A Symbolic Approach to Gene Expression Time Series Analysis. - Ivan G. Costa; Francisco de A. T. de Carvalho; Marcílio Carlos Pereira de Souto (SBRN, 2002)

Stability Evaluation of Clustering Algorithms for Time Series Gene Expression Data. - Ivan G. Costa; Francisco de A. T. de Carvalho; Marcílio Carlos Pereira de Souto (WOB, 2002)

Comparative study on proximity indices for cluster analysis of gene expression time series. - Ivan G. Costa; Francisco de A. T. de Carvalho; Marcílio Carlos Pereira de Souto (J. Intell. Fuzzy Syst., 2002)

On External Indices for Mixtures: Validating Mixtures of Genes. - Ivan G. Costa; Alexander Schliep (GfKl, 2005)

The Graphical Query Language: a tool for analysis of gene expression time-courses. - Ivan G. Costa; Alexander Schönhuth; Alexander Schliep (Bioinform., 2005)

Analyzing Gene Expression Time-Courses. - Alexander Schliep; Ivan G. Costa; Christine Steinhoff; Alexander Schönhuth (IEEE ACM Trans. Comput. Biol. Bioinform., 2005)

Validating Gene Clusterings by Selecting Informative Gene Ontology Terms with Mutual Information. - Ivan G. Costa; Marcílio Carlos Pereira de Souto; Alexander Schliep (BSB, 2007)

Semi-supervised learning for the identification of syn-expressed genes from fused microarray and in situ image data. - Ivan G. Costa; Roland Krause; Lennart Opitz; Alexander Schliep (BMC Bioinform., 2007)

On the Complexity of Gene Expression Classification Data Sets. - Ana Carolina Lorena; Ivan G. Costa; Marcílio Carlos Pereira de Souto (HIS, 2008)

Comparative study on normalization procedures for cluster analysis of gene expression datasets. - Marcílio Carlos Pereira de Souto; Daniel S. A. de Araujo; Ivan G. Costa; Rodrigo G. F. Soares; Teresa Bernarda Ludermir; Alexander Schliep (IJCNN, 2008)

Ranking and selecting clustering algorithms using a meta-learning approach. - 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 (IJCNN, 2008)

Inferring differentiation pathways from gene expression. - Ivan G. Costa; Stefan Roepcke; Christoph Hafemeister; Alexander Schliep (ISMB, 2008)

Clustering cancer gene expression data: a comparative study. - Marcílio Carlos Pereira de Souto; Ivan G. Costa; Daniel S. A. de Araujo; Teresa Bernarda Ludermir; Alexander Schliep (BMC Bioinform., 2008)

Mining Rules for the Automatic Selection Process of Clustering Methods Applied to Cancer Gene Expression Data. - André C. A. Nascimento; Ricardo Bastos Cavalcante Prudêncio; Marcílio Carlos Pereira de Souto; Ivan G. Costa (ICANN (2), 2009)

Using Supervised Complexity Measures in the Analysis of Cancer Gene Expression Data Sets. - Ivan G. Costa; Ana Carolina Lorena; Liciana R. M. P. y Peres; Marcílio Carlos Pereira de Souto (BSB, 2009)

Constrained mixture estimation for analysis and robust classification of clinical time series. - Ivan G. Costa; Alexander Schönhuth; Christoph Hafemeister; Alexander Schliep (Bioinform., 2009)

Complexity measures of supervised classifications tasks: A case study for cancer gene expression data. - Marcílio Carlos Pereira de Souto; Ana Carolina Lorena; Newton Spolaôr; Ivan Gesteira Costa (IJCNN, 2010)

On the Complexity of Gene Marker Selection. - Ana Carolina Lorena; Newton Spolaôr; Ivan G. Costa; Marcilio C. P. de Souto (SBRN, 2010)

Semi-supervised Approach for Finding Cancer Sub-classes on Gene Expression Data. - Clerton Ribeiro; Francisco de Assis Tenório de Carvalho; Ivan G. Costa (BSB, 2010)

PyMix - The Python mixture package - a tool for clustering of heterogeneous biological data. - Benjamin Georgi; Ivan Gesteira Costa; Alexander Schliep (BMC Bioinform., 2010)

pGQL: A probabilistic graphical query language for gene expression time courses. - Ruben Schilling; Ivan G. Costa; Alexander Schliep (BioData Min., 2011)

Classifying short gene expression time-courses with Bayesian estimation of piecewise constant functions. - Christoph Hafemeister; Ivan G. Costa; Alexander Schönhuth; Alexander Schliep (Bioinform., 2011)

Detection and interpretation of metabolite-transcript coresponses using combined profiling data. - Henning Redestig; Ivan G. Costa (Bioinform., 2011)

Predicting gene expression in T cell differentiation from histone modifications and transcription factor binding affinities by linear mixture models. - Ivan G. Costa; Helge G. Roider; Thaís Gaudencio do Rêgo; Francisco de A. T. de Carvalho (BMC Bioinform., 2011)

Predicting Gene Functions Using Semi-supervised Clustering Algorithms with Objective Function Optimization. - Valmir Macário Filho; Ivan G. Costa; João F. L. Oliveira; Francisco de A. T. de Carvalho (SBRN, 2012)

A Comparison of External Clustering Evaluation Indices in the Context of Imbalanced Data Sets. - Marcilio C. P. de Souto; André L. V. Coelho; Katti Faceli; Tiemi C. Sakata; Viviane Bonadia; Ivan G. Costa (SBRN, 2012)

Prediction of Transcription Factor Binding Sites by Integrating DNase Digestion and Histone Modification. - Eduardo G. Gusmão; Christoph Dieterich; Ivan G. Costa (BSB, 2012)

Evaluating Correlation Coefficients for Clustering Gene Expression Profiles of Cancer. - Pablo A. Jaskowiak; Ricardo J. G. B. Campello; Ivan G. Costa (BSB, 2012)

CLEVER: clique-enumerating variant finder. - Tobias Marschall; Ivan G. Costa; Stefan Canzar; Markus Bauer 001; Gunnar W. Klau; Alexander Schliep; Alexander Schönhuth (Bioinform., 2012)

Inferring epigenetic and transcriptional regulation during blood cell development with a mixture of sparse linear models. - Thaís Gaudencio do Rêgo; Helge G. Roider; Francisco de A. T. de Carvalho; Ivan G. Costa (Bioinform., 2012)

Analysis of complexity indices for classification problems: Cancer gene expression data. - Ana Carolina Lorena; Ivan G. Costa; Newton Spolaôr; Marcílio Carlos Pereira de Souto (Neurocomputing, 2012)

Random Forest and Gene Networks for Association of SNPs to Alzheimer's Disease. - Gilderlanio S. Araújo; Manuela R. B. Souza; João Ricardo M. Oliveira; Ivan G. Costa (BSB, 2013)

Discovering motifs that induce sequencing errors. - Manuel Allhoff; Alexander Schönhuth; Marcel Martin; Ivan G. Costa; Sven Rahmann; Tobias Marschall (BMC Bioinform., 2013)

Proximity Measures for Clustering Gene Expression Microarray Data: A Validation Methodology and a Comparative Analysis. - Pablo A. Jaskowiak; Ricardo J. G. B. Campello; Ivan G. Costa (IEEE ACM Trans. Comput. Biol. Bioinform., 2013)

Detection of active transcription factor binding sites with the combination of DNase hypersensitivity and histone modifications. - Eduardo G. Gusmão; Christoph Dieterich; Martin Zenke; Ivan G. Costa (Bioinform., 2014)

On the selection of appropriate distances for gene expression data clustering. - Pablo A. Jaskowiak; Ricardo J. G. B. Campello; Ivan G. Costa (BMC Bioinform., 2014)

Detecting differential peaks in ChIP-seq signals with ODIN. - Manuel Allhoff; Kristin Seré; Heike Chauvistré; Qiong Lin; Martin Zenke; Ivan G. Costa (Bioinform., 2015)

Impact of missing data imputation methods on gene expression clustering and classification. - Marcílio Carlos Pereira de Souto; Pablo A. Jaskowiak; Ivan G. Costa (BMC Bioinform., 2015)

Measuring the complexity of regression problems. - Aron I. Maciel; Ivan G. Costa; Ana Carolina Lorena (IJCNN, 2016)

A multiple kernel learning algorithm for drug-target interaction prediction. - André C. A. Nascimento; Ricardo B. C. Prudêncio; Ivan G. Costa (BMC Bioinform., 2016)

Data complexity meta-features for regression problems. - Ana Carolina Lorena; Aron I. Maciel; Péricles Barbosa C. de Miranda; Ivan G. Costa; Ricardo B. C. Prudêncio (Mach. Learn., 2018)

Prognostically Relevant Subtypes and Survival Prediction for Breast Cancer Based on Multimodal Genomics Data. - Md. Rezaul Karim 001; Galih Wicaksono; Ivan G. Costa; Stefan Decker; Oya Beyan (IEEE Access, 2019)

Deep learning-based clustering approaches for bioinformatics. - Md. Rezaul Karim 001; Oya Beyan; Achille Zappa; Ivan G. Costa; Dietrich Rebholz-Schuhmann; Michael Cochez; Stefan Decker (Briefings Bioinform., 2021)

CrossTalkeR: analysis and visualization of ligand-receptorne tworks. - James Shiniti Nagai; Nils B. Leimkühler; Michael T. Schaub; Rebekka K. Schneider; Ivan G. Costa (Bioinform., 2021)

MOJITOO: a fast and universal method for integration of multimodal single-cell data. - Mingbo Cheng; Zhijian Li; Ivan G. Costa (Bioinform., 2022)

Detection of cell markers from single cell RNA-seq with sc2marker. - Ronghui Li; Bella Banjanin; Rebekka K. Schneider; Ivan G. Costa (BMC Bioinform., 2022)

The area under the ROC curve as a measure of clustering quality. - Pablo A. Jaskowiak; Ivan G. Costa; Ricardo J. G. B. Campello (Data Min. Knowl. Discov., 2022)

Clustering Validation with The Area Under Precision-Recall Curves. - Pablo Andretta Jaskowiak; Ivan Gesteira Costa (CoRR, 2023)

RGT: a toolbox for the integrative analysis of high throughput regulatory genomics data. - Zhijian Li; Chao-Chung Kuo; Fabio Ticconi; Mina Shaigan; Julia Gehrmann; Eduardo G. Gusmão; Manuel Allhoff; Martin Manolov; Martin Zenke; Ivan G. Costa (BMC Bioinform., 2023)

Optimal Transport Distances for Directed, Weighted Graphs: A Case Study With Cell-Cell Communication Networks. - James Shiniti Nagai; Ivan G. Costa; Michael T. Schaub (ICASSP, 2024)

SIngle cell level Genotyping Using scRna Data (SIGURD). - Martin Grasshoff; Milena Kalmer; Nicolas Chatain; Kim Kricheldorf; Angela Maurer; Ralf Weiskirchen; Steffen Koschmieder; Ivan G. Costa (Briefings Bioinform., 2024)

tRigon: an R package and Shiny App for integrative (path-)omics data analysis. - David L. Hölscher; Michael Goedertier; Barbara Mara Klinkhammer; Patrick Droste; Ivan G. Costa; Peter Boor; Roman David Bülow (BMC Bioinform., 2024)

Advances and challenges in cell-cell communication inference: a comprehensive review of tools, resources, and future directions. - Giulia Cesaro; James Shiniti Nagai; Nicolò Gnoato; Alice Chiodi; Gaia Tussardi; Vanessa Klöker; Carmelo Vittorio Musumarra; Ettore Mosca; Ivan G. Costa; Barbara Di Camillo; Enrica Calura; Giacomo Baruzzo (Briefings Bioinform., 2025)