Author

R. Lister

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Plant Biology· 6 Evolutionary Biology· 3 Cancer Biology· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 8 Research Focus:cell type annotation· 7 Research Focus:chromatin & epigenetic regulation· 6 Organism:Arabidopsis· 5 Approach:statistical model· 5 Research Focus:gene regulatory network inference· 3 Assay:ChIP-seq· 2 Research Focus:development & morphogenesis· 2

Frequent Co-Authors

J. Cahn· 3 shared M. Oliva· 3 shared A. de Mendoza· 2 shared D. Poppe· 2 shared H. Millar· 2 shared J. Petereit· 2 shared J. Pflueger· 2 shared J. Whelan· 2 shared

Activity by Year

2017-2023 · peak 4/yr

Co-Author Collaboration Network

10 top collaborators · 20 mutual co-author links

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3 shared papersPlant Biology

J. Cahn

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Author profile →

10 papers

Recent·Most cited

Characterization of DNA methylation reader proteins of Arabidopsis thaliana

J. Cahn, J. P. B. Lloyd, I. D. Karemaker, P. W. Jansen, J. Pflueger, O. Duncan, J. Petereit, O. Bogdanovic, H. Millar, M. Vermeulen, R. Lister

The paper identifies and characterizes DNA methylation reader proteins in Arabidopsis thaliana, revealing context-specific binding preferences and functional roles.

bioRxiv · Dec 5, 2023Plant Biology

Establishment of cell transcriptional identity during seed germination

L. C. Liew, Y. You, M. Oliva, M. Peirats-Llobet, S. Ng, M. Tamiru-Oli, O. G. Berkowitz, U. V. T. Hong, A. Haslem, T. Stuart, M. E. Ritchie, G. Bassel, R. Lister, J. Whelan, Q. Gouil, M. G. Lewsey

This study maps the temporal changes in cell-type specific gene expression during Arabidopsis seed germination, revealing a shared initial transcriptional state followed by distinct regulatory programs.

bioRxiv · Jan 21, 2023 · PreprintPlant Biology

PHYTOMap: Multiplexed single-cell 3D spatial gene expression analysis in plant tissue

T. Nobori, M. Oliva, R. Lister, J. R. Ecker

PHYTOMap enables low-cost, transgene-free single-cell spatial gene expression analysis in plant tissue, demonstrating its ability to identify cell types in Arabidopsis roots.

bioRxiv · Jul 28, 2022 · PreprintPlant Biology

Single Nucleus RNA Sequencing of Pre-Malignant Liver Reveals Disease-Associated Hepatocyte State with HCC Prognostic Potential

R. Carlessi, E. Denisenko, E. Boslem, J. Koehn-Gaone, N. Main, N. D. B. A. Bakar, G. D. Shirolkar, M. Jones, D. Poppe, B. J. Dwyer, C. Jackaman, M. C. Tjiam, R. Lister, M. Karin, J. A. Fallowfield, , J. E. E. Tirnitz-Parker

The paper uses snRNA-seq to identify a disease-associated hepatocyte state in pre-malignant livers that correlates with HCC risk in mice and humans.

bioRxiv · Mar 25, 2022Cancer Biology

Systematic evaluation of chromatin immunoprecipitation sequencing to study histone occupancy in dormancy transitions of grapevine buds

D. Hermawaty, T. G. Chabikwa, J. Cahn, R. Lister, M. J. Considine

The paper develops and optimizes a ChIP-seq protocol for studying histone occupancy in dormant grapevine buds, demonstrating its effectiveness for woody tissues.

bioRxiv · Mar 14, 2022Plant Biology

An environmentally responsive transcriptional state modulates cell identities during root development

M. Oliva, T. Stuart, D. Tang, J. Pflueger, D. Poppe, J. S. Jabbari, S. Gigante, J. M. Dragwidge, J. Whelan, M. G. Lewsey, R. Lister

This study identifies an environmentally responsive transcriptional state that influences cell identities during root development in Arabidopsis, revealing a new layer of patterning independent of ontogenetic trajectories.

bioRxiv · Mar 4, 2022 · PreprintPlant Biology

Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri

N. J. Kenny, W. R. Francis, R. E. Rivera-Vicens, K. Juravel, A. de Mendoza, C. Diez-Vives, R. Lister, L. Bezares-Calderon, L. Grombacher, M. Roller, L. D. Barlow, S. Camilli, J. F. Ryan, G. Wörheide, A. L. Hill, , S. Leys

The paper presents the chromosomal-level genome assembly of Ephydatia muelleri and analyzes its genomic architecture and adaptation mechanisms.

bioRxiv · Feb 18, 2020Evolutionary Biology

Coordination and assembly of protein complexes encoded across mitochondrial and nuclear genomes is assisted by CLPP2 in Arabidopsis thaliana

J. Petereit, O. Duncan, M. Murcha, R. Fenske, E. Cincu, J. Cahn, A. Pruzinska, L. Kollipara, S. Wortekamp, A. Sickmann, J. Lee, R. Lister, H. Millar, S. HUANG

The paper shows that CLPP2 in Arabidopsis thaliana aids in coordinating and assembling protein complexes encoded by both mitochondrial and nuclear genomes, affecting mitochondrial protein homeostasis.

bioRxiv · Jan 22, 2020Plant Biology

Genomic adaptations to aquatic and aerial life in mayflies and the origin of wings in insects

I. Almudi, J. Vizueta, A. de Mendoza, C. Wyatt, F. Marletaz, P. Firbas, R. Feuda, G. Masiero, P. Medina, A. Alcaina, F. Cruz, J. Gomez-Garrido, M. Gut, T. S. Alioto, C. Vargas-Chavez, , F. Casares

This study analyzes the genome and gene expression of mayflies to uncover genomic adaptations related to aquatic and aerial life and the origin of wings in insects.

bioRxiv · Dec 29, 2019Evolutionary Biology

Regulatory remodeling in the allo-tetraploid frog Xenopus laevis

D. M. Elurbe, S. S. Paranjpe, G. Georgiou, I. van Kruijsbergen, O. Bogdanovic, R. Gibeaux, R. Heald, R. Lister, M. A. Huynen, S. J. van Heeringen, G. J. C. Veenstra

This study investigates the genomic and epigenomic consequences of whole genome duplication in Xenopus laevis, finding that subgenome degradation and regulatory element innovation are linked to repeats and non-allelic homologous recombination.

bioRxiv · Mar 24, 2017Evolutionary Biology