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ORCIDBibTeX records: Ivan G. Costa
@article{DBLP:journals/bmcbi/HolscherGKDCBB24,
author = {David L. H{\"{o}}lscher and
Michael Goedertier and
Barbara Mara Klinkhammer and
Patrick Droste and
Ivan G. Costa and
Peter Boor and
Roman David B{\"{u}}low},
title = {tRigon: an {R} package and Shiny App for integrative (path-)omics
data analysis},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {98},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05721-w},
doi = {10.1186/S12859-024-05721-W},
timestamp = {Mon, 11 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/HolscherGKDCBB24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiKTSGGAMZC23,
author = {Zhijian Li and
Chao{-}Chung Kuo and
Fabio Ticconi and
Mina Shaigan and
Julia Gehrmann and
Eduardo G. Gusm{\~{a}}o and
Manuel Allhoff and
Martin Manolov and
Martin Zenke and
Ivan G. Costa},
title = {{RGT:} a toolbox for the integrative analysis of high throughput regulatory
genomics data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {79},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05184-5},
doi = {10.1186/S12859-023-05184-5},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LiKTSGGAMZC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2304-01450,
author = {Pablo Andretta Jaskowiak and
Ivan Gesteira Costa},
title = {Clustering Validation with The Area Under Precision-Recall Curves},
journal = {CoRR},
volume = {abs/2304.01450},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2304.01450},
doi = {10.48550/ARXIV.2304.01450},
eprinttype = {arXiv},
eprint = {2304.01450},
timestamp = {Mon, 17 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2304-01450.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2309-07030,
author = {James Shiniti Nagai and
Ivan G. Costa and
Michael T. Schaub},
title = {Optimal transport distances for directed, weighted graphs: a case
study with cell-cell communication networks},
journal = {CoRR},
volume = {abs/2309.07030},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2309.07030},
doi = {10.48550/ARXIV.2309.07030},
eprinttype = {arXiv},
eprint = {2309.07030},
timestamp = {Tue, 19 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2309-07030.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiBSC22,
author = {Ronghui Li and
Bella Banjanin and
Rebekka K. Schneider and
Ivan G. Costa},
title = {Detection of cell markers from single cell RNA-seq with sc2marker},
journal = {{BMC} Bioinform.},
volume = {23},
number = {1},
pages = {276},
year = {2022},
url = {https://doi.org/10.1186/s12859-022-04817-5},
doi = {10.1186/S12859-022-04817-5},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LiBSC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/datamine/JaskowiakCC22,
author = {Pablo A. Jaskowiak and
Ivan G. Costa and
Ricardo J. G. B. Campello},
title = {The area under the {ROC} curve as a measure of clustering quality},
journal = {Data Min. Knowl. Discov.},
volume = {36},
number = {3},
pages = {1219--1245},
year = {2022},
url = {https://doi.org/10.1007/s10618-022-00829-0},
doi = {10.1007/S10618-022-00829-0},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/datamine/JaskowiakCC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KarimBZCRCD21,
author = {Md. Rezaul Karim and
Oya Beyan and
Achille Zappa and
Ivan G. Costa and
Dietrich Rebholz{-}Schuhmann and
Michael Cochez and
Stefan Decker},
title = {Deep learning-based clustering approaches for bioinformatics},
journal = {Briefings Bioinform.},
volume = {22},
number = {1},
pages = {393--415},
year = {2021},
url = {https://doi.org/10.1093/bib/bbz170},
doi = {10.1093/BIB/BBZ170},
timestamp = {Mon, 03 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/KarimBZCRCD21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NagaiLSSC21,
author = {James Shiniti Nagai and
Nils B. Leimk{\"{u}}hler and
Michael T. Schaub and
Rebekka K. Schneider and
Ivan G. Costa},
title = {CrossTalkeR: analysis and visualization of ligand-receptorne tworks},
journal = {Bioinform.},
volume = {37},
number = {22},
pages = {4263--4265},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab370},
doi = {10.1093/BIOINFORMATICS/BTAB370},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/NagaiLSSC21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2009-02400,
author = {Pablo Andretta Jaskowiak and
Ivan Gesteira Costa and
Ricardo Jos{\'{e}} Gabrielli Barreto Campello},
title = {The Area Under the {ROC} Curve as a Measure of Clustering Quality},
journal = {CoRR},
volume = {abs/2009.02400},
year = {2020},
url = {https://arxiv.org/abs/2009.02400},
eprinttype = {arXiv},
eprint = {2009.02400},
timestamp = {Wed, 16 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2009-02400.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/access/KarimWCDB19,
author = {Md. Rezaul Karim and
Galih Wicaksono and
Ivan G. Costa and
Stefan Decker and
Oya Beyan},
title = {Prognostically Relevant Subtypes and Survival Prediction for Breast
Cancer Based on Multimodal Genomics Data},
journal = {{IEEE} Access},
volume = {7},
pages = {133850--133864},
year = {2019},
url = {https://doi.org/10.1109/ACCESS.2019.2941796},
doi = {10.1109/ACCESS.2019.2941796},
timestamp = {Thu, 07 Nov 2019 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/access/KarimWCDB19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ml/LorenaMMCP18,
author = {Ana Carolina Lorena and
Aron I. Maciel and
P{\'{e}}ricles B. C. de Miranda and
Ivan G. Costa and
Ricardo B. C. Prud{\^{e}}ncio},
title = {Data complexity meta-features for regression problems},
journal = {Mach. Learn.},
volume = {107},
number = {1},
pages = {209--246},
year = {2018},
url = {https://doi.org/10.1007/s10994-017-5681-1},
doi = {10.1007/S10994-017-5681-1},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ml/LorenaMMCP18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/NascimentoPC16,
author = {Andr{\'{e}} C. A. Nascimento and
Ricardo B. C. Prud{\^{e}}ncio and
Ivan G. Costa},
title = {A multiple kernel learning algorithm for drug-target interaction prediction},
journal = {{BMC} Bioinform.},
volume = {17},
pages = {46},
year = {2016},
url = {https://doi.org/10.1186/s12859-016-0890-3},
doi = {10.1186/S12859-016-0890-3},
timestamp = {Sun, 25 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/NascimentoPC16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ijcnn/MacielCL16,
author = {Aron I. Maciel and
Ivan G. Costa and
Ana Carolina Lorena},
title = {Measuring the complexity of regression problems},
booktitle = {2016 International Joint Conference on Neural Networks, {IJCNN} 2016,
Vancouver, BC, Canada, July 24-29, 2016},
pages = {1450--1457},
publisher = {{IEEE}},
year = {2016},
url = {https://doi.org/10.1109/IJCNN.2016.7727369},
doi = {10.1109/IJCNN.2016.7727369},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ijcnn/MacielCL16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AllhoffSCLZC15,
author = {Manuel Allhoff and
Kristin Ser{\'{e}} and
Heike Chauvistr{\'{e}} and
Qiong Lin and
Martin Zenke and
Ivan G. Costa},
title = {Detecting differential peaks in ChIP-seq signals with {ODIN}},
journal = {Bioinform.},
volume = {31},
number = {6},
pages = {980},
year = {2015},
url = {https://doi.org/10.1093/bioinformatics/btv030},
doi = {10.1093/BIOINFORMATICS/BTV030},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/AllhoffSCLZC15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SoutoJC15,
author = {Marc{\'{\i}}lio Carlos Pereira de Souto and
Pablo A. Jaskowiak and
Ivan G. Costa},
title = {Impact of missing data imputation methods on gene expression clustering
and classification},
journal = {{BMC} Bioinform.},
volume = {16},
pages = {64:1--64:9},
year = {2015},
url = {https://doi.org/10.1186/s12859-015-0494-3},
doi = {10.1186/S12859-015-0494-3},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/SoutoJC15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GusmaoDZC14,
author = {Eduardo G. Gusm{\~{a}}o and
Christoph Dieterich and
Martin Zenke and
Ivan G. Costa},
title = {Detection of active transcription factor binding sites with the combination
of DNase hypersensitivity and histone modifications},
journal = {Bioinform.},
volume = {30},
number = {22},
pages = {3143--3151},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btu519},
doi = {10.1093/BIOINFORMATICS/BTU519},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GusmaoDZC14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AllhoffSCLZC14,
author = {Manuel Allhoff and
Kristin Ser{\'{e}} and
Heike Chauvistr{\'{e}} and
Qiong Lin and
Martin Zenke and
Ivan G. Costa},
title = {Detecting differential peaks in ChIP-seq signals with {ODIN}},
journal = {Bioinform.},
volume = {30},
number = {24},
pages = {3467--3475},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btu722},
doi = {10.1093/BIOINFORMATICS/BTU722},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/AllhoffSCLZC14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/JaskowiakCC14,
author = {Pablo A. Jaskowiak and
Ricardo J. G. B. Campello and
Ivan G. Costa},
title = {On the selection of appropriate distances for gene expression data
clustering},
journal = {{BMC} Bioinform.},
volume = {15},
number = {{S-2}},
pages = {S2},
year = {2014},
url = {https://doi.org/10.1186/1471-2105-15-S2-S2},
doi = {10.1186/1471-2105-15-S2-S2},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/JaskowiakCC14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AllhoffSMCRM13,
author = {Manuel Allhoff and
Alexander Sch{\"{o}}nhuth and
Marcel Martin and
Ivan G. Costa and
Sven Rahmann and
Tobias Marschall},
title = {Discovering motifs that induce sequencing errors},
journal = {{BMC} Bioinform.},
volume = {14},
number = {{S-5}},
pages = {S1},
year = {2013},
url = {https://doi.org/10.1186/1471-2105-14-S5-S1},
doi = {10.1186/1471-2105-14-S5-S1},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/AllhoffSMCRM13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/JaskowiakCC13,
author = {Pablo A. Jaskowiak and
Ricardo J. G. B. Campello and
Ivan G. Costa},
title = {Proximity Measures for Clustering Gene Expression Microarray Data:
{A} Validation Methodology and a Comparative Analysis},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {10},
number = {4},
pages = {845--857},
year = {2013},
url = {https://doi.org/10.1109/TCBB.2013.9},
doi = {10.1109/TCBB.2013.9},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/JaskowiakCC13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wob/AraujoSOC13,
author = {Gilderlanio S. Ara{\'{u}}jo and
Manuela R. B. Souza and
Jo{\~{a}}o Ricardo M. Oliveira and
Ivan G. Costa},
editor = {Jo{\~{a}}o C. Setubal and
Nalvo F. Almeida},
title = {Random Forest and Gene Networks for Association of SNPs to Alzheimer's
Disease},
booktitle = {Advances in Bioinformatics and Computational Biology - 8th Brazilian
Symposium on Bioinformatics, {BSB} 2013, Recife, Brazil, November
3-7, 2013, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {8213},
pages = {104--115},
publisher = {Springer},
year = {2013},
url = {https://doi.org/10.1007/978-3-319-02624-4\_10},
doi = {10.1007/978-3-319-02624-4\_10},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/wob/AraujoSOC13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RegoRCC12,
author = {Tha{\'{\i}}s Gaudencio do R{\^{e}}go and
Helge G. Roider and
Francisco de A. T. de Carvalho and
Ivan G. Costa},
title = {Inferring epigenetic and transcriptional regulation during blood cell
development with a mixture of sparse linear models},
journal = {Bioinform.},
volume = {28},
number = {18},
pages = {2297--2303},
year = {2012},
url = {https://doi.org/10.1093/bioinformatics/bts362},
doi = {10.1093/BIOINFORMATICS/BTS362},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RegoRCC12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MarschallCCBKSS12,
author = {Tobias Marschall and
Ivan G. Costa and
Stefan Canzar and
Markus Bauer and
Gunnar W. Klau and
Alexander Schliep and
Alexander Sch{\"{o}}nhuth},
title = {{CLEVER:} clique-enumerating variant finder},
journal = {Bioinform.},
volume = {28},
number = {22},
pages = {2875--2882},
year = {2012},
url = {https://doi.org/10.1093/bioinformatics/bts566},
doi = {10.1093/BIOINFORMATICS/BTS566},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MarschallCCBKSS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijon/LorenaCSS12,
author = {Ana Carolina Lorena and
Ivan G. Costa and
Newton Spola{\^{o}}r and
Marc{\'{\i}}lio Carlos Pereira de Souto},
title = {Analysis of complexity indices for classification problems: Cancer
gene expression data},
journal = {Neurocomputing},
volume = {75},
number = {1},
pages = {33--42},
year = {2012},
url = {https://doi.org/10.1016/j.neucom.2011.03.054},
doi = {10.1016/J.NEUCOM.2011.03.054},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ijon/LorenaCSS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/sbrn/SoutoCFSBC12,
author = {Marcilio C. P. de Souto and
Andr{\'{e}} L. V. Coelho and
Katti Faceli and
Tiemi C. Sakata and
Viviane Bonadia and
Ivan G. Costa},
editor = {Ana Carolina Lorena and
Carlos Eduardo Thomaz and
Aurora Trinidad Ramirez Pozo},
title = {A Comparison of External Clustering Evaluation Indices in the Context
of Imbalanced Data Sets},
booktitle = {2012 Brazilian Symposium on Neural Networks, Curitiba, Paran{\'{a}},
Brazil, October 20-25, 2012},
pages = {49--54},
publisher = {{IEEE} Computer Society},
year = {2012},
url = {https://doi.org/10.1109/SBRN.2012.25},
doi = {10.1109/SBRN.2012.25},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/sbrn/SoutoCFSBC12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/sbrn/FilhoCOC12,
author = {Valmir Mac{\'{a}}rio Filho and
Ivan G. Costa and
Jo{\~{a}}o F. L. Oliveira and
Francisco de A. T. de Carvalho},
editor = {Ana Carolina Lorena and
Carlos Eduardo Thomaz and
Aurora Trinidad Ramirez Pozo},
title = {Predicting Gene Functions Using Semi-supervised Clustering Algorithms
with Objective Function Optimization},
booktitle = {2012 Brazilian Symposium on Neural Networks, Curitiba, Paran{\'{a}},
Brazil, October 20-25, 2012},
pages = {61--66},
publisher = {{IEEE} Computer Society},
year = {2012},
url = {https://doi.org/10.1109/SBRN.2012.33},
doi = {10.1109/SBRN.2012.33},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/sbrn/FilhoCOC12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wob/GusmaoDC12,
author = {Eduardo G. Gusm{\~{a}}o and
Christoph Dieterich and
Ivan G. Costa},
editor = {Marc{\'{\i}}lio Carlos Pereira de Souto and
Maricel G. Kann},
title = {Prediction of Transcription Factor Binding Sites by Integrating DNase
Digestion and Histone Modification},
booktitle = {Advances in Bioinformatics and Computational Biology - 7th Brazilian
Symposium on Bioinformatics, {BSB} 2012, Campo Grande, Brazil, August
15-17, 2012. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {7409},
pages = {109--119},
publisher = {Springer},
year = {2012},
url = {https://doi.org/10.1007/978-3-642-31927-3\_10},
doi = {10.1007/978-3-642-31927-3\_10},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/wob/GusmaoDC12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wob/JaskowiakCC12,
author = {Pablo A. Jaskowiak and
Ricardo J. G. B. Campello and
Ivan G. Costa},
editor = {Marc{\'{\i}}lio Carlos Pereira de Souto and
Maricel G. Kann},
title = {Evaluating Correlation Coefficients for Clustering Gene Expression
Profiles of Cancer},
booktitle = {Advances in Bioinformatics and Computational Biology - 7th Brazilian
Symposium on Bioinformatics, {BSB} 2012, Campo Grande, Brazil, August
15-17, 2012. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {7409},
pages = {120--131},
publisher = {Springer},
year = {2012},
url = {https://doi.org/10.1007/978-3-642-31927-3\_11},
doi = {10.1007/978-3-642-31927-3\_11},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/wob/JaskowiakCC12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodatamining/SchillingCS11,
author = {Ruben Schilling and
Ivan G. Costa and
Alexander Schliep},
title = {pGQL: {A} probabilistic graphical query language for gene expression
time courses},
journal = {BioData Min.},
volume = {4},
pages = {9},
year = {2011},
url = {https://doi.org/10.1186/1756-0381-4-9},
doi = {10.1186/1756-0381-4-9},
timestamp = {Wed, 01 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodatamining/SchillingCS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HafemeisterCSS11,
author = {Christoph Hafemeister and
Ivan G. Costa and
Alexander Sch{\"{o}}nhuth and
Alexander Schliep},
title = {Classifying short gene expression time-courses with Bayesian estimation
of piecewise constant functions},
journal = {Bioinform.},
volume = {27},
number = {7},
pages = {946--952},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btr037},
doi = {10.1093/BIOINFORMATICS/BTR037},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HafemeisterCSS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RedestigC11,
author = {Henning Redestig and
Ivan G. Costa},
title = {Detection and interpretation of metabolite-transcript coresponses
using combined profiling data},
journal = {Bioinform.},
volume = {27},
number = {13},
pages = {357--365},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btr231},
doi = {10.1093/BIOINFORMATICS/BTR231},
timestamp = {Tue, 08 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RedestigC11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/CostaRRC11,
author = {Ivan G. Costa and
Helge G. Roider and
Tha{\'{\i}}s Gaudencio do R{\^{e}}go and
Francisco de A. T. de Carvalho},
title = {Predicting gene expression in {T} cell differentiation from histone
modifications and transcription factor binding affinities by linear
mixture models},
journal = {{BMC} Bioinform.},
volume = {12},
number = {{S-1}},
pages = {S29},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-S1-S29},
doi = {10.1186/1471-2105-12-S1-S29},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/CostaRRC11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/GeorgiCS10,
author = {Benjamin Georgi and
Ivan Gesteira Costa and
Alexander Schliep},
title = {PyMix - The Python mixture package - a tool for clustering of heterogeneous
biological data},
journal = {{BMC} Bioinform.},
volume = {11},
pages = {9},
year = {2010},
url = {https://doi.org/10.1186/1471-2105-11-9},
doi = {10.1186/1471-2105-11-9},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/GeorgiCS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ijcnn/SoutoLSC10,
author = {Marc{\'{\i}}lio Carlos Pereira de Souto and
Ana Carolina Lorena and
Newton Spola{\^{o}}r and
Ivan Gesteira Costa},
title = {Complexity measures of supervised classifications tasks: {A} case
study for cancer gene expression data},
booktitle = {International Joint Conference on Neural Networks, {IJCNN} 2010, Barcelona,
Spain, 18-23 July, 2010},
pages = {1--7},
publisher = {{IEEE}},
year = {2010},
url = {https://doi.org/10.1109/IJCNN.2010.5596305},
doi = {10.1109/IJCNN.2010.5596305},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ijcnn/SoutoLSC10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/sbrn/LorenaSCS10,
author = {Ana Carolina Lorena and
Newton Spola{\^{o}}r and
Ivan G. Costa and
Marcilio C. P. de Souto},
editor = {Teresa Bernarda Ludermir and
Karla Figueiredo and
Carlos E. Thomaz},
title = {On the Complexity of Gene Marker Selection},
booktitle = {11th Brazilian Symposium on Neural Networks {(SBRN} 2010), Sao Paulo,
23-28 October, 2010},
pages = {85--90},
publisher = {{IEEE} Computer Society},
year = {2010},
url = {https://doi.org/10.1109/SBRN.2010.23},
doi = {10.1109/SBRN.2010.23},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/sbrn/LorenaSCS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wob/RibeiroCC10,
author = {Clerton Ribeiro and
Francisco de Assis Ten{\'{o}}rio de Carvalho and
Ivan G. Costa},
editor = {Carlos Eduardo Ferreira and
Satoru Miyano and
Peter F. Stadler},
title = {Semi-supervised Approach for Finding Cancer Sub-classes on Gene Expression
Data},
booktitle = {Advances in Bioinformatics and Computational Biology, 5th Brazilian
Symposium on Bioinformatics, {BSB} 2010, Rio de Janeiro, Brazil, August
31-September 3, 2010. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6268},
pages = {25--34},
publisher = {Springer},
year = {2010},
url = {https://doi.org/10.1007/978-3-642-15060-9\_3},
doi = {10.1007/978-3-642-15060-9\_3},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/wob/RibeiroCC10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CostaSHS09,
author = {Ivan G. Costa and
Alexander Sch{\"{o}}nhuth and
Christoph Hafemeister and
Alexander Schliep},
title = {Constrained mixture estimation for analysis and robust classification
of clinical time series},
journal = {Bioinform.},
volume = {25},
number = {12},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btp222},
doi = {10.1093/BIOINFORMATICS/BTP222},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/CostaSHS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icann/NascimentoPSC09,
author = {Andr{\'{e}} C. A. Nascimento and
Ricardo Bastos Cavalcante Prud{\^{e}}ncio and
Marc{\'{\i}}lio Carlos Pereira de Souto and
Ivan G. Costa},
editor = {Cesare Alippi and
Marios M. Polycarpou and
Christos G. Panayiotou and
Georgios Ellinas},
title = {Mining Rules for the Automatic Selection Process of Clustering Methods
Applied to Cancer Gene Expression Data},
booktitle = {Artificial Neural Networks - {ICANN} 2009, 19th International Conference,
Limassol, Cyprus, September 14-17, 2009, Proceedings, Part {II}},
series = {Lecture Notes in Computer Science},
volume = {5769},
pages = {20--29},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-04277-5\_3},
doi = {10.1007/978-3-642-04277-5\_3},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icann/NascimentoPSC09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wob/CostaLPS09,
author = {Ivan G. Costa and
Ana Carolina Lorena and
Liciana R. M. P. y Peres and
Marc{\'{\i}}lio Carlos Pereira de Souto},
editor = {Katia S. Guimar{\~{a}}es and
Anna R. Panchenko and
Teresa M. Przytycka},
title = {Using Supervised Complexity Measures in the Analysis of Cancer Gene
Expression Data Sets},
booktitle = {Advances in Bioinformatics and Computational Biology, 4th Brazilian
Symposium on Bioinformatics, {BSB} 2009, Porto Alegre, Brazil, July
29-31, 2009. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5676},
pages = {48--59},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-03223-3\_5},
doi = {10.1007/978-3-642-03223-3\_5},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/wob/CostaLPS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SoutoCALS08,
author = {Marc{\'{\i}}lio Carlos Pereira de Souto and
Ivan G. Costa and
Daniel S. A. de Araujo and
Teresa Bernarda Ludermir and
Alexander Schliep},
title = {Clustering cancer gene expression data: a comparative study},
journal = {{BMC} Bioinform.},
volume = {9},
year = {2008},
url = {https://doi.org/10.1186/1471-2105-9-497},
doi = {10.1186/1471-2105-9-497},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/SoutoCALS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/his/LorenaCS08,
author = {Ana Carolina Lorena and
Ivan G. Costa and
Marc{\'{\i}}lio Carlos Pereira de Souto},
editor = {Fatos Xhafa and
Francisco Herrera and
Ajith Abraham and
Mario K{\"{o}}ppen and
Jos{\'{e}} Manuel Ben{\'{\i}}tez},
title = {On the Complexity of Gene Expression Classification Data Sets},
booktitle = {8th International Conference on Hybrid Intelligent Systems {(HIS}
2008), September 10-12, 2008, Barcelona, Spain},
pages = {825--830},
publisher = {{IEEE} Computer Society},
year = {2008},
url = {https://doi.org/10.1109/HIS.2008.163},
doi = {10.1109/HIS.2008.163},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/his/LorenaCS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ijcnn/SoutoACSLS08,
author = {Marc{\'{\i}}lio Carlos Pereira de Souto and
Daniel S. A. de Araujo and
Ivan G. Costa and
Rodrigo G. F. Soares and
Teresa Bernarda Ludermir and
Alexander Schliep},
title = {Comparative study on normalization procedures for cluster analysis
of gene expression datasets},
booktitle = {Proceedings of the International Joint Conference on Neural Networks,
{IJCNN} 2008, part of the {IEEE} World Congress on Computational Intelligence,
{WCCI} 2008, Hong Kong, China, June 1-6, 2008},
pages = {2792--2798},
publisher = {{IEEE}},
year = {2008},
url = {https://doi.org/10.1109/IJCNN.2008.4634191},
doi = {10.1109/IJCNN.2008.4634191},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ijcnn/SoutoACSLS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ijcnn/SoutoPSACLS08,
author = {Marc{\'{\i}}lio Carlos Pereira de Souto and
Ricardo Bastos Cavalcante Prud{\^{e}}ncio and
Rodrigo G. F. Soares and
Daniel S. A. de Araujo and
Ivan G. Costa and
Teresa Bernarda Ludermir and
Alexander Schliep},
title = {Ranking and selecting clustering algorithms using a meta-learning
approach},
booktitle = {Proceedings of the International Joint Conference on Neural Networks,
{IJCNN} 2008, part of the {IEEE} World Congress on Computational Intelligence,
{WCCI} 2008, Hong Kong, China, June 1-6, 2008},
pages = {3729--3735},
publisher = {{IEEE}},
year = {2008},
url = {https://doi.org/10.1109/IJCNN.2008.4634333},
doi = {10.1109/IJCNN.2008.4634333},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ijcnn/SoutoPSACLS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/CostaRHS08,
author = {Ivan G. Costa and
Stefan Roepcke and
Christoph Hafemeister and
Alexander Schliep},
title = {Inferring differentiation pathways from gene expression},
booktitle = {Proceedings 16th International Conference on Intelligent Systems for
Molecular Biology (ISMB), Toronto, Canada, July 19-23, 2008},
pages = {156--164},
year = {2008},
url = {https://doi.org/10.1093/bioinformatics/btn153},
doi = {10.1093/BIOINFORMATICS/BTN153},
timestamp = {Sat, 19 Oct 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ismb/CostaRHS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/CostaKOS07,
author = {Ivan G. Costa and
Roland Krause and
Lennart Opitz and
Alexander Schliep},
title = {Semi-supervised learning for the identification of syn-expressed genes
from fused microarray and \emph{in situ }image data},
journal = {{BMC} Bioinform.},
volume = {8},
number = {{S-10}},
year = {2007},
url = {https://doi.org/10.1186/1471-2105-8-S10-S3},
doi = {10.1186/1471-2105-8-S10-S3},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/CostaKOS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wob/CostaSS07,
author = {Ivan G. Costa and
Marc{\'{\i}}lio Carlos Pereira de Souto and
Alexander Schliep},
editor = {Marie{-}France Sagot and
Maria Em{\'{\i}}lia Telles Walter},
title = {Validating Gene Clusterings by Selecting Informative Gene Ontology
Terms with Mutual Information},
booktitle = {Advances in Bioinformatics and Computational Biology, Second Brazilian
Symposium on Bioinformatics, {BSB} 2007, Angra dos Reis, Brazil, August
29-31, 2007, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4643},
pages = {81--92},
publisher = {Springer},
year = {2007},
url = {https://doi.org/10.1007/978-3-540-73731-5\_8},
doi = {10.1007/978-3-540-73731-5\_8},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/wob/CostaSS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CostaSS05,
author = {Ivan G. Costa and
Alexander Sch{\"{o}}nhuth and
Alexander Schliep},
title = {The Graphical Query Language: a tool for analysis of gene expression
time-courses},
journal = {Bioinform.},
volume = {21},
number = {10},
pages = {2544--2545},
year = {2005},
url = {https://doi.org/10.1093/bioinformatics/bti311},
doi = {10.1093/BIOINFORMATICS/BTI311},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/CostaSS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/SchliepCSS05,
author = {Alexander Schliep and
Ivan G. Costa and
Christine Steinhoff and
Alexander Sch{\"{o}}nhuth},
title = {Analyzing Gene Expression Time-Courses},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {2},
number = {3},
pages = {179--193},
year = {2005},
url = {https://doi.org/10.1109/TCBB.2005.31},
doi = {10.1109/TCBB.2005.31},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/SchliepCSS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gfkl/CostaS05,
author = {Ivan G. Costa and
Alexander Schliep},
editor = {Myra Spiliopoulou and
Rudolf Kruse and
Christian Borgelt and
Andreas N{\"{u}}rnberger and
Wolfgang Gaul},
title = {On External Indices for Mixtures: Validating Mixtures of Genes},
booktitle = {From Data and Information Analysis to Knowledge Engineering, Proceedings
of the 29th Annual Conference of the Gesellschaft f{\"{u}}r Klassifikation
e.V., University of Magdeburg, March 9-11, 2005},
series = {Studies in Classification, Data Analysis, and Knowledge Organization},
pages = {662--669},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/3-540-31314-1\_81},
doi = {10.1007/3-540-31314-1\_81},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/gfkl/CostaS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jifs/CostaCS02,
author = {Ivan G. Costa and
Francisco de A. T. de Carvalho and
Marc{\'{\i}}lio Carlos Pereira de Souto},
title = {Comparative study on proximity indices for cluster analysis of gene
expression time series},
journal = {J. Intell. Fuzzy Syst.},
volume = {13},
number = {2-4},
pages = {133--142},
year = {2002},
url = {http://content.iospress.com/articles/journal-of-intelligent-and-fuzzy-systems/ifs00195},
timestamp = {Sat, 25 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jifs/CostaCS02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/sbrn/CostaCS02,
author = {Ivan G. Costa and
Francisco de A. T. de Carvalho and
Marc{\'{\i}}lio Carlos Pereira de Souto},
editor = {Teresa Bernarda Ludermir and
Marc{\'{\i}}lio Carlos Pereira de Souto},
title = {A Symbolic Approach to Gene Expression Time Series Analysis},
booktitle = {7th Brazilian Symposium on Neural Networks {(SBRN} 2002), 11-14 November
2002, Recife, Brazil},
pages = {25--30},
publisher = {{IEEE} Computer Society},
year = {2002},
url = {https://doi.org/10.1109/SBRN.2002.1181430},
doi = {10.1109/SBRN.2002.1181430},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/sbrn/CostaCS02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wob/CostaCS02,
author = {Ivan G. Costa and
Francisco de A. T. de Carvalho and
Marc{\'{\i}}lio Carlos Pereira de Souto},
editor = {Ana L. C. Bazzan},
title = {Stability Evaluation of Clustering Algorithms for Time Series Gene
Expression Data},
booktitle = {I Brazilian Workshop on Bioinformatics, October 18th, 2002, Gramado,
RS, Brazil},
pages = {88--90},
year = {2002},
timestamp = {Thu, 10 Mar 2005 15:02:43 +0100},
biburl = {https://dblp.org/rec/conf/wob/CostaCS02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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