Publications

You can also find my articles on my Google Scholar profile.

Preprints

• A realistic benchmark for the identification of differentially abundant taxa in (confounded) human microbiome studies
  bioRxiv (2024)
  ^{Jakob Wirbel, Morgan Essex, Sofia K Forslund, Georg Zeller}

• Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson’s disease
  bioRxiv (2023)
  ^{Stefano Romano, Jakob Wirbel, Rebecca Ansorge, Christian Schudoma, Quinten R Ducarmon, Arjan Narbad, Georg Zeller}

• ATF6 activation alters colonic lipid metabolism causing tumor-associated microbial adaptation
  bioRxiv (2023)
  ^{Olivia I Coleman, Adam Sorbie, Sandra Bierwith, Janine Kövilein, Miriam von Stern, Nikolai Köhler, Jakob Wirbel, Christina Schmidt, Tim Kacprowski, Andreas Dunkel, Josh K Pauling, Johannes Plagge, Diego Mediel-Cuadra, Sophia Wagner, Tingying Peng, Thomas Metzler, Clemens Schafmayer, Sebastian Hinz, Christian Röder, Christoph Röcken, Bärbel Stecher, Philip Rosenstiel, Katja Steiger, Moritz Jesinghaus, Gerhard Liebisch, Josef Ecker, Georg Zeller, Klaus-Peter Janssen, Dirk Haller}

• Intragenic DNA inversions expand bacterial coding capacity
  bioRxiv (2023)
  ^{Rachael B Chanin, Patrick T West, Ryan M Park, Jakob Wirbel, Gabriella ZM Green, Arjun M Miklos, Matthew O Gill, Angela S Hickey, Erin F Brooks, Ami S Bhatt}

Peer-reviewed publications

• C. difficile may be overdiagnosed in adults and is a prevalent commensal in infants
  eLife 12:RP90111 (2023)
  ^{Pamela Ferretti, Jakob Wirbel, Oleksandr M Maistrenko, Thea Van Rossum, Renato Alves, Anthony Fullam, Wasiu Akanni, Christian Schudoma, Anna Schwarz, Roman Thielemann, Leonie Thomas, Stefanie Kandels, Rajna Hercog, Anja Telzerow, Ivica Letunic, Michael Kuhn, Georg Zeller, Thomas SB Schmidt, Peer Bork}

• Location and condition based reconstruction of colon cancer microbiome from human RNA sequencing data
  Genome Medicine 15, 32 (2023)
  ^{Gaia Sambruni, Angeli D Macandog, Jakob Wirbel, Danilo Cagnina, Carlotta Catozzi, Tiziano Dallavilla, Francesca Borgo, Nicola Fazio, Uberto Fumagalli-Romario, Wanda L Petz, Teresa Manzo, Simona P Ravenda, Georg Zeller, Luigi Nezi, Martin H Schaefer}

• Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments
  Microbiome 10, 212 (2022)
  ^{Hans-Joachim Ruscheweyh, Alessio Milanese, Lucas Paoli, Nicolai Karcher, Quentin Clayssen, Marisa Isabell Keller, Jakob Wirbel, Peer Bork, Daniel R Mende, Georg Zeller, Shinichi Sunagawa}

• Depression and fatigue in active IBD from a microbiome perspective—a Bayesian approach to faecal metagenomics
  BMC Medicine 20, 366 (2022)
  ^{Anne Kerstin Thomann, Torsten Wüstenberg, Jakob Wirbel, Laura-Louise Knoedler, Philipp A Thomann, Georg Zeller, Matthias P Ebert, Stefanie Lis, Wolfgang Reindl}

• Calorie restriction improves metabolic state independently of gut microbiome composition: a randomized dietary intervention trial
  Genome Medicine 14, 30 (2022)
  ^{Solomon A Sowah, Alessio Milanese, Ruth Schübel, Jakob Wirbel, Ece Kartal, Theron S Johnson, Frank Hirche, Mirja Grafetstätter, Tobias Nonnenmacher, Romy Kirsten, Marina López-Nogueroles, Agustín Lahoz, Kathrin V Schwarz, Jürgen G Okun, Cornelia M Ulrich, Johanna Nattenmüller, Arnold von Eckardstein, Daniel Müller, Gabriele I Stangl, Rudolf Kaaks, Tilman Kühn, Georg Zeller}

• A faecal microbiota signature with high specificity for pancreatic cancer
  Gut 71:1359-1372 (2022)
  ^{Ece Kartal, Thomas SB Schmidt, Esther Molina-Montes, Sandra Rodríguez-Perales, Jakob Wirbel, Oleksandr M Maistrenko, Wasiu A Akanni, Bilal Alashkar Alhamwe, Renato J Alves, Alfredo Carrato, Hans-Peter Erasmus, Lidia Estudillo, Fabian Finkelmeier, Anthony Fullam, Anna M Glazek, Paulina Gómez-Rubio, Rajna Hercog, Ferris Jung, Stefanie Kandels, Stephan Kersting, Melanie Langheinrich, Mirari Márquez, Xavier Molero, Askarbek Orakov, Thea Van Rossum, Raul Torres-Ruiz, Anja Telzerow, Konrad Zych, Vladimir Benes, Georg Zeller, Jonel Trebicka, Francisco X Real, Nuria Malats, Peer Bork, MAGIC Study investigators, PanGenEU Study investigators}

• Microbiota-dependent activation of the myeloid calcineurin-NFAT pathway inhibits B7H3-and B7H4-dependent anti-tumor immunity in colorectal cancer
  Immunity 55, 701-717 (2022)
  ^{Kenneth Peuker, Anne Strigli, Daniele VF Tauriello, Alexander Hendricks, Witigo von Schönfels, Greta Burmeister, Mario Brosch, Alexander Herrmann, Sandra Krüger, Jessica Nitsche, Lea Južnić, Marc Marius Geissler, Andreas Hiergeist, André Gessner, Jakob Wirbel, Ruby Priyadarshini Ponnudurai, Antje Tunger, Rebekka Wehner, Daniel E Stange, Jürgen Weitz, Daniela E Aust, Gustavo B Baretton, Marc Schmitz, Christoph Röcken, Jochen Hampe, Sebastian Hinz, Georg Zeller, Triantafyllos Chavakis, Clemens Schafmayer, Eduard Batlle, Sebastian Zeissig}

• Identifying temporal and spatial patterns of variation from multimodal data using MEFISTO
  Nature Methods 19, 179-186 (2022)
  ^{Britta Velten, Jana M Braunger, Ricard Argelaguet, Damien Arnol, Jakob Wirbel, Danila Bredikhin, Georg Zeller, Oliver Stegle}

• Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox
  Genome Biology 22, 93 (2021)
  ^{Jakob Wirbel, Konrad Zych, Morgan Essex, Nicolai Karcher, Ece Kartal, Guillem Salazar, Peer Bork, Shinichi Sunagawa, Georg Zeller}

• Prediction of combination therapies based on topological modeling of the immune signaling network in Multiple Sclerosis
  Genome Medicine 13, 117 (2021)
  ^{Marti Bernardo-Faura, Melanie Rinas, Jakob Wirbel, Inna Pertsovskaya, Vicky Pliaka, Dimitris E Messinis, Gemma Vila, Theodore Sakellaropoulos, Wolfgang Faigle, Pernilla Stridh, Janina R Behrens, Tomas Olsson, Roland Martin, Friedemann Paul, Leonidas G Alexopoulos, Pablo Villoslada, Julio Saez-Rodriguez}

• Unravelling the collateral damage of antibiotics on gut bacteria
  Nature 599, 120-124 (2021)
  ^{Lisa Maier, Camille V Goemans, Jakob Wirbel, Michael Kuhn, Claudia Eberl, Mihaela Pruteanu, Patrick Müller, Sarela Garcia-Santamarina, Elisabetta Cacace, Boyao Zhang, Cordula Gekeler, Tisya Banerjee, Exene Erin Anderson, Alessio Milanese, Ulrike Löber, Sofia K Forslund, Kiran Raosaheb Patil, Michael Zimmermann, Bärbel Stecher, Georg Zeller, Peer Bork, Athanasios Typas}

• Commensal Clostridiales strains mediate effective anti-cancer immune response against solid tumors
  Cell Host & Microbe 29, 1573-1588 (2021)
  ^{Ana Montalban-Arques, Egle Katkeviciute, Philipp Busenhart, Anna Bircher, Jakob Wirbel, Georg Zeller, Yasser Morsy, Lubor Borsig, Jesus F Glaus Garzon, Anne Müller, Isabelle C Arnold, Mariela Artola-Boran, Michael Krauthammer, Anna Sintsova, Nicola Zamboni, Gabriel E Leventhal, Laura Berchtold, Tomas de Wouters, Gerhard Rogler, Katharina Baebler, Marlene Schwarzfischer, Larissa Hering, Ivan Olivares-Rivas, Kirstin Atrott, Claudia Gottier, Silvia Lang, Onur Boyman, Ralph Fritsch, Markus G Manz, Marianne R Spalinger, Michael Scharl}

• Metabolic models predict bacterial passengers in colorectal cancer
  Cancer & Metabolism 8, 1-13 (2020)
  ^{Daniel R. Garza, Rahwa Taddese, Jakob Wirbel, Georg Zeller, Annemarie Boleij, Martijn A Huynen, Bas E Dutilh}

• Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation
  Nature Medicine 25; pages 667-678 (2019)
  ^{Andrew Maltez Thomas, Paolo Manghi, Francesco Asnicar, Edoardo Pasolli, Federica Armanini, Moreno Zolfo, Francesco Beghini, Serena Manara, Nicolai Karcher, Chiara Pozzi, Sara Gandini, Davide Serrano, Sonia Tarallo, Antonio Francavilla, Gaetano Gallo, Mario Trompetto, Giulio Ferrero, Sayaka Mizutani, Hirotsugu Shiroma, Satoshi Shiba, Tatsuhiro Shibata, Shinichi Yachida, Takuji Yamada, Jakob Wirbel, Petra Schrotz-King, Cornelia M Ulrich, Hermann Brenner, Manimozhiyan Arumugam, Peer Bork, Georg Zeller, Francesca Cordero, Emmanuel Dias-Neto, João Carlos Setubal, Adrian Tett, Barbara Pardini, Maria Rescigno, Levi Waldron, Alessio Naccarati, Nicola Segata}

• Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer
  Nature Medicine 25; pages 679–689 (2019)
  ^{Jakob Wirbel, Paul Theodor Pyl, Ece Kartal, Konrad Zych, Alireza Kashani, Alessio Milanese, Jonas S Fleck, Anita Y Voigt, Albert Palleja, Ruby Ponnudurai, Shinichi Sunagawa, Luis Pedro Coelho, Petra Schrotz-King, Emily Vogtmann, Nina Habermann, Emma Niméus, Andrew M Thomas, Paolo Manghi, Sara Gandini, Davide Serrano, Sayaka Mizutani, Hirotsugu Shiroma, Satoshi Shiba, Tatsuhiro Shibata, Shinichi Yachida, Takuji Yamada, Levi Waldron, Alessio Naccarati, Nicola Segata, Rashmi Sinha, Cornelia M Ulrich, Hermann Brenner, Manimozhiyan Arumugam, Peer Bork, Georg Zeller}

• Extensive transmission of microbes along the gastrointestinal tract
  eLife 8:e42693 (2019)
  ^{Thomas SB Schmidt, Matthew R Hayward, Luis P Coelho, Simone S Li, Paul I Costea, Anita Y Voigt, Jakob Wirbel, Oleksandr M Maistrenko, Renato JC Alves, Emma Bergsten, Carine de Beaufort, Iradj Sobhani, Anna Heintz-Buschart, Shinichi Sunagawa, Georg Zeller, Paul Wilmes, Peer Bork}

• Phosphoproteomics-Based Profiling of Kinase Activities in Cancer Cells.
  Cancer Systems Biology pp 103-132 (2018)
  ^{Jakob Wirbel, Pedro Cutillas, Julio Saez-Rodriguez}

• Red Blood Cells Preconditioned with Hemin Are Less Permissive to Plasmodium Invasion In Vivo and In Vitro
  PLoS ONE 10(10): e0140805 (2015)
  ^{Véronique Gaudreault, Jakob Wirbel, Armando Jardim, Petra Rohrbach, Tatiana Scorza}