Peer Bork (Bork Peer)

ResearcherID ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 59

Top Venues

Nature

Nature communications

Nucleic acids research

Molecular systems biology

EMBL Heidelberg

University of Leipzig (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

EMBL Heidelberg

Germany

Strategic Head of Bioinformatics

EMBL Heidelberg

Germany

Joint Head of Unit, Senior Scientist :: Structural and Computational Biology

EMBL Heidelberg

Germany

Group Leader :: Structural and Computational Biology

Max Delbrück Centrum für Molekulare Medizin Berlin Buch

Germany

visiting group leader

EMBL Heidelberg

Germany

Visiting Group Leader :: Structural and Computational Biology

Education History

University of Leipzig

Germany

PHD :: Biochemistry

Publications

Ayele Argaw-Denboba, Thomas Sebastian Benedikt Schmidt, Monica Di Giacomo, Bobby Ranjan, Saravanan Devendran, Eleonora Mastrorilli, Catrin T Lloyd, Danilo Pugliese, Violetta Paribeni, Juliette Dabin, Alessandra Pisaniello, Sergio Martin Espinola, Alvaro Crevenna, Subhanita Ghosh, Neil E Humphreys, Olga Boruc, Peter Sarkies, Michael Zimmermann, Peer Bork, Jamie A Hackett
Paternal microbiome perturbations impact offspring fitness. Nature (2024)
Ayele Argaw-Denboba, Thomas Sebastian Benedikt Schmidt, Monica Di Giacomo, Bobby Ranjan, Saravanan Devendran, Eleonora Mastrorilli, Catrin T Lloyd, Danilo Pugliese, Violetta Paribeni, Juliette Dabin, Alessandra Pisaniello, Sergio Martin Espinola, Alvaro Crevenna, Subhanita Ghosh, Neil E Humphreys, Olga Boruc, Peter Sarkies, Michael Zimmermann, Peer Bork, Jamie A Hackett
Paternal microbiome perturbations impact offspring fitness. Nature 629 (8012) (2024)
Ayele Argaw-Denboba, Thomas Sebastian Benedikt Schmidt, Monica Di Giacomo, Bobby Ranjan, Saravanan Devendran, Eleonora Mastrorilli, Catrin T Lloyd, Danilo Pugliese, Violetta Paribeni, Juliette Dabin, Alessandra Pisaniello, Sergio Martin Espinola, Alvaro Crevenna, Subhanita Ghosh, Neil E Humphreys, Olga Boruc, Peter Sarkies, Michael Zimmermann, Peer Bork, Jamie A Hackett
Paternal microbiome perturbations impact offspring fitness. Nature 629 (8012) (2024)
Ayele Argaw-Denboba, Thomas Sebastian Benedikt Schmidt, Monica Di Giacomo, Bobby Ranjan, Saravanan Devendran, Eleonora Mastrorilli, Catrin T Lloyd, Danilo Pugliese, Violetta Paribeni, Juliette Dabin, Alessandra Pisaniello, Sergio Martin Espinola, Alvaro Crevenna, Subhanita Ghosh, Neil E Humphreys, Olga Boruc, Peter Sarkies, Michael Zimmermann, Peer Bork, Jamie A Hackett
Paternal microbiome perturbations impact offspring fitness. Nature 629 (8012) (2024)
Ayele Argaw-Denboba, Thomas Sebastian Benedikt Schmidt, Monica Di Giacomo, Bobby Ranjan, Saravanan Devendran, Eleonora Mastrorilli, Catrin T Lloyd, Danilo Pugliese, Violetta Paribeni, Juliette Dabin, Alessandra Pisaniello, Sergio Martin Espinola, Alvaro Crevenna, Subhanita Ghosh, Neil E Humphreys, Olga Boruc, Peter Sarkies, Michael Zimmermann, Peer Bork, Jamie A Hackett
Paternal microbiome perturbations impact offspring fitness. Nature 629 (8012) (2024)
Ayele Argaw-Denboba, Thomas Sebastian Benedikt Schmidt, Monica Di Giacomo, Bobby Ranjan, Saravanan Devendran, Eleonora Mastrorilli, Catrin T Lloyd, Danilo Pugliese, Violetta Paribeni, Juliette Dabin, Alessandra Pisaniello, Sergio Martin Espinola, Alvaro Crevenna, Subhanita Ghosh, Neil E Humphreys, Olga Boruc, Peter Sarkies, Michael Zimmermann, Peer Bork, Jamie A Hackett
Paternal microbiome perturbations impact offspring fitness. Nature 629 (8012) (2024)
Ayele Argaw-Denboba, Thomas Sebastian Benedikt Schmidt, Monica Di Giacomo, Bobby Ranjan, Saravanan Devendran, Eleonora Mastrorilli, Catrin T Lloyd, Danilo Pugliese, Violetta Paribeni, Juliette Dabin, Alessandra Pisaniello, Sergio Martin Espinola, Alvaro Crevenna, Subhanita Ghosh, Neil E Humphreys, Olga Boruc, Peter Sarkies, Michael Zimmermann, Peer Bork, Jamie A Hackett
Paternal microbiome perturbations impact offspring fitness. Nature (2024)
Ayele Argaw-Denboba, Thomas Sebastian Benedikt Schmidt, Monica Di Giacomo, Bobby Ranjan, Saravanan Devendran, Eleonora Mastrorilli, Catrin T Lloyd, Danilo Pugliese, Violetta Paribeni, Juliette Dabin, Alessandra Pisaniello, Sergio Martin Espinola, Alvaro Crevenna, Subhanita Ghosh, Neil E Humphreys, Olga Boruc, Peter Sarkies, Michael Zimmermann, Peer Bork, Jamie A Hackett
Paternal microbiome perturbations impact offspring fitness. Nature 629 (8012) (2024)
Yiqian Duan, Santos-Júnior Célio Dias, Thomas Sebastian Benedikt Schmidt, Anthony Fullam, Breno L S de Almeida, Chengkai Zhu, Michael Kuhn, Xing-Ming Zhao, Peer Bork, Luis Pedro Coelho
A catalog of small proteins from the global microbiome. Nature communications 15 (1) (2024)
Ayele Argaw-Denboba, Thomas Sebastian Benedikt Schmidt, Monica Di Giacomo, Bobby Ranjan, Saravanan Devendran, Eleonora Mastrorilli, Catrin T Lloyd, Danilo Pugliese, Violetta Paribeni, Juliette Dabin, Alessandra Pisaniello, Sergio Martin Espinola, Alvaro Crevenna, Subhanita Ghosh, Neil E Humphreys, Olga Boruc, Peter Sarkies, Michael Zimmermann, Peer Bork, Jamie A Hackett
Paternal microbiome perturbations impact offspring fitness. Nature 629 (8012) (2024)
Senying Lai, Huarui Wang, Peer Bork, Wei-Hua Chen, Xing-Ming Zhao
Long-read sequencing reveals extensive gut phageome structural variations driven by genetic exchange with bacterial hosts. Science advances 10 (33) (2024)
Ayele Argaw-Denboba, Thomas Sebastian Benedikt Schmidt, Monica Di Giacomo, Bobby Ranjan, Saravanan Devendran, Eleonora Mastrorilli, Catrin T Lloyd, Danilo Pugliese, Violetta Paribeni, Juliette Dabin, Alessandra Pisaniello, Sergio Martin Espinola, Alvaro Crevenna, Subhanita Ghosh, Neil E Humphreys, Olga Boruc, Peter Sarkies, Michael Zimmermann, Peer Bork, Jamie A Hackett
Paternal microbiome perturbations impact offspring fitness. Nature 629 (8012) (2024)
Ayele Argaw-Denboba, Thomas Sebastian Benedikt Schmidt, Monica Di Giacomo, Bobby Ranjan, Saravanan Devendran, Eleonora Mastrorilli, Catrin T Lloyd, Danilo Pugliese, Violetta Paribeni, Juliette Dabin, Alessandra Pisaniello, Sergio Martin Espinola, Alvaro Crevenna, Subhanita Ghosh, Neil E Humphreys, Olga Boruc, Peter Sarkies, Michael Zimmermann, Peer Bork, Jamie A Hackett
Paternal microbiome perturbations impact offspring fitness. Nature (2024)
Senying Lai, Huarui Wang, Peer Bork, Wei-Hua Chen, Xing-Ming Zhao
Long-read sequencing reveals extensive gut phageome structural variations driven by genetic exchange with bacterial hosts. Science advances 10 (33) (2024)
Janaina Rigonato, Marko Budinich, Alejandro A Murillo, Manoela C Brandão, Juan J Pierella Karlusich, Yawouvi Dodji Soviadan, Ann C Gregory, Hisashi Endo, Florian Kokoszka, Dean Vik, Nicolas Henry, Paul Frémont, Karine Labadie, Ahmed A Zayed, Céline Dimier, Marc Picheral, Sarah Searson, Julie Poulain, Stefanie Kandels, Stéphane Pesant, Eric Karsenti, null null, Peer Bork, Chris Bowler, Colomban de Vargas, Damien Eveillard, Marion Gehlen, Daniele Iudicone, Fabien Lombard, Hiroyuki Ogata, Lars Stemmann, Matthew B Sullivan, Shinichi Sunagawa, Patrick Wincker, Samuel Chaffron, Olivier Jaillon
Ocean-wide comparisons of mesopelagic planktonic community structures. ISME communications 3 (1) (2023)
Katherine M Kennedy, Marcus C de Goffau, Maria Elisa Perez-Munoz, Marie-Claire Arrieta, Fredrik Bäckhed, Peer Bork, Thorsten Braun, Frederic D Bushman, Joel Dore, Willem M de Vos, Ashlee M Earl, Jonathan A Eisen, Michal A Elovitz, Stephanie Christine Ganal-Vonarburg, Michael G Gaenzle, Wendy S Garrett, Lindsay J Hall, Mathias W Hornef, Curtis Huttenhower, Liza Konnikova, Sarah Lebeer, Andrew J Macpherson, Ruth C Massey, Alice Carolyn McHardy, Omry Koren, Trevor D Lawley, Ruth E Ley, Corina M Berset, Paul W O' Toole, Eric G Pamer, Julian Parkhill, Jeroen Raes, Thomas Rattei, Anne Salonen, Eran Segal, Nicola Segata, Fergus Shanahan, Deborah M Sloboda, Gordon C S Smith, Harry Sokol, Timothy D Spector, Michael G Surette, Gerald W Tannock, Alan William Walker, Moran Yassour, Jens Walter
Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature 613 (7945) (2023)
Katherine M Kennedy, Marcus C de Goffau, Maria Elisa Perez-Munoz, Marie-Claire Arrieta, Fredrik Bäckhed, Peer Bork, Thorsten Braun, Frederic D Bushman, Joel Dore, Willem M de Vos, Ashlee M Earl, Jonathan A Eisen, Michal A Elovitz, Stephanie Christine Ganal-Vonarburg, Michael G Gaenzle, Wendy S Garrett, Lindsay J Hall, Mathias W Hornef, Curtis Huttenhower, Liza Konnikova, Sarah Lebeer, Andrew J Macpherson, Ruth C Massey, Alice Carolyn McHardy, Omry Koren, Trevor D Lawley, Ruth E Ley, Corina M Berset, Paul W O' Toole, Eric G Pamer, Julian Parkhill, Jeroen Raes, Thomas Rattei, Anne Salonen, Eran Segal, Nicola Segata, Fergus Shanahan, Deborah M Sloboda, Gordon C S Smith, Harry Sokol, Timothy D Spector, Michael G Surette, Gerald W Tannock, Alan William Walker, Moran Yassour, Jens Walter
Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature 613 (7945) (2023)
Katherine M Kennedy, Marcus C de Goffau, Maria Elisa Perez-Munoz, Marie-Claire Arrieta, Fredrik Bäckhed, Peer Bork, Thorsten Braun, Frederic D Bushman, Joel Dore, Willem M de Vos, Ashlee M Earl, Jonathan A Eisen, Michal A Elovitz, Stephanie Christine Ganal-Vonarburg, Michael G Gaenzle, Wendy S Garrett, Lindsay J Hall, Mathias W Hornef, Curtis Huttenhower, Liza Konnikova, Sarah Lebeer, Andrew J Macpherson, Ruth C Massey, Alice Carolyn McHardy, Omry Koren, Trevor D Lawley, Ruth E Ley, Corina M Berset, Paul W O' Toole, Eric G Pamer, Julian Parkhill, Jeroen Raes, Thomas Rattei, Anne Salonen, Eran Segal, Nicola Segata, Fergus Shanahan, Deborah M Sloboda, Gordon C S Smith, Harry Sokol, Timothy D Spector, Michael G Surette, Gerald W Tannock, Alan William Walker, Moran Yassour, Jens Walter
Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature 613 (7945) (2023)
Katherine M Kennedy, Marcus C de Goffau, Maria Elisa Perez-Munoz, Marie-Claire Arrieta, Fredrik Bäckhed, Peer Bork, Thorsten Braun, Frederic D Bushman, Joel Dore, Willem M de Vos, Ashlee M Earl, Jonathan A Eisen, Michal A Elovitz, Stephanie Christine Ganal-Vonarburg, Michael G Gaenzle, Wendy S Garrett, Lindsay J Hall, Mathias W Hornef, Curtis Huttenhower, Liza Konnikova, Sarah Lebeer, Andrew J Macpherson, Ruth C Massey, Alice Carolyn McHardy, Omry Koren, Trevor D Lawley, Ruth E Ley, Corina M Berset, Paul W O' Toole, Eric G Pamer, Julian Parkhill, Jeroen Raes, Thomas Rattei, Anne Salonen, Eran Segal, Nicola Segata, Fergus Shanahan, Deborah M Sloboda, Gordon C S Smith, Harry Sokol, Timothy D Spector, Michael G Surette, Gerald W Tannock, Alan William Walker, Moran Yassour, Jens Walter
Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature 613 (7945) (2023)
Katherine M Kennedy, Marcus C de Goffau, Maria Elisa Perez-Munoz, Marie-Claire Arrieta, Fredrik Bäckhed, Peer Bork, Thorsten Braun, Frederic D Bushman, Joel Dore, Willem M de Vos, Ashlee M Earl, Jonathan A Eisen, Michal A Elovitz, Stephanie Christine Ganal-Vonarburg, Michael G Gaenzle, Wendy S Garrett, Lindsay J Hall, Mathias W Hornef, Curtis Huttenhower, Liza Konnikova, Sarah Lebeer, Andrew J Macpherson, Ruth C Massey, Alice Carolyn McHardy, Omry Koren, Trevor D Lawley, Ruth E Ley, Corina M Berset, Paul W O' Toole, Eric G Pamer, Julian Parkhill, Jeroen Raes, Thomas Rattei, Anne Salonen, Eran Segal, Nicola Segata, Fergus Shanahan, Deborah M Sloboda, Gordon C S Smith, Harry Sokol, Timothy D Spector, Michael G Surette, Gerald W Tannock, Alan William Walker, Moran Yassour, Jens Walter
Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature 613 (7945) (2023)
Santos-Júnior Célio Dias, Marcelo Der Torossian Torres, Yiqian Duan, Rodríguez Del Río Álvaro, Thomas Sebastian Benedikt Schmidt, Chong Hui, Anthony Fullam, Michael Kuhn, Zhu Chengkai, Houseman Amy, Somborski Jelena, Vines Anna, Xing-Ming Zhao, Peer Bork, Huerta-Cepas Jaime, de la Fuente-Nunez Cesar, Luis Pedro Coelho
Computational exploration of the global microbiome for antibiotic discovery. bioRxiv : the preprint server for biology (2023)
Katherine M Kennedy, Marcus C de Goffau, Maria Elisa Perez-Munoz, Marie-Claire Arrieta, Fredrik Bäckhed, Peer Bork, Thorsten Braun, Frederic D Bushman, Joel Dore, Willem M de Vos, Ashlee M Earl, Jonathan A Eisen, Michal A Elovitz, Stephanie Christine Ganal-Vonarburg, Michael G Gaenzle, Wendy S Garrett, Lindsay J Hall, Mathias W Hornef, Curtis Huttenhower, Liza Konnikova, Sarah Lebeer, Andrew J Macpherson, Ruth C Massey, Alice Carolyn McHardy, Omry Koren, Trevor D Lawley, Ruth E Ley, Corina M Berset, Paul W O' Toole, Eric G Pamer, Julian Parkhill, Jeroen Raes, Thomas Rattei, Anne Salonen, Eran Segal, Nicola Segata, Fergus Shanahan, Deborah M Sloboda, Gordon C S Smith, Harry Sokol, Timothy D Spector, Michael G Surette, Gerald W Tannock, Alan William Walker, Moran Yassour, Jens Walter
Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature 613 (7945) (2023)
Sander Wuyts, Renato Jc Alves, Maria Zimmermann-Kogadeeva, Suguru Nishijima, Sonja Blasche, Marja Driessen, Philipp E Geyer, Rajna Hercog, Ece Kartal, Lisa Maier, Johannes B Müller, Sarela Garcia Santamarina, Thomas Sebastian Benedikt Schmidt, Daniel C Sevin, Anja Telzerow, Peter V Treit, Tobias Wenzel, Athanasios Typas, Kiran Raosaheb Patil, Matthias Mann, Michael Kuhn, Peer Bork
Consistency across multi-omics layers in a drug-perturbed gut microbial community. Molecular systems biology (2023)
Petros Andrikopoulos, Judith Aron-Wisnewsky, Rima Chakaroun, Antonis Myridakis, Sofia Kirke Forslund-Startceva, Trine Nielsen, Solia Adriouch, Bridget Holmes, Julien Chilloux, Sara Vieira-Silva, Gwen Falony, Joe-Elie Salem, Fabrizio Andreelli, Eugeni Belda, Julius Kieswich, Kanta Chechi, Francesc Puig-Castellví, Mickael Chevalier, Emmanuelle Le Chatelier, Michael T Olanipekun, Lesley Hoyles, Renato Jc Alves, Gerard Helft, Richard Isnard, Lars Valeur Køber, Luis Pedro Coelho, Christine Rouault, Dominique Gauguier, Jens Peter Gøtze, Edi Prifti, Philippe Froguel, null null, Jean-Daniel Zucker, Fredrik Bäckhed, Henrik Vestergaard, Torben Hansen, Jean-Michel Oppert, Matthias Blüher, Jens Nielsen, Jeroen Raes, Peer Bork, Muhammad M Yaqoob, Michael Stumvoll, Oluf Pedersen, S Dusko Ehrlich, Karine Clément, Marc Emmanuel Dumas
Evidence of a causal and modifiable relationship between kidney function and circulating trimethylamine N-oxide. Nature communications 14 (1) (2023)
Katherine M Kennedy, Marcus C de Goffau, Maria Elisa Perez-Munoz, Marie-Claire Arrieta, Fredrik Bäckhed, Peer Bork, Thorsten Braun, Frederic D Bushman, Joel Dore, Willem M de Vos, Ashlee M Earl, Jonathan A Eisen, Michal A Elovitz, Stephanie Christine Ganal-Vonarburg, Michael G Gaenzle, Wendy S Garrett, Lindsay J Hall, Mathias W Hornef, Curtis Huttenhower, Liza Konnikova, Sarah Lebeer, Andrew J Macpherson, Ruth C Massey, Alice Carolyn McHardy, Omry Koren, Trevor D Lawley, Ruth E Ley, Corina M Berset, Paul W O' Toole, Eric G Pamer, Julian Parkhill, Jeroen Raes, Thomas Rattei, Anne Salonen, Eran Segal, Nicola Segata, Fergus Shanahan, Deborah M Sloboda, Gordon C S Smith, Harry Sokol, Timothy D Spector, Michael G Surette, Gerald W Tannock, Alan William Walker, Moran Yassour, Jens Walter
Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature 613 (7945) (2023)
Thomas Sebastian Benedikt Schmidt, Anthony Fullam, Pamela Ferretti, Askarbek Orakov, Oleksandr M Maistrenko, Hans-Joachim Ruscheweyh, Ivica Letunic, Yiqian Duan, Thea Van Rossum, Shinichi Sunagawa, Daniel R Mende, Robert D Finn, Michael Kuhn, Luis Pedro Coelho, Peer Bork
SPIRE: a Searchable, Planetary-scale mIcrobiome REsource. Nucleic acids research (2023)
Chuqing Sun, Jingchao Chen, Menglu Jin, Xueyang Zhao, Yun Li, Yanqi Dong, Na Gao, Zhi Liu, Peer Bork, Xing-Ming Zhao, Wei-Hua Chen
Long-Read Sequencing Reveals Extensive DNA Methylations in Human Gut Phagenome Contributed by Prevalently Phage-Encoded Methyltransferases. Advanced science (Weinheim, Baden-Wurttemberg, Germany) (2023)
Ana Hernández-Plaza, Damian Szklarczyk, Jorge Botas, Carlos P Cantalapiedra, Joaquín Giner-Lamia, Daniel R Mende, Rebecca Kirsch, Thomas Rattei, Ivica Letunic, Lars Juhl Jensen, Peer Bork, Christian von Mering, Huerta-Cepas Jaime
eggNOG 6.0: enabling comparative genomics across 12 535 organisms. Nucleic acids research (2022)
Ece Kartal, Thomas Sebastian Benedikt Schmidt, Esther Molina-Montes, Sandra Rodríguez-Perales, Jakob Wirbel, Oleksandr M Maistrenko, Wasiu A Akanni, Bilal Alashkar Alhamwe, Renato Jc Alves, Alfredo Carrato, Hans-Peter Erasmus, Lidia Estudillo, Fabian Finkelmeier, Anthony Fullam, Anna M Glazek, Paulina Gómez-Rubio, Rajna Hercog, Ferris E Jung, Stefanie Kandels-Lewis, Stephan Kersting, Melanie Langheinrich, Mirari Márquez, Xavier Molero, Askarbek Orakov, Thea Van Rossum, Raul Torres-Ruíz, Anja Telzerow, Konrad Zych, null null, null null, Vladimir Benes, Georg Zeller, Jonel Trebicka, Francisco X Real, Núria Malats, Peer Bork
A faecal microbiota signature with high specificity for pancreatic cancer. Gut 71 (7) (2022)
Typhaine Paysan-Lafosse, Matthias Blum, Sara Rocío Chuguransky, Tiago Grego, Beatriz Lázaro Pinto, Gustavo A Salazar, Maxwell L Bileschi, Peer Bork, Alan J Bridge, Lucy J Colwell, Julian Gough, Daniel H Haft, Ivica Letunic, Aron Marchler-Bauer, Huaiyu Mi, Darren A Natale, Christine A Orengo, Arun Prasad Pandurangan, Catherine Rivoire, Christian J A Sigrist, Ian Sillitoe, Narmada Thanki, Paul D Thomas, Silvio C E Tosatto, Cathy H Wu, Alex Bateman
InterPro in 2022. Nucleic acids research (2022)
Liang Xue, Swantje Lenz, Maria Zimmermann-Kogadeeva, Dimitry Tegunov, Patrick Cramer, Peer Bork, Juri Rappsilber, Julia Mahamid
Visualizing translation dynamics at atomic detail inside a bacterial cell. Nature 610 (7930) (2022)
Lucas Paoli, Hans-Joachim Ruscheweyh, Clarissa C Forneris, Florian Hubrich, Satria Kautsar, Agneya Bhushan, Alessandro Lotti, Quentin Clayssen, Guillem Salazar, Alessio Milanese, Charlotte I Carlström, Chrysa Papadopoulou, Daniel Gehrig, Mikhail Karasikov, Harun Mustafa, Martin Larralde, Laura M Carroll, Pablo Sánchez, Ahmed A Zayed, Dylan R Cronin, Silvia G Acinas, Peer Bork, Chris Bowler, Tom O Delmont, Josep M Gasol, Alvar D Gossert, André Kahles, Matthew B Sullivan, Patrick Wincker, Georg Zeller, Serina L Robinson, Jörn Piel, Shinichi Sunagawa
Biosynthetic potential of the global ocean microbiome. Nature 607 (7917) (2022)
Thomas Sebastian Benedikt Schmidt, Simone S Li, Oleksandr M Maistrenko, Wasiu A Akanni, Luis Pedro Coelho, Sibasish Dolai, Anthony Fullam, Anna M Glazek, Rajna Hercog, Hilde Herrema, Ferris Jung, Stefanie Kandels, Askarbek Orakov, Roman Thielemann, Moritz von Stetten, Thea Van Rossum, Vladimir Benes, Thomas J Borody, Willem Meindert de Vos, Cyriel Y Ponsioen, Max Nieuwdorp, Peer Bork
Drivers and determinants of strain dynamics following fecal microbiota transplantation. Nature medicine 28 (9) (2022)
Anthony Fullam, Ivica Letunic, Thomas Sebastian Benedikt Schmidt, Quinten R Ducarmon, Nicolai Karcher, Supriya Khedkar, Michael Kuhn, Martin Larralde, Oleksandr M Maistrenko, Lukas Malfertheiner, Alessio Milanese, Joao Frederico Matias Rodrigues, Claudia Sanchis-López, Christian Schudoma, Damian Szklarczyk, Shinichi Sunagawa, Georg Zeller, Huerta-Cepas Jaime, Christian von Mering, Peer Bork, Daniel R Mende
proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes. Nucleic acids research (2022)
Jakob Wirbel, Konrad Zych, Morgan Essex, Nicolai Karcher, Ece Kartal, Guillem Salazar, Peer Bork, Shinichi Sunagawa, Georg Zeller
Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox. Genome biology 22 (1) (2021)
Luis Pedro Coelho, Renato Jc Alves, Rodríguez Del Río Álvaro, Pernille Neve Myers, Carlos P Cantalapiedra, Joaquín Giner-Lamia, Thomas Sebastian Schmidt, Daniel R Mende, Askarbek Orakov, Ivica Letunic, Falk Hildebrand, Thea Van Rossum, Sofia Kirke Forslund-Startceva, Supriya Khedkar, Oleksandr M Maistrenko, Shaojun Pan, Longhao Jia, Pamela Ferretti, Shinichi Sunagawa, Xing-Ming Zhao, Henrik Bjørn Nielsen, Huerta-Cepas Jaime, Peer Bork
Towards the biogeography of prokaryotic genes. Nature 601 (7892) (2021)
Sofia Kirke Forslund-Startceva, Rima Chakaroun, Maria Zimmermann-Kogadeeva, Lajos Markó, Judith Aron-Wisnewsky, Trine Nielsen, Lucas Moitinho-Silva, Thomas S B Schmidt, Gwen Falony, Sara Vieira-Silva, Solia Adriouch, Renato Jc Alves, Karen Assmann, Jean-Philippe Bastard, Till Birkner, Robert Caesar, Julien Chilloux, Luis Pedro Coelho, Leopold Fezeu, Nathalie Galleron, Gerard Helft, Richard Isnard, Boyang Ji, Michael Kuhn, Emmanuelle Le Chatelier, Antonis Myridakis, Lisa M Olsson, Nicolas Pons, Edi Prifti, Benoit Quinquis, Hugo Roume, Joe-Elie Salem, Nataliya Sokolovska, Valentina Tremaroli, Mireia Valles-Colomer, Christian Lewinter, Nadja B Sønderskov, Helle Krogh Pedersen, Tue Haldor Hansen, null null, Jens Peter Gøtze, Lars Valeur Køber, Henrik Vestergaard, Torben Hansen, Jean-Daniel Zucker, Serge Hercberg, Jean-Michel Oppert, Ivica Letunic, Jens B Nielsen, Fredrik Bäckhed, Stanislav Dusko Ehrlich, Marc Emmanuel Dumas, Jeroen Raes, Oluf Pedersen, Karine Clement, Michael Stumvoll, Peer Bork
Combinatorial, additive and dose-dependent drug-microbiome associations. Nature (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 Loeber, Sofia Kirke Forslund-Startceva, Kiran Raosaheb Patil, Michael Zimmermann, Bärbel Stecher, Georg Zeller, Peer Bork, Athanasios Typas
Unravelling the collateral damage of antibiotics on gut bacteria. Nature 599 (7883) (2021)
Jacob M Musser, Klaske J Schippers, Michael Nickel, Giulia Mizzon, Andrea B Kohn, Constantin Pape, Paolo Ronchi, Nikolaos Papadopoulos, Alexander J Tarashansky, Jörg U Hammel, Florian Wolf, Cong Liang, Ana Hernández-Plaza, Carlos P Cantalapiedra, Kaia Achim, Nicole L Schieber, Leslie Pan, Fabian Ruperti, Warren R Francis, Sergio Vargas, Svenja Kling, Maike Renkert, Maxim Polikarpov, Gleb Bourenkov, Roberto Feuda, Imre Gaspar, Pawel Burkhardt, Bo Wang, Peer Bork, Martin Beck, Thomas R Schneider, Anna Kreshuk, Gert Wörheide, Jaime Huerta-Cepas, Yannick Schwab, Leonid L Moroz, Detlev Arendt
Profiling cellular diversity in sponges informs animal cell type and nervous system evolution. Science (New York, N.Y.) 374 (6568) (2021)
Martina Kluenemann, Sergej Andrejev, Sonja Blasche, André Mateus, Panagiotis L Kastritis, Saravanan Devendran, Johanna Vappiani, Bernd Simon, Timothy A Scott, Eleni Kafkia, Dimitrios Konstantinidis, Katharina Zirngibl, Eleonora Mastrorilli, Manuel Banzhaf, Marie-Therese Mackmull, Felix Hövelmann, Leo Nesme, Ana Rita Brochado, Lisa Maier, Thomas Bock, Vinita Periwal, Manjeet Kumar, Yongkyu Kim, Melanie Tramontano, Carsten Schultz, Martin Beck, Janosch Hennig, Michael Zimmermann, Daniel C Sévin, Filipe Cabreiro, Mikhail M Savitski, Peer Bork, Athanasios Typas, Kiran Raosaheb Patil
Bioaccumulation of therapeutic drugs by human gut bacteria. Nature 597 (7877) (2021)
Daniel Machado, Oleksandr M Maistrenko, Sergej Andrejev, Yongkyu Kim, Peer Bork, Kaustubh R Patil, Kiran Raosaheb Patil
Polarization of microbial communities between competitive and cooperative metabolism. Nature ecology & evolution 5 (2) (2021)
Silvia G Acinas, Pablo Sánchez, Guillem Salazar, Francisco Miguel Cornejo-Castillo, Marta Sebastián, Ramiro Logares, Marta Royo-Llonch, Lucas Paoli, Shinichi Sunagawa, Pascal Hingamp, Hiroyuki Ogata, Gipsi Lima-Mendez, Simon Roux, José M González, Jesús Maria Arrieta, Intikhab S Alam, Allan Kamau, Chris Bowler, Jeroen Raes, Stéphane Pesant, Peer Bork, Susana Agustí, Takashi Gojobori, Dolors Vaqué, Matthew B Sullivan, Carlos Pedrós-Alió, Ramon Massana, Carlos M Duarte, Josep M Gasol
Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities. Communications biology 4 (1) (2021)
Jonel Trebicka, Peer Bork, Aleksander Krag, Manimozhiyan Arumugam
Utilizing the gut microbiome in decompensated cirrhosis and acute-on-chronic liver failure. Nature reviews. Gastroenterology & hepatology 18 (3) (2020)
Antonio Molinaro, Pierre Bel Lassen, Marcus Henricsson, Hao Wu, Solia Adriouch, Eugeni Belda, Rima Chakaroun, Trine Nielsen, Per-Olof Bergh, Christine Rouault, Sébastien André, Florian Marquet, Fabrizio Andreelli, Joe-Elie Salem, Karen Assmann, Jean-Philippe Bastard, Sofia Forslund, Emmanuelle Le Chatelier, Gwen Falony, Nicolas Pons, Edi Prifti, Benoit Quinquis, Hugo Roume, Sara Vieira-Silva, Tue Haldor Hansen, Helle Krogh Pedersen, Christian Lewinter, Nadja B Sønderskov, null null, Lars Køber, Henrik Vestergaard, Torben Hansen, Jean-Daniel Zucker, Pilar Galan, Marc Emmanuel Dumas, Jeroen Raes, Jean-Michel Oppert, Ivica Letunic, Jens B Nielsen, Peer Bork, Stanislav Dusko Ehrlich, Michael Stumvoll, Oluf Pedersen, Judith Aron-Wisnewsky, Karine Clement, Fredrik Bäckhed
Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology. Nature communications 11 (1) (2020)
Antonio Molinaro, Pierre Bel Lassen, Marcus Henricsson, Hao Wu, Solia Adriouch, Eugeni Belda, Rima Chakaroun, Trine Nielsen, Per-Olof Bergh, Christine Rouault, Sébastien André, Florian Marquet, Fabrizio Andreelli, Joe-Elie Salem, Karen Assmann, Jean-Philippe Bastard, Sofia Forslund, Emmanuelle Le Chatelier, Gwen Falony, Nicolas Pons, Edi Prifti, Benoit Quinquis, Hugo Roume, Sara Vieira-Silva, Tue Haldor Hansen, Helle Krogh Pedersen, Christian Lewinter, Nadja B Sønderskov, null null, Lars Køber, Henrik Vestergaard, Torben Hansen, Jean-Daniel Zucker, Pilar Galan, Marc Emmanuel Dumas, Jeroen Raes, Jean-Michel Oppert, Ivica Letunic, Jens B Nielsen, Peer Bork, Stanislav Dusko Ehrlich, Michael Stumvoll, Oluf Pedersen, Judith Aron-Wisnewsky, Karine Clement, Fredrik Bäckhed
Author Correction: Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology. Nature communications 11 (1) (2020)
Shinichi Sunagawa, Silvia G Acinas, Peer Bork, Chris Bowler, null null, Damien Eveillard, Gabriel Gorsky, Lionel Guidi, Daniele Iudicone, Eric Karsenti, Fabien Lombard, Hiroyuki Ogata, Stephane Pesant, Matthew B Sullivan, Patrick Wincker, Colomban de Vargas
Tara Oceans: towards global ocean ecosystems biology. Nature reviews. Microbiology 18 (8) (2020)
Sara Vieira-Silva, Gwen Falony, Eugeni Belda, Trine Nielsen, Judith Aron-Wisnewsky, Rima Chakaroun, Sofia K Forslund, Karen Assmann, Mireia Valles-Colomer, Thi Thuy Duyen Nguyen, Sebastian Proost, Edi Prifti, Valentina Tremaroli, Nicolas Pons, Emmanuelle Le Chatelier, Fabrizio Andreelli, Jean-Phillippe Bastard, Luis Pedro Coelho, Nathalie Galleron, Tue H Hansen, Jean-Sébastien Hulot, Christian Lewinter, Helle K Pedersen, Benoit Quinquis, Christine Rouault, Hugo Roume, Joe-Elie Salem, Nadja B Sønderskov, Sothea Touch, null null, Marc Emmanuel Dumas, Stanislav Dusko Ehrlich, Pilar Galan, Jens P Gøtze, Torben Hansen, Jens Juul Holst, Lars Køber, Ivica Letunic, Jens B Nielsen, Jean-Michel Oppert, Michael Stumvoll, Henrik Vestergaard, Jean-Daniel Zucker, Peer Bork, Oluf Pedersen, Fredrik Bäckhed, Karine Clement, Jeroen Raes
Statin therapy is associated with lower prevalence of gut microbiota dysbiosis. Nature 581 (7808) (2020)
Thea Van Rossum, Pamela Ferretti, Oleksandr M Maistrenko, Peer Bork
Diversity within species: interpreting strains in microbiomes. Nature reviews. Microbiology 18 (9) (2020)
Alessio Milanese, Daniel R Mende, Lucas Paoli, Guillem Salazar, Hans-Joachim Ruscheweyh, Miguelangel Cuenca, Pascal Hingamp, Renato Jc Alves, Paul Igor Costea, Luis Pedro Coelho, Thomas Sebastian Benedikt Schmidt, Alexandre Almeida, Alex L Mitchell, Robert D Finn, Jaime Huerta-Cepas, Peer Bork, Georg Zeller, Shinichi Sunagawa
Microbial abundance, activity and population genomic profiling with mOTUs2. Nature communications 10 (1) (2019)
Helle Krogh Pedersen, Sofia K Forslund, Valborg Gudmundsdottir, Anders Østergaard Petersen, Falk Hildebrand, Tuulia Hyötyläinen, Trine Nielsen, Torben Hansen, Peer Bork, S Dusko Ehrlich, Søren Brunak, Matej Oresic, Oluf Pedersen, Henrik Bjørn Nielsen
A computational framework to integrate high-throughput '-omics' datasets for the identification of potential mechanistic links. Nature protocols 13 (12) (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 Maltez 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
Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer. Nature medicine 25 (4) (2019)
Thomas Sebastian Benedikt Schmidt, Matthew R Hayward, Luis Pedro 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
Extensive transmission of microbes along the gastrointestinal tract. eLife 8 (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
Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation. Nature medicine 25 (4) (2019)
Simon Roux, Evelien M Adriaenssens, Bas E Dutilh, Eugene V Koonin, Andrew M Kropinski, Mart Krupovic, Jens H Kuhn, Rob Lavigne, J Rodney Brister, Darren P Martin, Clara Amid, Ramy K Aziz, Seth R Bordenstein, Peer Bork, Mya Breitbart, Guy R Cochrane, Rebecca A Daly, Christelle Desnues, Melissa B Duhaime, Joanne B Emerson, François Enault, Jed A Fuhrman, Pascal Hingamp, Philip Hugenholtz, Bonnie L Hurwitz, Natalia N Ivanova, Jessica M Labonté, Kyung-Bum Lee, Rex R Malmstrom, Manuel Martinez-Garcia, Ilene Karsch Mizrachi, Hiroyuki Ogata, A David Páez-Espino, Marie-Agnès Petit, Catherine Putonti, Thomas Rattei, Alejandro Reyes, Francisco Rodriguez-Valera, Karyna Rosario, Lynn Schriml, Frederik Schulz, Grieg F Steward, Matthew B Sullivan, Shinichi Sunagawa, Curtis A Suttle, Ben Temperton, Susannah G Tringe, Rebecca Vega Thurber, Nicole Suzanne Webster, Katrine L Whiteson, Steven W Wilhelm, K Eric Wommack, Tanja Woyke, Kelly C Wrighton, Pelin Yilmaz, Takashi Yoshida, Mark J Young, Natalya Yutin, Lisa Zeigler Allen, Nikos C Kyrpides, Emiley A Eloe-Fadrosh
Minimum Information about an Uncultivated Virus Genome (MIUViG). Nature biotechnology 37 (1) (2018)
Marco L Hennrich, Natalie Romanov, Patrick Horn, Samira Jaeger, Volker Eckstein, Violetta Steeples, Fei Ye, Ximing Ding, Laura Poisa-Beiro, Mang Ching Lai, Benjamin Lang, Jacqueline Boultwood, Thomas Luft, Judith Barbara Zaugg, Andrea Pellagatti, Peer Bork, Patrick Aloy, Anne-Claude Gavin, Anthony Dick Ho
Cell-specific proteome analyses of human bone marrow reveal molecular features of age-dependent functional decline. Nature communications 9 (1) (2018)
Luca Parca, Martin Beck, Peer Bork, Alessandro Ori
Quantifying compartment-associated variations of protein abundance in proteomics data. Molecular systems biology 14 (7) (2018)
Albert Palleja, Kristian H Mikkelsen, Sofia K Forslund, Alireza Kashani, Kristine H Allin, Trine Nielsen, Tue Haldor Hansen, Suisha Liang, Qiang Feng, Chenchen Zhang, Paul Theodor Pyl, Luis Pedro Coelho, Huanming Yang, Jian Wang, Athanasios Typas, Morten F Nielsen, Henrik Bjorn Nielsen, Peer Bork, Jun Wang, Tina Vilsbøll, Torben Hansen, Filip K Krag Knop, Manimozhiyan Arumugam, Oluf Pedersen
Recovery of gut microbiota of healthy adults following antibiotic exposure. Nature microbiology 3 (11) (2018)
Melanie Tramontano, Sergej Andrejev, Mihaela Pruteanu, Martina Klünemann, Michael Kuhn, Marco Galardini, Paula Jouhten, Aleksej Zelezniak, Georg Zeller, Peer Bork, Athanasios Typas, Kiran Raosaheb Patil
Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies. Nature microbiology 3 (4) (2018)
Paul Igor Costea, Luis Pedro Coelho, Shinichi Sunagawa, Robin Munch, Jaime Huerta-Cepas, Kristoffer Forslund, Falk Hildebrand, Almagul Kushugulova, Georg Zeller, Peer Bork
Subspecies in the global human gut microbiome. Molecular systems biology 13 (12) (2017)

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