Keywords: paralog processing, deep learning, comparative transcriptomics, multi-omics

Latest 26 Papers

Pioneer bark beetle attacks induce multifaceted localized defense responses in Norway spruce

Authors: Ramires, M. J., Netherer, S., Schebeck, M., Hummel, K., Schlosser, S., Razzazi-Fazeli, E., Ertl, R., Ahmad, M., Espinosa-Ruiz, A., Carrera, E., Arc, E., Martinez-Godoy, M. A., Banos, J., Caballero, T., Ledermann, T., van Loo, M., Trujillo-Moya, C.

Date: 2025-08-07 · Version: 1

DOI: 10.1101/2025.08.06.668443

Model Organism: Picea abies

Norway spruce bark beetle defense multi-omics jasmonic acid phenolic compounds

Phenotypic scoring of Canola Blackleg severity using machine learning image analysis

Authors: Hu, Q., Anderson, S. N., Gardner, S., Ernst, T. W., Koscielny, C. B., Bahia, N. S., Johnson, C. G., Jarvis, A. C., Hynek, J., Coles, N., Falak, I., Charne, D. R., Ruidiaz, M. E., Linares, J. N., Mazis, A., Stanton, D. J.

Date: 2025-07-22 · Version: 1

DOI: 10.1101/2025.07.17.665372

Model Organism: Multi-species

blackleg disease canola (Brassica spp.)deep learning image-based phenotyping disease severity scoring

RegenPGC View: Semantic Segmentation of Perennial Groundcover Cropping Systems to Restore American Croplands

Authors: Meyering, B., Schlautman, B.

Date: 2025-07-06 · Version: 1

DOI: 10.1101/2025.07.03.663038

Model Organism: General

perennial groundcovers cover cropping deep learning convolutional neural network image‑based phenotyping

Virus-induced upregulation of mitochondrial metabolism modulates cytosolic redox balance and defense responses

Authors: Hou, L.-Y., Wu, C.-H., Lin, N.-S.

Date: 2025-07-06 · Version: 1

DOI: 10.1101/2025.07.05.663277

Model Organism: Nicotiana benthamiana

metabolic reprogramming Bamboo mosaic virus mitochondrial metabolism redox balance multi-omics

Multi-Omics Analysis of Heat Stress-Induced Memory in Arabidopsis

Authors: Thirumlaikumar, V. P. P., Yu, L., Arora, D., Mubeen, U., Wisniewski, A., Walther, D., Giavalisco, P., Alseekh, S., DL Nelson, A., Skirycz, A., Balazadeh, S.

Date: 2025-06-23 · Version: 1

DOI: 10.1101/2025.06.19.660594

Model Organism: Arabidopsis thaliana

heat stress acquired thermotolerance heat stress memory multi-omics Arabidopsis thaliana

Unraveling the cis-regulatory code controlling abscisic acid-dependent gene expression in Arabidopsis using deep learning

Authors: Opdebeeck, H., Smet, D., Thierens, S., Minne, M., De Beukelaer, H., Zuallaert, J., Van Bel, M., Van Montagu, M., Degroeve, S., De Rybel, B., Vandepoele, K.

Date: 2025-06-06 · Version: 1

DOI: 10.1101/2025.06.03.657584

Model Organism: Arabidopsis thaliana

Abscisic acid Arabidopsis thaliana deep learning promoter motifs ABF binding sites

Deciphering the Sequence Basis and Application of Transcriptional Initiation Regulation in Plant Genomes Through Deep Learning

Authors: Gao, P., Lian, L., Feng, W., Ma, Y., Lin, J., Qin, L., Hao, S., Zhao, H., Liu, X., Yuan, J., Lin, Z., Li, X., Guan, Y., Wang, X.

Date: 2025-04-24 · Version: 1

DOI: 10.1101/2025.04.22.649999

Model Organism: Glycine max

transcription start site promoter motifs deep learning soybean domestication plant gene regulation

2-Oxoglutarate-dependent dioxygenases contribute to cardenolide biosynthesis in Erysimum cheiranthoides (wormseed wallflower)

Authors: Younkin, G., Holland, C. K., Jander, G.

Date: 2025-04-16 · Version: 1

DOI: 10.1101/2025.04.10.648230

Model Organism: Erysimum cheiranthoides

cardenolide biosynthesis 2‑oxoglutarate‑dependent dioxygenases hydroxylation comparative transcriptomics enzyme modeling

Comparative transcriptomics uncovers plant and fungal genetic determinants of mycorrhizal compatibility

Authors: Marques-Galvez, J. E., de Freitas Pereira, M., Nehls, U., Ruytinx, J., Barry, K., Peter, M., Martin, F., Grigoriev, I. V., Veneault-Fourrey, C., Kohler, A.

Date: 2025-04-14 · Version: 1

DOI: 10.1101/2025.04.11.648352

Model Organism: Populus

ectomycorrhizal symbiosis poplar comparative transcriptomics gene regulons compatibility

High radiosensitivity in the conifer Norway spruce (Picea abies) due to lesscomprehensive mobilisation of protection and repair responses compared to the radiotolerant Arabidopsis thaliana

Authors: Bhattacharjee, P., Blagojevic, D., Lee, Y., Gillard, G. B., Gronvold, L., Hvidsten, T. R., Sandve, S. R., Lind, O. C., Salbu, B., Brede, D. A., Olsen, J. E.

Date: 2025-04-14 · Version: 3

DOI: 10.1101/2023.11.20.562501

Model Organism: Multi-species

ionising radiation radiosensitivity comparative transcriptomics DNA damage repair antioxidant response

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