Ivan G. Costa

54 papers A 1B 3C 1Misc 1Journal 35Unranked 13
YearRankTypeTitle / Venue / Authors
2025 J jnl
Advances and challenges in cell-cell communication inference: a comprehensive review of tools, resources, and future directions.
Briefings Bioinform.
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
2025 J jnl
PILOT-GM-VAE: patient-level analysis of single-cell disease atlas with optimal transport of Gaussian mixture variational autoencoders.
Briefings Bioinform.
Mehdi Joodaki, Mina Shaigan, Samaneh Samiei, James Shiniti Nagai, Tiago Maié, Christoph Kuppe, Ivan G. Costa
2025 J jnl
scACCorDiON: a clustering approach for explainable patient level cell-cell communication graph analysis.
Bioinform.
James Shiniti Nagai, Tiago Maié, Michael T. Schaub, Ivan G. Costa
2024 Misc conf
Optimal Transport Distances for Directed, Weighted Graphs: A Case Study With Cell-Cell Communication Networks.
ICASSP
James Shiniti Nagai, Ivan G. Costa, Michael T. Schaub
2024 J jnl
SIngle cell level Genotyping Using scRna Data (SIGURD).
Briefings Bioinform.
Martin Grasshoff, Milena Kalmer, Nicolas Chatain, Kim Kricheldorf, Angela Maurer, Ralf Weiskirchen, Steffen Koschmieder, Ivan G. Costa
2024 J jnl
tRigon: an R package and Shiny App for integrative (path-)omics data analysis.
BMC Bioinform.
David L. Hölscher, Michael Goedertier, Barbara Mara Klinkhammer, Patrick Droste, Ivan G. Costa, Peter Boor, Roman David Bülow
2023 J jnl
Optimal transport distances for directed, weighted graphs: a case study with cell-cell communication networks.
CoRR
James Shiniti Nagai, Ivan G. Costa, Michael T. Schaub
2023 J jnl
RGT: a toolbox for the integrative analysis of high throughput regulatory genomics data.
BMC Bioinform.
Zhijian Li, Chao-Chung Kuo, Fabio Ticconi, Mina Shaigan, Julia Gehrmann, Eduardo G. Gusmão, Manuel Allhoff, Martin Manolov, Martin Zenke, Ivan G. Costa
2022 J jnl
Detection of cell markers from single cell RNA-seq with sc2marker.
BMC Bioinform.
Ronghui Li, Bella Banjanin, Rebekka K. Schneider, Ivan G. Costa
2022 J jnl
MOJITOO: a fast and universal method for integration of multimodal single-cell data.
Bioinform.
Mingbo Cheng, Zhijian Li, Ivan G. Costa
2022 J jnl
The area under the ROC curve as a measure of clustering quality.
Data Min. Knowl. Discov.
Pablo A. Jaskowiak, Ivan G. Costa, Ricardo J. G. B. Campello
2021 J jnl
CrossTalkeR: analysis and visualization of ligand-receptorne tworks.
Bioinform.
James Shiniti Nagai, Nils B. Leimkühler, Michael T. Schaub, Rebekka K. Schneider, Ivan G. Costa
2021 J jnl
Deep learning-based clustering approaches for bioinformatics.
Briefings Bioinform.
Md. Rezaul Karim, Oya Beyan, Achille Zappa, Ivan G. Costa, Dietrich Rebholz-Schuhmann, Michael Cochez, Stefan Decker
2019 J jnl
Prognostically Relevant Subtypes and Survival Prediction for Breast Cancer Based on Multimodal Genomics Data.
IEEE Access
Md. Rezaul Karim, Galih Wicaksono, Ivan G. Costa, Stefan Decker, Oya Beyan
2018 J jnl
Data complexity meta-features for regression problems.
Mach. Learn.
Ana Carolina Lorena, Aron I. Maciel, Péricles Barbosa C. de Miranda, Ivan G. Costa, Ricardo B. C. Prudêncio
2016 J jnl
A multiple kernel learning algorithm for drug-target interaction prediction.
BMC Bioinform.
André C. A. Nascimento, Ricardo B. C. Prudêncio, Ivan G. Costa
2016 B conf
Measuring the complexity of regression problems.
IJCNN
Aron I. Maciel, Ivan G. Costa, Ana Carolina Lorena
2015 J jnl
Detecting differential peaks in ChIP-seq signals with ODIN.
Bioinform.
Manuel Allhoff, Kristin Seré, Heike Chauvistré, Qiong Lin, Martin Zenke, Ivan G. Costa
2015 J jnl
Impact of missing data imputation methods on gene expression clustering and classification.
BMC Bioinform.
Marcílio Carlos Pereira de Souto, Pablo A. Jaskowiak, Ivan G. Costa
2014 J jnl
Detecting differential peaks in ChIP-seq signals with ODIN.
Bioinform.
Manuel Allhoff, Kristin Seré, Heike Chauvistré, Qiong Lin, Martin Zenke, Ivan G. Costa
2014 J jnl
Detection of active transcription factor binding sites with the combination of DNase hypersensitivity and histone modifications.
Bioinform.
Eduardo G. Gusmão, Christoph Dieterich, Martin Zenke, Ivan G. Costa
2014 J jnl
On the selection of appropriate distances for gene expression data clustering.
BMC Bioinform.
Pablo A. Jaskowiak, Ricardo J. G. B. Campello, Ivan G. Costa
2013 J jnl
Discovering motifs that induce sequencing errors.
BMC Bioinform.
Manuel Allhoff, Alexander Schönhuth, Marcel Martin, Ivan G. Costa, Sven Rahmann, Tobias Marschall
2013 J jnl
Proximity Measures for Clustering Gene Expression Microarray Data: A Validation Methodology and a Comparative Analysis.
IEEE ACM Trans. Comput. Biol. Bioinform.
Pablo A. Jaskowiak, Ricardo J. G. B. Campello, Ivan G. Costa
2013 — conf
Random Forest and Gene Networks for Association of SNPs to Alzheimer's Disease.
BSB
Gilderlanio S. Araújo, Manuela R. B. Souza, João Ricardo M. Oliveira, Ivan G. Costa
2012 — conf
A Comparison of External Clustering Evaluation Indices in the Context of Imbalanced Data Sets.
SBRN
Marcilio C. P. de Souto, André L. V. Coelho, Katti Faceli, Tiemi C. Sakata, Viviane Bonadia dos Santos, Ivan G. Costa
2012 J jnl
Analysis of complexity indices for classification problems: Cancer gene expression data.
Neurocomputing
Ana Carolina Lorena, Ivan G. Costa, Newton Spolaôr, Marcílio Carlos Pereira de Souto
2012 J jnl
CLEVER: clique-enumerating variant finder.
Bioinform.
Tobias Marschall, Ivan G. Costa, Stefan Canzar, Markus Bauer, Gunnar W. Klau, Alexander Schliep, Alexander Schönhuth
2012 — conf
Evaluating Correlation Coefficients for Clustering Gene Expression Profiles of Cancer.
BSB
Pablo A. Jaskowiak, Ricardo J. G. B. Campello, Ivan G. Costa
2012 J jnl
Inferring epigenetic and transcriptional regulation during blood cell development with a mixture of sparse linear models.
Bioinform.
Thaís Gaudencio do Rêgo, Helge G. Roider, Francisco de A. T. de Carvalho, Ivan G. Costa
2012 — conf
Predicting Gene Functions Using Semi-supervised Clustering Algorithms with Objective Function Optimization.
SBRN
Valmir Macário Filho, Ivan G. Costa, João F. L. Oliveira, Francisco de A. T. de Carvalho
2012 — conf
Prediction of Transcription Factor Binding Sites by Integrating DNase Digestion and Histone Modification.
BSB
Eduardo G. Gusmão, Christoph Dieterich, Ivan G. Costa
2011 J jnl
Classifying short gene expression time-courses with Bayesian estimation of piecewise constant functions.
Bioinform.
Christoph Hafemeister, Ivan G. Costa, Alexander Schönhuth, Alexander Schliep
2011 J jnl
Detection and interpretation of metabolite-transcript coresponses using combined profiling data.
Bioinform.
Henning Redestig, Ivan G. Costa
2011 J jnl
Predicting gene expression in T cell differentiation from histone modifications and transcription factor binding affinities by linear mixture models.
BMC Bioinform.
Ivan G. Costa, Helge G. Roider, Thaís Gaudencio do Rêgo, Francisco de A. T. de Carvalho
2011 J jnl
pGQL: A probabilistic graphical query language for gene expression time courses.
BioData Min.
Ruben Schilling, Ivan G. Costa, Alexander Schliep
2010 — conf
On the Complexity of Gene Marker Selection.
SBRN
Ana Carolina Lorena, Newton Spolaôr, Ivan G. Costa, Marcilio C. P. de Souto
2010 — conf
Semi-supervised Approach for Finding Cancer Sub-classes on Gene Expression Data.
BSB
Clerton Ribeiro, Francisco de Assis Tenório de Carvalho, Ivan G. Costa
2009 J jnl
Constrained mixture estimation for analysis and robust classification of clinical time series.
Bioinform.
Ivan G. Costa, Alexander Schönhuth, Christoph Hafemeister, Alexander Schliep
2009 — conf
Mining Rules for the Automatic Selection Process of Clustering Methods Applied to Cancer Gene Expression Data.
ICANN (2)
André C. A. Nascimento, Ricardo Bastos Cavalcante Prudêncio, Marcílio Carlos Pereira de Souto, Ivan G. Costa
2009 — conf
Using Supervised Complexity Measures in the Analysis of Cancer Gene Expression Data Sets.
BSB
Ivan G. Costa, Ana Carolina Lorena, Liciana R. M. P. y Peres, Marcílio Carlos Pereira de Souto
2008 J jnl
Clustering cancer gene expression data: a comparative study.
BMC Bioinform.
Marcílio Carlos Pereira de Souto, Ivan G. Costa, Daniel S. A. de Araujo, Teresa Bernarda Ludermir, Alexander Schliep
2008 B conf
Comparative study on normalization procedures for cluster analysis of gene expression datasets.
IJCNN
Marcílio Carlos Pereira de Souto, Daniel S. A. de Araujo, Ivan G. Costa, Rodrigo G. F. Soares, Teresa Bernarda Ludermir, Alexander Schliep
2008 A conf
Inferring differentiation pathways from gene expression.
ISMB
Ivan G. Costa, Stefan Roepcke, Christoph Hafemeister, Alexander Schliep
2008 C conf
On the Complexity of Gene Expression Classification Data Sets.
HIS
Ana Carolina Lorena, Ivan G. Costa, Marcílio Carlos Pereira de Souto
2008 B conf
Ranking and selecting clustering algorithms using a meta-learning approach.
IJCNN
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
2007 J jnl
Semi-supervised learning for the identification of syn-expressed genes from fused microarray and
BMC Bioinform.
Ivan G. Costa, Roland Krause, Lennart Opitz, Alexander Schliep
2007 — conf
Validating Gene Clusterings by Selecting Informative Gene Ontology Terms with Mutual Information.
BSB
Ivan G. Costa, Marcílio Carlos Pereira de Souto, Alexander Schliep
2005 J jnl
Analyzing Gene Expression Time-Courses.
IEEE ACM Trans. Comput. Biol. Bioinform.
Alexander Schliep, Ivan G. Costa, Christine Steinhoff, Alexander Schönhuth
2005 — conf
On External Indices for Mixtures: Validating Mixtures of Genes.
GfKl
Ivan G. Costa, Alexander Schliep
2005 J jnl
The Graphical Query Language: a tool for analysis of gene expression time-courses.
Bioinform.
Ivan G. Costa, Alexander Schönhuth, Alexander Schliep
2002 — conf
A Symbolic Approach to Gene Expression Time Series Analysis.
SBRN
Ivan G. Costa, Francisco de A. T. de Carvalho, Marcílio Carlos Pereira de Souto
2002 J jnl
Comparative study on proximity indices for cluster analysis of gene expression time series.
J. Intell. Fuzzy Syst.
Ivan G. Costa, Francisco de A. T. de Carvalho, Marcílio Carlos Pereira de Souto
2002 — conf
Stability Evaluation of Clustering Algorithms for Time Series Gene Expression Data.
WOB
Ivan G. Costa, Francisco de A. T. de Carvalho, Marcílio Carlos Pereira de Souto