Publications


2023

Aguilar-Cruz A, Flores-Sandoval E, Gutierrez-Ramos X, et al. (2023) Control of cell fate specification and patterning by an ancestral microRNA. bioRxiv:2023.09.09.556951.

Ali MF, Shin JM, Fatema U, et al. (2023) Cellular dynamics of coenocytic endosperm development in Arabidopsis thaliana. Nat Plants 9(2):330-42 preprintbioRxiv:2022.04.01.485647.

Birklbauer MJ, Matzinger M, Müller F, et al. (2023) MS Annika 2.0 Identifies Cross-Linked Peptides in MS2-MS3-Based Workflows at High Sensitivity and Specificity. J Proteome Res 22(9):3009-21.

Bradamante G, Nguyen VH, Incarbone M, et al. (2023) Two ARG ONAUTE proteins loaded with transposon-derived small RNAs are associated with the reproductive cell lineage in Arabidopsis. Plant Cell 36(4):863-80 preprint bioRxiv:2022.01.25.477718.

Casey A and Dolan L (2023) Genes encoding cytochrome P450 monooxygenases and glutathione S-transferases associated with herbicide resistance evolved before the origin of land plants. PLoS One 18(2):e0273594.

Casey A, Köcher T, Caygill S, et al. (2023) Transcriptome changes in chlorsulfuron-treated plants are caused by acetolactate synthase inhibition and not induction of a herbicide detoxification system in Marchantia polymorpha. Pestic Biochem Physiol 191:105370 preprint bioRxiv:2022.08.31.505973.

Casey C, Köcher T, Champion C, et al. (2023) Reduced coenzyme Q synthesis confers non-target site resistance to the herbicide thaxtomin A. PLoS Genet 19(1):e1010423 preprint bioRxiv:2022.09.13.507736.

Caygill S and Dolan L (2023) ATP binding cassette transporters and uridine diphosphate glycosyltransferases are ancient protein families that evolved roles in herbicide resistance through exaptation. PLoS One 18(9):e0287356 preprint bioRxiv:2023.06.06.543864.

Clasen SJ, Bell MEW, Borbón A, et al. (2023) Silent recognition of flagellins from human gut commensal bacteria by Toll-like receptor 5. Sci Immunol 8(79):eabq7001 preprint bioRxiv:2022.04.12.488020.

Crego CG, Hess J, Yardeni G, et al. (2023) CAM evolution is associated with gene family expansion in an explosive bromeliad radiation. bioRxiv:2023.02.01.526631.

Ctortecka C, Hartlmayr D, Seth A, et al. (2023) An automated nanowell-array workflow for quantitative multiplexed single-cell proteomics sample preparation at high sensitivity. Mol Cell Proteomics 22(12):100665.

De la Concepcion JC (2023) The exocyst complex is an evolutionary battleground in plant-microbe interactions. Curr Opin Plant Biol [epub].

Dona M, Bradamante G, Bogojevic Z, et al. (2023) A versatile CRISPR-based system for lineage tracing in living plants. Plant J 115(5):1169-84 preprint bioRxiv:2023.02.09.527713.

Dorl S, Winkler S, Mechtler K, et al. (2023) MS Ana: Improving Sensitivity in Peptide Identification with Spectral Library Search. J Proteome Res 22(2):462-70.

Durut N, Kornienko AE, Schmidt HA, et al. (2023) Long non-coding RNAs contribute to DNA damage resistance in Arabidopsis thaliana. Genetics 225(1):iyad135 preprint bioRxiv:2023.03.20.533408

Feng C, Roitinger E, Hudecz O, et al. (2023) TurboID-based proteomic profiling of meiotic chromosome axes in Arabidopsis thaliana. Nat Plants 9(4):616-30.

Fridrich A, Salinas-Saaverda M, Kozlolvski I, et al. (2023) An ancient pan-cnidarian microRNA regulates stinging capsule biogenesis in Nematostella vectensis. Cell Rep 42(9):113072 preprint bioRxiv:2022.12.15.520629.

Hawkins TJ, Kopischke M, Duckney PJ, et al. (2023) NET4 and RabG3 link actin to the tonoplast and facilitate cytoskeletal remodelling during stomatal immunity. Nat Commun 14(1):5848 preprint bioRxiv:2021.09.29.461190.

Hisanaga T and Berger F (2023) Plant reproduction: Ancient origins of male germline differentiation. Curr Biol 33(22):R1190-2

Hisanaga T, Romani F, Wu S, et al. (2023) The Polycomb repressive complex 2 deposits H3K27me3 and represses transposable elements in a broad range of eukaryotes. Curr Biol 33(20):4367-80 preprint bioRxiv:2022.10.24.513474.

Hisanaga T, Wu S, Schafran P, et al. (2023) The ancestral chromatin landscape of land plants. New Phytol 240(5):2085-101 preprint bioRxiv:2022.10.21.513199.

Holla S, Zou Y, Sabljic I, et al. (2023) ATG8 delipidation is dispensable for plant autophagy. bioRxiv:2023.08.23.554513.

Imai R, Fujino T, Tomimoto S, et al. (2023) The molecular clock in long-lived tropical trees is independent of growth rate. bioRxiv:2023.01.26.525665

Incarbone M, Bradamante G, Pruckner F, et al. (2023) Salicylic acid and RNA interference mediate antiviral immunity of plant stem cells. Proc Natl Acad Sci USA 120(42):e2302069120 preprint bioRxiv:2022.12.18.520928.

Jaegle B, Soto-Jiménez LM, Burns R, et al. (2023) Extensive sequence duplication in Arabidopsis revealed by pseudo-heterozygosity.  Genome Biol 24(1):44 preprint bioRxiv:2021.11.15.468652.

Jamge B, Lorkovic ZJ, Axelsson E, et al. (2023) Histone variants shape chromatin states in Arabidopsis. Elife 12:RP87714 preprint bioRxiv:2023.03.08.531698.

Jiang D and Berger F (2023) Variation is important: Warranting chromatin function and dynamics by histone variants. Curr Opin Plant Biol 75:102408.

Jin M, Liu H, Liu X, et al. (2023) Complex genetic architecture underlying the plasticity of maize agronomic traits. Plant Commun 4(3):100473.

Kersten S, Chang J, Huber CD, et al. (2023) Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass. Proc Natl Acad Sci USA 120(16):e2206808120 preprint bioRxiv:2021.12.14.472587.

Khan M, Uhse S, Bindics J, et al. (2023) Tip of the iceberg? Three novel TOPLESS interacting effectors of the gall-inducing fungus Ustilago maydis. bioRxiv:2023.06.12.544640.

Kornienko AE, Nizhynska V, Molla Morales A, et al. (2023) Population-level annotation of lncRNAs in Arabidopsis thaliana reveals extensive expression variation associated with transposable element-like silencing. Plant Cell 36(1):85-111 preprint: bioRxiv:2023.03.14.532599.

Lebovka I, Hay Mele B, Liu X, et al. (2023) Computational modelling of cambium activity provides a regulatory framework for simulating radial plant growth. Elife 12:e66627.

Lee DH, Choi I, Park SJ, et al. (2023) Three consecutive cytosolic glycolysis enzymes modulate autophagic flux. Plant Physiol [epub].

Leiendecker L, Neumann T, Jung PS, et al. (2023) Human Papillomavirus 42 Drives Digital Papillary Adenocarcinoma and Elicits a Germ Cell-like Program Conserved in HPV-Positive Cancers. Cancer Discov 13(1):70-84.

Li B, Niu F, Zeng Y, et al. (2023) Ufmylation reconciles salt stress-induced unfolded protein responses via ER-phagy in Arabidopsis. Proc Natl Acad Sci USA 120(5):e2208351120.

Markusch H, Michl-Holzinger P, Obermeyer S, et al. (2023) ELF1 is a component of the Arabidopsis RNA polymerase II elongation complex and associates with a subset of transcribed genes. New Phytol 238(1):113-24.

Matzinger M and Mechtler K. (2023) Improving single cell proteomics experiments: how can we best utilize latest-generation data acquisition and MS instrument architecture? Expert Rev Proteomics [epub].

Matzinger M, Mayer RL, and Mechtler K (2023) Label-Free Single Cell Proteomics Utilizing Ultrafast LC and MS Instrumentation: A Valuable Complementary Technique to Multiplexing. Proteomics 23(13-14):e2200162.

Matzinger M, Mueller E, Duernberger G, et al. (2023) Robust and easy-to-use one pot workflow for label-free single-cell proteomics. Anal Cehm 95(9):4435-45 preprint bioRxiv:2022.10.03.510693.

Mayer RL and Mechtler K (2023) Immunopeptidomics in the Era of Single-Cell Proteomics. Biology (Basel) 12(12):1514.

Mérai Z, Xu F, Musilek A, et al. (2023) Phytochromes mediate germination inhibition under red, far-red, and white light in Aethionema arabicum. Plant Physiol 192(2):1584-602 preprint bioRxiv:2022.06.24.497527.

Montgomery S and Berger F (2023) Epigenetic reprogramming of imprinting at meiosis. bioRxiv:2023.05.17.541143.

Montgomery SA and Berger F (2023) Paternal imprinting in Marchantia polymorpha. New Phytol 241(3):1000-6.

Mulvey H and Dolan L (2023) RHO GTPase of plants regulates polarized cell growth and cell division orientation during morphogenesis. Curr Biol 33(14):2897-911 preprint bioRxiv:2023.05.23.541913.

Mulvey H and Dolan L (2023) RHO of plant signaling was established early in streptophyte evolution. Curr Biol 33(24):5515-25.

Murphy PJ and Berger F (2023) The chromatin source-sink hypothesis: a shared mode of chromatin-mediated regulations. Development 150(21):dev201989.

Nguyen VH, Mittelsten Scheid O, Gutzat R (2023) Heat stress response and transposon control in plant shoot stem cells. bioRxiv:2023.02.24.529891.

Osakabe A, Takizawa Y, Horikhosi N, et al. (2023) Molecular and structural basis of the heterochromatin-specific chromatin remodeling activity by Arabidopsis DDM1. bioRxiv:2023.07.10.548306.

Picchianti L, Sanchez de Medina Hernandez V, ..., Dagdas Y (2023) Shuffled ATG8 interacting motifs form an ancestral bridge between UFMylation and autophagy. EMBO J 42(10):e112053 preprint bioRxiv:2022.04.26.489478.

Pisupati R, Nizhynska V, Morales AM, et al. (2023) On the Causes of Gene-Body Methylation Variation in Arabidopsis thaliana. PLoS Genet 19(5):e1010728 preprint bioRxiv:2022.12.04.519028.

Poláček M, Arizpe A, ..., Swarts K (2023) Automation of tree-ring detection and measurements using deep learning. Methods in Ecol and Evol 14:2233-42 preprint bioRxiv:2022.01.10.475709.

Rogov VV, Nezis IP, Tsapras P, et al. (2023) Atg8 family proteins, LIR/AIM motifs and other interaction modes. Autophagy Rep. 2(1):2188523.

Saeed B, Deligne F, Brillada C, et al. (2023) K63-linked ubiquitin chains are a global signal for endocytosis and contribute to selective autophagy in plants. Curr Biol 33(7):1337-45.

Sammarco I, Díez Rodríguez B, Galanti D, et al. (2023) DNA methylation in the wild: epigenetic transgenerational inheritance can mediate adaptation in clones of wild strawberry (Fragaria vesca). New Phytol 241(4):1621-35.

Sidhaye J, Trepte P, Sepke N, et al. (2023) Integrated transcriptome and proteome analysis reveals posttranscriptional regulation of ribosomal genes in human brain organoids. Elife 12:e85135.

Streubel S, Deiber S, Roetzer J, et al. (2023) Meristem dormancy in Marchantia polymorpha is regulated by a liverwort-specific miRNA and a clade III SPL gene. Curr Biol 33(4):660-74 preprint bioRxiv:2022.10.03.510622.

Sundar G VH, Sotelo-Parrilla P, Raju S, et al. (2023) Oryza genera-specific novel Histone H4 variant predisposes H4 Lysine5 Acetylation marks to modulate salt stress responses. bioRxiv:2023.07.31.551207.

Tanasa S, Shukla N, Cairo A, et al. (2023) A complex role of Arabidopsis CDKD;3 in meiotic progression and cytokinesis. Plant Direct 7(3):e477 preprint bioRxiv:2022.08.08.503215.

Vainonen JP, Gossens R, Krasensky-Wrzaczek J, et al. (2023) Poly(ADP-ribose)-binding protein RCD1 is a plant PARylation reader regulated by Photoregulatory Protein Kinases. Commun Biol 6(1):429.

Vedanayagam J, Lin CJ, Papareddy R, et al. (2023) Regulatory logic of endogenous RNAi in silencing de novo genomic conflicts. PLoS Genet 19(6):e1010787.

Voichek Y, Hristova G, Mollá-Morales A, et al. (2023)Widespread transcriptional regulation from within transcribed regions in plants. bioRxiv:2023.09.15.557872

Voichek Y, Hurieva B, Michaud C, et al. (2023) Cell-cycle status of male and female gametes during Arabidopsis reproduction. Plant Physiol 194(1):412-21 preprint bioRxiv:2023.02.22.529524.

Wallner ES, Dolan L, Bergmann DC (2023) Arabidopsis stomatal lineage cells establish bipolarity and segregate differential signaling capacity to regulate stem cell potential. Dev Cell 58(18):1643-56.

Weiszmann J, Walther D, Clauw P, et al. (2023)  Metabolome plasticity in 241 Arabidopsis thaliana accessions reveals evolutionary cold adaptation processes. Plant Physiol 193(2):980-1000 preprint bioRxiv:2020.09.24.311092.

Wlodzimierz P, Rabanal FA, Burns R, et al. (2023) Cycles of satellite and transposon evolution in Arabidopsis centromeres. Nature [epub].

Yilmazer I, Vetrano P, Eicke S, et al. (2023) A conserved ESCRT-II-like protein participates in the biogenesis and maintenance of thylakoid membranes. bioRxiv:2023.10.10.561251.

Yuen ELH, Leary AY, Clavel M, et al. (2023) A RabGAP-Rab GTPase pair regulates plant autophagy and immunity. bioRxiv:2023.07.03.547386.

Zdrzałek R, Stone C, De la Concepcion JC, et al. (2023) Pathways to engineering plant intracellular NLR immune receptors. Curr Opin Plant Biol 74:102380.

Zecua-Ramirez P, Llamas E, Charura N, et al. (2023) Autophagy restricts fungal accommodation in the roots of Arabidopsis thaliana. bioRxiv:2023.07.21.550010

Zeng Y, Li B, Huang S, et al. (2023) The plant unique ESCRT component FREE1 regulates autophagosome closure. Nat Commun 14(1):1768.

Zheng R, Matzinger M, Mayer RL, et al. (2023) A high-sensitivity low-nanoflow LC-MS configuration for high-throughput sample-limited proteomics. Anal Chem 95(51):18673-8 preprint bioRxiv:2023.04.27.538542.

Zhou X, Wang L, Zhu P, et al.(2023) Comprehensive molecular characterization of complete mitogenome assemblies of 33 Eimeria isolates infecting domestic chickens. Parasit Vectors 16(1):109.

Zhu P, Schon M, Questa J, et al. (2023) Causal role of a promoter polymorphism in natural variation of the Arabidopsis floral repressor gene FLC. Curr Biol 33(20):4381-91.

Zuo Z, Roux ME, Chevalier J, et al.(2022) The mRNA decapping machinery targets LBD3/ASL9 to mediate apical hook and lateral root development. Life Sci Alliance 6(9):e202302090 preprint bioRxiv:2022.07.06.499076.