}ckl, Andrea and Fendt, Liane and Sottsas, Irma and Klocker, Helmut and Huck, Christian W. and Rasse, Michael and Kronenberg, Florian and Kloss, Frank R.}, journal={PloS one}, volume={10}, number={8}, pages={e0135643}, year={2015}, publisher={Public Library of Science} }
Julia Raschenberger, Barbara Kollerits, Stephanie Titze, Anna Koettgen, Barbara Baerthlein, Arif Ekici, Lukas Forer, Sebastian Schönherr, Hansi Weißensteiner, Margot Haun, Christoph Wanner, Kai-Uwe Eckardt and Florian Kronenberg: Association of Relative Telomere Length with Cardiovascular Disease in a Large Chronic Kidney Disease Cohort: The GCKD Study. In Atherosclerosis, vol. 242, no. 2, pages 529-534. Elsevier, 2015
@article{raschenberger2015association, title={Association of relative telomere length with cardiovascular disease in a large chronic kidney disease cohort: the GCKD study}, author = {Raschenberger, Julia and Kollerits, Barbara and Titze, Stephanie and {Koettgen}, Anna K and Baerthlein, Barbara B and Ekici, Arif B and Forer, Lukas and Sch, Sebastian and Sch\"onherr, and Weissensteiner, Hansi and Haun, Margot and Wanner, Christoph and Eckardt, Kai-Uwe and Kronenberg, Florian}, journal={Atherosclerosis}, volume={242}, number={2}, pages={529--534}, year={2015}, publisher={Elsevier} }
Fernanda Kehdy, Mateus Gouveia, Moara Machado, Wagner Magalhaes, Andrea Horimoto, Bernardo Horta, Rennan Moreira, Thiago Leal, Marilia Scliar, Giordano Soares-Souza and others: Origin and Dynamics of Admixture in Brazilians and its Effect on the Pattern of Deleterious Mutations. In Proceedings of the National Academy of Sciences, vol. 112, no. 28, pages 8696-8701. National Acad Sciences, 2015
@article{kehdy2015origin, title={Origin and dynamics of admixture in Brazilians and its effect on the pattern of deleterious mutations}, author={Kehdy, Fernanda SG and Gouveia, Mateus H and Machado, Moara and Magalh{\~a}es, Wagner CS and Horimoto, Andrea R and Horta, Bernardo L and Moreira, Rennan G and Leal, Thiago P and Scliar, Marilia O and Soares-Souza, Giordano B and others}, journal={Proceedings of the National Academy of Sciences}, volume={112}, number={28}, pages={8696--8701}, year={2015}, publisher={National Acad Sciences} }
Claudia Lamina, Johannes Linsenmeyer, Hansi Weißensteiner, Barbara Kollerits, Christa Meisinger, Barbara Rantner, Doris Stöckl, Marietta Stadler, Peter Klein-Weigel, Annette Peters and others: Correlation between a Positive Family Risk Score and Peripheral Artery Disease in One Case-Control and Two Population-Based Studies. In Atherosclerosis, vol. 237, no. 1, pages 243-250. Elsevier, 2014
@article{lamina2014correlation, title={Correlation between a positive family risk score and peripheral artery disease in one case-control and two population-based studies}, author={Lamina, Claudia and Linsenmeyer, Johannes and Weissensteiner, Hansi and Kollerits, Barbara and Meisinger, Christa and Rantner, Barbara and St{\"o}ckl, Doris and Stadler, Marietta and Klein-Weigel, Peter and Peters, Annette and others}, journal={Atherosclerosis}, volume={237}, number={1}, pages={243--250}, year={2014}, publisher={Elsevier} }
Lukas Forer, Tomislav Lipic, Sebastian Schönherr, Hansi Weißensteiner, Davor Davidovic, Florian Kronenberg and Enis Afgan: Delivering Bioinformatics MapReduce Applications in the Cloud. In Proceedings of the 37th International Convention on Information and Communication Technology, Electronics and Microelectronics (MIPRO 2014), pages 373-377. 2014
@inproceedings{forer2014delivering, title={Delivering bioinformatics mapreduce applications in the cloud}, author={Forer, Lukas and Lipic, Tomislav and Schonherr, Sebastian and Weissensteiner, Hansi and Davidovic, Davor and Kronenberg, Florian and Afgan, Enis}, booktitle={Information and Communication Technology, Electronics and Microelectronics (MIPRO), 2014 37th International Convention on}, pages={373--377}, year={2014}, organization={IEEE} }
Monika Summerer, Jürgen Horst, Gertraud Erhart, Hansi Weißensteiner, Sebastian Schönherr, Dominic Pacher, Lukas Forer, David Horst, Angelika Manhart, Basil Horst, Torpong Sanguansermsri and Anita Kloss-Brandstätter: Large-Scale Mitochondrial DNA Analysis in Southeast Asia Reveals Evolutionary Effects of Cultural Isolation in the Multi-Ethnic Population of Myanmar. In BMC Evolutionary Biology, vol. 14, no. 1, pages 17. BioMed Central, 2014
@article{summerer2014large, title={Large-scale mitochondrial DNA analysis in Southeast Asia reveals evolutionary effects of cultural isolation in the multi-ethnic population of Myanmar}, author = {Summerer, Monika and Horst, J{\"{u}}rgen and Erhart, Gertraud and Weissensteiner, Hansi and Sch{\"{o}}nherr, Sebastian and Pacher, Dominic and Forer, Lukas and Horst, David and Manhart, Angelika and Horst, Basil and Sanguansermsri, Torpong and Kloss-Brandst{\"{a}}tter, Anita}, journal={BMC evolutionary biology}, volume={14}, number={1}, pages={17}, year={2014}, publisher={BioMed Central} }
Hansi Weißensteiner, Margot Haun, Sebastian Schönherr, Mathias Neuner, Lukas Forer, Günther Specht, Anita Kloss-Brandstätter, Florian Kronenberg, Stefan Coassin: SNPflow: A Lightweight Application for the Processing, Storing and Automatic Quality Checking of Genotyping Assays. In PLOS ONE, vol. 8, no. 3, pages 1-9. Public Library of Science, 2013
@article{10.1371/journal.pone.0059508, author = {Weissensteiner, Hansi AND Haun, Margot AND Schönherr, Sebastian AND Neuner, Mathias AND Forer, Lukas AND Specht, Günther AND Kloss-Brandstätter, Anita AND Kronenberg, Florian AND Coassin, Stefan}, journal = {PLOS ONE}, publisher = {Public Library of Science}, title = {SNPflow: A Lightweight Application for the Processing, Storing and Automatic Quality Checking of Genotyping Assays}, year = {2013}, month = {03}, volume = {8}, url = {http://dx.doi.org/10.1371%2Fjournal.pone.0059508}, pages = {1-9}, abstract = {Single nucleotide polymorphisms (SNPs) play a prominent role in modern genetics. Current genotyping technologies such as Sequenom iPLEX, ABI TaqMan and KBioscience KASPar made the genotyping of huge SNP sets in large populations straightforward and allow the generation of hundreds of thousands of genotypes even in medium sized labs. While data generation is straightforward, the subsequent data conversion, storage and quality control steps are time-consuming, error-prone and require extensive bioinformatic support. In order to ease this tedious process, we developed SNPflow. SNPflow is a lightweight, intuitive and easily deployable application, which processes genotype data from Sequenom MassARRAY (iPLEX) and ABI 7900HT (TaqMan, KASPar) systems and is extendible to other genotyping methods as well. SNPflow automatically converts the raw output files to ready-to-use genotype lists, calculates all standard quality control values such as call rate, expected and real amount of replicates, minor allele frequency, absolute number of discordant replicates, discordance rate and the p-value of the HWE test, checks the plausibility of the observed genotype frequencies by comparing them to HapMap/1000-Genomes, provides a module for the processing of SNPs, which allow sex determination for DNA quality control purposes and, finally, stores all data in a relational database. SNPflow runs on all common operating systems and comes as both stand-alone version and multi-user version for laboratory-wide use. The software, a user manual, screenshots and a screencast illustrating the main features are available at http://genepi-snpflow.i-med.ac.at.}, number = {3}, doi = {10.1371/journal.pone.0059508} }
Lukas Forer, Sebastian Schönherr, Hansi Weißensteiner, Günther Specht, Florian Kronenberg and Anita Kloss-Brandstätter: Cloud Computing - Bringing Computational Power to Medical Genetics. In Zlatko Trajanoski (Ed.): Computational Medicine: Tools and Challenges, 203 p., Springer 2012, ISBN: 978-3-7091-0946-5, pp. 27-36
@incollection{forer2012cloud, title={Cloud Computing - Bringing computational power to medical genetics}, author={Forer, Lukas and Sch{\"o}nherr, Sebastian and Weissensteiner, Hansi and Specht, G{\"u}nther and Kronenberg, Florian and Kloss-Brandst{\"a}tter, Anita}, booktitle={Computational Medicine: Tools and Challenges}, pages={27--36}, year={2012}, publisher={Springer}, }
Sebastian Schönherr, Lukas Forer, Hansi Weißensteiner, Florian Kronenberg, Günther Specht and Anita Kloss-Brandstätter: Cloudgene: A Graphical Execution Platform for MapReduce Programs on Private and Public Clouds. In BMC Bioinformatics, vol. 13, no. 1, pages 200. 2012
@Article{Schönherr2012, author="Sch{\"o}nherr, Sebastian and Forer, Lukas and Wei{\ss}ensteiner, Hansi and Kronenberg, Florian and Specht, G{\"u}nther and Kloss-Brandst{\"a}tter, Anita", title="Cloudgene: A graphical execution platform for MapReduce programs on private and public clouds", journal="BMC Bioinformatics", year="2012", volume="13", number="1", pages="200", abstract="The MapReduce framework enables a scalable processing and analyzing of large datasets by distributing the computational load on connected computer nodes, referred to as a cluster. In Bioinformatics, MapReduce has already been adopted to various case scenarios such as mapping next generation sequencing data to a reference genome, finding SNPs from short read data or matching strings in genotype files. Nevertheless, tasks like installing and maintaining MapReduce on a cluster system, importing data into its distributed file system or executing MapReduce programs require advanced knowledge in computer science and could thus prevent scientists from usage of currently available and useful software solutions.", issn="1471-2105", doi="10.1186/1471-2105-13-200", url="http://dx.doi.org/10.1186/1471-2105-13-200" }
Sebastian Schönherr, Lukas Forer, Hansi Weißensteiner, Florian Kronenberg, Günther Specht and Anita Kloss-Brandstätter: A Feedback Guided Interface for Elastic Computing. In Proceedings of the 23rd GI-Workshop Grundlagen von Datenbanken (GvDB 2011), Obergurgl, Austria, pages 109-114. 2011
@inproceedings{schonherr2011feedback, title={A feedback guided interface for elastic computing.}, author={Sch{\"o}nherr, Sebastian and Forer, Lukas and Wei{\ss}ensteiner, Hansi and Kronenberg, Florian and Specht, G{\"u}nther and Kloss-Brandst{\"a}tter, Anita}, booktitle={Grundlagen von Datenbanken}, pages={109--114}, year={2011}, organization={Citeseer} }
Anita Kloss-Brandstätter, Dominic Pacher, Sebastian Schönherr, Hansi Weißensteiner, Robert Binna, Günther Specht and Florian Kronenberg: HaploGrep: A Fast and Reliable Algorithm for Automatic Classification of Mitochondrial DNA Haplogroups. In Human Mutation, vol. 32, no. 1, pages 25-32. Wiley Inc., 2011
@article {HUMU:HUMU21382, author = {Kloss-Brandstätter, Anita and Pacher, Dominic and Schönherr, Sebastian and Weissensteiner, Hansi and Binna, Robert and Specht, Günther and Kronenberg, Florian}, title = {HaploGrep: a fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups}, journal = {Human Mutation}, volume = {32}, number = {1}, publisher = {Wiley Subscription Services, Inc., A Wiley Company}, issn = {1098-1004}, url = {http://dx.doi.org/10.1002/humu.21382}, doi = {10.1002/humu.21382}, pages = {25--32}, keywords = {mitochondrial DNA, haplogroup, Phylotree, quality assurance}, year = {2011}, } Click to copy this citation from the text box above or download
Lukas Forer, Sebastian Schönherr, Hansi Weißensteiner, Florian Haider, Thomas Kluckner, Christian Gieger, Heinz-Erich Wichmann, Günther Specht, Florian Kronenberg and Anita Kloss-Brandstätter: CONAN: Copy Number Variation Analysis Software for Genome-wide Association Studies. In BMC Bioinformatics, vol. 11, no. 1, pages 318. 2010
@Article{Forer2010, author="Forer, Lukas and Sch{\"o}nherr, Sebastian and Weissensteiner, Hansi and Haider, Florian and Kluckner, Thomas and Gieger, Christian and Wichmann, Heinz-Erich and Specht, G{\"u}nther and Kronenberg, Florian and Kloss-Brandst{\"a}tter, Anita", title="CONAN: copy number variation analysis software for genome-wide association studies", journal="BMC Bioinformatics", year="2010", volume="11", number="1", pages="318", abstract="Genome-wide association studies (GWAS) based on single nucleotide polymorphisms (SNPs) revolutionized our perception of the genetic regulation of complex traits and diseases. Copy number variations (CNVs) promise to shed additional light on the genetic basis of monogenic as well as complex diseases and phenotypes. Indeed, the number of detected associations between CNVs and certain phenotypes are constantly increasing. However, while several software packages support the determination of CNVs from SNP chip data, the downstream statistical inference of CNV-phenotype associations is still subject to complicated and inefficient in-house solutions, thus strongly limiting the performance of GWAS based on CNVs.", issn="1471-2105", doi="10.1186/1471-2105-11-318", url="http://dx.doi.org/10.1186/1471-2105-11-318" }
Hansi Weißensteiner, Sebastian Schönherr, Günther Specht, Florian Kronenberg and Anita Brandstätter: eCOMPAGT integrates mtDNA: Import, Validation and Export of Mitochondrial DNA Profiles for Population Genetics, Tumour Dynamics and Genotype-Phenotype Association Studies. In BMC Bioinformatics, vol. 11, no. 1, pages 122. 2010
@Article{Weißensteiner2010, author="Weißensteiner, Hansi and Sch{\"o}nherr, Sebastian and Specht, G{\"u}nther and Kronenberg, Florian and Brandst{\"a}tter, Anita", title="eCOMPAGT integrates mtDNA: Import, Validation and Export of Mitochondrial DNA Profiles for Population Genetics, Tumour Dynamics and Genotype-Phenotype Association Studies", journal="BMC Bioinformatics", year="2010", volume="11", number="1", pages="122", abstract="Mitochondrial DNA (mtDNA) is widely being used for population genetics, forensic DNA fingerprinting and clinical disease association studies. The recent past has uncovered severe problems with mtDNA genotyping, not only due to the genotyping method itself, but mainly to the post-lab transcription, storage and report of mtDNA genotypes.", issn="1471-2105", doi="10.1186/1471-2105-11-122", url="http://dx.doi.org/10.1186/1471-2105-11-122" }