Exploring the human gut microbiome at strain resolution

Publikacje

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

Autorzy: Falk Hildebrand, Mark J Pallen, Peer Bork
Opublikowane w: Gut, Numer 69/7, 2020, Strona(/y) 1358.1-1359, ISSN 0017-5749
Wydawca: BMJ Publishing Group
DOI: 10.1136/gutjnl-2019-319045

Diversity within species: interpreting strains in microbiomes

Autorzy: Thea Van Rossum, Pamela Ferretti, Oleksandr M. Maistrenko, Peer Bork
Opublikowane w: Nature Reviews Microbiology, Numer 18/9, 2020, Strona(/y) 491-506, ISSN 1740-1526
Wydawca: 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

Autorzy: Anne-Claude Gavin; Peer Bork; Yuanyue Li; Michael Kuhn
Opublikowane w: Bioinformatics (2019), Numer 1, 2019, ISSN 1367-4803
Wydawca: Oxford University Press
DOI: 10.1101/573790

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

Autorzy: 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
Opublikowane w: Nucleic Acids Research, 2019, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkz1002

Combinatorial, additive and dose-dependent drug–microbiome associations

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

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

Autorzy: 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
Opublikowane w: Nature Medicine, Numer 25/4, 2019, Strona(/y) 679-689, ISSN 1078-8956
Wydawca: Nature Publishing Group
DOI: 10.1038/s41591-019-0406-6

A fecal microbiota signature with high specificity for pancreatic cancer

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

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

Autorzy: Ivica Letunic, Peer Bork
Opublikowane w: Nucleic Acids Research, Numer 47/W1, 2019, Strona(/y) W256-W259, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkz239

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

Autorzy: Cantalapiedra, C.P., Hernandez-Plaza, A., Letunic, I., Bork, P. and Huerta-Cepas, J.
Opublikowane w: Molecular Biology and Evolution, 2021, ISSN 1537-1719
Wydawca: Oxford Academic
DOI: 10.1093/molbev/msab293

GUNC: detection of chimerism and contamination in prokaryotic genomes

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

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

Autorzy: Luis Pedro Coelho, Renato Alves, Paulo Monteiro, Jaime Huerta-Cepas, Ana Teresa Freitas, Peer Bork
Opublikowane w: Microbiome, Numer 7/1, 2019, ISSN 2049-2618
Wydawca: Springer Nature
DOI: 10.1186/s40168-019-0684-8

Subspecies in the global human gut microbiome

Autorzy: Paul I Costea, Luis Pedro Coelho, Shinichi Sunagawa, Robin Munch, Jaime Huerta‐Cepas, Kristoffer Forslund, Falk Hildebrand, Almagul Kushugulova, Georg Zeller, Peer Bork
Opublikowane w: Molecular Systems Biology, Numer 13/12, 2017, Strona(/y) 960, ISSN 1744-4292
Wydawca: 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

Autorzy: J. R. Bedarf, F. Hildebrand, L. P. Coelho, S. Sunagawa, M. Bahram, F. Goeser, P. Bork, U. Wüllner
Opublikowane w: Genome Medicine, Numer 9/1, 2017, ISSN 1756-994X
Wydawca: 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

Autorzy: Jaime Huerta-Cepas, Kristoffer Forslund, Luis Pedro Coelho, Damian Szklarczyk, Lars Juhl Jensen, Christian von Mering, Peer Bork
Opublikowane w: Molecular Biology and Evolution, Numer 34/8, 2017, Strona(/y) 2115-2122, ISSN 0737-4038
Wydawca: Oxford University Press
DOI: 10.1093/molbev/msx148

metaSNV: A tool for metagenomic strain level analysis

Autorzy: Paul Igor Costea, Robin Munch, Luis Pedro Coelho, Lucas Paoli, Shinichi Sunagawa, Peer Bork
Opublikowane w: PLOS ONE, Numer 12/7, 2017, Strona(/y) e0182392, ISSN 1932-6203
Wydawca: Public Library of Science
DOI: 10.1371/journal.pone.0182392

Extensive transmission of microbes along the gastrointestinal tract

Autorzy: 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
Opublikowane w: eLife, Numer 8, 2019, ISSN 2050-084X
Wydawca: eLife Sciences Publications
DOI: 10.7554/elife.42693

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

Autorzy: 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
Opublikowane w: Frontiers in Ecology and Evolution, Numer 5, 2017, Strona(/y) 1-11, ISSN 2296-701X
Wydawca: Frontiers
DOI: 10.3389/fevo.2017.00137

Selective maternal seeding and environment shape the human gut microbiome

Autorzy: Katri Korpela, Paul Costea, Luis Pedro Coelho, Stefanie Kandels-Lewis, Gonneke Willemsen, Dorret I. Boomsma, Nicola Segata, Peer Bork
Opublikowane w: Genome Research, Numer 28/4, 2018, Strona(/y) 561-568, ISSN 1088-9051
Wydawca: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.233940.117

Antibiotics-induced monodominance of a novel gut bacterial order

Autorzy: 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
Opublikowane w: Gut, 2019, Strona(/y) gutjnl-2018-317715, ISSN 0017-5749
Wydawca: BMJ Publishing Group
DOI: 10.1136/gutjnl-2018-317715

Extensive impact of non-antibiotic drugs on human gut bacteria

Autorzy: 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
Opublikowane w: Nature, Numer 555/7698, 2018, Strona(/y) 623-628, ISSN 0028-0836
Wydawca: Nature Publishing Group
DOI: 10.1038/nature25979

The Human Gut Microbiome: From Association to Modulation

Autorzy: Thomas S.B. Schmidt, Jeroen Raes, Peer Bork
Opublikowane w: Cell, Numer 172/6, 2018, Strona(/y) 1198-1215, ISSN 0092-8674
Wydawca: Cell Press
DOI: 10.1016/j.cell.2018.02.044

iPath3.0: interactive pathways explorer v3

Autorzy: Youssef Darzi, Ivica Letunic, Peer Bork, Takuji Yamada
Opublikowane w: Nucleic Acids Research, Numer 46/W1, 2018, Strona(/y) W510-W513, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gky299

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

Autorzy: Daniel R. Mende, Ivica Letunic, Jaime Huerta-Cepas, Simone S. Li, Kristoffer Forslund, Shinichi Sunagawa, Peer Bork
Opublikowane w: Nucleic Acids Research, Numer 45/D1, 2017, Strona(/y) D529-D534, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkw989

Durable coexistence of donor and recipient strains after fecal microbiota transplantation

Autorzy: 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
Opublikowane w: Science, Numer 352/6285, 2016, Strona(/y) 586-589, ISSN 0036-8075
Wydawca: American Association for the Advancement of Science
DOI: 10.1126/science.aad8852

Dispersal strategies shape persistence and evolution of gut bacteria

Autorzy: Hildebrand, F., Gossmann, T.I., Frioux, C., Özkurt, E., Myers, P.N., Ferretti, P., Bahram, M., Nielsen, H.B. and Bork, P.
Opublikowane w: Cell Host & Microbe, 2021, ISSN 1934-6069
Wydawca: 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

Autorzy: 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.
Opublikowane w: NAR, 2019, ISSN 1362-4962
Wydawca: Oxford Academics
DOI: 10.1093/nar/gky1085

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

Autorzy: 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
Opublikowane w: The ISME Journal, Numer 14/5, 2020, Strona(/y) 1247-1259, ISSN 1751-7362
Wydawca: Nature Publishing Group
DOI: 10.1038/s41396-020-0600-z

SMART: recent updates, new developments and status in 2020

Autorzy: Ivica Letunic, Supriya Khedkar, Peer Bork
Opublikowane w: Nucleic Acids Research, Numer 49/D1, 2020, Strona(/y) D458-D460, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkaa937

metaSNV v2: detection of SNVs and subspecies in prokaryotic metagenomes

Autorzy: Van Rossum, T., Costea, P., Paoli, L., Alves, R., Thielemann, R., Sunugava, S. and Bork., P.
Opublikowane w: Bioinformatics, 2022, ISSN 1460-2059
Wydawca: oxford university press
DOI: 10.1093/bioinformatics/btab789

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

Autorzy: Mohammad Bahram, Sten Anslan, Falk Hildebrand, Peer Bork, Leho Tedersoo
Opublikowane w: Environmental Microbiology Reports, Numer 11/4, 2019, Strona(/y) 487-494, ISSN 1758-2229
Wydawca: 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

Autorzy: 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,
Opublikowane w: Nature Medicine, Numer 25/4, 2019, Strona(/y) 667-678, ISSN 1078-8956
Wydawca: Nature Publishing Group
DOI: 10.1038/s41591-019-0405-7

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