Institute of Bio- and Geosciences (IBG)

Bioinformatics (IBG-4)

Publications 2023

Publications of IBG-4 in 2023

Journal Article Becker, N.FZJ* ; Frieg, B.FZJ* ; Gremer, L.FZJ* ; Kupreichyk, T.FZJ* ; Gardon, L.FZJ* ; Freiburg, P. ; Neudecker, P.FZJ* ; Willbold, D.FZJ* ; Gohlke, H. (Corresponding author)FZJ* ; Heise, H. (Corresponding author)FZJ*
Atomic Resolution Insights into pH Shift Induced Deprotonation Events in LS-Shaped Aβ(1–42) Amyloid Fibrils
Journal of the American Chemical Society 145(4), 2161–2169 (2023) [10.1021/jacs.2c09231]2023 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Borggräfe, J. ; Gertzen, C. G. W. ; Viegas, A. ; Gohlke, H. (Corresponding author)FZJ* ; Etzkorn, M. (Corresponding author)FZJ*
The architecture of the 10‐23 DNA zyme and its implications for DNA ‐mediated catalysis
The FEBS journal 290(8), 2011-2021 (NA) [10.1111/febs.16698]NA Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Case, D. A. ; Aktulga, H. M. ; Belfon, K. ; Cerutti, D. S. ; Cisneros, G. A. ; Cruzeiro, V. W. D. ; Forouzesh, N. ; Giese, T. J. ; Götz, A. W. ; Gohlke, H.FZJ* ; Izadi, S. ; Kasavajhala, K. ; Kaymak, M. C. ; King, E. ; Kurtzman, T. ; Lee, T.-S. ; Li, P. ; Liu, J.FZJ* ; Luchko, T. ; Luo, R. ; Manathunga, M. ; Machado, M. R. ; Nguyen, H. M. ; O’Hearn, K. A. ; Onufriev, A. V. ; Pan, F. ; Pantano, S. ; Qi, R. ; Rahnamoun, A. ; Risheh, A. ; Schott-Verdugo, S.FZJ* ; Shajan, A. ; Swails, J. ; Wang, J. ; Wei, H. ; Wu, X. ; Wu, Y. ; Zhang, S.FZJ* ; Zhao, S. ; Zhu, Q. ; Cheatham, T. E. ; Roe, D. R. ; Roitberg, A. ; Simmerling, C. ; York, D. M. ; Nagan, M. C. (Corresponding author) ; Merz, K. M. (Corresponding author)
AmberTools
Journal of chemical information and modeling 63(20), 6183 - 6191 (2023) [10.1021/acs.jcim.3c01153]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Dittrich, J. ; Kolodzy, F. ; Töpel, A. ; Hofmann, A. ; Groth, G. ; Pich, A. (Corresponding author) ; Gohlke, H. (Corresponding author)FZJ*
Loading and Co-Solvent-Triggered Release of Okanin, a C4 Plant Key Enzyme Inhibitor, into/from Functional Microgels
The chemical engineering journal 460, 141631 (2023) [10.1016/j.cej.2023.141631]2023 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Dittrich, J. ; Popara, M. ; Kubiak, J. ; Dimura, M. ; Schepers, B. ; Verma, N. ; Schmitz, B. ; Dollinger, P. ; Kovacic, F.FZJ* ; Jaeger, K.-E. (Corresponding author)FZJ* ; Seidel, C. A. M. (Corresponding author) ; Peulen, T.-O. (Corresponding author) ; Gohlke, H. (Corresponding author)FZJ*
Resolution of Maximum Entropy Method-Derived Posterior Conformational Ensembles of a Flexible System Probed by FRET and Molecular Dynamics Simulations
Journal of chemical theory and computation 19(8), 2389 - 2409 (2023) [10.1021/acs.jctc.2c01090]2023 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Dumschott, K. (Corresponding author)FZJ* ; Dörpholz, H.FZJ* ; Laporte, M.-A. ; Brilhaus, D. ; Schrader, A. ; Usadel, B.FZJ* ; Neumann, S. ; Arnaud, E. ; Kranz, A. (Corresponding author)FZJ*
Ontologies for increasing the FAIRness of plant research data
Frontiers in plant science 14, 1279694 (2023) [10.3389/fpls.2023.1279694]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article El Harrar, T.FZJ* ; Gohlke, H. (Corresponding author)FZJ*
Cumulative Millisecond-Long Sampling for a Comprehensive Energetic Evaluation of Aqueous Ionic Liquid Effects on Amino Acid Interactions
Journal of chemical information and modeling 63(1), 281–298 (NA) [10.1021/acs.jcim.2c01123]NA Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Großkinsky, D. K. (Corresponding author) ; Faure, J.-D. ; Gibon, Y. ; Haslam, R. P. ; Usadel, B.FZJ* ; Zanetti, F. ; Jonak, C. (Corresponding author)
The potential of integrative phenomics to harness underutilized crops for improving stress resilience
Frontiers in plant science 14, 1216337 (2023) [10.3389/fpls.2023.1216337]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Gui, S. ; Martinez-Rivas, F. J. ; Wen, W. ; Meng, M. ; Yan, J. ; Usadel, B. (Corresponding author)FZJ* ; Fernie, A. R. (Corresponding author)
Going broad and deep: sequencing‐driven insights into plant physiology, evolution, and crop domestication
The plant journal 113(3), 446 - 459 (2023) [10.1111/tpj.16070]2023 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Haase, M.FZJ* ; David, B.FZJ* ; Paschold, B.FZJ* ; Classen, T.FZJ* ; Schneider, P. ; Pozhydaieva, N. ; Gohlke, H.FZJ* ; Pietruszka, J. (Corresponding author)FZJ*
Application of the C3-Methyltransferase StspM1 for the Synthesis of the Natural Pyrroloindole Motif
ACS catalysis 14(XXX), 227–236 (NA) [10.1021/acscatal.3c04952]NA OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Jayakodi, M. ; Golicz, A. A. ; Kreplak, J. ; et al
The giant diploid faba genome unlocks variation in a global protein crop
Nature <London> 615(7953), 652 - 659 (2023) [10.1038/s41586-023-05791-5]2023 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Julca, I. ; Mutwil-Anderwald, D. ; Manoj, V. ; Khan, Z. ; Lai, S. K. ; Yang, L. K. ; Beh, I. T. ; Dziekan, J. ; Lim, Y. P. ; Lim, S. K. ; Low, Y. W. ; Lam, Y. I. ; Tjia, S. ; Mu, Y. ; Tan, Q. W. ; Nuc, P. ; Choo, L. M. ; Khew, G. ; Shining, L. ; Kam, A. ; Tam, J. P. ; Bozdech, Z. ; Schmidt, M. ; Usadel, B.FZJ* ; Kanagasundaram, Y. ; Alseekh, S. ; Fernie, A. ; Li, H. Y. ; Mutwil, M. (Corresponding author)
Genomic, transcriptomic, and metabolomic analysis of Oldenlandia corymbosa reveals the biosynthesis and mode of action of anti‐cancer metabolites
Journal of integrative plant biology 65(6), 1442 - 1466 (2023) [10.1111/jipb.13469]2023 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Kaiser, J. ; Gertzen, C. G. W. ; Bernauer, T. ; Höfner, G. ; Niessen, K. V. ; Seeger, T. ; Paintner, F. F. ; Wanner, K. T. ; Worek, F. ; Thiermann, H. ; Gohlke, H. (Corresponding author)FZJ*
A novel binding site in the nicotinic acetylcholine receptor for MB327 can explain its allosteric modulation relevant for organophosphorus-poisoning treatment
Toxicology letters 373, 160-171 (2023) [10.1016/j.toxlet.2022.11.018]2023 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article König, P. (Corresponding author) ; Beier, S.FZJ* ; Mascher, M. ; Stein, N. ; Lange, M. ; Scholz, U.
DivBrowse—interactive visualization and exploratory data analysis of variant call matrices
GigaScience 12, giad025 (2023) [10.1093/gigascience/giad025]2023 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article La Sala, G. (Corresponding author) ; Pfleger, C. ; Käck, H. ; Wissler, L. ; Nevin, P. ; Böhm, K. ; Janet, J. P. ; Schimpl, M. ; Stubbs, C. J. ; De Vivo, M. ; Tyrchan, C. ; Hogner, A. ; Gohlke, H. (Corresponding author)FZJ* ; Frolov, A. I. (Corresponding author)
Combining structural and coevolution information to unveil allosteric sites
Chemical science 14(25), 7057-7067 (2023) [10.1039/D2SC06272K]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Lin, C. ; Kuffour, E. O. ; Fuchs, N. V. ; Gertzen, C. G. W. ; Kaiser, J. ; Hirschenberger, M. ; Tang, X. ; Xu, H. C. ; Michel, O. ; Tao, R. ; Haase, A. ; Martin, U. ; Kurz, T. ; Drexler, I. ; Görg, B. ; Lang, P. A. ; Luedde, T. ; Sparrer, K. M. J. ; Gohlke, H.FZJ* ; König, R. ; Münk, C. (Corresponding author)
Regulation of STING activity in DNA sensing by ISG15 modification
Cell reports 42(11), 113277 - (2023) [10.1016/j.celrep.2023.113277]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Lippi, N. ; Senger, E.FZJ* ; Karhu, S. ; Mezzetti, B. ; Cianciabella, M. ; Denoyes, B. ; Sönmez, D. A. ; Fidelis, M. ; Gatti, E. ; Höfer, M. ; Kafkas, N. E. ; Mazzoni, L. ; McCallum, S. ; Olbricht, K. ; Orsucci, S. ; Osorio, S. ; Pinczinger, D. ; Predieri, S. ; Rokka, S. ; Sánchez-Sevilla, J. F. ; Savini, G. ; Soria, C. ; Usadel, B.FZJ* ; Zucchi, P. ; Chiara, M. (Corresponding author)
Development and Validation of a Multilingual Lexicon as a Key Tool for the Sensory Analyses and Consumer Tests of Blueberry and Raspberry Fruit
Agriculture 13(2), 314 - (2023) [10.3390/agriculture13020314]2023 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Marasco, R. ; Fusi, M. ; Coscolín, C. ; Barozzi, A. ; Almendral, D. ; Bargiela, R. ; Nutschel, C. G. n.FZJ* ; Pfleger, C. ; Dittrich, J. ; Gohlke, H.FZJ* ; Matesanz, R. ; Sanchez-Carrillo, S. ; Mapelli, F. ; Chernikova, T. N. ; Golyshin, P. N. ; Ferrer, M. (Corresponding author) ; Daffonchio, D. (Corresponding author)
Enzyme adaptation to habitat thermal legacy shapes the thermal plasticity of marine microbiomes
Nature Communications 14(1), 1045 (2023) [10.1038/s41467-023-36610-0]2023 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Muñoz, P. ; Castillejo, C. ; Gómez, J. A. ; Miranda, L. ; Lesemann, S. ; Olbricht, K. ; Petit, A. ; Chartier, P. ; Haugeneder, A. ; Trinkl, J. ; Mazzoni, L. ; Masny, A. ; Zurawicz, E. ; Ziegler, F. M. R.FZJ* ; Usadel, B.FZJ* ; Schwab, W. ; Denoyes, B. ; Mezzetti, B. ; Osorio, S. ; Sánchez-Sevilla, J. F. ; Amaya, I. (Corresponding author)
QTL analysis for ascorbic acid content in strawberry fruit reveals a complex genetic architecture and association with GDP-L-galactose phosphorylase
Horticulture research 10(3), uhad006 (2023) [10.1093/hr/uhad006]2023 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Musyaffa, F. A. ; Rapp, K. ; Gohlke, H. (Corresponding author)FZJ*
LISTER: Semiautomatic Metadata Extraction from Annotated Experiment Documentation in eLabFTW
Journal of chemical information and modeling 63(20), 6224 - 6238 (2023) [10.1021/acs.jcim.3c00744]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Osorio, S. (Corresponding author) ; Costa, F. (Corresponding author) ; Gibon, Y. ; Usadel, B.FZJ* ; Vicente, A.
Advances in fruit development and ripening
The journal of experimental botany 74(20), 6205 - 6206 (2023) [10.1093/jxb/erad379]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Pandya, A.FZJ* ; Thiele, B.FZJ* ; Köppchen, S.FZJ* ; Zurita-Silva, A.Extern* ; Usadel, B.FZJ* ; Fiorani, F. (Corresponding author)FZJ*
Characterization of Bioactive Phenolic Compounds in Seeds of Chilean Quinoa (Chenopodium quinoa Willd.) Germplasm
Agronomy 13(8), 2170 - (2023) [10.3390/agronomy13082170]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Perez-Garcia, P. ; Chow, J. ; Costanzi, E. ; Gurschke, M. ; Dittrich, J. ; Dierkes, R. F. ; Molitor, R.FZJ* ; Applegate, V. ; Feuerriegel, G. ; Tete, P. ; Danso, D. ; Thies, S.FZJ* ; Schumacher, J. ; Pfleger, C. ; Jaeger, K.-E.FZJ* ; Gohlke, H.FZJ* ; Smits, S. H. J. ; Schmitz, R. A. (Corresponding author) ; Streit, W. R. (Corresponding author)
An archaeal lid-containing feruloyl esterase degrades polyethylene terephthalate
Communications chemistry 6(1), 193 (2023) [10.1038/s42004-023-00998-z]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Peulen, T. O. ; Hengstenberg, C. S. ; Biehl, R.FZJ* ; Dimura, M. ; Lorenz, C. ; Valeri, A. ; Folz, J. ; Hanke, C. A. ; Ince, S. ; Vöpel, T. ; Farago, B. ; Gohlke, H.FZJ* ; Klare, J. P. (Corresponding author) ; Stadler, A. M. (Corresponding author)FZJ* ; Seidel, C. A. (Corresponding author) ; Herrmann, C. (Corresponding author)
Integrative dynamic structural biology unveils conformers essential for the oligomerization of a large GTPase
eLife 12, e79565 (2023) [10.7554/eLife.79565]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Poorter, H. (Corresponding author)FZJ* ; Hummel, G. M. ; Nagel, K. A.FZJ* ; Fiorani, F.FZJ* ; von Gillhaussen, P.Extern* ; Virnich, O. ; Schurr, U.FZJ* ; Postma, J. A.FZJ* ; van de Zedde, R. ; Wiese-Klinkenberg, A.FZJ*
Pitfalls and potential of high-throughput plant phenotyping platforms
Frontiers in plant science 14, 1233794 (2023) [10.3389/fpls.2023.1233794] special issue: "Plant Phenotyping for a Sustainable Future"2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Pott, D. M. ; Durán-Soria, S. ; Allwood, J. W. ; Pont, S. ; Gordon, S. L. ; Jennings, N. ; Austin, C. ; Stewart, D. ; Brennan, R. M. ; Masny, A. ; Sønsteby, A. ; Krüger, E. ; Jarret, D. ; Vallarino, J. G. ; Usadel, B.FZJ* ; Osorio, S. (Corresponding author)
Dissecting the impact of environment, season and genotype on blackcurrant fruit quality traits
Food chemistry 402, 134360 - (2023) [10.1016/j.foodchem.2022.134360]2023 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Radchuk, V. (Corresponding author) ; Belew, Z. M. ; Gündel, A. ; Mayer, S. ; Hilo, A. ; Hensel, G. ; Sharma, R. ; Neumann, K. ; Ortleb, S. ; Wagner, S. ; Muszynska, A. ; Crocoll, C. ; Xu, D. ; Hoffie, I. ; Kumlehn, J. ; Fuchs, J. ; Peleke, F. F. ; Szymanski, J. J.FZJ* ; Rolletschek, H. ; Nour-Eldin, H. H. ; Borisjuk, L.
SWEET11b transports both sugar and cytokinin in developing barley grains
The plant cell 35(6), 2186 - 2207 (2023) [10.1093/plcell/koad055]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Specka, X. ; Martini, D. (Corresponding author) ; Weiland, C. ; Arend, D. ; Asseng, S. ; Boehm, F. ; Feike, T. ; Fluck, J. ; Gackstetter, D. ; Gonzales-Mellado, A. ; Hartmann, T. ; Haunert, J.-H. ; Hoedt, F. ; Hoffmann, C. ; König, P. ; Lange, M. ; Lesch, S. ; Lindstädt, B. ; Lischeid, G. ; Möller, M. ; Rascher, U.FZJ* ; Reif, J. C. ; Schmalzl, M. ; Senft, M. ; Stahl, U. ; Svoboda, N. ; Usadel, B.FZJ* ; Webber, H. ; Ewert, F.
FAIRagro: Ein Konsortium in der Nationalen Forschungsdateninfrastruktur (NFDI) für Forschungsdaten in der Agrosystemforschung
Informatik-Spektrum 46, 24-35 (2023) [10.1007/s00287-022-01520-w]2023 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Stalke, A. (Corresponding author) ; Behrendt, A. ; Hennig, F. ; Gohlke, H.FZJ* ; Buhl, N. ; Reinkens, T. ; Baumann, U. ; Schlegelberger, B. ; Illig, T. ; Pfister, E.-D. ; Skawran, B.
Functional characterization of novel or yet uncharacterized ATP7B missense variants detected in patients with clinical Wilson's disease
Clinical genetics 104(2), 174-185 (2023) [10.1111/cge.14352]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Tiozon, R. J. N. ; Sreenivasulu, N. ; Alseekh, S. ; Sartagoda, K. J. D. ; Usadel, B.FZJ* ; Fernie, A. R. (Corresponding author)
Metabolomics and machine learning technique revealed that germination enhances the multi-nutritional properties of pigmented rice
Communications biology 6(1), 1000 (2023) [10.1038/s42003-023-05379-9]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Twizerimana, A. P. ; Becker, D.FZJ* ; Zhu, S. ; Luedde, T. ; Gohlke, H.FZJ* ; Münk, C. (Corresponding author)
The cyclophilin A-binding loop of the capsid regulates the human TRIM5α sensitivity of nonpandemic HIV-1
Proceedings of the National Academy of Sciences of the United States of America 120(48), e2306374120 (2023) [10.1073/pnas.2306374120]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article van der Weg, K. J.FZJ* ; Gohlke, H. (Corresponding author)FZJ*
TopEnzyme: a framework and database for structural coverage of the functional enzyme space
Bioinformatics 39(3), btad116 (2023) [10.1093/bioinformatics/btad116]2023 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Weil, H. L. ; Schneider, K. ; Tschöpe, M. ; Bauer, J. ; Maus, O. ; Frey, K. ; Brilhaus, D. ; Martins Rodrigues, C. ; Doniparthi, G. ; Wetzels, F. ; Lukasczyk, J. ; Kranz, A.FZJ* ; Grüning, B. ; Zimmer, D. ; Deßloch, S. ; von Suchodoletz, D. ; Usadel, B.FZJ* ; Garth, C. ; Mühlhaus, T. (Corresponding author)
PLANTdataHUB : a collaborative platform for continuous FAIR data sharing in plant research
The plant journal 116(4), 974-988 (2023) [10.1111/tpj.16474]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Yakici, N. ; Kreins, A. Y. ; Catak, M. C. ; Babayeva, R. ; Erman, B. ; Kenney, H. ; Gungor, H. E. ; Cea, P. A. ; Kawai, T. ; Bosticardo, M. ; Delmonte, O. M. ; Adams, S. ; Fan, Y.-T. ; Pala, F. ; Turkyilmaz, A. ; Howley, E. ; Worth, A. ; Kot, H. ; Sefer, A. P. ; Kara, A. ; Bulutoglu, A. ; Eltan, S. B. ; Altunbas, M. Y. ; Bayram, F. ; Karakus, I. S. ; Karatay, E. ; Tekeoglu, S. D. ; Eser, M. ; Albayrak, D. ; Citli, S. ; Kiykim, A. ; Karakoc-Aydiner, E. ; Ozen, A. ; Ghosh, S. ; Gohlke, H.FZJ* ; Orhan, F. ; Notarangelo, L. D. ; Davies, E. G. ; Baris, S. (Corresponding author)
Expanding the clinical and immunological phenotypes of PAX1-deficient SCID and CID patients
Clinical immunology 255, 109757 (2023) [10.1016/j.clim.2023.109757]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Zhou, X.-R. (Corresponding author)FZJ* ; Beier, S.FZJ* ; Brilhaus, D. ; Martins Rodrigues, C. ; Mühlhaus, T. ; von Suchodoletz, D. ; Twyman, R. M. ; Usadel, B.FZJ* ; Kranz, A. (Corresponding author)FZJ*
DataPLAN: A Web-Based Data Management Plan Generator for the Plant Sciences
Data 8(11), 159 - (2023) [10.3390/data8110159]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Zrenner, R. (Corresponding author) ; Genzel, F.FZJ* ; Baldermann, S. ; Guerra, T. ; Grosch, R.
Does Constitutive Expression of Defense-Related Genes and Salicylic Acid Concentrations Correlate with Field Resistance of Potato to Black Scurf Disease?
Bioengineering 10(11), 1244 - (2023) [10.3390/bioengineering10111244]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Last Modified: 09.01.2025