Publications of D. Walther

Leer, M.; Soultoukis, G. A.; Jähnert, M.; Oveisi, M.; Walther, D.; Schulz, T. J.: pubCounteR: an R package for interrogating published literature for experimentally-derived gene lists within a user-defined biological context. Frontiers in Bioinformatics Volume 5, 1523184 (2025)

Wagner, M.; Kang, J.; Mercado, C.; Thirumlaikumar, V. P.; Gorka, M.; Zillmer, H.; Guo, J.; Minen, R. I.; Plecki, C. F.; Dehesh, K. et al.; Schroeder, F. C.; Walther, D.; Skirycz, A.: Mapping protein-metabolite interactions in E. coli by integrating chromatographic techniques and co-fractionation mass spectrometry. iScience, 112611 (2025)

Paajanen, P.; Tomkins, M.; Hoerbst, F.; Veevers, R.; Heeney, M.; Thomas, H. R.; Apelt, F.; Saplaoura, E.; Gupta, S.; Frank, M. et al.; Walther, D.; Faulkner, C.; Kehr, J.; Kragler, F.; Morris, R. J.: Re-analysis of mobile mRNA datasets raises questions about the extent of long-distance mRNA communication. Nature Plants (2025)

Hernández-Sánchez, I.E.; Rindfleisch, T.; Alpers, J.; Dulle, M.; Garvey, C. J.; Knox-Brown, P.; Miettinen, M. S.; Nagy, G.; Pusterla, J. M.; Rekas, A. et al.; Shou, K.; Stadler, A. M.; Walther, D.; Wolff, M.; Zuther, E.; Thalhammer, A.: Functional in vitro diversity of an intrinsically disordered plant protein during freeze–thawing is encoded by its structural plasticity. Protein Science 33 (5), e4989 (2024)

Uflewski, M.; Rindfleisch, T.; Korkmaz, K.; Tietz, E.; Mielke, S.; Correa Galvis, V.; Dünschede, B.; Luzarowski, M.; Skirycz, A.; Schwarzländer, M. et al.; Strand, D.; Hertle, A. P.; Schünemann, D.; Walther, D.; Thalhammer, A.; Wolff, M.; Armbruster, U.: The thylakoid proton antiporter KEA3 regulates photosynthesis in response to the chloroplast energy status. Nature Communications 15, 2792 (2024)

Murik, O.; Geffen, O.; Shotland, Y.; Fernandez-Pozo, N.; Ullrich, K. K.; Walther, D.; Rensing, S. A.; Treves, H.: Genomic imprints of unparalleled growth. New Phytologist 241 (3), pp. 1144 - 1160 (2023)

Back, G.; Walther, D.: Predictions of DNA mechanical properties at a genomic scale reveal potentially new functional roles of DNA flexibility. NAR: genomics and bioinformatics 5 (4), lqad097 (2023)

Giese, J.; Eirich, J.; Walther, D.; Zhang, Y.; Lassowskat, I.; Fernie, A. R.; Elsässer, M.; Maurino, V. G.; Schwarzländer, M.; Finkemeier, I.: The interplay of post-translational protein modifications in Arabidopsis leaves during photosynthesis induction. The Plant Journal 116 (4), pp. 1172 - 1193 (2023)

Weiszmann, J.; Walther, D.; Clauw, P.; Back, G.; Gunis, J.; Reichardt, I.; Koemeda, S.; Jez, J.; Nordborg, M.; Schwarzerova, J. et al.; Pierides, I.; Nägele, T.; Weckwerth, W.: Metabolome plasticity in 241 Arabidopsis thaliana accessions reveals evolutionary cold adaptation processes. Plant Physiology 193 (2), pp. 980 - 1000 (2023)

Qiu, Y.; Li, Z.; Walther, D.; Köhler, C.: Updated phylogeny and protein structure predictions revise the hypothesis on the origin of MADS-box transcription factors in land plants. Molecular Biology and Evolution 40 (9), msad194 (2023)

Loiacono, F.V.; Walther, D.; Seeger, S.; Thiele, W.; Gerlach, I.; Karcher, D.; Schöttler, M. A.; Zoschke, R.; Bock, R.: Emergence of novel RNA editing sites by changes in the binding affinity of a conserved PPR protein. Molecular Biology and Evolution 39 (12), msac222 (2022)

Chen, L.; Zhao, H.; Chen, Y.; Jiang, F.; Zhou, F.; Liu, Q.; Fan, Y.; Liu, T.; Tu, W.; Walther, D. et al.; Song, B.: Comparative transcriptomics analysis reveals a calcineurin B-like gene to positively regulate constitutive and acclimated freezing tolerance in potato. Plant, Cell and Environment 45 (11), pp. 3305 - 3321 (2022)

Fischer, A.; Dotzek, J.; Walther, D.; Greiner, S.: Graph-based models of the Oenothera mitochondrial genome capture the enormous complexity of higher plant mitochondrial DNA organization. NAR: genomics and bioinformatics 4 (2), lqac027 (2022)

Hoang, Y.; Gryzik, S.; Hoppe, I.; Rybak, A.; Schädlich, M.; Kadner, I.; Walther, D.; Vera, J.; Radbruch, A.; Groth, D. et al.; Baumgart, S.; Baumgrass, R.: PRI: Re-analysis of a public mass cytometry dataset reveals patterns of effective tumor treatments. Frontiers in immunology 13, 849329 (2022)

Thieme, S.; Walther, D.: Biclique extension as an effective approach to identify missing links in metabolic compound-protein interaction networks. Bioinformatics advances 2 (1), vbac001 (2022)

Martinez-Seidel, F.; Hsieh, Y.-C.; Walther, D.; Kopka, J.; Firmino, A.: COSNet(i): ComplexOme-Structural Network Interpreter used to study spatial enrichment in metazoan ribosomes. BMC Bioinformatics 22, 605 (2021)

Moreno, J.C.; Rojas, B.E.; Vicente, R.; Gorka, M.; Matz, T.; Kosmacz, M.; Peralta-Ariza, J.S.; Zhang, Y.; Alseekh, S.; Childs, D. et al.; Luzarowski, M.; Nikoloski, Z.; Zarivach, R.; Walther, D.; Hartman, M.D.; Figueroa, C.M.; Iglesias, A.A.; Fernie, A. R.; Skirycz, A.: Tyr-Asp inhibition of glyceraldehyde 3-phosphate dehydrogenase affects plant redox metabolism. EMBO Journal 40 (15), e106800 (2021)

Back, G.; Walther, D.: Identification of cis-regulatory motifs in first introns and the prediction of intron-mediated enhancement of gene expression in Arabidopsis thaliana. BMC Genomics 22 (1), 390 (2021)

Kuang, J.-F.; Wu, C.-J.; Guo, Y.-F.; Walther, D.; Shan, W.; Chen, J.-Y.; Chen, L.; Lu, W.-J.: Deciphering Transcriptional Regulators of Banana Fruit Ripening by Regulatory Network Analysis. Plant Biotechnology Journal 19 (3), pp. 477 - 489 (2021)

Martinez-Seidel, F.; Beine-Golovchuk, O.; Hsieh, Y.-C.; El Eshraky, K.; Gorka, M.; Cheong, B.-E.; Jimenez‐posada, E.V.; Walther, D.; Skirycz, A.; Roessner, U. et al.; Kopka, J.; Firmino, A.: Spatially enriched paralog rearrangements argue functionally diverse ribosomes arise during cold acclimation in arabidopsis. International Journal of Molecular Sciences 22 (11), 6160 (2021)