Bioinformatics

@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"
}

@article{jacquemont2011mirror,
  title={Mirror extreme BMI phenotypes associated with gene dosage at the chromosome 16p11. 2 locus},
  author={Jacquemont, S{\'e}bastien and Reymond, Alexandre and Zufferey, Flore and Harewood, Louise and Walters, Robin G and Kutalik, Zolt{\'a}n and Martinet, Danielle and Shen, Yiping and Valsesia, Armand and Beckmann, Noam D and others},
  journal={Nature},
  volume={478},
  number={7367},
  pages={97--102},
  year={2011},
  publisher={Nature Publishing Group}
}

@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}
}

@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},
}

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@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"
}

@MISC{M_chaosor,
    author = {Borovicka M and Laschitz L and Reiter D and Gächter E and Specht G},
    title = {Chaos or Content: Towards Generic Structuring of Medical Documents by Utilisation of Archetype-Classes},
    year = {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"
}

@Article{Schönherr2009,
author="Sch{\"o}nherr, Sebastian
and Wei{\ss}ensteiner, Hansi
and Coassin, Stefan
and Specht, G{\"u}nther
and Kronenberg, Florian
and Brandst{\"a}tter, Anita",
title="eCOMPAGT -- efficient Combination and Management of Phenotypes and Genotypes for Genetic Epidemiology",
journal="BMC Bioinformatics",
year="2009",
volume="10",
number="1",
pages="139",
abstract="High-throughput genotyping and phenotyping projects of large epidemiological study populations require sophisticated laboratory information management systems. Most epidemiological studies include subject-related personal information, which needs to be handled with care by following data privacy protection guidelines. In addition, genotyping core facilities handling cooperative projects require a straightforward solution to monitor the status and financial resources of the different projects.",
issn="1471-2105",
doi="10.1186/1471-2105-10-139",
url="http://dx.doi.org/10.1186/1471-2105-10-139"
}

@inproceedings{snowmed_holzner_1996,
  author = {M. Holzner and M. Adler and M. Fischer and G. Specht},
  title = {Graphische Darstellung von Differentialdiagnosen in einem Begriffsnetz unter Verwendung von Snomed-kodierten Hypothesen},
  booktitle = {Proceedings of the 41. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie (GMDS '96)},
  location = {15.-19.9.96 in Bonn},
  year = {1996},
}

@article{specht1995multimed,
  title={MultiMED-ein Multimedia-Datenbanksystem zur Aus-und Weiterbildung in der R{\"o}ntgendiagnostik in der Orthop{\"a}die},
  author={Specht, Gunther and Bauer, Martin},
  journal={Hypermedia in der Aus-und Weiterbildung, Schriften zur Informationswissenschaft},
  volume={17},
  pages={209--210},
  year={1995}
}