Publications:
2025
Engelhorn, J.; Snodgrass, S. J.; Kok, A.; Seetharam, A. S.; Schneider, M.; Kiwit, T.; Singh, A.; Banf, M.; Khaipho-Burch, M.; Runcie, D. E.; Sanchez-Camargo, V. A.; Torres-Rodriguez, J. V.; Sun, G.; Stam, M.; Fiorani, F.; Beier, S.; Schnable, J. C.; Bass, H. W.; Hufford, M. B.; Stich, B.; Frommer, W. B.; Ross-Ibarra, J.; Hartwig, T. Genetic Variation at Transcription Factor Binding Sites Largely Explains Phenotypic Heritability in Maize. Nature Genetics 2025, in press, 2023.08.08.551183. https://doi.org/10.1101/2023.08.08.551183.
2024
Kühl, M.; Wu, P.-Y.; Shrestha, A.; Engelhorn, J.; Hartwig, T.; Stich, B. Investigating the Barley Methylome, Its Variation and Association with Genomic, Transcriptomic, and Phenotypic Variation. Plant Biology October 22, 2024. https://doi.org/10.1101/2024.10.21.619366.
Kaur, A.; Best, N. B.; Hartwig, T.; Budka, J.; Khangura, R. S.; McKenzie, S.; Aragón-Raygoza, A.; Strable, J.; Schulz, B.; Dilkes, B. P. A Maize Semi-Dwarf Mutant Reveals a GRAS Transcription Factor Involved in Brassinosteroid Signaling. Plant Physiology 2024, 195 (4), 3072–3096. https://doi.org/10.1093/plphys/kiae147.
Casale, F.; Arlt, C.; Kühl, M.; Li, J.; Engelhorn, J.; Hartwig, T.; Stich, B. The Role of Methylation and Structural Variants in Shaping the Recombination Landscape of Barley. Genomics July 23, 2024. https://doi.org/10.1101/2024.07.22.604552.
Manosalva Pérez, N.; Ferrari, C.; Engelhorn, J.; Depuydt, T.; Nelissen, H.; Hartwig, T.; Vandepoele, K. MINI‐AC : Inference of Plant Gene Regulatory Networks Using Bulk or Single‐cell Accessible Chromatin Profiles. The Plant Journal 2024, 117 (1), 280–301. https://doi.org/10.1111/tpj.16483.
2023
Banf, M.; Zhao, K.; Hartwig, T. Editorial: Modern Machine Learning Approaches for Quantitative Inference of Gene Regulation from Genomic and Epigenomic Features. Front. Plant Sci. 2023, 14, 1330793. https://doi.org/10.3389/fpls.2023.1330793.
Hartwig, T.; Banf, M.; Prietsch, G. P.; Zhu, J.-Y.; Mora-Ramírez, I.; Schippers, J. H. M.; Snodgrass, S. J.; Seetharam, A. S.; Huettel, B.; Kolkman, J. M.; Yang, J.; Engelhorn, J.; Wang, Z.-Y. Hybrid Allele-Specific ChIP-Seq Analysis Identifies Variation in Brassinosteroid-Responsive Transcription Factor Binding Linked to Traits in Maize. Genome Biol 2023, 24 (1), 108. https://doi.org/10.1186/s13059-023-02909-w.
Myers, Z. A.; Wootan, C. M.; Liang, Z.; Zhou, P.; Engelhorn, J.; Hartwig, T.; Nathan, S. M. Conserved and Variable Heat Stress Responses of the Heat Shock Factor Transcription Factor Family in Maize and Setaria viridis . Plant Direct 2023, 7 (4), e489. https://doi.org/10.1002/pld3.489.
2022
Liang, Z.; Myers, Z. A.; Petrella, D.; Engelhorn, J.; Hartwig, T.; Springer, N. M. Mapping Responsive Genomic Elements to Heat Stress in a Maize Diversity Panel. Genome Biol 2022, 23 (1), 234. https://doi.org/10.1186/s13059-022-02807-7.
Weisweiler, M.; Arlt, C.; Wu, P.-Y.; Van Inghelandt, D.; Hartwig, T.; Stich, B. Structural Variants in the Barley Gene Pool: Precision and Sensitivity to Detect Them Using Short-Read Sequencing and Their Association with Gene Expression and Phenotypic Variation. Theor Appl Genet 2022, 135 (10), 3511–3529. https://doi.org/10.1007/s00122-022-04197-7.
Z. A. Myers, C. M. Wootan, Z. Liang, P. Zhou, J. Englehorn, T. Hartwig, N. M. Springer (2022). Conserved and variable responses of the HEAT SHOCK FACTOR transcription factor family in maize and Setaria viridis. doi.org/10.1101/2022.05.19.492695
2021
M. Banf; T. Hartwig (2021). The Reasonable Effectiveness of Randomness in Scalable and Integrative Gene Regulatory Network Inference and Beyond. Computation
S. D. Savadel**, T. Hartwig**, Z M. Turpin, D. L. Vera, P.-Y. Lung, X. Sui, M. Blank, W. B. Frommer, J. H. Dennis, J. Zhang, H. W. Bass (2021). The native cistrome and sequence motif families of the maize ear. PLOS Genetics
J. Moe-Lange, N. M. Gappel, M. Machado, M. M. Wudick, C. S. A. Sies, S. N. Schott-Verdugo, M. Bonus, S. Mishra, T. Hartwig, M. Bezrutczyk, D. Basu, E. E. Farmer, H. Gohlke, A. Malkovskiy, E. S. Haswell, M. J. Lercher, D. W. Ehrhardt, W. B. Frommer, T. J Kleist 2021. Interdependence of a mechanosensitive anion channel and glutamate receptors in distal wound signaling. Science Advances
M. Bezrutczyk, N. R Zöllner, C. PS Kruse, T. Hartwig, T. Lautwein, K. Köhrer, W. B Frommer, J. Kim (2021). Evidence for phloem loading via the abaxial bundle sheath cells in maize leaves. Plant Cell
J-K. Kim, E. Symeonidi, T. Y. Pang, T. Denyer, D. Weidauer, M. Bezrutczyk, M. Miras, N. Zöllner, T. Hartwig, M. M. Wudick, M. Lercher, L. Chen, M. CP Timmermans, W. B. Frommer (2021). Distinct identities of leaf phloem cells revealed by single cell transcriptomics. Plant Cell
Y. Bi, Z. Deng, W. Ni, R. Shrestha, D. Savage, T. Hartwig, S. Patil, S. H. Hong, Z. Zhang, J. A Oses-Prieto, K. H Li, P. H. Quail, A. L. Burlingame, S. Xu, Z. Wang (2021). Arabidopsis ACINUS is O-glycosylated and regulates transcription and alternative splicing of regulators of reproductive transitions. Nature Comm.
2020
J. Moreno-Romero, A. V. Probst, I. Trindade, Kalyanikrishna, J. Engelhorn, and S. Farrona (2020). “Looking At the Past and Heading to the Future: Meeting Summary of the 6th European Workshop on Plant Chromatin 2019 in Cologne, Germany” (2020). Frontiers in Plant Science 10.
P. Comelli, D. Glowa, A. Frerichs, J. Engelhorn, J. W. Chandler, and W. Werr (2020). “Functional dissection of the DORNRÖSCHEN-LIKE enhancer 2 during embryonic and phyllotactic patterning”. Planta 251.4.
Selected 2019 and earlier
A. Frerichs, J. Engelhorn, J. Altmüller, J. Gutierrez-Marcos, and W. Werr (2019). “Specific chromatin changes mark lateral organ founder cells in the Arabidopsis inflorescence meristem”. J. Exp. Bot. 70.15.
Y. Lu, S. A. Hokin, J. L. Kermicle, T. Hartwig, M. M. S. Evans (2019). A Pistil-Expressed Pectin Methylesterase Confers Cross-Incompatibility Between Strains of Zea mays. Nature Comm.
W. Yan, D. Chen, J. Schumacher, D. Durantini, J. Engelhorn, M. Chen, C. C. Carles, K. Kaufmann (2019). “Dynamic control of enhancer activity drives stage-specific gene expression during flower morphogenesis”. Nature Comm. 10.1.
Y. Lu, S. A. Hokin, J. L. Kermicle, T. Hartwig, M. M. S. Evans (2019). A Pistil-Expressed Pectin Methylesterase Confers Cross-Incompatibility Between Strains of Zea mays. Nature Comm.
M. Bezrutczyk, T. Hartwig, M. Horshman, S. N. Char, J. Yang, B. Yang, W. B. Frommer, D. Sosso (2018). Impaired phloem loading in genome edited triple knock-out mutants of SWEET sucrose transporters. New Phytologist
M. K. Dhami, T. Hartwig, A. Letten, M. Banf, T. Fukami (2018). Genomic diversity of a nectar yeast clusters into metabolically, but not geographically, distinct lineages. Mol. Ecology M. Bezrutczyk, J. Yang, J. Eom, M. Prior, D. Sosso, T. Hartwig, B. Szurek, R. Oliva, V-C. Casiana, W. Frank, B. Yang, W. Frommer (2017). Nutrient flux and/or nutrient signaling in biotic interactions. Plant J.
M. Bezrutczyk, T. Hartwig, M. Horshman, S. N. Char, J. Yang, B. Yang, W. B. Frommer, D. Sosso (2018). Impaired phloem loading in genome edited triple knock-out mutants of SWEET sucrose transporters. New Phytologist
M. K. Dhami, T. Hartwig, T. Fukami (2016). Genetic basis of priority effects: insights from nectar yeast. Proc. R. Soc. B