BibTeX entries of Ulrich Bodenhofer's publications

2017

@article{GreiffWeberPalmeBodenhoferMihoMenzelReddy17,
  author = {V. Greiff and C. R. Weber and J. Palme and
                  U. Bodenhofer and E. Miho and U. Menzel and
                  S. T. Reddy},
  title = {Learning the high-dimensional immunogenomic features
                  that predict public and private antibody
                  repertoires},
  journal = {J. Immunol.},
  doi = {10.4049/jimmunol.1700594},
  volume = 199,
  number = 8,
  pages = {2985--2997},
  year = 2017
}
@inproceedings{BodenhoferHochreiter17,
  author = {U. Bodenhofer and S. Hochreiter},
  title = {Position Kernels as a Key to Making Sense of Very
                  Rare and Private Single-Nucleotide Variants},
  booktitle = {NIPS Workshop on Machine Learning in Computational
                  Biology},
  month = {December},
  year = 2017,
  address = {Long Beach, CA},
  note = {(accepted)}
}
@inproceedings{BodenhoferHaslinger-EistererMinichmayerHermanutzMeier17,
  author = {U. Bodenhofer and B. Haslinger-Eisterer and
                  A. Minichmayer and G. Hermanutz and J. Meier},
  title = {Machine Learning-Based Risk Profile Classification:
                  A Case Study for Heart Valve Surgery},
  booktitle = {NIPS Workshop on Machine Learning for Health},
  month = {December},
  year = 2017,
  address = {Long Beach, CA},
  note = {(accepted)}
}

2016

@article{ZehentmayrHauser-KronbergerZellingerHlubekSchusterBodenhoferFastner16,
  author = {F. Zehentmayr and C. Hauser-Kronberger and
                  B. Zellinger and F. Hlubek and C. Schuster and
                  U. Bodenhofer and G. Fastner and H. Deutschmann and
                  P. Steininger and R. Reitsamer and T. Fischer and
                  F. Sedlmayer},
  title = {{Hsa-miR-375} is a predictor of local control in
                  early stage breast cancer},
  journal = {Clin. Epigenetics},
  doi = {10.1186/s13148-016-0198-1},
  volume = 8,
  pages = 28,
  year = 2016
}
@article{Perualila-TanKasimTalloenVerbistGoehlmannShkedy16,
  author = {N. Perualila-Tan and A. Kasim and W. Talloen and
                  B. Verbist and H. W. H. G\"ohlmann and {The QSTAR Consortium}
		  and Z. Shkedy},
  title = {A joint modeling approach for uncovering
                  associations between gene expression, bioactivity
                  and chemical structure in early drug discovery to
                  guide lead selection and genomic biomarker
                  development},
  journal = {Stat. Appl. Genet. Mol. Biol.},
  doi = {10.1515/sagmb-2014-0086},
  volume = 15,
  number = 4,
  pages = {291--304},
  year = 2016
}
@article{Perualila-TanShkedyTalloenGoehlmannMoerbekeKasim16,
  author = {N. Perualila-Tan and Z. Shkedy and W. Talloen and
                  H. W. H. G\"ohlmann and {The QSTAR Consortium} and
                  M. V. Moerbeke and A. Kasim},
  title = {Weighted similarity-based clustering of chemical
                  structures and bioactivity data in early drug
                  discovery},
  journal = {J. Bioinform. Comput. Biol.},
  volume = 14,
  pages = 1650018,
  doi = {10.1142/S0219720016500189},
  year = 2016
}
@article{KhalediSchniederjansPohlRainerBodenhoferXiaKlawonn16,
  author = {A. Khaledi and M. Schniederjans and S. Pohl and
                  R. Rainer and U. Bodenhofer and B. Xia and
                  F. Klawonn and S. Bruchmann and M. Preusse and
                  D. Eckweiler and A. D\"otsch and S. H\"aussler},
  title = {Transcriptome profiling of antimicrobial resistance
                  in {{\em Pseudomonas aeruginosa}}},
  journal = {Antimicrob. Agents Chemother.},
  volume = 60,
  number = 8,
  pages = {4722--4733},
  doi = {10.1128/AAC.00075-16},
  year = 2016
}

2015

@article{BehounekBodenhoferCintulaSaminger-PlatzSarkoci15,
  author = {L. B\v{e}hounek and U. Bodenhofer and P. Cintula and
                  S. Saminger-Platz and P. Sarkoci},
  title = {Graded dominance and related graded properties of
                  fuzzy connectives},
  journal = {Fuzzy Sets and Systems},
  doi = {10.1016/j.fss.2014.04.025},
  volume = 262,
  pages = {78--101},
  year = 2015
}
@article{RavindranathPerualila-TanKasimDrakakisLiggiBrewertonMason15,
  author = {A. C. Ravindranath and N. Perualila-Tan and A. Kasim
                  and G. Drakakis and S. Liggi and S. C. Brewerton and
                  D.~Mason and M. J. Bodkin and D. A. Evans and
                  A. Bhagwat and W. Talloen and H. W. G\"ohlmann and
                  Z. Shkedy and A. Bender and {The QSTAR Consortium}},
  title = {Connecting gene expression data from connectivity
                  map and in silico target predictions for small
                  molecule mechanism-of-action analysis},
  journal = {Mol. Biosyst.},
  doi = {10.1039/C4MB00328D},
  volume = 11,
  number = 1,
  pages = {86--96},
  year = 2015
}
@article{VerbistKlambauerVervoortTalloenQStarConsortiumShkedyBender15,
  author = {B. Verbist and G. Klambauer and L. Vervoort and
                  W. Talloen and {The QSTAR Consortium} and Z. Shkedy
                  and O. Thas and A. Bender and H. W. G\"ohlmann and
                  S. Hochreiter},
  title = {Using transcriptomics to guide lead optimization in
                  drug discovery projects: Lessons learned from the
                  {QSTAR} project},
  journal = {Drug Discov. Today},
  doi = {10.1016/j.drudis.2014.12.014},
  volume = 20,
  number = 5,
  pages = {505--513},
  year = 2015
}
@article{PalmeHochreiterBodenhofer15,
  author = {J. Palme and S. Hochreiter and U. Bodenhofer},
  title = {{KeBABS}: an {R} package for kernel-based analysis
                  of biological sequences},
  journal = {Bioinformatics},
  year = 2015,
  volume = 31,
  number = 15,
  pages = {2574--2576},
  doi = {10.1093/bioinformatics/btv176}
}
@article{VerbistVerheyenVervoortCrabbeBeerensBosmansJaensch15,
  author = {B. M. P. Verbist and G. R. Verheyen and L. Vervoort
                  and M. Crabbe and D. Beerens and C. Bosmans and
                  S. Jaensch and S. Osselaer and W. Talloen and
                  I. {Van den Wyngaert} and G. {Van Hecke} and
                  D. Wuyts and {The QSTAR Consortium} and F. {Van
                  Goethem} and H. W. H. G\"ohlmann},
  title = {Integrating high-dimensional transcriptomics and
                  image analysis tools into early safety screening:
                  proof of concept for a new early drug development
                  strategy},
  journal = {Chem. Res. Toxicol.},
  doi = {10.1021/acs.chemrestox.5b00103},
  volume = 28,
  number = 10,
  pages = {1914--1925},
  year = 2015
}
@article{BodenhoferBonatestaHorejs-KainrathHochreiter15,
  author = {U. Bodenhofer and E. Bonatesta and
                  C. Horej\v{s}-Kainrath and S. Hochreiter},
  title = {{msa}: an {R} package for multiple sequence
                  alignment},
  journal = {Bioinformatics},
  doi = {10.1093/bioinformatics/btv494},
  volume = 31,
  number = 24,
  pages = {3997--3999},
  year = 2015
}

2014

@article{LippJuhaszPaarOgrisEckerstorferThuenauerHesse14,
  author = {A. M. Lipp and K. Juhasz and C. Paar and C. Ogris
                  and P. Eckerstorfer and R. Thuenauer and J. Hesse
                  and B. Nimmervoll and H. Stockinger and
                  G. J. Sch\"utz and U. Bodenhofer and Z. Balogi and
                  A. Sonnleitner},
  title = {{Lck} Mediates Signal Transmission from {CD59} to
                  the {TCR/CD3} Pathway in {Jurkat T} Cells},
  journal = {PLoS ONE},
  year = 2014,
  doi = {10.1371/journal.pone.0085934},
  volume = 9,
  number = 1,
  pages = {e85934}
}

2013

@article{BodenhoferKroneKlawonn13,
  author = {U. Bodenhofer and M. Krone and F. Klawonn},
  title = {Testing noisy numerical data for monotonic
                  association},
  journal = {Inform. Sci.},
  volume = 245,
  pages = {21--37},
  year = 2013,
  doi = {10.1016/j.ins.2012.11.026}
}

2012

@article{KlambauerSchwarzbauerMayrClevertMittereckerBodenhoferHochreiter12,
  author = {G. Klambauer and K. Schwarzbauer and A. Mayr and
                  D.-A. Clevert and A. Mitterecker and U. Bodenhofer
                  and S. Hochreiter},
  title = {{cn.MOPS:} mixture of {Poissons} for discovering
                  copy number variations in next-generation sequencing
                  data with a low false discovery rate},
  journal = {Nucleic Acids Res.},
  year = 2012,
  doi = {10.1093/nar/gks003},
  volume = 40,
  number = 9,
  pages = {e69}
}
@article{SchwarzbauerBodenhoferHochreiter12,
  author = {K. Schwarzbauer and U. Bodenhofer and S. Hochreiter},
  title = {Genome-Wide Chromatin Remodeling Identified at
                  {GC}-Rich Long Nucleosome-Free Regions},
  journal = {PLoS ONE},
  year = 2012,
  doi = {10.1371/journal.pone.0047924},
  volume = 7,
  number = 11,
  pages = {e47924}
}

2011

@article{MahrenholzAbfalterBodenhoferVolkmerHochreiter11,
  author = {C. C. Mahrenholz and I. G. Abfalter and
                  U. Bodenhofer and R. Volkmer and S. Hochreiter},
  title = {Complex networks govern coiled coil oligomerization
                  --- Predicting and profiling by means of a machine
                  learning approach},
  journal = {Mol. Cell. Proteomics},
  year = {2011},
  volume = {10},
  number = {5},
  pages = {M110.004994},
  doi = {10.1074/mcp.M110.004994}
}
@article{BodenhoferKothmeierHochreiter11,
  author = {U. Bodenhofer and A. Kothmeier and S. Hochreiter},
  title = {{APCluster:} an {R} package for affinity propagation
                  clustering},
  journal = {Bioinformatics},
  volume = 27,
  number = 17,
  pages = {2463--2464},
  year = 2011,
  doi = {10.1093/bioinformatics/btr406}
}

2010

@article{StepnickaBodenhoferDankovaNovak10,
  author = {M. \v{S}t\v{e}pni\v{c}ka and U. Bodenhofer and
                  M. Da\v{n}kov\'{a} and V. Nov\'{a}k},
  title = {Continuity issues of the implicational
                  interpretation of fuzzy rules},
  journal = {Fuzzy Sets and Systems},
  volume = {161},
  number = {14},
  pages = {1959--1972},
  year = {2010},
  doi = {10.1016/j.fss.2010.03.009}
}
@article{HochreiterBodenhoferHeuselMayrMittereckerKasimKhamiakova10,
  author = {S. Hochreiter and U. Bodenhofer and M. Heusel and
                  A. Mayr and A. Mitterecker and A. Kasim and
                  T. Khamiakova and S. {Van Sanden} and D. Lin and
                  W. Talloen and L. Bijnens and H. W. H. G\"ohlmann
                  and Z. Shkedy and D.-A. Clevert},
  title = {{FABIA:} factor analysis for bicluster acquisition},
  journal = {Bioinformatics},
  volume = {26},
  number = {12},
  pages = {1520--1527},
  year = {2010},
  doi = {10.1093/bioinformatics/btq227}
}
@inproceedings{BehounekCintulaBodenhoferSaminger-PlatzSarkoci10,
  author = {L. B\v{e}hounek and P. Cintula and U. Bodenhofer and
                  S. Saminger-Platz and P. Sarkoci},
  title = {On a graded notion of t-norm and dominance},
  booktitle = {Proc. 40th IEEE Int. Symp. on Multiple-Valued Logic},
  pages = {73--78},
  publisher = {IEEE Computer Society},
  year = {2010},
  doi = {10.1109/ISMVL.2010.21}
}

2009

@article{SoukupBodenhoferMittendorfer-HolzerMayer09,
  author = {D. Soukup and U. Bodenhofer and
                  M. Mittendorfer-Holzer and K. Mayer},
  title = {Semi-automatic identification of print layers from a
                  sequence of sample images: a case study from
                  banknote print inspection},
  journal = {Image Vision Comput.},
  year = {2009},
  volume = {27},
  number = {8},
  pages = {989--998},
  doi = {10.1016/j.imavis.2008.08.008}
}
@inproceedings{BodenhoferSchwarzbauerIonescuHochreiter09,
  author = {U. Bodenhofer and K. Schwarzbauer and M. Ionescu and
                  S. Hochreiter},
  title = {Modeling position specificity in sequence kernels by
                  fuzzy equivalence relations},
  booktitle = {Proc. Joint 13th IFSA World Congress and 6th EUSFLAT
                  Conference},
  editor = {J. P. Carvalho and D. Dubois and U. Kaymak and
                  J. M. C. Sousa},
  address = {Lisbon},
  month = {July},
  year = {2009},
  pages = {1376--1381},
  pdf = {http://www.eusflat.org/proceedings/IFSA-EUSFLAT_2009/pdf/tema_1376.pdf}
}
@inproceedings{Bodenhofer09,
  author = {U. Bodenhofer},
  title = {A survey of applications of fuzzy orderings: from
                  databases to statistics and machine learning},
  booktitle = {Proc. 14 Recontres Francophones sur la Logique Floue
                  et ses Applications},
  address = {Annecy},
  month = {November},
  year = {2009},
  pages = {3--9},
  pdf = {http://www.bioinf.jku.at/people/bodenhofer/private/publications/pdf/Bodenhofer09.pdf}
}

2008

@incollection{Bodenhofer08c,
  author = {U. Bodenhofer},
  title = {Lexicographic composition of similarity-based fuzzy
                  orderings},
  editor = {B. Bouchon-Meunier and C. Marsala and M. Rifqi and
                  R. R. Yager},
  booktitle = {Uncertainty and Intelligent Information Systems},
  publisher = {World-Scientific},
  chapter = {33},
  year = {2008},
  pages = {457--469},
  pdf = {http://www.bioinf.jku.at/people/bodenhofer/private/publications/pdf/Bodenhofer08c.pdf}
}
@article{BehounekBodenhoferCintula08,
  author = {L. B\v{e}hounek and U. Bodenhofer and P. Cintula},
  title = {Relations in {F}uzzy {C}lass {T}heory: Initial
                  steps},
  journal = {Fuzzy Sets and Systems},
  year = {2008},
  volume = {159},
  number = {14},
  pages = {1729--1772},
  doi = {10.1016/j.fss.2007.10.012}
}
@article{BodenhoferDemirci08,
  author = {U. Bodenhofer and M. Demirci},
  title = {Strict fuzzy orderings with a given context of
                  similarity},
  journal = {Internat. J. Uncertain. Fuzziness Knowledge-Based
                  Systems},
  volume = {16},
  number = {2},
  pages = {147--178},
  year = {2008},
  doi = {10.1142/S021848850800511X}
}
@article{BodenhoferKlawonn08,
  author = {U. Bodenhofer and F. Klawonn},
  title = {Robust rank correlation coefficients on the basis of
                  fuzzy orderings: initial steps},
  journal = {Mathware Soft Comput.},
  volume = {15},
  number = {1},
  pages = {5--20},
  year = {2008},
  url = {http://ic.ugr.es/Mathware/index.php/Mathware/article/view/25},
  pdf = {http://www.bioinf.jku.at/people/bodenhofer/private/publications/pdf/BodenhoferKlawonn08.pdf}
}
@article{Bodenhofer08,
  author = {U. Bodenhofer},
  title = {Orderings of fuzzy sets based on fuzzy
                  orderings. part {I}: the basic approach},
  journal = {Mathware Soft Comput.},
  volume = {15},
  number = {2},
  year = {2008},
  pages = {201--218},
  url = {http://ic.ugr.es/Mathware/index.php/Mathware/article/view/30},
  pdf = {http://www.bioinf.jku.at/people/bodenhofer/private/publications/pdf/Bodenhofer08.pdf}
}
@article{Bodenhofer08b,
  author = {U. Bodenhofer},
  title = {Orderings of fuzzy sets based on fuzzy
                  orderings. part {II}: generalizations},
  journal = {Mathware Soft Comput.},
  volume = {15},
  number = {3},
  year = {2008},
  pages = {219--249},
  url = {http://ic.ugr.es/Mathware/index.php/Mathware/article/view/354},
  pdf = {http://www.bioinf.jku.at/people/bodenhofer/private/publications/pdf/Bodenhofer08b.pdf}
}

2007

@article{BodenhoferDeBaetsFodor07,
  author = {U. Bodenhofer and B. {De Baets} and J. Fodor},
  title = {A compendium of fuzzy weak orders: Representations
                  and constructions},
  journal = {Fuzzy Sets and Systems},
  year = {2007},
  volume = {158},
  number = {8},
  pages = {811--829},
  doi = {10.1016/j.fss.2006.10.005}
}
@inproceedings{BodenhoferDankovaStepnickaNovak07,
  author = {U. Bodenhofer and M. Da\v{n}kov\'{a} and
                  M. \v{S}t\v{e}pni\v{c}ka and V. Nov\'{a}k},
  title = {A plea for the usefulness of the deductive
                  interpretation of fuzzy rules in engineering
                  applications},
  booktitle = {Proc. 16th IEEE Int. Conf. on Fuzzy Systems},
  address = {London},
  month = {July},
  year = {2007},
  pages = {1567--1572},
  doi = {10.1109/FUZZY.2007.4295600 }
}
@inproceedings{BehounekBodenhoferCintula07,
  author = {L. B\v{e}hounek and U. Bodenhofer and P. Cintula},
  title = {Valverde-style representation results in a graded
                  framework},
  editor = {M. \v{S}t\v{e}pni\v{c}ka and V. Nov{\'a}k and
                  U. Bodenhofer},
  booktitle = {Proc. 5th Conference of the European Society for
                  Fuzzy Logic and Technology},
  address = {Ostrava},
  month = {September},
  year = {2007},
  volume = {{I}},
  pages = {153--160},
  pdf = {http://www.eusflat.org/proceedings/EUSFLAT_2007/papers/Behounek_Libor_(167).pdf}
}
@inproceedings{BodenhoferKlawonn07,
  author = {U. Bodenhofer and F. Klawonn},
  title = {Towards robust rank correlation measures for
                  numerical observations on the basis of fuzzy
                  orderings},
  editor = {M. \v{S}t\v{e}pni\v{c}ka and V. Nov{\'a}k and
                  U. Bodenhofer},
  booktitle = {Proc. 5th Conference of the European Society for
                  Fuzzy Logic and Technology},
  address = {Ostrava},
  month = {September},
  year = {2007},
  volume = {{I}},
  pages = {321--327},
  pdf = {http://www.eusflat.org/proceedings/EUSFLAT_2007/papers/Bodenhofer_Ulrich_(140).pdf}
}

2006

@incollection{SamingerBodenhoferKlementMesiar06,
  author = {S. Saminger and U. Bodenhofer and E. P. Klement and
                  R. Mesiar},
  title = {Aggregration of fuzzy relations and preservation of
                  transitivity},
  editor = {H. C. M. {de Swart} and E. Or\l owska and M. Roubens
                  and G. Schmidt},
  booktitle = {Theory and Applications of Relational Structures as
                  Knowledge Instruments II},
  publisher = {Springer},
  address = {Berlin},
  volume = {4342},
  series = {Lecture Notes in Artificial Intelligence},
  pages = {185--206},
  year = {2006},
  doi = {10.1007/11964810}
}
@incollection{BodenhoferKuengSaminger06,
  author = {U. Bodenhofer and J. K\"{u}ng and S. Saminger},
  title = {Flexible query answering using distance-based fuzzy
                  relations},
  editor = {H. C. M. {de Swart} and E. Or\l owska and M. Roubens
                  and G. Schmidt},
  booktitle = {Theory and Applications of Relational Structures as
                  Knowledge Instruments II},
  publisher = {Springer},
  address = {Berlin},
  volume = {4342},
  series = {Lecture Notes in Artificial Intelligence},
  pages = {207--228},
  year = {2006},
  doi = {10.1007/11964810}
}
@incollection{BodenhoferDeBaetsFodor06,
  author = {U. Bodenhofer and B. {De Baets} and J. Fodor},
  title = {General representation theorems for fuzzy weak
                  orders},
  editor = {H. C. M. {de Swart} and E. Or\l owska and M. Roubens
                  and G. Schmidt},
  booktitle = {Theory and Applications of Relational Structures as
                  Knowledge Instruments II},
  publisher = {Springer},
  address = {Berlin},
  volume = {4342},
  series = {Lecture Notes in Artificial Intelligence},
  pages = {229--244},
  year = {2006},
  doi = {10.1007/11964810}
}
@inproceedings{LughoferBodenhofer06,
  author = {E. Lughofer and U. Bodenhofer},
  title = {Incremental learning of fuzzy basis function
                  networks with a modified version of vector
                  quantization},
  booktitle = {Proc. 11th Int. Conf. on Information Processing and
                  Management of Uncertainty in Knowledge-Based
                  Systems},
  address = {Paris},
  month = {July},
  pages = {56--63},
  volume = {1},
  year = {2006},
  pdf = {http://www.bioinf.jku.at/people/bodenhofer/private/publications/pdf/LughoferBodenhofer06.pdf}
}
@inproceedings{Bodenhofer06,
  author = {U. Bodenhofer},
  title = {Lexicographic composition of fuzzy orderings},
  booktitle = {Proc. 11th Int. Conf. on Information Processing and
                  Management of Uncertainty in Knowledge-Based
                  Systems},
  address = {Paris},
  month = {July},
  pages = {2430--2437},
  volume = {3},
  year = {2006},
  pdf = {http://www.bioinf.jku.at/people/bodenhofer/private/publications/pdf/Bodenhofer06.pdf}
}
@inproceedings{BergmairBodenhofer06,
  author = {R. Bergmair and U. Bodenhofer},
  title = {Syntax-driven analysis of context-free languages
                  with respect to fuzzy relational semantics},
  booktitle = {Proc. 15th IEEE Int. Conf. on Fuzzy Systems},
  address = {Vancouver, BC},
  month = {July},
  year = {2006},
  pages = {9647--9654},
  doi = {10.1109/FUZZY.2006.1681988 }
}
@inproceedings{MoserBodenhofer06,
  author = {B. Moser and U. Bodenhofer},
  title = {Correspondences between fuzzy equivalence relations
                  and kernels: theoretical results and potential
                  applications},
  booktitle = {Proc. 15th IEEE Int. Conf. on Fuzzy Systems},
  address = {Vancouver, BC},
  month = {July},
  year = {2006},
  pages = {10217--10223},
  doi = {10.1109/FUZZY.2006.1682001 }
}

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