Ivan G. Costa

发表

Analysis of complexity indices for classification problems: Cancer gene expression data

Ana Carolina Lorena, Ivan G. Costa, Newton Spolaôr, 2012, Neurocomputing.

Detecting differential peaks in ChIP-seq signals with ODIN

Ivan G. Costa, Manuel Allhoff, Kristin Seré, 2014, Bioinform..

On the Feasibility of Heterogeneous Analysis of Large Scale Biological Data

Alexander Schliep, Ivan G. Costa, Alexander Schliep, 2006 .

Inferring epigenetic and transcriptional regulation during blood cell development with a mixture of sparse linear models

Francisco de A. T. de Carvalho, Ivan G. Costa, Helge G. Roider, 2012, Bioinform..

CLEVER: clique-enumerating variant finder

Alexander Schliep, Alexander Schönhuth, Ivan G. Costa, 2012, Bioinform..

On the Complexity of Gene Expression Classification Data Sets

Ana Carolina Lorena, Ivan G. Costa, Marcílio Carlos Pereira de Souto, 2008, 2008 Eighth International Conference on Hybrid Intelligent Systems.

Inferring differentiation pathways from gene expression

Alexander Schliep, Ivan G. Costa, Stefan Roepcke, 2008, ISMB.

A multiple kernel learning algorithm for drug-target interaction prediction

Ivan G. Costa, Ricardo B. C. Prudêncio, André C. A. Nascimento, 2016, BMC Bioinformatics.

Mining Rules for the Automatic Selection Process of Clustering Methods Applied to Cancer Gene Expression Data

Ivan G. Costa, Marcílio Carlos Pereira de Souto, Ricardo B. C. Prudêncio, 2009, ICANN.

On the Complexity of Gene Marker Selection

Ana Carolina Lorena, Ivan G. Costa, Newton Spolaôr, 2010, 2010 Eleventh Brazilian Symposium on Neural Networks.

PyMix - The Python mixture package - a tool for clustering of heterogeneous biological data

Benjamin Georgi, Alexander Schliep, Ivan G. Costa, 2010, BMC Bioinformatics.

Predicting Gene Functions Using Semi-supervised Clustering Algorithms with Objective Function Optimization

Francisco de A. T. de Carvalho, Ivan G. Costa, Valmir Macário Filho, 2012, 2012 Brazilian Symposium on Neural Networks.

pGQL: A probabilistic graphical query language for gene expression time courses

Alexander Schliep, Ivan G. Costa, Ruben Schilling, 2010, BioData Mining.

A Comparison of External Clustering Evaluation Indices in the Context of Imbalanced Data Sets

Ivan G. Costa, Marcílio Carlos Pereira de Souto, André L. V. Coelho, 2012, 2012 Brazilian Symposium on Neural Networks.

Semi-supervised learning for the identification of syn-expressed genes from fused microarray and in situ image data

Alexander Schliep, Ivan G. Costa, Lennart Opitz, 2007, BMC Bioinformatics.

Predicting gene expression in T cell differentiation from histone modifications and transcription factor binding affinities by linear mixture models

Francisco de A. T. de Carvalho, Ivan G. Costa, Helge G. Roider, 2011, BMC Bioinformatics.

Prediction of Transcription Factor Binding Sites by Integrating DNase Digestion and Histone Modification

Ivan G. Costa, Christoph Dieterich, Eduardo G. Gusmão, 2012, BSB.

Classifying short gene expression time-courses with Bayesian estimation of piecewise constant functions

Alexander Schliep, Alexander Schönhuth, Ivan G. Costa, 2011, Bioinform..

Constrained mixture estimation for analysis and robust classification of clinical time series

Alexander Schliep, Alexander Schönhuth, Ivan G. Costa, 2009, Bioinform..

Evaluating Correlation Coefficients for Clustering Gene Expression Profiles of Cancer

Ricardo J. G. B. Campello, Ivan G. Costa, Pablo A. Jaskowiak, 2012, BSB.

Proximity Measures for Clustering Gene Expression Microarray Data: A Validation Methodology and a Comparative Analysis

Ricardo J. G. B. Campello, Ivan G. Costa, Pablo A. Jaskowiak, 2013, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Detection and interpretation of metabolite–transcript coresponses using combined profiling data

Ivan G. Costa, Henning Redestig, Henning Redestig, 2011, Bioinform..

Ranking and selecting clustering algorithms using a meta-learning approach

Alexander Schliep, Ivan G. Costa, Marcílio Carlos Pereira de Souto, 2008, 2008 IEEE International Joint Conference on Neural Networks (IEEE World Congress on Computational Intelligence).

Detecting differential peaks in ChIP-seq signals with ODIN

Ivan G. Costa, Manuel Allhoff, Kristin Seré, 2015, Bioinform..

On External Indices for Mixtures: Validating Mixtures of Genes

Alexander Schliep, Ivan G. Costa, Alexander Schliep, 2005, GfKl.

Discovering motifs that induce sequencing errors

Alexander Schönhuth, Sven Rahmann, Ivan G. Costa, 2013, BMC Bioinformatics.

Random Forest and Gene Networks for Association of SNPs to Alzheimer's Disease

João Ricardo M. Oliveira, Ivan G. Costa, Gilderlanio S. Araújo, 2013, BSB.

Impact of missing data imputation methods on gene expression clustering and classification

Ivan G. Costa, Marcílio Carlos Pereira de Souto, Pablo A. Jaskowiak, 2015, BMC Bioinformatics.

Semi-supervised Approach for Finding Cancer Sub-classes on Gene Expression Data

Francisco de A. T. de Carvalho, Ivan G. Costa, Clerton Ribeiro, 2010, BSB.

The Graphical Query Language: a tool for analysis of gene expression time-courses

Alexander Schliep, Alexander Schönhuth, Ivan G. Costa, 2005 .

Using Supervised Complexity Measures in the Analysis of Cancer Gene Expression Data Sets

Ana Carolina Lorena, Ivan G. Costa, Marcílio Carlos Pereira de Souto, 2009, BSB.

On the selection of appropriate distances for gene expression data clustering

Ricardo J. G. B. Campello, Ivan G. Costa, Pablo A. Jaskowiak, 2014, BMC Bioinformatics.

Data complexity meta-features for regression problems

Ana Carolina Lorena, Ivan G. Costa, Ricardo B. C. Prudêncio, 2017, Machine Learning.

Validating Gene Clusterings by Selecting Informative Gene Ontology Terms with Mutual Information

Alexander Schliep, Ivan G. Costa, Marcílio Carlos Pereira de Souto, 2007, BSB.

Analyzing Gene Expression Time-Courses

Alexander Schliep, Alexander Schönhuth, Christine Steinhoff, 2005, IEEE ACM Trans. Comput. Biol. Bioinform..

The General Hidden Markov Model Library : Analyzing Systems with Unobservable States

Benjamin Georgi, Alexander Schönhuth, Ivan G. Costa, 2004 .

Comparative study on normalization procedures for cluster analysis of gene expression datasets

Alexander Schliep, Ivan G. Costa, Marcílio Carlos Pereira de Souto, 2008, 2008 IEEE International Joint Conference on Neural Networks (IEEE World Congress on Computational Intelligence).

Stability Evaluation of Clustering Algorithms for Time Series Gene Expression Data

Francisco de A. T. de Carvalho, Ivan G. Costa, Marcílio Carlos Pereira de Souto, 2002, WOB.

Comparative study on proximity indices for cluster analysis of gene expression time series

Francisco de A. T. de Carvalho, Ivan G. Costa, Marcílio Carlos Pereira de Souto, 2002, J. Intell. Fuzzy Syst..

Measuring the complexity of regression problems

Ana Carolina Lorena, Ivan G. Costa, Aron I. Maciel, 2016, 2016 International Joint Conference on Neural Networks (IJCNN).

Detection of active transcription factor binding sites with the combination of DNase hypersensitivity and histone modifications

Ivan G. Costa, Christoph Dieterich, Martin Zenke, 2014, Bioinform..

Complexity measures of supervised classifications tasks: A case study for cancer gene expression data

Ana Carolina Lorena, Ivan G. Costa, Newton Spolaôr, 2010, The 2010 International Joint Conference on Neural Networks (IJCNN).

Clustering cancer gene expression data: a comparative study

Alexander Schliep, Ivan G. Costa, Marcílio Carlos Pereira de Souto, 2008, BMC Bioinformatics.

Gene expression trees in lymphoid development

Ivan G. Costa, Alexander Schliep, Stefan Roepcke, 2007, BMC Immunology.

Unique and assay specific features of NOMe-, ATAC- and DNase I-seq data

Marcel H. Schulz, Ivan G. Costa, Thomas Lengauer, 2019, bioRxiv.

Chromatin-accessibility estimation of single-cell on ATAC data

Ivan G. Costa, Mingbo Cheng, M. Zenke, 2019, bioRxiv.

Semi-supervised Clustering of Yeast Gene Expression Data

Alexander Schönhuth, Ivan G. Costa, Alexander Schliep, 2009 .

DNA methylation levels at individual age-associated CpG sites can be indicative for life expectancy

Ian J. Deary, Ivan G. Costa, Wolfgang Wagner, 2016, Aging.

Comparative analysis of clustering methods for gene expression time course data

Francisco de A. T. de Carvalho, Ivan G. Costa, Marcilio C. P. de Souto, 2004, Genetics and Molecular Biology.

A symbolic approach to gene expression time series analysis

Francisco de A. T. de Carvalho, Ivan G. Costa, Marcílio Carlos Pereira de Souto, 2002, VII Brazilian Symposium on Neural Networks, 2002. SBRN 2002. Proceedings..

Gene Expression Trees in Blood Cell Development

Ivan G. Costa, Stefan Roepcke, Alexander Schliep, 2005 .

The interaction of MYC with the trithorax protein ASH2L promotes gene transcription by regulating H3K27 modification

Ivan G. Costa, E. Kremmer, E. Gusmão, 2014, Nucleic acids research.

Topological demarcation by HMGB2 is disrupted early upon senescence entry across cell types and induces CTCF clustering

Ivan G. Costa, J. Mallm, K. Rippe, 2017, bioRxiv.

Mapping the cardiac vascular niche in heart failure

Ivan G. Costa, Michael T. Schaub, M. Schaub, 2022, Nature Communications.

The area under the ROC curve as a measure of clustering quality

Ricardo J. G. B. Campello, Ivan G. Costa, Pablo A. Jaskowiak, 2020, Data Mining and Knowledge Discovery.

BIOINFORMATICS Inferring differentiation pathways from gene expression

Ivan G. Costa, Alexander Schliep, Stefan Roepcke, 2008 .

Detection of cell markers from single cell RNA-seq with sc2marker

Ivan G. Costa, R. Schneider, Ronghui Li, 2022, BMC Bioinform..

Early and late stage MPN patients show distinct gene expression profiles in CD34+ cells

Ivan G. Costa, J. Eschweiler, A. Schuppert, 2021, Annals of Hematology.

SARS-CoV-2 infects the human kidney and drives fibrosis in kidney organoids

Ivan G. Costa, Vincent A. Voelz, Matthew F. D. Hurley, 2021, Cell Stem Cell.

Adult human kidney organoids originate from CD24+ cells and represent an advanced model for adult polycystic kidney disease

Ivan G. Costa, Benjamin S. Freedman, P. Boor, 2022, Nature Genetics.

scMEGA: single-cell multi-omic enhancer-based gene regulatory network inference

Ivan G. Costa, J. Nagai, C. Kuppe, 2022, bioRxiv.

Dissecting CD8+ T cell pathology of severe SARS-CoV-2 infection by single-cell immunoprofiling

Ivan G. Costa, J. Saez-Rodriguez, R. Schneider, 2022, Frontiers in Immunology.

Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)

Ivan G. Costa, Mingbo Cheng, R. Coppo, 2022, bioRxiv.

Platelet-instructed SPP1+ macrophages drive myofibroblast activation in fibrosis in a CXCL4-dependent manner

Ivan G. Costa, P. Boor, R. Schneider, 2023, Cell reports.

CALR frameshift mutations in MPN patient-derived iPS cells accelerate maturation of megakaryocytes

Ivan G. Costa, P. Boor, T. Brümmendorf, 2021, bioRxiv.

Replicative senescence is associated with nuclear reorganization and with DNA methylation at specific transcription factor binding sites

Ivan G. Costa, V. Beneš, T. Brümmendorf, 2015, Clinical Epigenetics.

SARS-CoV-2 infects the human kidney and drives fibrosis in kidney organoids

Ivan G. Costa, Vincent A. Voelz, Matthew F. D. Hurley, 2021, Cell Stem Cell.

RGT: a toolbox for the integrative analysis of high throughput regulatory genomics data

Ivan G. Costa, E. Gusmão, Manuel Allhoff, 2023, bioRxiv.

Identification of transcription factor binding sites using ATAC-seq

Marcel H. Schulz, Ivan G. Costa, M. Zenke, 2018, Genome Biology.

Infliximab therapy together with tyrosine kinase inhibition targets leukemic stem cells in chronic myeloid leukemia

Ivan G. Costa, T. Luedde, T. Brümmendorf, 2019, BMC Cancer.

Next-Generation Morphometry for pathomics-data mining in histopathology

Ivan G. Costa, P. Boor, Mingbo Cheng, 2023, Nature Communications.

Analyzing gene expression time-courses

Ivan G. Costa, A. Schliep, I.G. Costa, 2005, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Clustering Validation with The Area Under Precision-Recall Curves

Ivan G. Costa, Pablo A. Jaskowiak, 2023, ArXiv.

A multiple kernel learning algorithm for drug-target interaction prediction

Ivan G. Costa, André C. A. Nascimento, R. Prudêncio, 2016, BMC Bioinformatics.

KIT D816V Mast Cells Derived from Induced Pluripotent Stem Cells Recapitulate Systemic Mastocytosis Transcriptional Profile

Ivan G. Costa, P. Boor, T. Brümmendorf, 2023, International journal of molecular sciences.

Mast cell deficiency prevents BCR::ABL1 induced splenomegaly and cytokine elevation in a CML mouse model

Ivan G. Costa, T. Brummer, S. Koschmieder, 2023, Leukemia.

Myelofibrosis at diagnosis is associated with the failure of treatment-free remission in CML patients

Ivan G. Costa, T. Brümmendorf, H. Jacobi, 2023, Frontiers in Pharmacology.

Targeting cytokine-induced leukemic stem cell persistence in chronic myeloid leukemia by IKK2-inhibition

Ivan G. Costa, T. Brümmendorf, M. Schemionek, 2022, Haematologica.

Sublethal necroptosis signaling promotes inflammation and liver cancer.

Ivan G. Costa, Jakob Nikolas Kather, T. Luedde, 2023, Immunity.

Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)

Ivan G. Costa, Mingbo Cheng, R. Coppo, 2023, bioRxiv.

Combined Genome-Wide CSF Aβ-42’s Associations and Simple Network Properties Highlight New Risk Factors for Alzheimer’s Disease

Ivan G. Costa, for the Alzheimer’s Disease Neuroimaging Initiative, G. Araújo, 2015, Journal of Molecular Neuroscience.

Clustering cancer gene expression data: a comparative study

Ivan G. Costa, Teresa B Ludermir, Alexander Schliep, 2008, BMC Bioinform..

Mining rules for selection of clustering methods on cancer gene expression

Ivan G. Costa, André C. A. Nascimento, M. D. Souto, 2009 .

Gene expression trees in lymphoid development

Ivan G. Costa, Alexander Schliep, S. Roepcke, 2007, BMC Immunology.

Detection of active transcription factor binding sites with the combination of DNase hypersensitivity and histone modifications

Ivan G. Costa, C. Dieterich, E. Gusmão, 2014, Bioinform..

Comparative analysis of clustering methods for gene expression time course data

Ivan G. Costa, M. D. Souto, F. D. Carvalho, 2004, Genetics and Molecular Biology.

Targeted DNA Methylation Analysis Facilitates Leukocyte Counts in Dried Blood Samples.

Ivan G. Costa, Tiago Maié, W. Wagner, 2023, Clinical chemistry.

Extending the landscape of omics technologies by pathomics

Ivan G. Costa, P. Boor, R. D. Bülow, 2023, NPJ systems biology and applications.

Enhanced fatty acid oxidation through Metformin and Baicalin as therapy for COVID-19 and associated inflammatory states in lung and kidney

Ivan G. Costa, J. Nagai, J. M. Rodríguez González-Moro, 2023, Free Radical Biology and Medicine.