Zobrazeno 1 - 10
of 63
pro vyhledávání: '"Tomáš, Pluskal"'
Publikováno v:
BMC Bioinformatics, Vol 24, Iss 1, Pp 1-11 (2023)
Abstract Background RNA-seq followed by de novo transcriptome assembly has been a transformative technique in biological research of non-model organisms, but the computational processing of RNA-seq data entails many different software tools. The comp
Externí odkaz:
https://doaj.org/article/d93eded9aae04aa187bcae13e6236923
Autor:
Robin Schmid, Daniel Petras, Louis-Félix Nothias, Mingxun Wang, Allegra T. Aron, Annika Jagels, Hiroshi Tsugawa, Johannes Rainer, Mar Garcia-Aloy, Kai Dührkop, Ansgar Korf, Tomáš Pluskal, Zdeněk Kameník, Alan K. Jarmusch, Andrés Mauricio Caraballo-Rodríguez, Kelly C. Weldon, Melissa Nothias-Esposito, Alexander A. Aksenov, Anelize Bauermeister, Andrea Albarracin Orio, Carlismari O. Grundmann, Fernando Vargas, Irina Koester, Julia M. Gauglitz, Emily C. Gentry, Yannick Hövelmann, Svetlana A. Kalinina, Matthew A. Pendergraft, Morgan Panitchpakdi, Richard Tehan, Audrey Le Gouellec, Gajender Aleti, Helena Mannochio Russo, Birgit Arndt, Florian Hübner, Heiko Hayen, Hui Zhi, Manuela Raffatellu, Kimberly A. Prather, Lihini I. Aluwihare, Sebastian Böcker, Kerry L. McPhail, Hans-Ulrich Humpf, Uwe Karst, Pieter C. Dorrestein
Publikováno v:
Nature Communications, Vol 12, Iss 1, Pp 1-12 (2021)
Abstract Molecular networking connects mass spectra of molecules based on the similarity of their fragmentation patterns. However, during ionization, molecules commonly form multiple ion species with different fragmentation behavior. As a result, the
Externí odkaz:
https://doaj.org/article/c79c811ddd0b40428c0ef8e4c5a7fe4c
Autor:
Colin Y. Kim, Andrew J. Mitchell, Christopher M. Glinkerman, Fu-Shuang Li, Tomáš Pluskal, Jing-Ke Weng
Publikováno v:
Nature Communications, Vol 11, Iss 1, Pp 1-7 (2020)
Halogenated plant natural products are rare and plant halogenation enzymes are thus far unknown. Here Kim et al. identify a dechloroacutumine halogenase from Common Moonseed that catalyzes the final chlorination step in the biosynthesis of acutumine,
Externí odkaz:
https://doaj.org/article/ce648d60171844778ff00a7c3876dcf5
Autor:
Zhixu Ni, Michele Wölk, Geoff Jukes, Karla Mendivelso Espinosa, Robert Ahrends, Lucila Aimo, Jorge Alvarez-Jarreta, Simon Andrews, Robert Andrews, Alan Bridge, Geremy C. Clair, Matthew J. Conroy, Eoin Fahy, Caroline Gaud, Laura Goracci, Jürgen Hartler, Nils Hoffmann, Dominik Kopczyinki, Ansgar Korf, Andrea F. Lopez-Clavijo, Adnan Malik, Jacobo Miranda Ackerman, Martijn R. Molenaar, Claire O’Donovan, Tomáš Pluskal, Andrej Shevchenko, Denise Slenter, Gary Siuzdak, Martina Kutmon, Hiroshi Tsugawa, Egon L. Willighagen, Jianguo Xia, Valerie B. O’Donnell, Maria Fedorova
Publikováno v:
Nature Methods, 20, 193-204. Nature Publishing Group
Nat Methods
Nat Methods
Recent progress in mass spectrometry (MS) lipidomics has led to a rapid proliferation of studies across biology and biomedicine and facilitating important discoveries. These generate extremely large raw datasets requiring sophisticated tailored solut
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4703f5cdf9d5a93e8e3707020004fffc
https://doi.org/10.1038/s41592-022-01710-0
https://doi.org/10.1038/s41592-022-01710-0
Autor:
Tito Damiani, Stefano Bonciarelli, Gerhard G. Thallinger, Nikolai Koehler, Christoph A. Krettler, Arif K. Salihoğlu, Ansgar Korf, Josch K. Pauling, Tomáš Pluskal, Zhixu Ni, Laura Goracci
Publikováno v:
Analytical Chemistry. 95:287-303
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2614398f9781cd17d961a55fdcc50886
https://doi.org/10.1021/acs.analchem.2c04406
https://doi.org/10.1021/acs.analchem.2c04406
Autor:
Robin Schmid, Steffen Heuckeroth, Ansgar Korf, Aleksandr Smirnov, Owen Myers, Thomas S. Dyrlund, Roman Bushuiev, Kevin J. Murray, Nils Hoffmann, Miaoshan Lu, Abinesh Sarvepalli, Zheng Zhang, Markus Fleischauer, Kai Dührkop, Mark Wesner, Shawn J. Hoogstra, Edward Rudt, Olena Mokshyna, Corinna Brungs, Kirill Ponomarov, Lana Mutabdžija, Tito Damiani, Chris J. Pudney, Mark Earll, Patrick O. Helmer, Timothy R. Fallon, Tobias Schulze, Albert Rivas-Ubach, Aivett Bilbao, Henning Richter, Louis-Félix Nothias, Mingxun Wang, Matej Orešič, Jing-Ke Weng, Sebastian Böcker, Astrid Jeibmann, Heiko Hayen, Uwe Karst, Pieter C. Dorrestein, Daniel Petras, Xiuxia Du, Tomáš Pluskal
Publikováno v:
Nature Biotechnology. 41:447-449
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::517e511eb2b7d07daaa666f95c83bafb
https://doi.org/10.1038/s41587-023-01690-2
https://doi.org/10.1038/s41587-023-01690-2
Autor:
Egon L. Willighagen, John W. Mayfield, Jonathan Alvarsson, Arvid Berg, Lars Carlsson, Nina Jeliazkova, Stefan Kuhn, Tomáš Pluskal, Miquel Rojas-Chertó, Ola Spjuth, Gilleain Torrance, Chris T. Evelo, Rajarshi Guha, Christoph Steinbeck
Publikováno v:
Journal of Cheminformatics, Vol 9, Iss 1, Pp 1-19 (2017)
Abstract Background The Chemistry Development Kit (CDK) is a widely used open source cheminformatics toolkit, providing data structures to represent chemical concepts along with methods to manipulate such structures and perform computations on them.
Externí odkaz:
https://doaj.org/article/04d9c1e269724925b7979d21a9dd3f92
Schizosaccharomyces pombeis a popular model organism in molecular biology and cell physiology. With its ease of genetic manipulation and growth, supported by in-depth functional annotation in the PomBase database and genome-wide metabolic models,S. p
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::053beda863a6fac78864a07a79d12615
https://doi.org/10.1101/2023.05.24.542151
https://doi.org/10.1101/2023.05.24.542151
Autor:
Meera Shah, Dan Su, Judith S. Scheliga, Tomáš Pluskal, Susanna Boronat, Khatereh Motamedchaboki, Alexandre Rosa Campos, Feng Qi, Elena Hidalgo, Mitsuhiro Yanagida, Dieter A. Wolf
Publikováno v:
Cell Reports, Vol 16, Iss 7, Pp 1891-1902 (2016)
The multi-subunit eukaryotic translation initiation factor eIF3 is thought to assist in the recruitment of ribosomes to mRNA. The expression of eIF3 subunits is frequently disrupted in human cancers, but the specific roles of individual subunits in m
Externí odkaz:
https://doaj.org/article/1ec21db44c76446c99eebbfd733118c1
Autor:
Kenichi Sajiki, Yuria Tahara, Alejandro Villar-Briones, Tomáš Pluskal, Takayuki Teruya, Ayaka Mori, Mitsuko Hatanaka, Masahiro Ebe, Takahiro Nakamura, Keita Aoki, Yukinobu Nakaseko, Mitsuhiro Yanagida
Publikováno v:
Open Biology, Vol 8, Iss 3 (2018)
Rapamycin inhibits TOR (target of rapamycin) kinase, and is being used clinically to treat various diseases ranging from cancers to fibrodysplasia ossificans progressiva. To understand rapamycin mechanisms of action more comprehensively, 1014 tempera
Externí odkaz:
https://doaj.org/article/371540c6d1bd4831ba52b1813cdd9460