Modern Metaproteomics: A Unique Tool to Characterize the Active Microbiome in Health and Diseases, and Pave the Road towards New Biomarkers—Example of Crohn’s Disease and Ulcerativ... by Céline Henry, Ariane Bassignani, Magali Berland, Olivier Langella, Harry Sokol, Catherine Juste

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A combined test for feature selection on sparse metaproteomics data—an alternative to missing value imputation by Sandra Plancade, Magali Berland, Mélisande Blein-Nicolas, Olivier Langella, Ariane Bassignani, Catherine Juste

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StrainFLAIR: strain-level profiling of metagenomic samples using variation graphs by Kévin Da Silva, Nicolas Pons, Magali Berland, Florian Plaza Oñate, Mathieu Almeida, Pierre Peterlongo

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Overview of data preprocessing for machine learning applications in human microbiome research by Eliana Ibrahimi, Marta B. Lopes, Marta B. Lopes, Xhilda Dhamo, Andrea Simeon, Rajesh Shigdel, Karel Hron, Blaž Stres, Blaž Stres, Blaž Stres, Blaž Stres, Domenica D’Elia, Magali Berland, Laura Judith Marcos-Zambrano

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Alteration of Gut Microbiome in Patients With Schizophrenia Indicates Links Between Bacterial Tyrosine Biosynthesis and Cognitive Dysfunction by Florence Thirion, Helene Speyer, Tue Haldor Hansen, Trine Nielsen, Yong Fan, Emmanuelle Le Chatelier, Sébastien Fromentin, Magali Berland, Florian Plaza Oñate, Nicolas Pons, Nathalie Galleron, Florence Levenez, Lajos Markó, Till Birkner, Torben Jørgensen, Sofia K. Forslund, Henrik Vestergaard, Torben Hansen, Merete Nordentoft, Ole Mors, Michael E. Benros, Oluf Pedersen, Stanislav D. Ehrlich

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Machine learning approaches in microbiome research: challenges and best practices by Georgios Papoutsoglou, Georgios Papoutsoglou, Sonia Tarazona, Marta B. Lopes, Marta B. Lopes, Thomas Klammsteiner, Thomas Klammsteiner, Eliana Ibrahimi, Julia Eckenberger, Julia Eckenberger, Pierfrancesco Novielli, Pierfrancesco Novielli, Alberto Tonda, Alberto Tonda, Andrea Simeon, Rajesh Shigdel, Stéphane Béreux, Stéphane Béreux, Giacomo Vitali, Sabina Tangaro, Sabina Tangaro, Leo Lahti, Andriy Temko, Marcus J. Claesson, Marcus J. Claesson, Magali Berland

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Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment by Laura Judith Marcos-Zambrano, Kanita Karaduzovic-Hadziabdic, Tatjana Loncar Turukalo, Piotr Przymus, Vladimir Trajkovik, Oliver Aasmets, Oliver Aasmets, Magali Berland, Aleksandra Gruca, Jasminka Hasic, Karel Hron, Thomas Klammsteiner, Mikhail Kolev, Leo Lahti, Marta B. Lopes, Marta B. Lopes, Victor Moreno, Victor Moreno, Victor Moreno, Victor Moreno, Irina Naskinova, Elin Org, Inês Paciência, Georgios Papoutsoglou, Rajesh Shigdel, Blaz Stres, Baiba Vilne, Malik Yousef, Malik Yousef, Eftim Zdravevski, Ioannis Tsamardinos, Enrique Carrillo de Santa Pau, Marcus J. Claesson, Isabel Moreno-Indias, Isabel Moreno-Indias, Jaak Truu

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Advancing microbiome research with machine learning: key findings from the ML4Microbiome COST action by Domenica D’Elia, Jaak Truu, Leo Lahti, Magali Berland, Georgios Papoutsoglou, Georgios Papoutsoglou, Michelangelo Ceci, Aldert Zomer, Marta B. Lopes, Marta B. Lopes, Eliana Ibrahimi, Aleksandra Gruca, Alina Nechyporenko, Alina Nechyporenko, Marcus Frohme, Thomas Klammsteiner, Thomas Klammsteiner, Enrique Carrillo-de Santa Pau, Laura Judith Marcos-Zambrano, Karel Hron, Gianvito Pio, Andrea Simeon, Ramona Suharoschi, Isabel Moreno-Indias, Andriy Temko, Miroslava Nedyalkova, Elena-Simona Apostol, Ciprian-Octavian Truică, Rajesh Shigdel, Jasminka Hasić Telalović, Erik Bongcam-Rudloff, Piotr Przymus, Naida Babić Jordamović, Naida Babić Jordamović, Laurent Falquet, Sonia Tarazona, Alexia Sampri, Alexia Sampri, Gaetano Isola, David Pérez-Serrano, Vladimir Trajkovik, Lubos Klucar, Tatjana Loncar-Turukalo, Aki S. Havulinna, Aki S. Havulinna, Christian Jansen, Christian Jansen, Randi J. Bertelsen, Marcus Joakim Claesson

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A toolbox of machine learning software to support microbiome analysis by Laura Judith Marcos-Zambrano, Víctor Manuel López-Molina, Burcu Bakir-Gungor, Marcus Frohme, Kanita Karaduzovic-Hadziabdic, Thomas Klammsteiner, Eliana Ibrahimi, Leo Lahti, Tatjana Loncar-Turukalo, Xhilda Dhamo, Andrea Simeon, Alina Nechyporenko, Alina Nechyporenko, Gianvito Pio, Gianvito Pio, Piotr Przymus, Alexia Sampri, Vladimir Trajkovik, Blanca Lacruz-Pleguezuelos, Oliver Aasmets, Oliver Aasmets, Ricardo Araujo, Ioannis Anagnostopoulos, Ioannis Anagnostopoulos, Önder Aydemir, Magali Berland, M. Luz Calle, M. Luz Calle, Michelangelo Ceci, Michelangelo Ceci, Hatice Duman, Aycan Gündoğdu, Aycan Gündoğdu, Aki S. Havulinna, Aki S. Havulinna, Kardokh Hama Najib Kaka Bra, Eglantina Kalluci, Sercan Karav, Daniel Lode, Marta B. Lopes, Marta B. Lopes, Patrick May, Bram Nap, Miroslava Nedyalkova, Inês Paciência, Inês Paciência, Lejla Pasic, Meritxell Pujolassos, Rajesh Shigdel, Antonio Susín, Ines Thiele, Ines Thiele, Ciprian-Octavian Truică, Paul Wilmes, Paul Wilmes, Ercument Yilmaz, Malik Yousef, Malik Yousef, Marcus Joakim Claesson, Marcus Joakim Claesson, Jaak Truu, Enrique Carrillo de Santa Pau

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