BibTeX entries of Ulrich Bodenhofer's publications
2018
@article{FischerFreulingMuellerPfaffBodenhoferHoeperFischer18,
author = {S. Fischer and C. M. Freuling and T. M\"uller and
F. Pfaff and U. Bodenhofer and D. H\"oper and
M. Fischer and D. A. Marston and A. R. Fooks and
T. C. Mettenleitner and F. J. Conraths and
T. Homeier-Bachmann},
title = {Defining objective clusters for rabies virus
sequences using affinity propagation clustering},
journal = {PLoS Neglect. Trop. Dis.},
volume = 12,
number = 1,
pages = {e0006182},
doi = {10.1371/journal.pntd.0006182},
year = 2018
}
@article{SteinwandterSismisSagmeisterBodenhoferHerwig18,
author = {V. Steinwandter and M. \v{S}i\v{s}mi\v{s} and
P. Sagmeister and U. Bodenhofer and C. Herwig},
title = {Multivariate analytics of chromatographic data:
Visual computing based on moving window factor
models},
journal = {J. Chromatogr. B.},
volume = 1092,
pages = {179--190},
doi = {10.1016/j.jchromb.2018.06.010},
year = 2018
}
2017
@incollection{KlementBauerBodenhoferMittendorfer-HolzerPollakRichterExner17,
author = {E. P. Klement and P. Bauer and U. Bodenhofer and
M. Mittendorfer-Holzer and R. Pollak and R. Richter
and H. Exner},
title = {{PapaGeno --- vollautomatische menschen\"ahnliche
Qualit\"atskontrolle f\"ur Aufdrucke auf Compact
Discs}},
editor = {M. Wirth and A. Reichl and M. Gr\"aser},
booktitle = {{50 Jahre Johannes Kepler Universit\"at
Linz. Innovationsfelder in Forschung, Lehre und
universit\"arem Alltag}},
publisher = {B\"ohlau},
address = {Vienna, Austria},
year = 2017,
pages = {265--282}
}
@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}
}
@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}
}
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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