Hassan Salem, Eugen Bauer, Anja S. Strauss, Heiko Vogel, Manja Marz, Martin Kaltenpoth (2014). "Vitamin supplementation by gut symbionts ensures metabolic homeostasis in an insect host" Proceedings of the Royal Society B: Biological Sciences. 281(1796).
Felipe C. Wouters, Michael Reichelt, Gaetan Glauser, Eugen Bauer, Matthias Erb, Jonathan Gershenzon, Daniel G. Vassao (2014). "Reglucosylation of the Benzoxazinoid DIMBOA with Inversion of Stereochemical Configuration is a Detoxification Strategy in Lepidopteran Herbivores" Angewandte Chemie International Edition. 53(42).
Eugen Bauer, Hassan Salem, Manja Marz, Heiko Vogel, Martin Kaltenpoth (2014). "Transcriptomic Immune Response of the Cotton Stainer Dysdercus fasciatus to Experimental Elimination of Vitamin-Supplementing Intestinal Symbionts" PLoS ONE. 9(12).
Eugen Bauer, Niclas Lampert, Aram Mikaelyan, Tim Kohler, Kiyoto Maekawa, Andreas Brune (2014). "Physicochemical conditions, metabolites, and community structure of the bacterial microbiota in the gut of wood-feeding cockroaches (Blaberidae: Panesthiinae)" FEMS Microbiology. 91(2).
Eugen Bauer, Cedric C. Laczny, Stefania Magnusdottir, Paul Wilmes, Ines Thiele (2015). "Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires" Microbiome. 3(1).
Ali Ebrahim, Eivind Almaas, Eugen Bauer, Aarash Bordbar, Anthony P Burgard, Roger L Chang, Andreas Drager, Imam Famili, Adam M Feist, Ronan M. T. Fleming, Stephen S Fong, Vassily Hatzimanikatis, Markus J Herrgard, Allen Holder, Michael Hucka, Daniel Hyduke, Neema Jamshidi, Sang Yup Lee, Nicolas Le Novere, Joshua A Lerman, Nathan E Lewis, Ding Ma, Radhakrishnan Mahadevan, Costas Maranas, Harish Nagarajan, Ali Navid, Jens Nielsen, Lars K Nielsen, Juan Nogales, Alberto Noronha, Csaba Pal, Bernhard O Palsson, Jason A Papin, Kiran R Patil, Nathan D Price, Jennifer L Reed, Michael Saunders, Ryan S Senger, Nikolaus Sonnenschein, Yuekai Sun, Ines Thiele (2015). "Do genome‐scale models need exact solvers or clearer standards?" Molecular systems biology. 11(10).
Hassan Salem, Thomas O. Onchuru, Eugen Bauer, Martin Kaltenpoth. (2015). "Symbiont transmission entails the risk of parasite infection" Biology letters. 11(12).
Stefania Magnusdottir, Almut Heinken, Laura Kutt, Dmitry A. Ravcheev, Eugen Bauer, Alberto Noronha, Kacy Greenhalgh, Christian Jaeger, Joanna Baginska, Paul Wilmes, Ronan M. T. Fleming, Ines Thiele. (2016). "Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota" Nature Biotechnology. 35(1).
Eugen Bauer, Johannes Zimmermann, Federico Baldini, Ines Thiele, Christoph Kaleta. (2017). "BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities" PLoS Computational Biology. 13(5).
Hassan Salem, Eugen Bauer, Roy Kirsch, Aileen Berasategui, Michael Cripps, Benjamin Weiss, Ryuichi Koga, Kayoko Fukumori, Heiko Vogel, Takema Fukatsu, Martin Kaltenpoth. (2017). "Drastic Genome Reduction in an Herbivore’s Pectinolytic Symbiont" Cell. 171(7).
Eugen Bauer, Ines Thiele. (2018). "From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota" mSystems. 3(3).
Eugen Bauer, Ines Thiele. (2018). "From metagenomic data to personalized computational microbiotas: Predicting dietary supplements for Crohns disease." NPG Systems Biology and Applications. 4(1).
Sayane Shome, R Gonzalo Parra, Nazeefa Fatima, Alexander Miguel Monzon, Bart Cuypers, Yumna Moosa, Nilson Da Rocha Coimbra, Juliana Assis, Carla Giner-Delgado, Handan Melike Dönertaş, Yesid Cuesta-Astroz, Geetha Saarunya, Imane Allali, Shruti Gupta, Ambuj Srivastava, Manisha Kalsan, Catalina Valdivia, Gabriel J Olguin-Orellana, Sofia Papadimitriou, Daniele Parisi, Nikolaj Pagh Kristensen, Leonor Rib, Marouen Ben Guebila, Eugen Bauer, Gaia Zaffaroni, Amel Bekkar, Efejiro Ashano, Lisanna Paladin, Marco Necci, Nicolás N Moreyra, Martin Rydén, Jordan Villalobos-Solís, Nikolaos Papadopoulos, Candice Rafael, Tülay Karakulak, Yasin Kaya, Yvonne Gladbach, Sandeep Kumar Dhanda, Nikolina Šoštarić, Aishwarya Alex, Dan DeBlasio, Farzana Rahman (2019). "Global network of computational biology communities: ISCBs Regional Student Groups breaking barriers" F1000Research. 8.
Eugen Bauer, Martin Kaltenpoth, Hassan Salem. (2020). "Minimal fermentative metabolism fuels extracellular symbiont in a leaf beetle." The ISME Journal. 14(3).
Frank Reis, Roy Kirsch, Yannick Pauchet, Eugen Bauer, Lisa Carolin Bilz, Kayoko Fukumori, Takema Fukatsu, Gregor Kölsch, and Martin Kaltenpoth. (2020). "Bacterial symbionts support larval sap feeding and adult folivory in (semi-) aquatic reed beetles." Nature Communications. 11(1), 1-15.
Julian Kiefer, Suvdanselengee Batsukh, Eugen Bauer, Bin Hirota, Benjamin Weiss, Jurgen Wierz, Takema Fukatsu, Martin Kaltenpoth, and Tobias Engl. "Inhibition of a nutritional endosymbiont by glyphosate abolishes mutualistic benefit on cuticle synthesis in Oryzaephilus surinamensis." Communications biology. 4(1), 554.
Julian Kiefer, Eugen Bauer, Genta Okude, Takema Fukatsu, Martin Kaltenpoth, and Tobias Engl. "Cuticle supplementation and nitrogen recycling by a dual bacterial symbiosis in a family of xylophagous beetles." The ISME Journal. 17(7), 1029-1039.
Anna Michalik, Eugen Bauer, Teresa Szklarzewicz, and Martin Kaltenpoth. "Nutrient supplementation by genome-eroded Burkholderia symbionts of scale insects." The ISME Journal. 17(12), 2221-2231.