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Journal Articles
- 2024
[j30]David L. Hölscher
, Michael Goedertier, Barbara Mara Klinkhammer, Patrick Droste, Ivan G. Costa, Peter Boor, Roman David Bülow:
tRigon: an R package and Shiny App for integrative (path-)omics data analysis. BMC Bioinform. 25(1): 98 (2024)- 2023
- [j29]Zhijian Li, Chao-Chung Kuo, Fabio Ticconi, Mina Shaigan, Julia Gehrmann, Eduardo G. Gusmão, Manuel Allhoff, Martin Manolov, Martin Zenke, Ivan G. Costa:
RGT: a toolbox for the integrative analysis of high throughput regulatory genomics data. BMC Bioinform. 24(1): 79 (2023) - 2022
- [j28]Ronghui Li, Bella Banjanin, Rebekka K. Schneider, Ivan G. Costa:
Detection of cell markers from single cell RNA-seq with sc2marker. BMC Bioinform. 23(1): 276 (2022) - [j27]Pablo A. Jaskowiak, Ivan G. Costa, Ricardo J. G. B. Campello:
The area under the ROC curve as a measure of clustering quality. Data Min. Knowl. Discov. 36(3): 1219-1245 (2022) - 2021
- [j26]Md. Rezaul Karim, Oya Beyan, Achille Zappa, Ivan G. Costa, Dietrich Rebholz-Schuhmann, Michael Cochez, Stefan Decker:
Deep learning-based clustering approaches for bioinformatics. Briefings Bioinform. 22(1): 393-415 (2021) - [j25]James Shiniti Nagai, Nils B. Leimkühler, Michael T. Schaub, Rebekka K. Schneider, Ivan G. Costa:
CrossTalkeR: analysis and visualization of ligand-receptorne tworks. Bioinform. 37(22): 4263-4265 (2021) - 2019
- [j24]Md. Rezaul Karim, Galih Wicaksono, Ivan G. Costa, Stefan Decker, Oya Beyan:
Prognostically Relevant Subtypes and Survival Prediction for Breast Cancer Based on Multimodal Genomics Data. IEEE Access 7: 133850-133864 (2019) - 2018
- [j23]Ana Carolina Lorena, Aron I. Maciel, Péricles B. C. de Miranda, Ivan G. Costa, Ricardo B. C. Prudêncio:
Data complexity meta-features for regression problems. Mach. Learn. 107(1): 209-246 (2018) - 2016
- [j22]André C. A. Nascimento, Ricardo B. C. Prudêncio, Ivan G. Costa:
A multiple kernel learning algorithm for drug-target interaction prediction. BMC Bioinform. 17: 46 (2016) - 2015
- [j21]Manuel Allhoff, Kristin Seré, Heike Chauvistré, Qiong Lin, Martin Zenke, Ivan G. Costa:
Detecting differential peaks in ChIP-seq signals with ODIN. Bioinform. 31(6): 980 (2015) - [j20]Marcílio Carlos Pereira de Souto, Pablo A. Jaskowiak, Ivan G. Costa:
Impact of missing data imputation methods on gene expression clustering and classification. BMC Bioinform. 16: 64:1-64:9 (2015) - 2014
- [j19]Eduardo G. Gusmão, Christoph Dieterich, Martin Zenke, Ivan G. Costa:
Detection of active transcription factor binding sites with the combination of DNase hypersensitivity and histone modifications. Bioinform. 30(22): 3143-3151 (2014) - [j18]Manuel Allhoff, Kristin Seré, Heike Chauvistré, Qiong Lin, Martin Zenke, Ivan G. Costa:
Detecting differential peaks in ChIP-seq signals with ODIN. Bioinform. 30(24): 3467-3475 (2014) - [j17]Pablo A. Jaskowiak, Ricardo J. G. B. Campello, Ivan G. Costa:
On the selection of appropriate distances for gene expression data clustering. BMC Bioinform. 15(S-2): S2 (2014) - 2013
- [j16]Manuel Allhoff, Alexander Schönhuth, Marcel Martin, Ivan G. Costa, Sven Rahmann, Tobias Marschall:
Discovering motifs that induce sequencing errors. BMC Bioinform. 14(S-5): S1 (2013) - [j15]Pablo A. Jaskowiak, Ricardo J. G. B. Campello, Ivan G. Costa:
Proximity Measures for Clustering Gene Expression Microarray Data: A Validation Methodology and a Comparative Analysis. IEEE ACM Trans. Comput. Biol. Bioinform. 10(4): 845-857 (2013) - 2012
- [j14]Thaís Gaudencio do Rêgo, Helge G. Roider, Francisco de A. T. de Carvalho, Ivan G. Costa:
Inferring epigenetic and transcriptional regulation during blood cell development with a mixture of sparse linear models. Bioinform. 28(18): 2297-2303 (2012) - [j13]Tobias Marschall, Ivan G. Costa, Stefan Canzar, Markus Bauer, Gunnar W. Klau, Alexander Schliep, Alexander Schönhuth:
CLEVER: clique-enumerating variant finder. Bioinform. 28(22): 2875-2882 (2012) - [j12]Ana Carolina Lorena, Ivan G. Costa, Newton Spolaôr, Marcílio Carlos Pereira de Souto:
Analysis of complexity indices for classification problems: Cancer gene expression data. Neurocomputing 75(1): 33-42 (2012) - 2011
- [j11]Ruben Schilling, Ivan G. Costa, Alexander Schliep:
pGQL: A probabilistic graphical query language for gene expression time courses. BioData Min. 4: 9 (2011) - [j10]Christoph Hafemeister, Ivan G. Costa, Alexander Schönhuth, Alexander Schliep:
Classifying short gene expression time-courses with Bayesian estimation of piecewise constant functions. Bioinform. 27(7): 946-952 (2011) - [j9]Henning Redestig, Ivan G. Costa:
Detection and interpretation of metabolite-transcript coresponses using combined profiling data. Bioinform. 27(13): 357-365 (2011) - [j8]Ivan G. Costa, Helge G. Roider, Thaís Gaudencio do Rêgo, Francisco de A. T. de Carvalho:
Predicting gene expression in T cell differentiation from histone modifications and transcription factor binding affinities by linear mixture models. BMC Bioinform. 12(S-1): S29 (2011) - 2010
- [j7]Benjamin Georgi, Ivan Gesteira Costa, Alexander Schliep:
PyMix - The Python mixture package - a tool for clustering of heterogeneous biological data. BMC Bioinform. 11: 9 (2010) - 2009
- [j6]Ivan G. Costa, Alexander Schönhuth, Christoph Hafemeister, Alexander Schliep:
Constrained mixture estimation for analysis and robust classification of clinical time series. Bioinform. 25(12) (2009) - 2008
- [j5]Marcílio Carlos Pereira de Souto, Ivan G. Costa, Daniel S. A. de Araujo, Teresa Bernarda Ludermir, Alexander Schliep:
Clustering cancer gene expression data: a comparative study. BMC Bioinform. 9 (2008) - 2007
- [j4]Ivan G. Costa, Roland Krause, Lennart Opitz, Alexander Schliep:
Semi-supervised learning for the identification of syn-expressed genes from fused microarray and in situ image data. BMC Bioinform. 8(S-10) (2007) - 2005
- [j3]Ivan G. Costa, Alexander Schönhuth, Alexander Schliep:
The Graphical Query Language: a tool for analysis of gene expression time-courses. Bioinform. 21(10): 2544-2545 (2005) - [j2]Alexander Schliep, Ivan G. Costa, Christine Steinhoff, Alexander Schönhuth:
Analyzing Gene Expression Time-Courses. IEEE ACM Trans. Comput. Biol. Bioinform. 2(3): 179-193 (2005) - 2002
- [j1]Ivan G. Costa, Francisco de A. T. de Carvalho, Marcílio Carlos Pereira de Souto:
Comparative study on proximity indices for cluster analysis of gene expression time series. J. Intell. Fuzzy Syst. 13(2-4): 133-142 (2002)
Conference and Workshop Papers
- 2024
- [c20]James Shiniti Nagai, Ivan G. Costa, Michael T. Schaub:
Optimal Transport Distances for Directed, Weighted Graphs: A Case Study With Cell-Cell Communication Networks. ICASSP 2024: 9856-9860 - 2016
- [c19]Aron I. Maciel, Ivan G. Costa, Ana Carolina Lorena:
Measuring the complexity of regression problems. IJCNN 2016: 1450-1457 - 2013
- [c18]Gilderlanio S. Araújo, Manuela R. B. Souza, João Ricardo M. Oliveira, Ivan G. Costa:
Random Forest and Gene Networks for Association of SNPs to Alzheimer's Disease. BSB 2013: 104-115 - 2012
- [c17]Marcilio C. P. de Souto, André L. V. Coelho, Katti Faceli, Tiemi C. Sakata, Viviane Bonadia, Ivan G. Costa:
A Comparison of External Clustering Evaluation Indices in the Context of Imbalanced Data Sets. SBRN 2012: 49-54 - [c16]Valmir Macário Filho, Ivan G. Costa, João F. L. Oliveira, Francisco de A. T. de Carvalho:
Predicting Gene Functions Using Semi-supervised Clustering Algorithms with Objective Function Optimization. SBRN 2012: 61-66 - [c15]Eduardo G. Gusmão, Christoph Dieterich, Ivan G. Costa:
Prediction of Transcription Factor Binding Sites by Integrating DNase Digestion and Histone Modification. BSB 2012: 109-119 - [c14]Pablo A. Jaskowiak, Ricardo J. G. B. Campello, Ivan G. Costa:
Evaluating Correlation Coefficients for Clustering Gene Expression Profiles of Cancer. BSB 2012: 120-131 - 2010
- [c13]Marcílio Carlos Pereira de Souto, Ana Carolina Lorena, Newton Spolaôr, Ivan Gesteira Costa:
Complexity measures of supervised classifications tasks: A case study for cancer gene expression data. IJCNN 2010: 1-7 - [c12]Ana Carolina Lorena, Newton Spolaôr, Ivan G. Costa, Marcilio C. P. de Souto:
On the Complexity of Gene Marker Selection. SBRN 2010: 85-90 - [c11]Clerton Ribeiro, Francisco de Assis Tenório de Carvalho, Ivan G. Costa:
Semi-supervised Approach for Finding Cancer Sub-classes on Gene Expression Data. BSB 2010: 25-34 - 2009
- [c10]André C. A. Nascimento, Ricardo Bastos Cavalcante Prudêncio, Marcílio Carlos Pereira de Souto, Ivan G. Costa:
Mining Rules for the Automatic Selection Process of Clustering Methods Applied to Cancer Gene Expression Data. ICANN (2) 2009: 20-29 - [c9]Ivan G. Costa, Ana Carolina Lorena, Liciana R. M. P. y Peres, Marcílio Carlos Pereira de Souto:
Using Supervised Complexity Measures in the Analysis of Cancer Gene Expression Data Sets. BSB 2009: 48-59 - 2008
- [c8]Ana Carolina Lorena, Ivan G. Costa, Marcílio Carlos Pereira de Souto:
On the Complexity of Gene Expression Classification Data Sets. HIS 2008: 825-830 - [c7]Marcílio Carlos Pereira de Souto, Daniel S. A. de Araujo, Ivan G. Costa, Rodrigo G. F. Soares, Teresa Bernarda Ludermir, Alexander Schliep:
Comparative study on normalization procedures for cluster analysis of gene expression datasets. IJCNN 2008: 2792-2798 - [c6]Marcílio Carlos Pereira de Souto, Ricardo Bastos Cavalcante Prudêncio, Rodrigo G. F. Soares, Daniel S. A. de Araujo, Ivan G. Costa, Teresa Bernarda Ludermir, Alexander Schliep:
Ranking and selecting clustering algorithms using a meta-learning approach. IJCNN 2008: 3729-3735 - [c5]Ivan G. Costa, Stefan Roepcke, Christoph Hafemeister, Alexander Schliep:
Inferring differentiation pathways from gene expression. ISMB 2008: 156-164 - 2007
- [c4]Ivan G. Costa, Marcílio Carlos Pereira de Souto, Alexander Schliep:
Validating Gene Clusterings by Selecting Informative Gene Ontology Terms with Mutual Information. BSB 2007: 81-92 - 2005
- [c3]Ivan G. Costa, Alexander Schliep:
On External Indices for Mixtures: Validating Mixtures of Genes. GfKl 2005: 662-669 - 2002
- [c2]Ivan G. Costa, Francisco de A. T. de Carvalho, Marcílio Carlos Pereira de Souto:
A Symbolic Approach to Gene Expression Time Series Analysis. SBRN 2002: 25-30 - [c1]Ivan G. Costa, Francisco de A. T. de Carvalho, Marcílio Carlos Pereira de Souto:
Stability Evaluation of Clustering Algorithms for Time Series Gene Expression Data. WOB 2002: 88-90
Informal and Other Publications
- 2023
- [i3]Pablo Andretta Jaskowiak, Ivan Gesteira Costa:
Clustering Validation with The Area Under Precision-Recall Curves. CoRR abs/2304.01450 (2023) - [i2]James Shiniti Nagai, Ivan G. Costa, Michael T. Schaub:
Optimal transport distances for directed, weighted graphs: a case study with cell-cell communication networks. CoRR abs/2309.07030 (2023) - 2020
- [i1]Pablo Andretta Jaskowiak, Ivan Gesteira Costa, Ricardo José Gabrielli Barreto Campello:
The Area Under the ROC Curve as a Measure of Clustering Quality. CoRR abs/2009.02400 (2020)
Coauthor Index
aka: Francisco de Assis Tenório de Carvalho
aka: Marcilio C. P. de Souto
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