Exploring the human gut microbiome at strain resolution

Publicaciones

Towards standardisation of naming novel prokaryotic taxa in the age of high-throughput microbiology

Autores: Falk Hildebrand, Mark J Pallen, Peer Bork
Publicado en: Gut, Edición 69/7, 2020, Página(s) 1358.1-1359, ISSN 0017-5749
Editor: BMJ Publishing Group
DOI: 10.1136/gutjnl-2019-319045

Diversity within species: interpreting strains in microbiomes

Autores: Thea Van Rossum, Pamela Ferretti, Oleksandr M. Maistrenko, Peer Bork
Publicado en: Nature Reviews Microbiology, Edición 18/9, 2020, Página(s) 491-506, ISSN 1740-1526
Editor: Nature Publishing Group
DOI: 10.1038/s41579-020-0368-1

Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features

Autores: Anne-Claude Gavin; Peer Bork; Yuanyue Li; Michael Kuhn
Publicado en: Bioinformatics (2019), Edición 1, 2019, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1101/573790

proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes

Autores: Daniel R Mende, Ivica Letunic, Oleksandr M Maistrenko, Thomas S B Schmidt, Alessio Milanese, Lucas Paoli, Ana Hernández-Plaza, Askarbek N Orakov, Sofia K Forslund, Shinichi Sunagawa, Georg Zeller, Jaime Huerta-Cepas, Luis Pedro Coelho, Peer Bork
Publicado en: Nucleic Acids Research, 2019, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gkz1002

Combinatorial, additive and dose-dependent drug–microbiome associations

Autores: "Forslund, S.*, Chakaroun, R.*, Zimmermann-Kogodeeva, M.* …[36 authors].... Metacardis consortium ....[14 authors]… Clement, K#, Stumvogel, M.# and Bork, P.#"
Publicado en: Nature, 2021, ISSN 1476-4687
Editor: Springer Nature
DOI: 10.1038/s41586-021-04177-9

Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer

Autores: 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, Shinich
Publicado en: Nature Medicine, Edición 25/4, 2019, Página(s) 679-689, ISSN 1078-8956
Editor: Nature Publishing Group
DOI: 10.1038/s41591-019-0406-6

A fecal microbiota signature with high specificity for pancreatic cancer

Autores: "Kartal, E.*, Schmidt, S.*, Molina-Montes, E.* ...[21 authors]... PanGenEU study investigators, Benes, V., Zeller, G., Real, F.X., Malats, N.# And Bork, P.#"
Publicado en: Gut, 2022, ISSN 1468-3288
Editor: BMJ publishing group
DOI: 10.1136/gutjnl-2021-324755

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

Autores: Ivica Letunic, Peer Bork
Publicado en: Nucleic Acids Research, Edición 47/W1, 2019, Página(s) W256-W259, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gkz239

eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale

Autores: Cantalapiedra, C.P., Hernandez-Plaza, A., Letunic, I., Bork, P. and Huerta-Cepas, J.
Publicado en: Molecular Biology and Evolution, 2021, ISSN 1537-1719
Editor: Oxford Academic
DOI: 10.1093/molbev/msab293

GUNC: detection of chimerism and contamination in prokaryotic genomes

Autores: Orakov, A.N., Fullam, A.N., Coelho, L.P., Khefkar, S., Szklarczyk, D., Mende, D.R., Schmidt, T.S.B. and Bork, P.
Publicado en: Genome Biology, 2021, ISSN 1474-760X
Editor: Biomed central - springer nature
DOI: 10.1186/s13059-021-02393-0

NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language

Autores: Luis Pedro Coelho, Renato Alves, Paulo Monteiro, Jaime Huerta-Cepas, Ana Teresa Freitas, Peer Bork
Publicado en: Microbiome, Edición 7/1, 2019, ISSN 2049-2618
Editor: Springer Nature
DOI: 10.1186/s40168-019-0684-8

Subspecies in the global human gut microbiome

Autores: Paul I Costea, Luis Pedro Coelho, Shinichi Sunagawa, Robin Munch, Jaime Huerta‐Cepas, Kristoffer Forslund, Falk Hildebrand, Almagul Kushugulova, Georg Zeller, Peer Bork
Publicado en: Molecular Systems Biology, Edición 13/12, 2017, Página(s) 960, ISSN 1744-4292
Editor: Nature Publishing Group
DOI: 10.15252/msb.20177589

Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson’s disease patients

Autores: J. R. Bedarf, F. Hildebrand, L. P. Coelho, S. Sunagawa, M. Bahram, F. Goeser, P. Bork, U. Wüllner
Publicado en: Genome Medicine, Edición 9/1, 2017, ISSN 1756-994X
Editor: BioMed Central
DOI: 10.1186/s13073-017-0428-y

Erratum to: Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson’s disease patients

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

Autores: Jaime Huerta-Cepas, Kristoffer Forslund, Luis Pedro Coelho, Damian Szklarczyk, Lars Juhl Jensen, Christian von Mering, Peer Bork
Publicado en: Molecular Biology and Evolution, Edición 34/8, 2017, Página(s) 2115-2122, ISSN 0737-4038
Editor: Oxford University Press
DOI: 10.1093/molbev/msx148

metaSNV: A tool for metagenomic strain level analysis

Autores: Paul Igor Costea, Robin Munch, Luis Pedro Coelho, Lucas Paoli, Shinichi Sunagawa, Peer Bork
Publicado en: PLOS ONE, Edición 12/7, 2017, Página(s) e0182392, ISSN 1932-6203
Editor: Public Library of Science
DOI: 10.1371/journal.pone.0182392

Extensive transmission of microbes along the gastrointestinal tract

Autores: 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
Publicado en: eLife, Edición 8, 2019, ISSN 2050-084X
Editor: eLife Sciences Publications
DOI: 10.7554/elife.42693

Pole-to-Pole Connections: Similarities between Arctic and Antarctic Microbiomes and Their Vulnerability to Environmental Change

Autores: Julia Kleinteich, Falk Hildebrand, Mohammad Bahram, Anita Y. Voigt, Susanna A. Wood, Anne D. Jungblut, Frithjof C. Küpper, Antonio Quesada, Antonio Camacho, David A. Pearce, Peter Convey, Warwick F. Vincent, Christiane Zarfl, Peer Bork, Daniel R. Dietrich
Publicado en: Frontiers in Ecology and Evolution, Edición 5, 2017, Página(s) 1-11, ISSN 2296-701X
Editor: Frontiers
DOI: 10.3389/fevo.2017.00137

Selective maternal seeding and environment shape the human gut microbiome

Autores: Katri Korpela, Paul Costea, Luis Pedro Coelho, Stefanie Kandels-Lewis, Gonneke Willemsen, Dorret I. Boomsma, Nicola Segata, Peer Bork
Publicado en: Genome Research, Edición 28/4, 2018, Página(s) 561-568, ISSN 1088-9051
Editor: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.233940.117

Antibiotics-induced monodominance of a novel gut bacterial order

Autores: Falk Hildebrand, Lucas Moitinho-Silva, Sonja Blasche, Martin T Jahn, Toni Ingolf Gossmann, Jaime Huerta-Cepas, Rajna Hercog, Mechthild Luetge, Mohammad Bahram, Anna Pryszlak, Renato J Alves, Sebastian M Waszak, Ana Zhu, Lumeng Ye, Paul Igor Costea, Steven Aalvink, Clara Belzer, Sofia K Forslund, Shinichi Sunagawa, Ute Hentschel, Christoph Merten, Kiran Raosaheb Patil, Vladimir Benes, Peer Bork
Publicado en: Gut, 2019, Página(s) gutjnl-2018-317715, ISSN 0017-5749
Editor: BMJ Publishing Group
DOI: 10.1136/gutjnl-2018-317715

Extensive impact of non-antibiotic drugs on human gut bacteria

Autores: Lisa Maier, Mihaela Pruteanu, Michael Kuhn, Georg Zeller, Anja Telzerow, Exene Erin Anderson, Ana Rita Brochado, Keith Conrad Fernandez, Hitomi Dose, Hirotada Mori, Kiran Raosaheb Patil, Peer Bork, Athanasios Typas
Publicado en: Nature, Edición 555/7698, 2018, Página(s) 623-628, ISSN 0028-0836
Editor: Nature Publishing Group
DOI: 10.1038/nature25979

The Human Gut Microbiome: From Association to Modulation

Autores: Thomas S.B. Schmidt, Jeroen Raes, Peer Bork
Publicado en: Cell, Edición 172/6, 2018, Página(s) 1198-1215, ISSN 0092-8674
Editor: Cell Press
DOI: 10.1016/j.cell.2018.02.044

iPath3.0: interactive pathways explorer v3

Autores: Youssef Darzi, Ivica Letunic, Peer Bork, Takuji Yamada
Publicado en: Nucleic Acids Research, Edición 46/W1, 2018, Página(s) W510-W513, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gky299

proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes

Autores: Daniel R. Mende, Ivica Letunic, Jaime Huerta-Cepas, Simone S. Li, Kristoffer Forslund, Shinichi Sunagawa, Peer Bork
Publicado en: Nucleic Acids Research, Edición 45/D1, 2017, Página(s) D529-D534, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gkw989

Durable coexistence of donor and recipient strains after fecal microbiota transplantation

Autores: Simone S. Li, Ana Zhu, Vladimir Benes, Paul I. Costea, Rajna Hercog, Falk Hildebrand, Jaime Huerta-Cepas, Max Nieuwdorp, Jarkko Salojärvi, Anita Y. Voigt, Georg Zeller, Shinichi Sunagawa, Willem M. de Vos, Peer Bork
Publicado en: Science, Edición 352/6285, 2016, Página(s) 586-589, ISSN 0036-8075
Editor: American Association for the Advancement of Science
DOI: 10.1126/science.aad8852

Dispersal strategies shape persistence and evolution of gut bacteria

Autores: Hildebrand, F., Gossmann, T.I., Frioux, C., Özkurt, E., Myers, P.N., Ferretti, P., Bahram, M., Nielsen, H.B. and Bork, P.
Publicado en: Cell Host & Microbe, 2021, ISSN 1934-6069
Editor: Cell Press
DOI: 10.1016/j.chom.2021.05.008

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

Autores: Huerta-Cepas, J.*, Szklarczyk, D.*, Heller, D., Hernandez-Plaza, A., Forslund, S.K., Cook, H., Mende, D., Letunic, I., Rattei, T., Jensen, L.J., von Mering, C. and Bork, P.
Publicado en: NAR, 2019, ISSN 1362-4962
Editor: Oxford Academics
DOI: 10.1093/nar/gky1085

Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity

Autores: Oleksandr M. Maistrenko, Daniel R. Mende, Mechthild Luetge, Falk Hildebrand, Thomas S. B. Schmidt, Simone S. Li, João F. Matias Rodrigues, Christian von Mering, Luis Pedro Coelho, Jaime Huerta-Cepas, Shinichi Sunagawa, Peer Bork
Publicado en: The ISME Journal, Edición 14/5, 2020, Página(s) 1247-1259, ISSN 1751-7362
Editor: Nature Publishing Group
DOI: 10.1038/s41396-020-0600-z

SMART: recent updates, new developments and status in 2020

Autores: Ivica Letunic, Supriya Khedkar, Peer Bork
Publicado en: Nucleic Acids Research, Edición 49/D1, 2020, Página(s) D458-D460, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gkaa937

metaSNV v2: detection of SNVs and subspecies in prokaryotic metagenomes

Autores: Van Rossum, T., Costea, P., Paoli, L., Alves, R., Thielemann, R., Sunugava, S. and Bork., P.
Publicado en: Bioinformatics, 2022, ISSN 1460-2059
Editor: oxford university press
DOI: 10.1093/bioinformatics/btab789

Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment

Autores: Mohammad Bahram, Sten Anslan, Falk Hildebrand, Peer Bork, Leho Tedersoo
Publicado en: Environmental Microbiology Reports, Edición 11/4, 2019, Página(s) 487-494, ISSN 1758-2229
Editor: Wiley-Blackwell
DOI: 10.1111/1758-2229.12684

Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation

Autores: 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,
Publicado en: Nature Medicine, Edición 25/4, 2019, Página(s) 667-678, ISSN 1078-8956
Editor: Nature Publishing Group
DOI: 10.1038/s41591-019-0405-7

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