Ioannis Tsamardinos

Publications (40)

The γ-OMP Algorithm for Feature Selection With Application to Gene Expression Data.

IEEE/ACM transactions on computational biology and bioinformatics

Avec: Michail Tsagris , Zacharias Papadovasilakis , Kleanthi Lakiotaki , Ioannis Tsamardinos

STATegra: Multi-Omics Data Integration - A Conceptual Scheme With a Bioinformatics Pipeline.

Frontiers in genetics

Avec: Nuria Planell , Vincenzo Lagani , Patricia Sebastian-Leon , Frans van der Kloet , Ewoud Ewing , Nestoras Karathanasis , Arantxa Urdangarin , Imanol Arozarena , Maja Jagodic , Ioannis Tsamardinos , Sonia Tarazona , Ana Conesa , Jesper Tegner , David Gomez-Cabrero

Automated machine learning for genome wide association studies.

Bioinformatics (Oxford, England)

Avec: Kleanthi Lakiotaki , Zaharias Papadovasilakis , Vincenzo Lagani , Stefanos Fafalios , Paulos Charonyktakis , Michail Tsagris , Ioannis Tsamardinos

The HUNT lung-SNP model: genetic variants plus clinical variables improve lung cancer risk assessment over clinical models.

Journal of cancer research and clinical oncology

Avec: Olav Toai Duc Nguyen , Ioannis Fotopoulos , Therese Haugdahl Nøst , Maria Markaki , Vincenzo Lagani , Ioannis Tsamardinos , Oluf Dimitri Røe

Deciphering the Methylation Landscape in Breast Cancer: Diagnostic and Prognostic Biosignatures through Automated Machine Learning.

Cancers

Avec: Maria Panagopoulou , Makrina Karaglani , Vangelis G Manolopoulos , Ioannis Iliopoulos , Ioannis Tsamardinos , Ekaterini Chatzaki

Forecasting military mental health in a complete sample of Danish military personnel deployed between 1992-2013.

Journal of affective disorders

Avec: Lars R Nissen , Ioannis Tsamardinos , Kasper Eskelund , Jaimie L Gradus , Søren B Andersen , Karen-Inge Karstoft

Structural Basis of the Subcellular Topology Landscape of

Frontiers in microbiology

Avec: Maria S Loos , Reshmi Ramakrishnan , Wim Vranken , Alexandra Tsirigotaki , Evrydiki-Pandora Tsare , Valentina Zorzini , Jozefien De Geyter , Biao Yuan , Ioannis Tsamardinos , Maria Klappa , Joost Schymkowitz , Frederic Rousseau , Spyridoula Karamanou , Anastassios Economou

A unified approach for sparse dynamical system inference from temporal measurements.

Bioinformatics (Oxford, England)

Avec: Yannis Pantazis , Ioannis Tsamardinos

Learning Pathway Dynamics from Single-Cell Proteomic Data: A Comparative Study.

Cytometry. Part A : the journal of the International Society for Analytical Cytology

Avec: Kleio-Maria Verrou , Ioannis Tsamardinos , Georgios Papoutsoglou

The Essentials of Multiomics.

The oncologist

Avec: John L Marshall , Beth N Peshkin , Takayuki Yoshino , Jakob Vowinckel , Håvard E Danielsen , Gerry Melino , Ioannis Tsamardinos , Christian Haudenschild , David J Kerr , Carlos Sampaio , Sun Young Rha , Kevin T FitzGerald , Eric C Holland , David Gallagher , Jesus Garcia-Foncillas , Hartmut Juhl

Combining evidence from four immune cell types identifies DNA methylation patterns that implicate functionally distinct pathways during Multiple Sclerosis progression.

EBioMedicine

Avec: Ewoud Ewing , Lara Kular , Sunjay J Fernandes , Nestoras Karathanasis , Vincenzo Lagani , Sabrina Ruhrmann , Ioannis Tsamardinos , Jesper Tegner , Fredrik Piehl , David Gomez-Cabrero , Maja Jagodic

Feedforward regulation of Myc coordinates lineage-specific with housekeeping gene expression during B cell progenitor cell differentiation.

PLoS biology

Avec: Isabel Ferreirós-Vidal , Thomas Carroll , Tianyi Zhang , Vincenzo Lagani , Ricardo N Ramirez , Elizabeth Ing-Simmons , Alicia G Gómez-Valadés , Lee Cooper , Ziwei Liang , Georgios Papoutsoglou , Gopuraja Dharmalingam , Ya Guo , Sonia Tarazona , Sunjay J Fernandes , Peri Noori , Gilad Silberberg , Amanda G Fisher , Ioannis Tsamardinos , Ali Mortazavi , Boris Lenhard , Ana Conesa , Jesper Tegner , Matthias Merkenschlager , David Gomez-Cabrero

STATegra, a comprehensive multi-omics dataset of B-cell differentiation in mouse.

Scientific data

Avec: David Gomez-Cabrero , Sonia Tarazona , Isabel Ferreirós-Vidal , Ricardo N Ramirez , Carlos Company , Andreas Schmidt , Theo Reijmers , Veronica von Saint Paul , Francesco Marabita , Javier Rodríguez-Ubreva , Antonio Garcia-Gomez , Thomas Carroll , Lee Cooper , Ziwei Liang , Gopuraja Dharmalingam , Frans van der Kloet , Amy C Harms , Leandro Balzano-Nogueira , Vincenzo Lagani , Ioannis Tsamardinos , Michael Lappe , Dieter Maier , Johan A Westerhuis , Thomas Hankemeier , Axel Imhof , Esteban Ballestar , Ali Mortazavi , Matthias Merkenschlager , Jesper Tegner , Ana Conesa

Extending greedy feature selection algorithms to multiple solutions.

Data mining and knowledge discovery

Avec: Giorgos Borboudakis , Ioannis Tsamardinos

Liquid Biopsy in Type 2 Diabetes Mellitus Management: Building Specific Biosignatures via Machine Learning.

Journal of clinical medicine

Avec: Makrina Karaglani , Maria Panagopoulou , Christina Cheimonidi , Ioannis Tsamardinos , Efstratios Maltezos , Nikolaos Papanas , Dimitrios Papazoglou , George Mastorakos , Ekaterini Chatzaki

Improving Lung Cancer Screening Selection: The HUNT Lung Cancer Risk Model for Ever-Smokers Versus the NELSON and 2021 United States Preventive Services Task Force Criteria in the Cohort of Norway: A Population-Based Prospective Study.

JTO clinical and research reports

Avec: Olav Toai Duc Nguyen , Ioannis Fotopoulos , Maria Markaki , Ioannis Tsamardinos , Vincenzo Lagani , Oluf Dimitri Røe

Out-of-Sample Tuning for Causal Discovery.

IEEE transactions on neural networks and learning systems

Avec: Konstantina Biza , Ioannis Tsamardinos , Sofia Triantafillou

Correction: Prediction of outcome in patients with non-small cell lung cancer treated with second line PD-1/PDL-1 inhibitors based on clinical parameters: Results from a prospective, single institution study.

PloS one

Avec: Konstantinos Rounis , Dimitrios Makrakis , Chara Papadaki , Alexia Monastirioti , Lambros Vamvakas , Konstantinos Kalbakis , Krystallia Gourlia , Iordanis Xanthopoulos , Ioannis Tsamardinos , Dimitrios Mavroudis , Sofia Agelaki

A characteristic cerebellar biosignature for bipolar disorder, identified with fully automatic machine learning.

IBRO neuroscience reports

Avec: Georgios V Thomaidis , Konstantinos Papadimitriou , Sotirios Michos , Evangelos Chartampilas , Ioannis Tsamardinos

Challenges in the Multivariate Analysis of Mass Cytometry Data: The Effect of Randomization.

Cytometry. Part A : the journal of the International Society for Analytical Cytology

Avec: Georgios Papoutsoglou , Vincenzo Lagani , Angelika Schmidt , Konstantinos Tsirlis , David-Gómez Cabrero , Jesper Tegnér , Ioannis Tsamardinos

A data driven approach reveals disease similarity on a molecular level.

NPJ systems biology and applications

Avec: Kleanthi Lakiotaki , George Georgakopoulos , Elias Castanas , Oluf Dimitri Røe , Giorgos Borboudakis , Ioannis Tsamardinos

Prediction of outcome in patients with non-small cell lung cancer treated with second line PD-1/PDL-1 inhibitors based on clinical parameters: Results from a prospective, single institution study.

PloS one

Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment.

Frontiers in microbiology

Avec: Laura Judith Marcos-Zambrano , Kanita Karaduzovic-Hadziabdic , Tatjana Loncar Turukalo , Piotr Przymus , Vladimir Trajkovik , Oliver Aasmets , Magali Berland , Aleksandra Gruca , Jasminka Hasic , Karel Hron , Thomas Klammsteiner , Mikhail Kolev , Leo Lahti , Marta B Lopes , Victor Moreno , Irina Naskinova , Elin Org , Inês Paciência , Georgios Papoutsoglou , Rajesh Shigdel , Blaz Stres , Baiba Vilne , Malik Yousef , Eftim Zdravevski , Ioannis Tsamardinos , Enrique Carrillo de Santa Pau , Marcus J Claesson , Isabel Moreno-Indias , Jaak Truu

Just Add Data: automated predictive modeling for knowledge discovery and feature selection.

NPJ precision oncology

Avec: Ioannis Tsamardinos , Paulos Charonyktakis , Georgios Papoutsoglou , Giorgos Borboudakis , Kleanthi Lakiotaki , Jean Claude Zenklusen , Hartmut Juhl , Ekaterini Chatzaki , Vincenzo Lagani

A machine learning approach utilizing DNA methylation as an accurate classifier of COVID-19 disease severity.

Scientific reports

Avec: Scott Bowler , Georgios Papoutsoglou , Aristides Karanikas , Ioannis Tsamardinos , Michael J Corley , Lishomwa C Ndhlovu

Learning biologically-interpretable latent representations for gene expression data: Pathway Activity Score Learning Algorithm.

Machine learning

Avec: Ioulia Karagiannaki , Krystallia Gourlia , Vincenzo Lagani , Yannis Pantazis , Ioannis Tsamardinos

XPF interacts with TOP2B for R-loop processing and DNA looping on actively transcribed genes.

Science advances

Avec: Georgia Chatzinikolaou , Kalliopi Stratigi , Athanasios Siametis , Evi Goulielmaki , Alexia Akalestou-Clocher , Ioannis Tsamardinos , Pantelis Topalis , Caroline Austin , Britta A M Bouwman , Nicola Crosetto , Janine Altmüller , George A Garinis

Don't lose samples to estimation.

Patterns (New York, N.Y.)

Avec: Ioannis Tsamardinos

Promising microRNAs in pre-diagnostic serum associated with lung cancer up to eight years before diagnosis: a HUNT study.

Journal of cancer research and clinical oncology

Avec: Ioannis Fotopoulos , Olav Toai Duc Nguyen , Therese Haugdahl Nøst , Maria Markaki , Vincenzo Lagani , Robin Mjelle , Torkjel Manning Sandanger , Pål Sætrom , Ioannis Tsamardinos , Oluf Dimitri Røe

Applicability of an Automated Model and Parameter Selection in the Prediction of Screening-Level PTSD in Danish Soldiers Following Deployment: Development Study of Transferable Predictive Models Using Automated Machine Learning.

JMIR medical informatics

Avec: Karen-Inge Karstoft , Ioannis Tsamardinos , Kasper Eskelund , Søren Bo Andersen , Lars Ravnborg Nissen

Non-parametric combination analysis of multiple data types enables detection of novel regulatory mechanisms in T cells of multiple sclerosis patients.

Scientific reports

Avec: Sunjay Jude Fernandes , Hiromasa Morikawa , Ewoud Ewing , Sabrina Ruhrmann , Rubin Narayan Joshi , Vincenzo Lagani , Nestoras Karathanasis , Mohsen Khademi , Nuria Planell , Angelika Schmidt , Ioannis Tsamardinos , Tomas Olsson , Fredrik Piehl , Ingrid Kockum , Maja Jagodic , Jesper Tegnér , David Gomez-Cabrero

Translating vitamin D transcriptomics to clinical evidence: Analysis of data in asthma and chronic obstructive pulmonary disease, followed by clinical data meta-analysis.

The Journal of steroid biochemistry and molecular biology

Avec: Niki Malliaraki , Kleanthi Lakiotaki , Rodanthi Vamvoukaki , George Notas , Ioannis Tsamardinos , Marilena Kampa , Elias Castanas

Circulating cell-free DNA in breast cancer: size profiling, levels, and methylation patterns lead to prognostic and predictive classifiers.

Oncogene

Avec: Maria Panagopoulou , Makrina Karaglani , Ioanna Balgkouranidou , Eirini Biziota , Triantafillia Koukaki , Evaggelos Karamitrousis , Evangelia Nena , Ioannis Tsamardinos , George Kolios , Evi Lianidou , Stylianos Kakolyris , Ekaterini Chatzaki

Scanning of Genetic Variants and Genetic Mapping of Phenotypic Traits in Gilthead Sea Bream Through ddRAD Sequencing.

Frontiers in genetics

Avec: Dimitrios Kyriakis , Alexandros Kanterakis , Tereza Manousaki , Alexandros Tsakogiannis , Michalis Tsagris , Ioannis Tsamardinos , Leonidas Papaharisis , Dimitris Chatziplis , George Potamias , Costas S Tsigenopoulos

A greedy feature selection algorithm for Big Data of high dimensionality.

Machine learning

Avec: Ioannis Tsamardinos , Giorgos Borboudakis , Pavlos Katsogridakis , Polyvios Pratikakis , Vassilis Christophides

Accurate Blood-Based Diagnostic Biosignatures for Alzheimer's Disease via Automated Machine Learning.

Journal of clinical medicine

Avec: Makrina Karaglani , Krystallia Gourlia , Ioannis Tsamardinos , Ekaterini Chatzaki

'Reduced' HUNT model outperforms NLST and NELSON study criteria in predicting lung cancer in the Danish screening trial.

BMJ open respiratory research

Avec: Oluf Dimitri Røe , Maria Markaki , Ioannis Tsamardinos , Vincenzo Lagani , Olav Toai Duc Nguyen , Jesper Holst Pedersen , Zaigham Saghir , Haseem Gary Ashraf

Automated machine learning optimizes and accelerates predictive modeling from COVID-19 high throughput datasets.

Scientific reports

Avec: Georgios Papoutsoglou , Makrina Karaglani , Vincenzo Lagani , Naomi Thomson , Oluf Dimitri Røe , Ioannis Tsamardinos , Ekaterini Chatzaki

Tissue-Specific Methylation Biosignatures for Monitoring Diseases: An In Silico Approach.

International journal of molecular sciences

Avec: Makrina Karaglani , Maria Panagopoulou , Ismini Baltsavia , Paraskevi Apalaki , Theodosis Theodosiou , Ioannis Iliopoulos , Ioannis Tsamardinos , Ekaterini Chatzaki

Corrigendum to "A characteristic cerebellar biosignature for bipolar disorder, identified with fully automatic machine learning" [IBRO Neurosci Rep. 15 (2023) 77-89].

IBRO neuroscience reports

Avec: Georgios V Thomaidis , Konstantinos Papadimitriou , Sotirios Michos , Evangelos Chartampilas , Ioannis Tsamardinos

Réseau de co-auteurs

Vincenzo Lagani 14 collaborations

Ekaterini Chatzaki 7 collaborations

Georgios Papoutsoglou 7 collaborations

Oluf Dimitri Røe 6 collaborations

Makrina Karaglani 6 collaborations

Kleanthi Lakiotaki 5 collaborations

David Gomez-Cabrero 5 collaborations

Jesper Tegner 4 collaborations

Olav Toai Duc Nguyen 4 collaborations

Maria Markaki 4 collaborations

Maria Panagopoulou 4 collaborations

Giorgos Borboudakis 4 collaborations

Krystallia Gourlia 4 collaborations

Ewoud Ewing 3 collaborations

Nestoras Karathanasis 3 collaborations

Maja Jagodic 3 collaborations

Sonia Tarazona 3 collaborations

Ana Conesa 3 collaborations

Ioannis Fotopoulos 3 collaborations

Michail Tsagris 2 collaborations

Nuria Planell 2 collaborations

Frans van der Kloet 2 collaborations

Paulos Charonyktakis 2 collaborations

Therese Haugdahl Nøst 2 collaborations

Ioannis Iliopoulos 2 collaborations

Kasper Eskelund 2 collaborations

Karen-Inge Karstoft 2 collaborations

Yannis Pantazis 2 collaborations

Hartmut Juhl 2 collaborations

Sunjay J Fernandes 2 collaborations

Sabrina Ruhrmann 2 collaborations

Fredrik Piehl 2 collaborations

Isabel Ferreirós-Vidal 2 collaborations

Thomas Carroll 2 collaborations

Ricardo N Ramirez 2 collaborations

Lee Cooper 2 collaborations

Ziwei Liang 2 collaborations

Gopuraja Dharmalingam 2 collaborations

Ali Mortazavi 2 collaborations

Matthias Merkenschlager 2 collaborations

Konstantinos Rounis 2 collaborations

Dimitrios Makrakis 2 collaborations

Chara Papadaki 2 collaborations

Alexia Monastirioti 2 collaborations

Lambros Vamvakas 2 collaborations

Konstantinos Kalbakis 2 collaborations

Iordanis Xanthopoulos 2 collaborations

Dimitrios Mavroudis 2 collaborations

Sofia Agelaki 2 collaborations

Georgios V Thomaidis 2 collaborations

Konstantinos Papadimitriou 2 collaborations

Sotirios Michos 2 collaborations

Evangelos Chartampilas 2 collaborations

Angelika Schmidt 2 collaborations

Jesper Tegnér 2 collaborations

Elias Castanas 2 collaborations

Zacharias Papadovasilakis 1 collaboration

Patricia Sebastian-Leon 1 collaboration

Arantxa Urdangarin 1 collaboration

Imanol Arozarena 1 collaboration

Zaharias Papadovasilakis 1 collaboration

Stefanos Fafalios 1 collaboration

Vangelis G Manolopoulos 1 collaboration

Lars R Nissen 1 collaboration

Jaimie L Gradus 1 collaboration

Søren B Andersen 1 collaboration

Maria S Loos 1 collaboration

Reshmi Ramakrishnan 1 collaboration

Wim Vranken 1 collaboration

Alexandra Tsirigotaki 1 collaboration

Evrydiki-Pandora Tsare 1 collaboration

Valentina Zorzini 1 collaboration

Jozefien De Geyter 1 collaboration

Biao Yuan 1 collaboration

Maria Klappa 1 collaboration

Joost Schymkowitz 1 collaboration

Frederic Rousseau 1 collaboration

Spyridoula Karamanou 1 collaboration

Anastassios Economou 1 collaboration

Kleio-Maria Verrou 1 collaboration

John L Marshall 1 collaboration

Beth N Peshkin 1 collaboration

Takayuki Yoshino 1 collaboration

Jakob Vowinckel 1 collaboration

Håvard E Danielsen 1 collaboration

Gerry Melino 1 collaboration

Christian Haudenschild 1 collaboration

David J Kerr 1 collaboration

Carlos Sampaio 1 collaboration

Sun Young Rha 1 collaboration

Kevin T FitzGerald 1 collaboration

Eric C Holland 1 collaboration

David Gallagher 1 collaboration

Jesus Garcia-Foncillas 1 collaboration

Lara Kular 1 collaboration

Tianyi Zhang 1 collaboration

Elizabeth Ing-Simmons 1 collaboration

Alicia G Gómez-Valadés 1 collaboration

Ya Guo 1 collaboration

Peri Noori 1 collaboration

Gilad Silberberg 1 collaboration

Amanda G Fisher 1 collaboration

Boris Lenhard 1 collaboration

Carlos Company 1 collaboration

Andreas Schmidt 1 collaboration

Theo Reijmers 1 collaboration

Veronica von Saint Paul 1 collaboration

Francesco Marabita 1 collaboration

Javier Rodríguez-Ubreva 1 collaboration

Antonio Garcia-Gomez 1 collaboration

Amy C Harms 1 collaboration

Leandro Balzano-Nogueira 1 collaboration

Michael Lappe 1 collaboration

Dieter Maier 1 collaboration

Johan A Westerhuis 1 collaboration

Thomas Hankemeier 1 collaboration

Axel Imhof 1 collaboration

Esteban Ballestar 1 collaboration

Christina Cheimonidi 1 collaboration

Efstratios Maltezos 1 collaboration

Nikolaos Papanas 1 collaboration

Dimitrios Papazoglou 1 collaboration

George Mastorakos 1 collaboration

Konstantina Biza 1 collaboration

Sofia Triantafillou 1 collaboration

Konstantinos Tsirlis 1 collaboration

David-Gómez Cabrero 1 collaboration

George Georgakopoulos 1 collaboration

Laura Judith Marcos-Zambrano 1 collaboration

Kanita Karaduzovic-Hadziabdic 1 collaboration

Tatjana Loncar Turukalo 1 collaboration

Piotr Przymus 1 collaboration

Vladimir Trajkovik 1 collaboration

Oliver Aasmets 1 collaboration

Magali Berland 1 collaboration

Aleksandra Gruca 1 collaboration

Jasminka Hasic 1 collaboration

Karel Hron 1 collaboration

Thomas Klammsteiner 1 collaboration

Mikhail Kolev 1 collaboration

Leo Lahti 1 collaboration

Marta B Lopes 1 collaboration

Victor Moreno 1 collaboration

Irina Naskinova 1 collaboration

Elin Org 1 collaboration

Inês Paciência 1 collaboration

Rajesh Shigdel 1 collaboration

Blaz Stres 1 collaboration

Baiba Vilne 1 collaboration

Malik Yousef 1 collaboration

Eftim Zdravevski 1 collaboration

Enrique Carrillo de Santa Pau 1 collaboration

Marcus J Claesson 1 collaboration

Isabel Moreno-Indias 1 collaboration

Jaak Truu 1 collaboration

Jean Claude Zenklusen 1 collaboration

Scott Bowler 1 collaboration

Aristides Karanikas 1 collaboration

Michael J Corley 1 collaboration

Lishomwa C Ndhlovu 1 collaboration

Ioulia Karagiannaki 1 collaboration

Georgia Chatzinikolaou 1 collaboration

Kalliopi Stratigi 1 collaboration

Athanasios Siametis 1 collaboration

Evi Goulielmaki 1 collaboration

Alexia Akalestou-Clocher 1 collaboration

Pantelis Topalis 1 collaboration

Caroline Austin 1 collaboration

Britta A M Bouwman 1 collaboration

Nicola Crosetto 1 collaboration

Janine Altmüller 1 collaboration

George A Garinis 1 collaboration

Robin Mjelle 1 collaboration

Torkjel Manning Sandanger 1 collaboration

Pål Sætrom 1 collaboration

Søren Bo Andersen 1 collaboration

Lars Ravnborg Nissen 1 collaboration

Sunjay Jude Fernandes 1 collaboration

Hiromasa Morikawa 1 collaboration

Rubin Narayan Joshi 1 collaboration

Mohsen Khademi 1 collaboration

Tomas Olsson 1 collaboration

Ingrid Kockum 1 collaboration

Niki Malliaraki 1 collaboration

Rodanthi Vamvoukaki 1 collaboration

George Notas 1 collaboration

Marilena Kampa 1 collaboration

Ioanna Balgkouranidou 1 collaboration

Eirini Biziota 1 collaboration

Triantafillia Koukaki 1 collaboration

Evaggelos Karamitrousis 1 collaboration

Evangelia Nena 1 collaboration

George Kolios 1 collaboration

Evi Lianidou 1 collaboration

Stylianos Kakolyris 1 collaboration

Dimitrios Kyriakis 1 collaboration

Alexandros Kanterakis 1 collaboration

Tereza Manousaki 1 collaboration

Alexandros Tsakogiannis 1 collaboration

Michalis Tsagris 1 collaboration

Leonidas Papaharisis 1 collaboration

Dimitris Chatziplis 1 collaboration

George Potamias 1 collaboration

Costas S Tsigenopoulos 1 collaboration

Pavlos Katsogridakis 1 collaboration

Polyvios Pratikakis 1 collaboration

Vassilis Christophides 1 collaboration

Jesper Holst Pedersen 1 collaboration

Zaigham Saghir 1 collaboration

Haseem Gary Ashraf 1 collaboration

Naomi Thomson 1 collaboration

Ismini Baltsavia 1 collaboration

Paraskevi Apalaki 1 collaboration

Theodosis Theodosiou 1 collaboration