Search Results - "Wirbel, Jakob"

Identifying temporal and spatial patterns of variation from multimodal data using MEFISTO by Velten, Britta, Braunger, Jana M., Argelaguet, Ricard, Arnol, Damien, Wirbel, Jakob, Bredikhin, Danila, Zeller, Georg, Stegle, Oliver

“…Factor analysis is a widely used method for dimensionality reduction in genome biology, with applications from personalized health to single-cell biology…”
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Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox by Wirbel, Jakob, Zych, Konrad, Essex, Morgan, Karcher, Nicolai, Kartal, Ece, Salazar, Guillem, Bork, Peer, Sunagawa, Shinichi, Zeller, Georg

“…The human microbiome is increasingly mined for diagnostic and therapeutic biomarkers using machine learning (ML). However, metagenomics-specific software is…”
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Extensive transmission of microbes along the gastrointestinal tract by Schmidt, Thomas Sb, Hayward, Matthew R, Coelho, Luis P, Li, Simone S, Costea, Paul I, Voigt, Anita Y, Wirbel, Jakob, Maistrenko, Oleksandr M, Alves, Renato Jc, Bergsten, Emma, de Beaufort, Carine, Sobhani, Iradj, Heintz-Buschart, Anna, Sunagawa, Shinichi, Zeller, Georg, Wilmes, Paul, Bork, Peer

“…The gastrointestinal tract is abundantly colonized by microbes, yet the translocation of oral species to the intestine is considered a rare aberrant event, and…”
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Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer by Wirbel, Jakob, Pyl, Paul Theodor, Kartal, Ece, Zych, Konrad, Kashani, Alireza, Milanese, Alessio, Fleck, Jonas S., Voigt, Anita Y., Palleja, Albert, Ponnudurai, Ruby, Sunagawa, Shinichi, Coelho, Luis Pedro, Schrotz-King, Petra, Vogtmann, Emily, Habermann, Nina, Niméus, Emma, Thomas, Andrew M., Manghi, Paolo, Gandini, Sara, Serrano, Davide, Mizutani, Sayaka, Shiroma, Hirotsugu, Shiba, Satoshi, Shibata, Tatsuhiro, Yachida, Shinichi, Yamada, Takuji, Waldron, Levi, Naccarati, Alessio, Segata, Nicola, Sinha, Rashmi, Ulrich, Cornelia M., Brenner, Hermann, Arumugam, Manimozhiyan, Bork, Peer, Zeller, Georg

“…Association studies have linked microbiome alterations with many human diseases. However, they have not always reported consistent results, thereby…”
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Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation by Thomas, Andrew Maltez, Manghi, Paolo, Asnicar, Francesco, Pasolli, Edoardo, Armanini, Federica, Zolfo, Moreno, Beghini, Francesco, Manara, Serena, Karcher, Nicolai, Pozzi, Chiara, Gandini, Sara, Serrano, Davide, Tarallo, Sonia, Francavilla, Antonio, Gallo, Gaetano, Trompetto, Mario, Ferrero, Giulio, Mizutani, Sayaka, Shiroma, Hirotsugu, Shiba, Satoshi, Shibata, Tatsuhiro, Yachida, Shinichi, Yamada, Takuji, Wirbel, Jakob, Schrotz-King, Petra, Ulrich, Cornelia M., Brenner, Hermann, Arumugam, Manimozhiyan, Bork, Peer, Zeller, Georg, Cordero, Francesca, Dias-Neto, Emmanuel, Setubal, João Carlos, Tett, Adrian, Pardini, Barbara, Rescigno, Maria, Waldron, Levi, Naccarati, Alessio, Segata, Nicola

“…Several studies have investigated links between the gut microbiome and colorectal cancer (CRC), but questions remain about the replicability of biomarkers…”
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A realistic benchmark for differential abundance testing and confounder adjustment in human microbiome studies by Wirbel, Jakob, Essex, Morgan, Forslund, Sofia Kirke, Zeller, Georg

“…In microbiome disease association studies, it is a fundamental task to test which microbes differ in their abundance between groups. Yet, consensus on suitable…”
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Phosphoproteomics-Based Profiling of Kinase Activities in Cancer Cells by Wirbel, Jakob, Cutillas, Pedro, Saez-Rodriguez, Julio

“…Cellular signaling, predominantly mediated by phosphorylation through protein kinases, is found to be deregulated in most cancers. Accordingly, protein kinases…”
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Depression and fatigue in active IBD from a microbiome perspective—a Bayesian approach to faecal metagenomics by Thomann, Anne Kerstin, Wüstenberg, Torsten, Wirbel, Jakob, Knoedler, Laura-Louise, Thomann, Philipp Arthur, Zeller, Georg, Ebert, Matthias Philip, Lis, Stefanie, Reindl, Wolfgang

“…Abstract Background Extraintestinal symptoms are common in inflammatory bowel diseases (IBD) and include depression and fatigue. These are highly prevalent…”
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Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments by Ruscheweyh, Hans-Joachim, Milanese, Alessio, Paoli, Lucas, Karcher, Nicolai, Clayssen, Quentin, Keller, Marisa Isabell, Wirbel, Jakob, Bork, Peer, Mende, Daniel R, Zeller, Georg, Sunagawa, Shinichi

“…Taxonomic profiling is a fundamental task in microbiome research that aims to detect and quantify the relative abundance of microorganisms in biological…”
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Calorie restriction improves metabolic state independently of gut microbiome composition: a randomized dietary intervention trial by Sowah, Solomon A, Milanese, Alessio, Schübel, Ruth, Wirbel, Jakob, Kartal, Ece, Johnson, Theron S, Hirche, Frank, Grafetstätter, Mirja, Nonnenmacher, Tobias, Kirsten, Romy, López-Nogueroles, Marina, Lahoz, Agustín, Schwarz, Kathrin V, Okun, Jürgen G, Ulrich, Cornelia M, Nattenmüller, Johanna, von Eckardstein, Arnold, Müller, Daniel, Stangl, Gabriele I, Kaaks, Rudolf, Kühn, Tilman, Zeller, Georg

“…The gut microbiota has been suggested to play a significant role in the development of overweight and obesity. However, the effects of calorie restriction on…”
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Location and condition based reconstruction of colon cancer microbiome from human RNA sequencing data by Sambruni, Gaia, Macandog, Angeli D, Wirbel, Jakob, Cagnina, Danilo, Catozzi, Carlotta, Dallavilla, Tiziano, Borgo, Francesca, Fazio, Nicola, Fumagalli-Romario, Uberto, Petz, Wanda L, Manzo, Teresa, Ravenda, Simona P, Zeller, Georg, Nezi, Luigi, Schaefer, Martin H

“…The association between microbes and cancer has been reported repeatedly; however, it is not clear if molecular tumour properties are connected to specific…”
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Red Blood Cells Preconditioned with Hemin Are Less Permissive to Plasmodium Invasion In Vivo and In Vitro by Gaudreault, Véronique, Wirbel, Jakob, Jardim, Armando, Rohrbach, Petra, Scorza, Tatiana

“…Malaria is a parasitic disease that causes severe hemolytic anemia in Plasmodium-infected hosts, which results in the release and accumulation of oxidized heme…”
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Prediction of combination therapies based on topological modeling of the immune signaling network in multiple sclerosis by Bernardo-Faura, Marti, Rinas, Melanie, Wirbel, Jakob, Pertsovskaya, Inna, Pliaka, Vicky, Messinis, Dimitris E, Vila, Gemma, Sakellaropoulos, Theodore, Faigle, Wolfgang, Stridh, Pernilla, Behrens, Janina R, Olsson, Tomas, Martin, Roland, Paul, Friedemann, Alexopoulos, Leonidas G, Villoslada, Pablo, Saez-Rodriguez, Julio

“…Multiple sclerosis (MS) is a major health problem, leading to a significant disability and patient suffering. Although chronic activation of the immune system…”
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Metabolic models predict bacterial passengers in colorectal cancer by Garza, Daniel R, Taddese, Rahwa, Wirbel, Jakob, Zeller, Georg, Boleij, Annemarie, Huynen, Martijn A, Dutilh, Bas E

“…Colorectal cancer (CRC) is a complex multifactorial disease. Increasing evidence suggests that the microbiome is involved in different stages of CRC initiation…”
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Unravelling the collateral damage of antibiotics on gut bacteria by Maier, Lisa, Goemans, Camille V., Wirbel, Jakob, Kuhn, Michael, Eberl, Claudia, Pruteanu, Mihaela, Müller, Patrick, Garcia-Santamarina, Sarela, Cacace, Elisabetta, Zhang, Boyao, Gekeler, Cordula, Banerjee, Tisya, Anderson, Exene Erin, Milanese, Alessio, Löber, Ulrike, Forslund, Sofia K., Patil, Kiran Raosaheb, Zimmermann, Michael, Stecher, Bärbel, Zeller, Georg, Bork, Peer, Typas, Athanasios

“…Antibiotics are used to fight pathogens but also target commensal bacteria, disturbing the composition of gut microbiota and causing dysbiosis and disease 1 …”
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The journey to understand previously unknown microbial genes by Wirbel, Jakob, Bhatt, Ami S., Probst, Alexander J.

“…The analysis of DNA sequences sheds light on microbial biology, but it is difficult to assess the function of genes that have little or no similarity to…”
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A faecal microbiota signature with high specificity for pancreatic cancer by Kartal, Ece, Schmidt, Thomas S B, Molina-Montes, Esther, Rodríguez-Perales, Sandra, Wirbel, Jakob, Maistrenko, Oleksandr M, Akanni, Wasiu A, Alashkar Alhamwe, Bilal, Alves, Renato J, Carrato, Alfredo, Erasmus, Hans-Peter, Estudillo, Lidia, Finkelmeier, Fabian, Fullam, Anthony, Glazek, Anna M, Gómez-Rubio, Paulina, Hercog, Rajna, Jung, Ferris, Kandels, Stefanie, Kersting, Stephan, Langheinrich, Melanie, Márquez, Mirari, Molero, Xavier, Orakov, Askarbek, Van Rossum, Thea, Torres-Ruiz, Raul, Telzerow, Anja, Zych, Konrad, Benes, Vladimir, Zeller, Georg, Trebicka, Jonel, Real, Francisco X, Malats, Nuria, Bork, Peer

“…Recent evidence suggests a role for the microbiome in pancreatic ductal adenocarcinoma (PDAC) aetiology and progression. To explore the faecal and salivary…”
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Commensal Clostridiales strains mediate effective anti-cancer immune response against solid tumors by Montalban-Arques, Ana, Katkeviciute, Egle, Busenhart, Philipp, Bircher, Anna, Wirbel, Jakob, Zeller, Georg, Morsy, Yasser, Borsig, Lubor, Glaus Garzon, Jesus F., Müller, Anne, Arnold, Isabelle C., Artola-Boran, Mariela, Krauthammer, Michael, Sintsova, Anna, Zamboni, Nicola, Leventhal, Gabriel E., Berchtold, Laura, de Wouters, Tomas, Rogler, Gerhard, Baebler, Katharina, Schwarzfischer, Marlene, Hering, Larissa, Olivares-Rivas, Ivan, Atrott, Kirstin, Gottier, Claudia, Lang, Silvia, Boyman, Onur, Fritsch, Ralph, Manz, Markus G., Spalinger, Marianne R., Scharl, Michael

“…Despite overall success, T cell checkpoint inhibitors for cancer treatment are still only efficient in a minority of patients. Recently, intestinal microbiota…”
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Abstract A40: The SIAMCAT R package enables statistical and machine learning analyses for case-control microbiome datasets by Wirbel, Jakob, Zych, Konrad, Essex, Morgan, Karcher, Nicolai, Kartal, Ece, Salazar, Guillem, Bork, Peer, Sunagawa, Shinichi, Zeller, Georg

“…Abstract Alterations in microbiome composition have been linked to many human diseases, including colorectal cancer or precancerous liver diseases. Findings…”
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Microbiota-dependent activation of the myeloid calcineurin-NFAT pathway inhibits B7H3- and B7H4-dependent anti-tumor immunity in colorectal cancer by Peuker, Kenneth, Strigli, Anne, Tauriello, Daniele V.F., Hendricks, Alexander, von Schönfels, Witigo, Burmeister, Greta, Brosch, Mario, Herrmann, Alexander, Krüger, Sandra, Nitsche, Jessica, Južnić, Lea, Geissler, Marc Marius, Hiergeist, Andreas, Gessner, André, Wirbel, Jakob, Ponnudurai, Ruby Priyadarshini, Tunger, Antje, Wehner, Rebekka, Stange, Daniel E., Weitz, Jürgen, Aust, Daniela E., Baretton, Gustavo B., Schmitz, Marc, Röcken, Christoph, Hampe, Jochen, Hinz, Sebastian, Zeller, Georg, Chavakis, Triantafyllos, Schafmayer, Clemens, Batlle, Eduard, Zeissig, Sebastian

“…Bacterial sensing by intestinal tumor cells contributes to tumor growth through cell-intrinsic activation of the calcineurin-NFAT axis, but the role of this…”
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