Institute of Bio- and Geosciences (IBG)

Publications

Here you will find all of our institute's publications, sorted by date of publication.

Dataset Alexander SczyrbaFZJ* ; Peter BelmannFZJ* ; Benedikt OsterholzFZJ* ; Nils KleinböltingFZJ* ; Alfred Pühler ; Andreas Schlüter
Replication Data for: Metagenomics-Toolkit: the flexible and efficient cloud-based metagenomics workflow featuring machine learning-enabled resource allocation
[10.26165/juelich-data/kxdwii] BibTeX | EndNote: XML, Text | RIS

Journal Article Klein, J. ; Lam, H. ; Mak, T. D. ; Bittremieux, W. ; Perez-Riverol, Y. ; Gabriels, R. ; Shofstahl, J. ; Hecht, H. ; Binz, P.-A. ; Kawano, S. ; Van Den Bossche, T. ; Carver, J. ; Neely, B. A. ; Mendoza, L. ; Suomi, T. ; Claeys, T. ; Payne, T. ; Schulte, D. ; Sun, Z. ; Hoffmann, N.FZJ* ; Zhu, Y. ; Neumann, S. ; Jones, A. R. ; Bandeira, N. ; Vizcaíno, J. A. ; Deutsch, E. W.
The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: mzSpecLib and mzPAF
Analytical chemistry 96(46), 18491 - 18501 (2024) [10.1021/acs.analchem.4c04091]2024 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Lick, S. ; Wibberg, D.FZJ* ; Busche, T. ; Blom, J. ; Grimmler, C. ; Goesmann, A. ; Kalinowski, J.
Pseudomonas kulmbachensis sp. nov. and Pseudomonas paraveronii sp. nov., originating from chilled beef and chicken breast
International journal of systematic and evolutionary microbiology 74(4), 1 (2024) [10.1099/ijsem.0.006293]2024 BibTeX | EndNote: XML, Text | RIS

Journal Article Berckx, F. ; Van Nguyen, T. ; Hilker, R. ; Wibberg, D.FZJ* ; Battenberg, K. ; Kalinowski, J. ; Berry, A. ; Pawlowski, K. (Corresponding author)
Host dependent specialized metabolism of nitrogen export in actinorhizal nodules induced by Frankia cluster-2
The journal of experimental botany 76(4), 1164–1178 (2024) [10.1093/jxb/erae446]2024 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Torta, F. ; Hoffmann, N.FZJ* ; Burla, B. ; et al
Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards
Nature Communications 15(1), 8562 (2024) [10.1038/s41467-024-52087-x]2024 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Kopczynski, D. (Corresponding author) ; Ejsing, C. S. ; McDonald, J. G. ; Bamba, T. ; Baker, E. S. ; Bertrand-Michel, J. ; Brügger, B. ; Coman, C. ; Ellis, S. R. ; Garrett, T. J. ; Griffiths, W. J. ; Guan, X. L. ; Han, X. ; Höring, M. ; Holčapek, M. ; Hoffmann, N.FZJ* ; Huynh, K. ; Lehmann, R. ; Jones, J. W. ; Kaddurah-Daouk, R. ; Köfeler, H. C. ; Meikle, P. J. ; Metz, T. O. ; O’Donnell, V. B. ; Saigusa, D. ; Schwudke, D. ; Shevchenko, A. ; Torta, F. ; Vizcaíno, J. A. ; Welti, R. ; Wenk, M. R. ; Wolrab, D. ; Xia, Y. ; Ekroos, K. ; Ahrends, R. ; Liebisch, G.
The lipidomics reporting checklist a framework for transparency of lipidomic experiments and repurposing resource data
Journal of lipid research 65(9), 100621 - (2024) [10.1016/j.jlr.2024.100621]2024 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Bielow, C. ; Hoffmann, N.FZJ* ; Jimenez-Morales, D. ; Van Den Bossche, T. ; Vizcaíno, J. A. ; Tabb, D. L. ; Bittremieux, W. ; Walzer, M.
Communicating Mass Spectrometry Quality Information in mzQC with Python, R, and Java
Journal of the American Society for Mass Spectrometry 35(8), 1875–1882 (2024) [10.1021/jasms.4c00174]2024 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Helm, T.FZJ* ; Stausberg, T. ; Previati, M. ; Ernst, P.FZJ* ; Klein, B.FZJ* ; Busche, T. ; Kalinowski, J. ; Wibberg, D.FZJ* ; Wiechert, W.FZJ* ; Claerhout, L. ; Wierckx, N.FZJ* ; Noack, S. (Corresponding author)FZJ*
Itaconate Production from Crude Substrates with U. maydis: Scale-up of an Industrially Relevant Bioprocess
Microbial cell factories 23(1), 29 (2024) [10.1186/s12934-024-02295-3]2024 DBCoverage Files BibTeX | EndNote: XML, Text | RIS

Journal Article Witting, M. (First author) ; Malik, A. ; Leach, A. ; Bridge, A. ; Aimo, L. ; Conroy, M. J. ; O’Donnell, V. B. ; Hoffmann, N.FZJ* ; Kopczynski, D. ; Giacomoni, F. ; Paulhe, N. ; Gassiot, A. C. ; Poupin, N. ; Jourdan, F. ; Bertrand-Michel, J. (Corresponding author)
Challenges and perspectives for naming lipids in the context of lipidomics
Metabolomics 20(1), 15 (2024) [10.1007/s11306-023-02075-x]2024 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Heyer, R. ; Hellwig, P. (Corresponding author) ; Maus, I.FZJ* ; Walke, D. ; Schlüter, A. ; Hassa, J. ; Sczyrba, A.FZJ* ; Tubbesing, T. ; Klocke, M. ; Mächtig, T. ; Schallert, K. ; Seick, I. ; Reichl, U. ; Benndorf, D.
Breakdown of hardly degradable carbohydrates (lignocellulose) in a two-stage anaerobic digestion plant is favored in the main fermenter
Water research 250, 121020 - (2024) [10.1016/j.watres.2023.121020]2024 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Vondrackova, M. ; Kopczynski, D. ; Hoffmann, N.FZJ* ; Kuda, O. (Corresponding author)
LORA, Lipid Over-Representation Analysis Based on Structural Information
Analytical chemistry 95(34), 12600 - 12604 (2023) [10.1021/acs.analchem.3c02039]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article de Jonckheere, B. ; Kollotzek, F. ; Münzer, P. ; Göb, V. ; Fischer, M. ; Mott, K. ; Coman, C. ; Troppmair, N. N. ; Manke, M.-C. ; Zdanyte, M. ; Harm, T. ; Sigle, M. ; Kopczynski, D. ; Bileck, A. ; Gerner, C. ; Hoffmann, N.FZJ* ; Heinzmann, D. ; Assinger, A. ; Gawaz, M. ; Stegner, D. ; Schulze, H. ; Borst, O. (Corresponding author) ; Ahrends, R. (Corresponding author)
Critical shifts in lipid metabolism promote megakaryocyte differentiation and proplatelet formation
Nature cardiovascular research 2(9), 835 - 852 (2023) [10.1038/s44161-023-00325-8]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article/Contribution to a conference proceedings/Contribution to a book Hoffmann, N.FZJ* ; Maus, I.FZJ* ; Beier, S.FZJ* ; Belmann, P.FZJ* ; Krüger, J.FZJ* ; Tauch, A. ; Goesmann, A. ; Eils, R. ; Bork, P. ; Kohlbacher, O. ; Kummer, U. ; Backofen, R. ; Buchhalter, I. ; Sczyrba, A. (Corresponding author)FZJ*
Embedding the de.NBI Cloud in the National Research Data Infrastructure Activities
2023NFDI Conference on Research Data Infrastructure, CORDI, KarlsruheKarlsruhe, Germany, 12 Sep 2023 - 14 Sep 20232023-09-122023-09-14 Proceedings of the conference on research data infrastructure 1, (2023) [10.52825/cordi.v1i.387]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Contribution to a book Holčapek, M. (Editor) ; Ekroos, K. (Editor) ; Kopczynski, D. ; Krause, D. ; Al Machot,, F. ; Schwudke, D. ; Hoffmann, N.FZJ* ; Ahrends, R. (Corresponding author)
The Past and Future of Lipidomics Bioinformatics
2023Mass Spectrometry for Lipidomics / Holčapek, Michal (Editor) ; : Wiley, 2023, ; ISBN: 9783527350155 ; doi:10.1002/9783527836512 Weinheim : Wiley 1, 271-290 (2023) [10.1002/9783527836512.ch10]2023 BibTeX | EndNote: XML, Text | RIS

Journal Article Ni, Z. ; Wölk, M. ; Jukes, G. ; Mendivelso Espinosa, K. ; Ahrends, R. ; Aimo, L. ; Alvarez-Jarreta, J. ; Andrews, S. ; Andrews, R. ; Bridge, A. ; Clair, G. C. ; Conroy, M. J. ; Fahy, E. ; Gaud, C. ; Goracci, L. ; Hartler, J. ; Hoffmann, N.FZJ* ; Kopczyinki, D. ; Korf, A. ; Lopez-Clavijo, A. F. ; Malik, A. ; Ackerman, J. M. ; Molenaar, M. R. ; O’Donovan, C. ; Pluskal, T. ; Shevchenko, A. ; Slenter, D. ; Siuzdak, G. ; Kutmon, M. ; Tsugawa, H. ; Willighagen, E. L. ; Xia, J. ; O’Donnell, V. B. (Corresponding author) ; Fedorova, M. (Corresponding author)
Guiding the choice of informatics software and tools for lipidomics research applications
Nature methods 20(2), 193 - 204 (2023) [10.1038/s41592-022-01710-0]2023 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Deutsch, E. W. (Corresponding author) ; Vizcaíno, J. A. ; Jones, A. R. ; Binz, P.-A. ; Lam, H. ; Klein, J. ; Bittremieux, W. ; Perez-Riverol, Y. ; Tabb, D. L. ; Walzer, M. ; Ricard-Blum, S. ; Hermjakob, H. ; Neumann, S. ; Mak, T. D. ; Kawano, S. ; Mendoza, L. ; Van Den Bossche, T. ; Gabriels, R. ; Bandeira, N. ; Carver, J. ; Pullman, B. ; Sun, Z. ; Hoffmann, N.FZJ* ; Shofstahl, J. ; Zhu, Y. ; Licata, L. ; Quaglia, F. ; Tosatto, S. C. E. ; Orchard, S. E.
Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work
Journal of proteome research 22(2), 287 - 301 (2023) [10.1021/acs.jproteome.2c00637]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Schmid, R. ; Heuckeroth, S. ; Korf, A. ; Smirnov, A. ; Myers, O. ; Dyrlund, T. S. ; Bushuiev, R. ; Murray, K. J. ; Hoffmann, N.FZJ* ; Lu, M. ; Sarvepalli, A. ; Zhang, Z. ; Fleischauer, M. ; Dührkop, K. ; Wesner, M. ; Hoogstra, S. J. ; Rudt, E. ; Mokshyna, O. ; Brungs, C. ; Ponomarov, K. ; Mutabdžija, L. ; Damiani, T. ; Pudney, C. J. ; Earll, M. ; Helmer, P. O. ; Fallon, T. R. ; Schulze, T. ; Rivas-Ubach, A. ; Bilbao, A. ; Richter, H. ; Nothias, L.-F. ; Wang, M. ; Orešič, M. ; Weng, J.-K. ; Böcker, S. ; Jeibmann, A. ; Hayen, H. ; Karst, U. ; Dorrestein, P. C. ; Petras, D. ; Du, X. ; Pluskal, T. (Corresponding author)
Integrative analysis of multimodal mass spectrometry data in MZmine 3
Nature biotechnology 41(4), 447 - 449 (2023) [10.1038/s41587-023-01690-2]2023 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Kopczynski, D. (First author) ; Hoffmann, N. (First author)FZJ* ; Peng, B. ; Liebisch, G. ; Spener, F. ; Ahrends, R. (Corresponding author)
Goslin 2.0 Implements the Recent Lipid Shorthand Nomenclature for MS-Derived Lipid Structures
Analytical chemistry 94(16), 6097 - 6101 (2022) [10.1021/acs.analchem.1c05430]2022 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article McDonald, J. G. ; Ejsing, C. S. ; Kopczynski, D. ; Holčapek, M. ; Aoki, J. ; Arita, M. ; Arita, M. ; Baker, E. S. ; Bertrand-Michel, J. ; Bowden, J. A. ; Brügger, B. ; Ellis, S. R. ; Fedorova, M. ; Griffiths, W. J. ; Han, X. ; Hartler, J. ; Hoffmann, N.FZJ* ; Koelmel, J. P. ; Köfeler, H. C. ; Mitchell, T. W. ; O’Donnell, V. B. ; Saigusa, D. ; Schwudke, D. ; Shevchenko, A. ; Ulmer, C. Z. ; Wenk, M. R. ; Witting, M. ; Wolrab, D. ; Xia, Y. ; Ahrends, R. (Corresponding author) ; Liebisch, G. (Corresponding author) ; Ekroos, K. (Corresponding author)
Introducing the Lipidomics Minimal Reporting Checklist
Nature metabolism 4(9), 1086 - 1088 (2022) [10.1038/s42255-022-00628-3]2022 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Philippe, A.-M. (Corresponding author) ; Sill, C. ; Westermann, S.FZJ* ; Allgaier, J.FZJ* ; Staropoli, M. ; Monkenbusch, M.FZJ* ; Gerstner, D. ; Fleming, Y. ; Wischnewski, A.FZJ* ; Hoffmann, N. ; Zolnierczuk, P.FZJ* ; Do, C. ; Pyckhout-Hintzen, W.FZJ*
Quantifying structure and dynamics of bound and bulk polymer in tailor-made rubber-silica nanocomposites
Frontiers in physics 10, 1023234 (2022) [10.3389/fphy.2022.1023234]2022 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Schafhauser, T. (Corresponding author) ; Wibberg, D.FZJ* ; Binder, A. ; Rückert, C. ; Busche, T. ; Wohlleben, W. ; Kalinowski, J.
Genome Assembly and Genetic Traits of the Pleuromutilin-Producer Clitopilus passeckerianus DSM1602
Journal of Fungi 8(8), 862 - (2022) [10.3390/jof8080862]2022 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Hoffmann, N. (Corresponding author)FZJ* ; Mayer, G. ; Has, C. ; Kopczynski, D. ; Al Machot, F. ; Schwudke, D. ; Ahrends, R. ; Marcus, K. ; Eisenacher, M. ; Turewicz, M.
A Current Encyclopedia of Bioinformatics Tools, Data Formats and Resources for Mass Spectrometry Lipidomics
Metabolites 12(7), 584 - (2022) [10.3390/metabo12070584]2022 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Uszkoreit, J. (Corresponding author)FZJ* ; Barkovits, K. ; Pacharra, S. ; Pfeiffer, K. ; Steinbach, S. ; Marcus, K. ; Eisenacher, M.
Dataset containing physiological amounts of spike-in proteins into murine C2C12 background as a ground truth quantitative LC-MS/MS reference
Data in Brief 43, 108435 - (2022) [10.1016/j.dib.2022.108435]2022 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Schenk, J. (Corresponding author) ; Höss, S. ; Kleinbölting, N.FZJ* ; Traunspurger, W.
Suitability of molecular taxonomy for assessing polluted sediments using the NemaSPEAR[%] index
Ecological indicators 137, 108761 - (2022) [10.1016/j.ecolind.2022.108761]2022 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Last Modified: 23.10.2024