Zobrazeno 1 - 10
of 30
pro vyhledávání: '"Jan P. Buchmann"'
Autor:
Vanessa R. Marcelino, Philip T. L. C. Clausen, Jan P. Buchmann, Michelle Wille, Jonathan R. Iredell, Wieland Meyer, Ole Lund, Tania C. Sorrell, Edward C. Holmes
Publikováno v:
Genome Biology, Vol 21, Iss 1, Pp 1-15 (2020)
Abstract There is an increasing demand for accurate and fast metagenome classifiers that can not only identify bacteria, but all members of a microbial community. We used a recently developed concept in read mapping to develop a highly accurate metag
Externí odkaz:
https://doaj.org/article/603ad5e8d3794c12b57c37afbe8c7179
Autor:
Joan Martí-Carreras, Alejandro Rafael Gener, Sierra D. Miller, Anderson F. Brito, Christiam E. Camacho, Ryan Connor, Ward Deboutte, Cody Glickman, David M. Kristensen, Wynn K. Meyer, Sejal Modha, Alexis L. Norris, Surya Saha, Anna K. Belford, Evan Biederstedt, James Rodney Brister, Jan P. Buchmann, Nicholas P. Cooley, Robert A. Edwards, Kiran Javkar, Michael Muchow, Harihara Subrahmaniam Muralidharan, Charles Pepe-Ranney, Nidhi Shah, Migun Shakya, Michael J. Tisza, Benjamin J. Tully, Bert Vanmechelen, Valerie C. Virta, JL Weissman, Vadim Zalunin, Alexandre Efremov, Ben Busby
Publikováno v:
Viruses, Vol 12, Iss 12, p 1424 (2020)
Viruses represent important test cases for data federation due to their genome size and the rapid increase in sequence data in publicly available databases. However, some consequences of previously decentralized (unfederated) data are lack of consens
Externí odkaz:
https://doaj.org/article/45441b170084430eaf943eb545346079
Autor:
Jemma L. Geoghegan, Vanessa Pirotta, Erin Harvey, Alastair Smith, Jan P. Buchmann, Martin Ostrowski, John-Sebastian Eden, Robert Harcourt, Edward C. Holmes
Publikováno v:
Viruses, Vol 10, Iss 6, p 300 (2018)
There is growing interest in characterizing the viromes of diverse mammalian species, particularly in the context of disease emergence. However, little is known about virome diversity in aquatic mammals, in part due to difficulties in sampling. We ch
Externí odkaz:
https://doaj.org/article/f2d142241432442ab29ca13c9d857db3
Transposable elements contribute to the establishment of the glycine shuttle in Brassicaceae species
Autor:
Sebastian Triesch, Alisandra K. Denton, Jan P. Buchmann, Vanessa Reichel-Deland, Ricardo Nuno Ferreira Martins Guerreiro, Urte Schlüter, Benjamin Stich, Andreas P.M. Weber
C3-C4intermediate photosynthesis has evolved multiple times convergently and independently in the Brassicaceae, although the family lacksbona fideC4species. Evolution of C3-C4intermediate photosynthesis requires a reconfiguration of gene-regulatory n
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::8214c29d43f81ffb69e9815c6d6a7dd7
https://doi.org/10.1101/2022.12.06.519256
https://doi.org/10.1101/2022.12.06.519256
Publikováno v:
Virus evolution. 8(2)
Despite a rapid expansion in the number of known RNA viruses following the advent of metagenomic sequencing, the identification and annotation of highly divergent RNA viruses remains challenging, particularly from poorly characterized hosts and envir
Autor:
Edward C. Holmes, Philip Thomas Lanken Conradsen Clausen, Tania C. Sorrell, Wieland Meyer, Jonathan R. Iredell, Ole Lund, Jan P. Buchmann, Vanessa R. Marcelino, Michelle Wille
Publikováno v:
Genome Biology, Vol 21, Iss 1, Pp 1-15 (2020)
Genome Biology
Marcelino, V R, Clausen, P T L C, Buchmann, J P, Wille, M, Iredell, J R, Meyer, W, Lund, O, Sorrell, T C & Holmes, E C 2020, ' CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data ', Genome Biology (Online Edition), vol. 21, 103 . https://doi.org/10.1186/s13059-020-02014-2
Genome Biology
Marcelino, V R, Clausen, P T L C, Buchmann, J P, Wille, M, Iredell, J R, Meyer, W, Lund, O, Sorrell, T C & Holmes, E C 2020, ' CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data ', Genome Biology (Online Edition), vol. 21, 103 . https://doi.org/10.1186/s13059-020-02014-2
High-throughput sequencing of DNA and RNA from environmental and host-associated samples (metagenomics and metatranscriptomics) is a powerful tool to assess which organisms are present in a sample. Taxonomic identification software usually align indi
Autor:
Jan P. Buchmann, Edward C. Holmes
Publikováno v:
Bioinformatics
Summary We present NCBI-taxonomist—a command-line tool written in Python that collects and manages taxonomic data from the National Center for Biotechnology Information (NCBI). NCBI-taxonomist does not depend on a pre-downloaded taxonomic database
Autor:
Edward C. Holmes, Jan P. Buchmann
Publikováno v:
Bioinformatics
Summary Entrezpy is a Python library that automates the querying and downloading of data from the Entrez databases at National Center for Biotechnology Information by interacting with E-Utilities. Entrezpy implements complex queries by automatically
Autor:
Christiam Camacho, Ben Busby, Evan Biederstedt, Benjamin J. Tully, David M. Kristensen, Nicholas P. Cooley, Ward Deboutte, Alexis L. Norris, Sierra D. Miller, Kiran Javkar, Cody Glickman, Alexandre Efremov, Ryan Connor, Anderson F. Brito, Nidhi Shah, Michael Muchow, Alejandro Rafael Gener, Bert Vanmechelen, Michael J. Tisza, Sejal Modha, Vadim Zalunin, Charles Pepe-Ranney, Jan P. Buchmann, Jake L. Weissman, Migun Shakya, Harihara Subrahmaniam Muralidharan, Surya Saha, Robert Edwards, Valerie C. Virta, Joan Martí-Carreras, James Rodney Brister, Wynn K. Meyer, Anna K. Belford
Publikováno v:
Viruses, Vol 12, Iss 1424, p 1424 (2020)
Viruses
Viruses; Volume 12; Issue 12; Pages: 1424
Viruses
Viruses; Volume 12; Issue 12; Pages: 1424
Viruses represent important test cases for data federation due to their genome size and the rapid increase in sequence data in publicly available databases. However, some consequences of previously decentralized (unfederated) data are lack of consens
Autor:
Ashleigh F. Porter, John-Sebastian Eden, Craig Moritz, Karrie Rose, Jan P. Buchmann, Erin Harvey, Edward C. Holmes, John H.-O. Pettersson, Wei-Shan Chang, Mang Shi
The RNA virus family Flaviviridae harbours several important pathogens of humans and other animals, including Zika virus, dengue virus and hepatitis C virus. The Flaviviridae are currently divided into four genera - Hepacivirus, Pegivirus, Pestivirus
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::bc02e6cc96d59f0b01badca31b41f3c8
https://doi.org/10.1101/2020.05.16.100149
https://doi.org/10.1101/2020.05.16.100149