Bezvoda R, Landeo-Ríos YM, Kubátová Z, et al. (2025) A genome-wide association screen for genes affecting leaf trichome development and epidermal metal accumulation in Arabidopsis. Plant Cell Environ 48(5):3708-34 preprint bioRxiv:2024.09.10.612273.
Birklbauer MJ, Buur LM, Kaser S, et al. (2025) Unified down-stream analysis of crosslinking mass spectrometry results with pyXLMS. bioRxiv:2025.12.18.695169.
Boo KH, Oh YK, Møller C, et al. (2025) Dasineura asteriae Reprograms the Flower Gene Expressions of Vegetative Organs to Create Flower-Like Gall in Aster scaber. Plant Cell Environ 48(11):8217-231.
Bourguet P, Lorkovic ZJ, Kripkiy Casado K, et al. (2025) Major alleles of CDCA7α shape CG-methylation in Arabidopsis thaliana. Nat Plants 11(12):2511-30 preprint bioRxiv:2025.09.03.673934.
Brachi B, Filiault D, Pisupati R, et al. (2025) Life-history trade-offs explain local adaptation in Arabidopsis thaliana. bioRxiv:2025.05.18.654693.
Braeuer P, Tirian L, Mueller F, et al. (2025) In vivo crosslinking and effective 2D enrichment for interactome studies of the nucleosome. bioRxiv:2025.02.25.640081.
Bräuer P, Tirian L, Müller F, et al. (2025) In vivo crosslinking and effective 2D enrichment for proteome wide interactome studies. Commun Chem 8(1):245.
Bubis JA, Arrey TN, Damoc E, et al. (2025) Challenging the Astral mass analyzer to quantify up to 5,300 proteins per single cell at unseen accuracy to uncover cellular heterogeneity. Nat Methods 22(3):510-9 preprint bioRxiv:2024.02.01.578358.
Campos-Dominguez L, Kongsted TE, Cure L, et al. (2025) Genome dynamics across the radiation of a mega-diverse genus. bioRxiv:2025.09.17.676772.
Capparotto A, Salvucci P, Ciampanelli A, et al. (2025) Plant genetic and root-associated microbial diversity modulate Lactuca sativa responsiveness to a soil inoculum under phosphate deficiency. bioRxiv:2025.04.02.646582.
Cheng C, McCauley BS, Matulionis N, et al. (2025) Histone H3 cysteine 110 enhances iron metabolism and modulates replicative life span in Saccharomyces cerevisiae. Sci Adv 11(15):eadv4082.
Clauw P, Ellis TJ, Liu HJ, et al. (2025) Beyond the Standard GWAS-A Guide for Plant Biologists. Plant Cell Physiol 66(4):431-43.
De la Concepcion JC, Duverge H, ... Dagdas Y (2025) Electrostatic changes enabled the diversification of an exocyst subunit via protein complex escape. Nat Plants 11(11):2350-67 preprint bioRxiv:2024.08.26.609756.
Del Chiaro A, Grujic N, ..., Dagdas Y (2025) Nonuple atg8 mutant provides genetic evidence for functional specialization of ATG8 isoforms in Arabidopsis thaliana. J Cell Sci 138(17):jcs263803 preprint bioRxiv:2024.12.10.627464.
Dombey R, Buendía-Ávila D, ..., Marí-Ordóñez A (2025) Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducing Spirodela polyrhiza. Genome Res 35(3):522-44 preprint bioRxiv: 2024.04.03.587901.
Ellis TJ, Field DL, Barton NH (2025) Joint Estimation of Paternity, Sibships and Pollen Dispersal in a Snapdragon Hybrid Zone. Mol Ecol 34(18):e70051.
Ellis TJ, Nizhynska V, Pisupati R, et al. (2025) Bisulphite sequencing in the presence of cytosine-conversion errors. PLoS One 20(5):e0322539 preprint bioRxiv:2024.09.16.613193.
Fridrich A and Irwin NAT (2026) Cross-kingdom gene transfer as a driver of land plant evolution. Curr Opin Plant Biol 89:102850.
Gandhivel VH, Sotelo-Parrilla P, Raju S, et al. (2025) An Oryza-specific histone H4 variant predisposes H4 lysine 5 acetylation to modulate salt stress responses. Nat Plants 11(4):790-807.
Giannini C, Loefke C, Brunoud G, et al. (2025) Nuclear auxin signalling induces autophagy for developmental reprogramming. bioRxiv:2025.11.04.686542.
Gross AS, Raffeiner M,..., Dagdas Y (2025) Autophagy in Plant Health and Disease. Annu Rev Plant Biol 76(1):197-227.
Harvey ZH, Stevens KM, Kok JY, et al. (2025) The histone core domain evolves at single-residue resolution to directly orchestrate transcription. Cell Rep 44(8):116079.
Hoffman-Sommer M, Piłka N, Anielska-Mazur A, et al. (2025) The TRAPPC8/TRS85 subunit of the Arabidopsis TRAPPIII tethering complex regulates endoplasmic reticulum function and autophagy. Plant Physiol 197(3):kiaf042 preprint bioRxiv:2024.01.11.575191.
Hoffmann G, Sadhu SP, Bradamante G, et al. (2025) AGO5 restricts virus vertical transmission in plant gametophytes. bioRxiv:2025.11.28.691182.
Hure V, Piron-Prunier F, Yehouessi T, et al. (2025) Alternative silencing states of transposable elements in Arabidopsis associated with H3K27me3. Genome Biol 26(1):11 preprint bioRxiv:2024.03.16.585326.
Husremović T, Meier V, Piëch L, et al. (2025) PHLPP2 is a pseudophosphatase that lost activity in the metazoan ancestor. PNAS 122(14):e2417218122 preprint bioRxiv:2024.12.03.625870.
Igolkina A, Vorbrugg S, Rabanal F, et al. (2025) A comparison of 27 Arabidopsis thaliana genomes and the path toward an unbiased characterization of genetic polymorphism. Nat Genet 57(9):2289-301 preprint bioRxiv 2024.05.30.596703
Igolkina AA, Bezlepksky AD, Nordborg M (2025) Pannagram: unbiased pangenome alignment and the Mobilome calling. bioRxiv:2025.02.07.637071.
Jacko-Reynolds VKL, Kwong WK, Livingston SJ, et al. (2025) Phylogenomics of coral-infecting corallicolids reveal multiple independent losses of chlorophyll biosynthesis in apicomplexan parasites. Curr Biol 35(5):1156-63.
Jaegle B, Voichek Y, Haupt M, et al. (2025) k-mer-based GWAS in a wheat collection reveals novel and diverse sources of powdery mildew resistance. Genome Biol 26(1):172 preprint bioRxiv:2024.10.03.616421.
Janse van Rensburg H, Schandry N, Waelchli J, et al. (2025) A TNL receptor mediates microbiome feedbacks in Arabidopsis. bioRxiv:2025.02.25.640125.
Julian J, Gao P, ... Dagdas Y (2025) ATG8ylation of vacuolar membrane protects plants against cell wall damage. Nat Plants 11(2):321-39 preprint bioRxiv:2024.04.21.590262.
Julian Y and Dagdas Y (2025) Vacuolar signaling, biogenesis, and quality control in plants. Curr Opin Plant Biol 86:102756.
Liu HJ, Fu J, Xu S, et al. (2025) Potential synthetic associations created by epistasis. Genome Biol 26(1):336.
Lopez-Valdivia I, Vallebueno-Estrada M, Rangarajan H, et al. (2025) In silico analysis of the evolution of root phenotypes during maize domestication in Neolithic soils of Tehuacan. New Phytol 248(1):339-53 preprint bioRxiv:2024.11.18.623787.
Ma Y, Şen ZB, Ng HP (2025) Plant galls induced by insects: Coordinated developmental reprogramming and defence manipulation. Curr Opin Plant Biol 86:102757.
Mathur V, Irwin N, Galindo LJ, et al. (2025) Phagocytosis repurposed: infection strategies in a global marine diatom-parasite interaction. bioRxiv:2025.07.29.667418.
Merai Z, Xu F, Hajdu A, et al. (2025) Phytochrome A is required for light-inhibited germination of Aethionema arabicum seed. New Phytol 247(5):2134-46 preprint bioRxiv:2025.02.26.640300.
Müller F, Birklbauer MJ, Bubis J, et al. (2025) Breaking barriers in crosslinking mass spectrometry with enhanced throughput and sensitivity using Orbitrap Astral. Nat Commun 16(1):9877.
Müller F, Brutiu BR, Saridakis I, et al. (2025) Developing a new cleavable crosslinker reagent for in-cell crosslinking. Commun Chem 8(1):191.
Mulvey H and Dolan L (2025) The evolution of RHO of plant (ROP) proteins and their morphogenetic functions. New Phytol 248(2):542-8.
Nguyen VH, Mittelsten Scheid O, Gutzat R (2025) Heat stress response and transposon control in plant shoot stem cells. Plant Physiol 197(4):kiaf110 preprint bioRxiv:2023.02.24.529891.
Omenge K, Werner S, Deecke K, et al. (2025) LysM Receptor Proteins are Required for Ectomycorrhizal Symbiosis in Poplar. bioRxiv:2025.12.17.694584.
Park C, Cho HS, Lim Y, et al. (2025) Evolution of the JULGI-SMXL4/5 module for phloem development in angiosperms. PNAS 122(10):e2416674122.
Petroll R, Papareddy RK, Krela R, et al. (2025) The expansion and diversification of epigenetic regulatory networks underpins major transitions in the evolution of land plants. Mol Biol Evol 42(4):msaf064 preprint bioRxiv:2024.09.22.614159.
Plott S, Dagdas YF, Ibl V (2025) Microautophagy in cereal grains: protein storage or degradation? Trends Plant Sci S1360-85.
Rappsilber J, Bruce J, Combe C, et al. (2025) A Roadmap for Improving Reliability and Data Sharing in Crosslinking Mass Spectrometry. Mol Cell Proteomics 24(8):101024.
Saddala S, Shukla N, Fulnecek J, et al. (2025) Post-transcriptional regulation of meiotic transcripts by the RNA binding protein CDM1 is associated with cytoplasmic condensate assemblies. bioRxiv:2025.08.17.670746.
Sadiku P, Brenes AJ, Mayer RL, et al. (2025) Single cell proteomic analysis defines discrete neutrophil functional states in human glioblastoma. Nat Commun 17(1)621 preprint bioRxiv:2025.07.23.666094.
Sanchez de Medina Hernandez V, Nava Garcia MM, ... Yasin D (2026) Cross-species interactome analysis uncovers a conserved selective autophagy mechanism for protein quality control in plants. Dev Cell 61(3):655-75 preprint bioRxiv:2024.09.08.611708.
Solé-Gil A, Sakai Y, Catarino B, et al. (2024) Divergent evolution of a thermospermine-dependent regulatory pathway in land plants. Dev Cell 60(9):1348-58.
Son N, Kim H, Kim J, et al. (2025) The histone variant H2A.W restricts heterochromatic crossovers in Arabidopsis. PNAS 122(14):e2413698122.
Spencer V, Casey C, Mosiolek M, et al. (2025) The cytochrome P450 enzyme MpCYP78E1 inhibits meristem initiation and activity in Marchantia polymorpha. Curr Biol 35(15):3723-35 preprint bioRxiv:2025.04.28.651025.
Struck TJ, Vaughn AH, Daigle A, et al. (2025) GHIST 2024: The 1st Genomic History Inference Strategies Tournament. Mol Biol Evol 42(11):msaf257 preprint bioRxiv:2025.08.05.668560.
Tanizawa Y, Mochizuki T, Yagura M, et al. (2025) MarpolBase: Genome database for Marchantia polymorpha featuring high quality reference genome sequences. Plant Cell Physiol 67(3):377-88 preprint bioRxiv:2025.03.30.646155.
Tsukahara S, Bousios A, Perez-Roman E, et al. (2024) Centrophilic retrotransposon integration via CENH3 chromatin in Arabidopsis. Nature 637(8046):744-8.
Walker J, Zhang J, Liu Y, et al. (2025) Extensive N4 cytosine methylation is essential for Marchantia sperm function. Cell 188(11):2890-906 preprint bioRxiv:2021.02.12.428880.
Wu S, Jandrasits K, Swarts K, et al. (2025) Population genomics of Marchantia polymorpha subsp. ruderalis reveals evidence of climate adaptation. Curr Biol 35(5):970-80.
Wyman J, Bateman RM, Dolan L, et al. (2026) Comparative rhizotaxy of fossil and living isoetalean rhizomorphs reveals development through rootlet intercalation within a triangular lattice. Ann Bot 137(6):1709-25.
Zaidi SS, Shakir S, De Kort H, et al. (2025) A comprehensive atlas of full-length Arabidopsis eccDNA populations identifies their genomic origins and epigenetic regulation. PLoS Biol 23(7):e3003275.
Zecua-Ramirez P, Dunken N, Charura NM, et al. (2025) Autophagy restricts symbiosis-associated cell death and regulates colonization by Serendipita indica in Arabidopsis. Plant Physiol 199(4):kiaf590 preprint bioRxiv:2023.07.21.550010.
Zhong T, Mullens A, Morales L, et al. (2025) A maize near-isogenic line population designed for gene discovery and characterization of allelic effects. Plant J 122(5):e70228.
Zou Y, Ohlsson JA, Holla S, et al. (2025) ATG8 delipidation is not universally critical for autophagy in plants. Nat Commun 16(1):403.
