Keywords: paralog processing, codon usage, transcriptome analysis, gene regulatory network

Latest 19 Papers

Gene regulatory network analysis of somatic embryogenesis identifies morphogenic genes that increase maize transformation frequency

Authors: Renema, J., Luckicheva, S., Verwaerde, I., Aesaert, S., Coussens, G., De Block, J., Grones, C., Eekhout, T., De Rybel, B., Brew-Appiah, R. A. T., Bagley, C. A., Hoengenaert, L., Vandepoele, K., Pauwels, L.

Date: 2025-06-23 · Version: 1

DOI: 10.1101/2025.06.22.659756

Model Organism: Zea mays

somatic embryogenesis transcription factors Zea mays single-cell transcriptomics gene regulatory network

Ethylene Receptor Gain- and Loss-of-function Mutants Reveal an ETR1-dependent Transcriptional Network in Roots

Authors: White, M. G., Harkey, A., Muhlemann, J. K., Olex, A. L., Pfeffer, N. J., Houben, M., Binder, B., Muday, G. K.

Date: 2025-06-22 · Version: 3

DOI: 10.1101/2024.06.26.600793

Model Organism: Arabidopsis thaliana

ethylene signaling ETR1 root development gene regulatory network Arabidopsis

Single-Nucleus Transcriptomics Reveals How Tissue Context Shapes the Circadian Transcriptome of the Arabidopsis Leaf

Authors: Zulfiqar, A., Myers, Z. A., Menon, A., Greenham, K.

Date: 2025-06-16 · Version: 1

DOI: 10.1101/2025.06.12.659411

Model Organism: Arabidopsis thaliana

circadian regulation single-nucleus RNA-seq cell-type-specific expression Arabidopsis thaliana leaf gene regulatory network

Stage-resolved gene regulatory network analysis reveals developmental reprogramming and genes with robust stem-preferred expression in sorghum

Authors: Fu, J., James, B., Hetti-Arachchilage, M., Lei, Y., McKinley, B., Kurtz, E., Barry, K., Moose, S. P., Mullet, J. E., Swaminathan, K., Marshall-Colon, A.

Date: 2025-05-30 · Version: 1

DOI: 10.1101/2025.05.27.656329

Model Organism: Sorghum bicolor

Sorghum bicolor stem organ-specific expression stem-specific transcription factors gene regulatory network bioenergy feedstock

Physiological characterization in a somaclonal mutant for fruit shape derived from persimmon 'Hiratanenashi'

Authors: Horiuchi, A., Matsuzaki, R., Onoue, N., Ushijima, K., Kubo, Y., Akagi, T., Minamikawa, M. F.

Date: 2025-05-19 · Version: 1

DOI: 10.1101/2025.05.19.654774

Model Organism: Diospyros kaki

fruit shape persimmon (Diospyros kaki)elliptic Fourier descriptor transcriptome analysis WOX13

Revisiting the Central Dogma: the distinct roles of genome, methylation, transcription, and translation on protein expression in Arabidopsis thaliana

Authors: Zhong, Z., Bailey, M., Kim, Y.-I., Pesaran-Afsharyan, N., Parker, B., Arathoon, L., Li, X., Rundle, C. A., Behrens, A., Nedialkova, D. D., Slavov, G., Hassani-Pak, K., Lilley, K. S., Theodoulou, F. L., Mott, R.

Date: 2025-03-31 · Version: 2

DOI: 10.1101/2025.01.08.631880

Model Organism: Arabidopsis thaliana

Arabidopsis thaliana codon usage gene expression DNA methylation ribosome profiling