Zobrazeno 1 - 10
of 19
pro vyhledávání: '"Oliver Alka"'
Autor:
Eftychia E. Kontou, Axel Walter, Oliver Alka, Julianus Pfeuffer, Timo Sachsenberg, Omkar S. Mohite, Matin Nuhamunada, Oliver Kohlbacher, Tilmann Weber
Publikováno v:
Journal of Cheminformatics, Vol 15, Iss 1, Pp 1-12 (2023)
Abstract Metabolomics experiments generate highly complex datasets, which are time and work-intensive, sometimes even error-prone if inspected manually. Therefore, new methods for automated, fast, reproducible, and accurate data processing and derepl
Externí odkaz:
https://doaj.org/article/3eac90bcea8046f0b2c75985a30b6984
Autor:
Oliver Alka, Premy Shanthamoorthy, Michael Witting, Karin Kleigrewe, Oliver Kohlbacher, Hannes L. Röst
Publikováno v:
Nature Communications, Vol 13, Iss 1, Pp 1-9 (2022)
The extraction of meaningful biological knowledge from high-throughput mass spectrometry data relies on limiting false discoveries to a manageable amount. Here the authors establish an automated, false discovery rate-controlled targeted analysis work
Externí odkaz:
https://doaj.org/article/ff39f31ef3ae4b09b3f9f82ade6676b4
Autor:
Tamara Scheidt, Oliver Alka, Humberto Gonczarowska-Jorge, Wolfgang Gruber, Florian Rathje, Margherita Dell’Aica, Marc Rurik, Oliver Kohlbacher, René P. Zahedi, Fritz Aberger, Christian G. Huber
Publikováno v:
Cell Communication and Signaling, Vol 18, Iss 1, Pp 1-18 (2020)
Abstract Background Aberrant hedgehog (HH) signaling is implicated in the development of various cancer entities such as medulloblastoma. Activation of GLI transcription factors was revealed as the driving force upon pathway activation. Increased pho
Externí odkaz:
https://doaj.org/article/274b593e3c1b42f79ca06a9c78081fdb
Autor:
Eftychia Eva Kontou, Axel Walter, Timo Sachsenberg, Tilmann Weber, Oliver Alka, Julianus Pfeuffer, Matin Nuhamunada, Omkar Mohite, Oliver Kohlbacher
Publikováno v:
Kontou, E E, Walter, A, Alka, O, Pfeuffer, J, Sachsenberg, T, Mohite, O S, Nuhamunada, M, Kohlbacher, O & Weber, T 2023, ' UmetaFlow : an untargeted metabolomics workflow for high-throughput data processing and analysis ', Journal of Cheminformatics, vol. 15, 52 . https://doi.org/10.1186/s13321-023-00724-w
Metabolomics experiments generate highly complex datasets, which are time and work-intensive, sometimes even error-prone if inspected manually. Therefore, new methods for automated, fast, reproducible, and accurate data processing and dereplication a
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::42768bcc0bdb98824df709466c0750d6
https://doi.org/10.26434/chemrxiv-2022-z0t4g-v2
https://doi.org/10.26434/chemrxiv-2022-z0t4g-v2
Autor:
Markus J. Herrgård, Bo Burla, Lars Schrübbers, Douglas McCloskey, Pasquale Colaianni, Lars K. Nielsen, Oliver Kohlbacher, Timo Sachsenberg, Federico Torta, Mette Kristensen, Hannes L. Röst, Svetlana Kutuzova, Oliver Alka
Publikováno v:
Kutuzova, S, Colaianni, P D, Röst, H, Sachsenberg, T, Alka, O, Kohlbacher, O, Burla, B, Torta, F, Schrübbers, L, Kristensen, M, Nielsen, L, Herrgård, M J & McCloskey, D 2020, ' SmartPeak Automates Targeted and Quantitative Metabolomics Data Processing ', Analytical Chemistry, vol. 94, no. 24, pp. 15968–15974 . https://doi.org/10.1021/acs.analchem.0c03421
SmartPeak is an application that encapsulates advanced algorithms to enable fast, accurate, and automated processing of CE-, GC- and LC-MS(/MS) data, and HPLC data for targeted and semi-targeted metabolomics, lipidomics, and fluxomics experiments.Hig
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::81646679062477bb3b4748b6948f4ccd
https://doi.org/10.1021/acs.analchem.0c03421
https://doi.org/10.1021/acs.analchem.0c03421
Autor:
Robert A. Quinn, Mélissa Nothias-Esposito, Oriane Moyne, Neha Garg, Fernando Vargas, Hiroshi Tsugawa, Zdeněk Kameník, Bindesh Shrestha, Julia M. Gauglitz, Sven W. Meyer, Tam Dang, Pieter C. Dorrestein, Michael Witting, Abinesh Sarvepalli, Madeleine Ernst, Alexey Gurevich, Giorgis Isaac, Nikolas Kessler, Zheng Zhang, Robin Schmid, Marcus Ludwig, Ngoc Hung Nguyen, Johannes Rainer, Mingxun Wang, Theodore Alexandrov, Laura-Isobel McCall, Ivan Protsyuk, Audrey Le Gouellec, Pierre-Marie Allard, Sebastian Böcker, Alan K. Jarmusch, Ricardo Silva, Heiko Neuweger, Irina Koester, Ansgar Korf, Oliver Kohlbacher, Anupriya Tripathi, Daniel Petras, Kai Dührkop, Simon Rogers, Julien Paolini, Alexander A. Aksenov, Markus Fleischauer, Oliver Alka, Fabian Aicheler, Steffen Neumann, Kelly C. Weldon, Louis-Félix Nothias, Mustafa Morsy, Christian Martin H, Hosein Mohimani, Vanessa V. Phelan, Nuno Bandeira, Jonathan McSayles, Xavier Cachet, Justin J. J. van der Hooft, Kyo Bin Kang, Florian Zubeil, Tomáš Pluskal, Aiko Barsch, Heejung Yang, Andrés Mauricio Caraballo-Rodríguez
Publikováno v:
Nature methods, vol 17, iss 9
Nature methods
Nature Methods
Nature Methods, Nature Publishing Group, 2020, 17 (9), pp.905-908. ⟨10.1038/s41592-020-0933-6⟩
Nat. Methods 17, 905–908 (2020)
Nature Methods 17 (2020) 9
Nature Methods, 17(9), 905-908
Nature methods
Nature Methods
Nature Methods, Nature Publishing Group, 2020, 17 (9), pp.905-908. ⟨10.1038/s41592-020-0933-6⟩
Nat. Methods 17, 905–908 (2020)
Nature Methods 17 (2020) 9
Nature Methods, 17(9), 905-908
Feature-based molecular networking allows the generation of molecular networks for mass spectrometry data that can recognize isomers, incorporate relative quantification and integrate ion mobility data.Molecular networking has become a key method to
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6a31c0489fe436e78d33f542d30efe91
https://doi.org/10.1038/s41592-020-0933-6
https://doi.org/10.1038/s41592-020-0933-6
Autor:
Oliver, Alka, Premy, Shanthamoorthy, Michael, Witting, Karin, Kleigrewe, Oliver, Kohlbacher, Hannes L, Röst
Publikováno v:
Nat. Commun. 13:1347 (2022)
The extraction of meaningful biological knowledge from high-throughput mass spectrometry data relies on limiting false discoveries to a manageable amount. For targeted approaches in metabolomics a main challenge is the detection of false positive met
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=pmid_dedup__::49e274e7cc953f076882690ae796873d
https://push-zb.helmholtz-muenchen.de/frontdoor.php?source_opus=64639
https://push-zb.helmholtz-muenchen.de/frontdoor.php?source_opus=64639
Autor:
Leon Bichmann, George Rosenberger, Phil Ewels, Hannes L. Röst, Timo Sachsenberg, Oliver Kohlbacher, Leon Kuchenbecker, Shubham Gupta, Julianus Pfeuffer, Oliver Alka
Publikováno v:
Journal of proteome research. 20(7)
Data-independent acquisition (DIA) is becoming a leading analysis method in biomedical mass spectrometry. The main advantages include greater reproducibility and sensitivity and a greater dynamic range compared with data-dependent acquisition (DDA).
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::561c8bbf69747e1cd77c6172d3116065
https://pubmed.ncbi.nlm.nih.gov/34153189
https://pubmed.ncbi.nlm.nih.gov/34153189
Autor:
George Rosenberger, Oliver Kohlbacher, Shubham Gupta, Leon Bichmann, Hannes L. Röst, Leon Kuchenbecker, Timo Sachsenberg, Oliver Alka, Julianus Pfeuffer
Data-independent acquisition (DIA) is becoming a leading analysis method in biomedical mass spectrometry. Main advantages include greater reproducibility, sensitivity and dynamic range compared to data-dependent acquisition (DDA). However, data analy
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::ea50c251176ceec77725264943440a0c
https://doi.org/10.1101/2020.12.08.415844
https://doi.org/10.1101/2020.12.08.415844
Publikováno v:
Methods in molecular biology (Clifton, N.J.). 2104
This chapter describes the open-source tool suite OpenMS. OpenMS contains more than 180 tools which can be combined to build complex and flexible data-processing workflows. The broad range of functionality and the interoperability of these tools enab
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=pmid________::185fac97356de989b565c05c23c10e57
https://pubmed.ncbi.nlm.nih.gov/31953812
https://pubmed.ncbi.nlm.nih.gov/31953812