Keywords: paralog processing, transcriptomic analysis, deep learning, lipidomics

Latest 23 Papers

Gain and loss of gene function shaped the nickel hyperaccumulation trait in Noccaea caerulescens

Authors: Belloeil, C., Garcia de la Torre, V. S., Contreras Aguilera, R., Kupper, H., Lopez-Roques, C., Iampetro, C., Vandecasteele, C., Klopp, C., Launay-Avon, A., Leemhuis, W., Yamjabok, J., van den Heuvel, J., Aarts, M. G. M., Quintela Sabaris, C., Thomine, S., MERLOT, S.

Date: 2025-07-25 · Version: 1

DOI: 10.1101/2025.07.22.664359

Model Organism: Noccaea caerulescens

nickel hyperaccumulation Noccaea caerulescens genome assembly transcriptomic analysis metal transporters

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

MdBRC1 and MdFT2 Interaction Fine-Tunes Bud Break Regulation in Apple

Authors: Gioppato, H. A., Estevan, J., Al Bolbol, M., Soriano, A., Garighan, J., Jeong, K., Georget, C., Soto, D. G., El Khoury, S., Falavigna, V. d. S., George, S., Perales, M., Andres, F.

Date: 2025-06-24 · Version: 1

DOI: 10.1101/2025.06.20.660803

Model Organism: Malus domestica

bud dormancy MdBRC1 MdFT2 transcriptomic analysis protein interaction

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

Constitutive expression of full-length or partial of SOC1 genes for yield enhancement in tomato

Authors: Danial, G. H., Jaikham, J., Song, G.-q.

Date: 2025-06-06 · Version: 1

DOI: 10.1101/2025.06.03.657751

Model Organism: Solanum lycopersicum

SOC1 tomato fruit yield heterologous gene expression branching transcriptomic analysis

Thermotolerance in Chia (Salvia hispanica L.) is Mediated by Rapid Heat-Induced Transcriptomic Reprogramming and Lipid Remodelling in Leaves

Authors: Zare, T., Kehelpannala, C., Bhatnagar, A., Rupasinghe, T., Ebert, B., Fournier-Level, A., Roessner, U.

Date: 2025-06-02 · Version: 1

DOI: 10.1101/2025.05.30.656991

Model Organism: Salvia hispanica

heat stress Salvia hispanica transcriptomics lipidomics calcium signaling

Dynamic changes to the plastoglobule lipidome and proteome in water-deficient maize

Authors: Devadasu, E., Schilmiller, A. L., Gonzalez, N., Lundquist, P. K.

Date: 2025-05-30 · Version: 1

DOI: 10.1101/2025.05.26.656201

Model Organism: Zea mays

drought resilience plastoglobules lipidomics quantitative proteomics Zea mays

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

Arabidopsis root lipid droplets are hubs for membrane homeostasis under heat stress, and triterpenoid synthesis and storage.

Authors: Scholz, P., Dabisch, J., Clews, A. C., Niemeyer, P. W., Vilchez, A. C., Lim, M. S. S., Sun, S., Hembach, L., Dreier, F., Blersch, K., Preuss, L., Bonin, M., Lesch, E., Iwai, Y., Shimada, T., Eirich, J., Finkemeier, I., Gutbrod, K., Doermann, P., Wang, Y., Mullen, R. T., Ischebeck, T.

Date: 2025-03-26 · Version: 1

DOI: 10.1101/2025.03.24.644787

Model Organism: Arabidopsis thaliana

lipid droplets heat stress Arabidopsis thaliana roots triterpene biosynthesis lipidomics

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