Publications of A Ruaud

Ruaud, A.; Pfister, N.; Ley, R.; Youngblut, N.: Interpreting tree ensemble machine learning models with endoR. PLoS Computational Biology 18 (12), e1010714 (2022)

Welter, D.; Ruaud, A.; Henseler, Z.; De Jong, H.; van Coeverden de Groot, P.; Michaux, J.; Gormezano, L.; Waters, J.; Youngblut, N.; Ley, R.: Free-living psychrophilic bacteria of the genus Psychrobacter are descendants of pathobionts. mSystems (accepted)

Welter, D.; Ruaud, A.; Henseler, Z.; De Jong, H.; van Coeverden de Groot, P.; Michaux, J.; Gormezano, L.; Waters, J.; Youngblut, N.; Ley, R.: Free-Living, Psychrotrophic Bacteria of the Genus Psychrobacter Are Descendants of Pathobionts. mSystems 6 (2), e00258-21 (2021)

Faktorová, D.; Nisbet, R.; Fernández Robledo , J.; Casacuberta, E.; Sudek, L.; Allen, A.; Ares, M.; Balestreri, C.; Barbrook, A.; Beardslee, P. et al.; Bender, S.; Booth, D.; Bouget, Y.-F.; Bowler, C.; Breglia, S.; Brownlee, C.; Burger, G.; Cerutti, H.; Cesaroni, R.; Chiurillo, M.; Clemente, T.; Coles, D.; Collier, J.; Cooney, E.; Coyne, K.; Docampo, R.; Dupont, C.; Edgcomb, V.; Einarsson, E.; Elustondo, P.; Federici, F.; Freire-Beneitez, V.; Freyria, N.; Fukuda, K.; García, P.; Girguis, P.; Gomaa, R.; Gornik, S.; Guo, J.; Hampl, V.; Hanawa, Y.; Haro-Contreras, E.; Hehenberger, E.; Highfield, A.; Hirakawa, Y.; Hopes, A.; Howe, C.; Hu, I.; Ibañez, J.; Irwin, N.; Ishii, Y.; Janowicz, N.; Jones, A.; Kachele, A.; Fujimura-Kamada, K.; Kaur, B.; Kaye, J.; Kazana, A.; Keeling, P.; King, N.; Klobutcher, L.; Lander, N.; Lassadi, I.; Li, Z.; Lin, S.; Lozano, J.-C.; Luan, F.; Maruyama, S.; Matute, T.; Miceli, C.; Minagawa, J.; Moosburner, M.; Najle, S.; Nanjappa, D.; Nimmo, I.; Noble, L.; Novák Vanclová, A.; Nowacki, M.; Nuñez, I.; Pain, A.; Piersanti, A.; Pucciarelli, S.; Pyrih, J.; Rest, J.; Rius, M.; Robertson, D.; Ruaud, A.; Ruiz-Trillo, I.; Sigg, M.; Silver, P.; Slamovits, C.; Smith, G.; Sprecher, B.; Stern, R.; Swart, E.; Tsaousis, A.; Tsypin, L.; Turkewitz, A.; Turnšek, J.; Valach, M.; Vergé, V.; von Dassow, P.; von der Haar, T.; Waller, R.; Wang, L.; Wen, X.; Wheeler, G.; Woods, A.; Zhang, H.; Mock, T.; Worden, A.; Lukeš, J.: Publisher Correction: Genetic tool development in marine protists: emerging model organisms for experimental cell biology. Nature Methods 17 (5), 551 (2020)

Faktorová, D.; Nisbet, R.; Fernández Robledo , J.; Casacuberta, E.; Sudek, L.; Allen, A.; Ares, M.; Balestreri, C.; Barbrook, A.; Beardslee, P. et al.; Bender, S.; Booth, D.; Bouget, Y.-F.; Bowler, C.; Breglia, S.; Brownlee, C.; Burger, G.; Cerutti, H.; Cesaroni, R.; Chiurillo, M.; Clemente, T.; Coles, D.; Collier, J.; Cooney, E.; Coyne, K.; Docampo, R.; Dupont, C.; Edgcomb, V.; Einarsson, E.; Elustondo, P.; Federici, F.; Freire-Beneitez, V.; Freyria, N.; Fukuda, K.; García, P.; Girguis, P.; Gomaa, R.; Gornik, S.; Guo, J.; Hampl, V.; Hanawa, Y.; Haro-Contreras, E.; Hehenberger, E.; Highfield, A.; Hirakawa, Y.; Hopes, A.; Howe, C.; Hu, I.; Ibañez, J.; Irwin, N.; Ishii, Y.; Janowicz, N.; Jones, A.; Kachele, A.; Fujimura-Kamada, K.; Kaur, B.; Kaye, J.; Kazana, A.; Keeling, P.; King, N.; Klobutcher, L.; Lander, N.; Lassadi, I.; Li, Z.; Lin, S.; Lozano, J.-C.; Luan, F.; Maruyama, S.; Matute, T.; Miceli, C.; Minagawa, J.; Moosburner, M.; Najle, S.; Nanjappa, D.; Nimmo, I.; Noble, L.; Novák Vanclová, A.; Nowacki, M.; Nuñez, I.; Pain, A.; Piersanti, A.; Pucciarelli, S.; Pyrih, J.; Rest, J.; Rius, M.; Robertson, D.; Ruaud, A.; Ruiz-Trillo, I.; Sigg, M.; Silver, P.; Slamovits, C.; Smith, G.; Sprecher, B.; Stern, R.; Swart, E.; Tsaousis, A.; Tsypin, L.; Turkewitz, A.; Turnšek, J.; Valach, M.; Vergé, V.; von Dassow, P.; von der Haar, T.; Waller, R.; Wang, L.; Wen, X.; Wheeler, G.; Woods, A.; Zhang, H.; Mock, T.; Worden, A.; Lukeš, J.: Genetic tool development in marine protists: emerging model organisms for experimental cell biology. Nature Methods 17 (5), pp. 481 - 494 (2020)

Ruaud, A.; Esquivel-Elizondo, S.; de la Cuesta-Zuluaga, J.; Waters, J.; Angenent, L.; Youngblut, N.; Ley, R.: Syntrophy via Interspecies H2 Transfer between Christensenella and Methanobrevibacter Underlies Their Global Cooccurrence in the Human Gut. mBio 11 (1), e03235-19 (2020)

Poole, A.; Goodrich, J.; Youngblut, N.; Luque, G.; Ruaud, A.; Sutter, J.; Waters, J.; Shi, Q.; El-Hadidi, M.; Johnson, L. et al.; Bar, H.; Huson, D.; Booth, J.; Ley, R.: Human Salivary Amylase Gene Copy Number Impacts Oral and Gut Microbiomes. Cell Host & Microbe 25 (4), pp. 553 - 564 (2019)

Fitzstevens, L.; Liu, X.; Ruaud, A.; Schmidt, V.; Mbong Ngwese, M.; Youngblut, N.; Rauch, J.; Suzuki, T.; Ha, N.; Arzamasov, A. et al.; Rodionov, D.; Pfister, N.; Thams, N.; Adegbite, B.; Zinsou, J.; Esen, M.; Velavan, T.; Adegnika, A.; Song, L.; Kremsner, P.; Ostermann, A.; Tyakht, A.; Ley, R.: Bifidobacteria compensate for genotype in lactose tolerance. 75th Mosbacher Kolloquium "The Microbiome - from Understanding to Modulation", Mosbach, Germany (2024)

Fitzstevens, L.; Liu, X.; Ruaud, A.; Schmidt, V.; Mbong, M.; Rauch, J.; Nguyen Thu, H.; Adegbite, B.; Zinsou, J.; Esen, M. et al.; Velavan, T.; Adegnika, A.; Song, L.; Kremsner, P.; Youngblut, N.; Tyakht, A.; Ley, R.: Bifidobacteria confer microbiome-acquired lactose tolerance in genetically lactase-non persistent humansrts. 3rd International Conference Controlling Microbes to Fight Infections (CMFI 2023), Tübingen, Germany (2023)

Ruaud, A.; Pfister, N.; Ley, R.; Youngblut, N.: Enhancing the application of machine learning models to microbiome data with endoR. Cell Symposia: Infection Biology in the Age of the Microbiome, Paris, France (2023)

Ruaud, A.; Pfister, N.; Ley, R.; Youngblut, N.: Interpretation of Tree Ensemble Machine Learning Models with EndoR. World Microbe Forum 2021 (2021)