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Marco Pagni

swiss institute of bioinformatics

37H-index
300Paper Count
6.3KCitation Count
Published Papers 49
Publication Date
MetaboT: an LLM-based multi-agent framework for interactive analysis of mass spectrometry metabolomics knowledge graphs
err2026-07-24
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errMadina Bekbergenova; Lucas Pradi; Benjamin Navet; Emma Tysinger; Franck Michel; Matthieu Feraud; Yousouf Taghzouti; Yan Zhou Chen; Olivier Kirchhoffer; Florence Mehl; Martin Legrand; Tao Jiang; Marco Pagni; Soha Hassoun; Jean-Luc Wolfender; Wout Bittremieux; Fabien Gandon; Louis-Félix Nothias
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MetaNetX: a bridge between metabolic resources for enhanced curation and multi-omics data harmonization
err2025-11-01
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errMoretti, Sebastien; Niknejad, Anne; Pagni, Marco; Mehl, Florence
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A large collection of bioinformatics question–query pairs over federated knowledge graphs: methodology and applications
err2025-05-16
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errJerven Bolleman; Vincent Emonet; Adrian Altenhoff; Amos Bairoch; Marie-Claude Blatter; Alan Bridge; Séverine Duvaud; Elisabeth Gasteiger; Dmitry Kuznetsov; Sébastien Moretti; Pierre-Andre Michel; Anne Morgat; Marco Pagni; Nicole Redaschi; Monique Zahn-Zabal; Tarcisio Mendes de Farias; Ana Claudia Sima
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Selective expression of Pneumocystis antigens in different patients during a suspected outbreak of Pneumocystis pneumonia
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IF4.7
err2025-05-14
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errMeier, Caroline S.; Pagni, Marco; Richard, Sophie; Muhlethaler, Konrad; Hauser, Philippe M.
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Melanin and Neurotransmitter Signalling Genes Are Differentially Co-Expressed in Growing Feathers of White and Rufous Barn Owls
err2025-02-05
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errDucrest, Anne-Lyse; San-Jose, Luis M.; Neuenschwander, Samuel; Schmid-Siegert, Emanuel; Simon, Celine; Pagni, Marco; Iseli, Christian; Richter, Hannes; Guex, Nicolas; Cumer, Tristan; Beaudoing, Emmanuel; Dupasquier, Melanie; Charruau, Pauline; Ducouret, Pauline; Xenarios, Ioannis; Goudet, Jerome; Roulin, Alexandre
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Prioritization of novel anti-infective stilbene derivatives by combining metabolomic data organization and a stringent 3R-infection model in a knowledge graph
err2025-01-01
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errKirchhoffer, Olivier Auguste; Quiros-Guerrero, Luis; Nitschke, Jahn; Nothias, Louis-Felix; Burdet, Frederic; Marcourt, Laurence; Hanna, Nabil; Mehl, Florence; David, Bruno; Grondin, Antonio; Queiroz, Emerson Ferreira; Pagni, Marco; Soldati, Thierry; Wolfender, Jean-Luc
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One-Step Soft Agar Enrichment and Isolation of Human Lung Bacteria Inhibiting the Germination of Aspergillus fumigatus Conidia
err2024-10-07
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errPalmieri, Fabio; Diserens, Jeremy; Gresse, Manon; Magnin, Margo; Helle, Julina; Salamin, Benoit; Bisanti, Lorenzo; Bernasconi, Eric; Pernot, Julie; Shanmuganathan, Apiha; Trompette, Aurelien; von Garnier, Christophe; Junier, Thomas; Neuenschwander, Samuel; Bindschedler, Saskia; Pagni, Marco; Koutsokera, Angela; Ubags, Niki; Junier, Pilar
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A Sample-Centric and Knowledge-Driven Computational Framework for Natural Products Drug Discovery
err2024-02-20
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errGaudry, Arnaud; Pagni, Marco; Mehl, Florence; Moretti, Sebastien; Quiros-Guerrero, Luis-Manuel; Cappelletti, Luca; Rutz, Adriano; Kaiser, Marcel; Marcourt, Laurence; Queiroz, Emerson Ferreira; Ioset, Jean-Robert; Grondin, Antonio; David, Bruno; Wolfender, Jean-Luc; Allard, Pierre-Marie
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Fungal antigenic variation using mosaicism and reassortment of subtelomeric genes' repertoires (vol 14, 7026, 2023)
err2023-12-01
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errMeier, Caroline S.; Pagni, Marco; Richard, Sophie; Muhlethaler, Konrad; Almeida, Joao M. G. C. F.; Nevez, Gilles; Cushion, Melanie T.; Calderon, Enrique J.; Hauser, Philippe M.
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The SIB Swiss Institute of Bioinformatics Semantic Web of data
err2023-10-25
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errAltenhoff, Adrian; Bairoch, Amos; Bansal, Parit; Baratin, Delphine; Bastian, Frederic; Bolleman, Jerven; Bridge, Alan; Burdet, Frederic; Crameri, Katrin; Dauvillier, Jerome; Dessimoz, Christophe; Gehant, Sebastien; Glover, Natasha; Gnodtke, Kristin; Hayes, Catherine; Ibberson, Mark; Kriventseva, Evgenia; Kuznetsov, Dmitry; Lisacek, Frederique; Mehl, Florence; de Farias, Tarcisio Mendes; Michel, Pierre-Andre; Moretti, Sebastien; Morgat, Anne; Osterle, Sabine; Pagni, Marco; Redaschi, Nicole; Robinson-Rechavi, Marc; Samarasinghe, Kasun; Sima, Ana-Claudia; Szklarczyk, Damian; Topalov, Orlin; Toure, Vasundra; Unni, Deepak; von Mering, Christian; Wollbrett, Julien; Zahn-Zabal, Monique; Zdobnov, Evgeny
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Candida albicans commensalism in the oral mucosa is favoured by limited virulence and metabolic adaptation
err2022-04-11
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errLemberg, Christina; Vicente, Kontxi Martinez de San; Frois-Martins, Ricardo; Altmeier, Simon; Tran, Van Du T.; Mertens, Sarah; Amorim-Vaz, Sara; Rai, Laxmi Shanker; D'Enfert, Christophe; Pagni, Marco; Sanglard, Dominique; LeibundGut-Landmann, Salome
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Predicting spatial patterns of soil bacteria under current and future environmental conditions
err2021-03-12
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errMod, Heidi K.; Buri, Aline; Yashiro, Erika; Guex, Nicolas; Malard, Lucie; Pinto-Figueroa, Eric; Pagni, Marco; Niculita-Hirzel, Helene; van der Meer, Jan Roelof; Guisan, Antoine
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MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models
err2020-11-06
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errMoretti, Sebastien; Tran, Van Du T.; Mehl, Florence; Ibberson, Mark; Pagni, Marco
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Greater topoclimatic control of above- versus below-ground communities
err2020-09-27
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errMod, Heidi K.; Scherrer, Daniel; Di Cola, Valeria; Broennimann, Olivier; Blandenier, Quentin; Breiner, Frank T.; Buri, Aline; Goudet, Jerome; Guex, Nicolas; Lara, Enrique; Mitchell, Edward A. D.; Niculita-Hirzel, Helene; Pagni, Marco; Pellissier, Loic; Pinto-Figueroa, Eric; Sanders, Ian R.; Schmidt, Benedikt R.; Seppey, Christophe V. W.; Singer, David; Ursenbacher, Sylvain; Yashiro, Erika; van der Meer, Jan R.; Guisan, Antoine
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Vacuolins and myosin VII are required for phagocytic uptake and phagosomal membrane recycling in Dictyostelium discoideum
err2020-07-06
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errBosmani, Cristina; Leuba, Florence; Hanna, Nabil; Bach, Frauke; Burdet, Frederic; Pagni, Marco; Hagedorn, Monica; Soldati, Thierry
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Expression Pattern of the Pneumocystis jirovecii Major Surface Glycoprotein Superfamily in Patients with Pneumonia
err2020-06-19
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errSchmid-Siegert, Emanuel; Richard, Sophie; Luraschi, Amanda; Muhlethaler, Konrad; Pagni, Marco; Hauser, Philippe M.
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Anti-adipogenic signals at the onset of obesity-related inflammation in white adipose tissue
err2020-03-11
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errCaputo, Tiziana; Tran, Van Du T.; Bararpour, Nasim; Winkler, Carine; Aguileta, Gabriela; Trang, Khanh Bao; Attianese, Greta M. P.; Wilson, Anne; Thomas, Aurelien; Pagni, Marco; Guex, Nicolas; Desvergne, Beatrice; Gilardi, Federica
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Transcriptional Responses of Dictyostelium discoideum Exposed to Different Classes of Bacteria
err2020-03-10
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errLamrabet, Otmane; Melotti, Astrid; Burdet, Frederic; Hanna, Nabil; Perrin, Jackie; Nitschke, Jahn; Pagni, Marco; Hilbi, Hubert; Soldati, Thierry; Cosson, Pierre
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Identification of Anti-Mycobacterium and Anti-Legionella Compounds With Potential Distinctive Structural Scaffolds From an HD-PBL Using Phenotypic Screens in Amoebae Host Models
err2020-02-21
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errHanna, Nabil; Kicka, Sebastien; Chiriano, Gianpaolo; Harrison, Christopher; Sakouhi, Hajer Ouertatani; Trofimov, Valentin; Kranjc, Agata; Nitschke, Jahn; Pagni, Marco; Cosson, Pierre; Hilbi, Hubert; Scapozza, Leonardo; Soldati, Thierry
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