Research output per year
Research output per year
- 1 - 50 out of 123 results
Search results
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2024
Advancing programmable gene expression in plants using CRISPRi-based Boolean gates
Khan, A. & Lister, R., 20 May 2024, In: Nature Biotechnology. 2 p.Research output: Contribution to journal › Article
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A modular dCas9-based recruitment platform for combinatorial epigenome editing
Swain, T., Pflueger, C., Freytag, S., Poppe, D., Pflueger, J., Nguyen, T. V., Li, J. K. & Lister, R., Jan 2024, In: Nucleic Acids Research. 52, 1, p. 474-491 18 p., gkad1108.Research output: Contribution to journal › Article › peer-review
Open Access7 Citations (Scopus) -
Approaches for the Analysis and Interpretation of Whole-Genome Bisulfite Sequencing Data
Stuart, T., Buckberry, S., Nguyen, T. V. & Lister, R., 2024, Epigenome Editing: Methods and Protocols. Jeltsch, A. & Rots, M. G. (eds.). 2 ed. Humana Press Inc., p. 391-403 13 p. (Methods in Molecular Biology; vol. 2842).Research output: Chapter in Book/Conference paper › Chapter › peer-review
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CRISPRi-based circuits to control gene expression in plants
Khan, M. A., Herring, G., Zhu, J. Y., Oliva, M., Fourie, E., Johnston, B., Zhang, Z., Potter, J., Pineda, L., Pflueger, J., Swain, T., Pflueger, C., Lloyd, J. P. B., Secco, D., Small, I., Kidd, B. N. & Lister, R., 20 May 2024, (E-pub ahead of print) In: Nature Biotechnology. 20 p.Research output: Contribution to journal › Article › peer-review
1 Citation (Scopus) -
Early moderate prenatal alcohol exposure and maternal diet impact offspring DNA methylation across species
Bestry, M., Larcombe, A. N., Kresoje, N., Chivers, E. K., Bakker, C., Fitzpatrick, J. P., Elliott, E. J., Craig, J. M., Muggli, E., Halliday, J., Hutchinson, D., Buckberry, S., Lister, R., Symons, M. & Martino, D., 6 Sept 2024, In: eLife. 12Research output: Contribution to journal › Article › peer-review
Open Access -
Establishment of single-cell transcriptional states during seed germination
Liew, L. C., You, Y., Auroux, L., Oliva, M., Peirats-Llobet, M., Ng, S., Tamiru-Oli, M., Berkowitz, O., Hong, U. V. T., Haslem, A., Stuart, T., Ritchie, M. E., Bassel, G. W., Lister, R., Whelan, J., Gouil, Q. & Lewsey, M. G., 10 Sept 2024, In: Nature Plants. 10, 9, p. 1418-1434 17 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Generation of Whole-Genome Bisulfite Sequencing Libraries for Comprehensive DNA Methylome Analysis
Vargas-Landin, D. B., Pflüger, J., Nguyen, T. V. & Lister, R., 2024, Methods in Molecular Biology: Methods and Protocols. New York: Humana Press Inc., p. 383-390 8 p. (Methods in Molecular Biology; vol. 2842).Research output: Chapter in Book/Conference paper › Chapter › peer-review
3 Citations (Scopus) -
Precisely programming gene expression in plants
Khan, A., Kidd, B. & Lister, R., 21 May 2024, Springer Nature.Research output: Other contribution
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RNA variant assessment using transactivation and transdifferentiation
PERSYST Investigator Team & Pflueger, C., 8 Aug 2024, In: American Journal of Human Genetics. 111, 8, p. 1673-1699 27 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Transient Naive Treatment (TNT) iPS cells do not feature Sendai virus expression: Response to Sendai virus persistence questions the transient naive reprogramming method for iPSC generation
Buckberry, S., Liu, X., Poppe, D., Tan, J. P., Faulkner, G. J., Polo, J. M. & Lister, R., 11 Jul 2024, bioRxiv, 13 p.Research output: Working paper › Preprint
Open Access -
2023
Embryonic Stem Cell-Derived Neurons as a Model System for Epigenome Maturation during Development
Martin, S., Poppe, D., Olova, N., O'Leary, C., Ivanova, E., Pflueger, J., Dechka, J., Simmons, R. K., Cooper, H. M., Reik, W., Lister, R. & Wolvetang, E. J., May 2023, In: Genes. 14, 5, 957.Research output: Contribution to journal › Article › peer-review
Open Access1 Citation (Scopus) -
Exploring the identity of individual plant cells in space and time
Oliva, M. & Lister, R., Oct 2023, In: The New Phytologist. 240, 1, p. 61-67 7 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Multiplexed single-cell 3D spatial gene expression analysis in plant tissue using PHYTOMap
Nobori, T., Oliva, M., Lister, R. & Ecker, J. R., Jul 2023, In: Nature Plants. 9, 7, p. 1026-1033 8 p.Research output: Contribution to journal › Article › peer-review
Open Access25 Citations (Web of Science) -
Single-nucleus RNA sequencing of pre-malignant liver reveals disease-associated hepatocyte state with HCC prognostic potential
Carlessi, R., Denisenko, E., Boslem, E., Köhn-Gaone, J., Main, N., Abu Bakar, N. D. B., Shirolkar, G. D., Jones, M., Beasley, A. B., Poppe, D., Dwyer, B. J., Jackaman, C., Tjiam, C., Lister, R., Karin, M., Fallowfield, J. A., Kendall, T. J., Forbes, S. J., Gray, E., Olynyk, J. K., & 5 others, 10 May 2023, In: Cell Genomics. 3, 5, p. 100301 100301.Research output: Contribution to journal › Article › peer-review
Open Access7 Citations (Scopus) -
Synthetic Epigenetic Reprogramming of Mesenchymal to Epithelial States Using the CRISPR/dCas9 Platform in Triple Negative Breast Cancer
Waryah, C., Cursons, J., Foroutan, M., Pflueger, C., Wang, E., Molania, R., Woodward, E., Sorolla, A., Wallis, C., Moses, C., Glas, I., Magalhães, L., Thompson, E. W., Fearnley, L. G., Chaffer, C. L., Davis, M., Papenfuss, A. T., Redfern, A., Lister, R., Esteller, M., & 1 others, 4 Aug 2023, In: Advanced Science. 10, 22, 2301802.Research output: Contribution to journal › Article › peer-review
Open Access10 Citations (Scopus) -
Systematic evaluation of chromatin immunoprecipitation sequencing to study histone occupancy in dormancy transitions of grapevine buds
Hermawaty, D., Cahn, J., Lister, R. & Considine, M. J., 12 Apr 2023, In: Tree Physiology. 43, 4, p. 675-689 15 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Transient naive reprogramming corrects hiPS cells functionally and epigenetically
Buckberry, S., Liu, X., Poppe, D., Tan, J. P., Sun, G., Chen, J., Nguyen, T. V., de Mendoza Soler, A., Pflueger, J., Frazer, T., Vargas Landin, D., Paynter, J. M., Smits, N., Liu, N., Ouyang, J. F., Rossello, F. J., Chy, H. S., Rackham, O. J. L., Laslett, A. L., Breen, J., & 4 others, 24 Aug 2023, In: Nature. 620, 7975, p. 863-872 10 p.Research output: Contribution to journal › Article › peer-review
Open Access17 Citations (Scopus) -
2022
A modular dCas9-based recruitment platform for combinatorial epigenome editing
Swain, T., Pflueger, C., Freytag, S., Poppe, D., Pflueger, J., Nguyen, T. V., Li, J. K. & Lister, R., 2 Jul 2022, bioRxiv, 37 p.Research output: Working paper › Preprint
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An environmentally-responsive transcriptional state modulates cell identities during root development
Oliva, M., Stuart, T., Tang, D., Pflueger, J., Poppe, D., Jabbari, J. S., Gigante, S., Dragwidge, J. M., Whelan, J., Lewsey, M. G. & Lister, R., 4 Mar 2022, bioRxiv, 53 p.Research output: Working paper › Preprint
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Comprehensive evaluation of deconvolution methods for human brain gene expression
Sutton, G. J., Poppe, D., Simmons, R. K., Walsh, K., Nawaz, U., Lister, R., Gagnon-Bartsch, J. A. & Voineagu, I., Dec 2022, In: Nature Communications. 13, 1, 1358.Research output: Contribution to journal › Article › peer-review
Open Access42 Citations (Scopus) -
CRISPRi-based circuits for genetic computation in plants
Khan, A., Herring, G., Oliva, M., Fourie, E., Zhu, J. Y., Johnston, B., Pflueger, J., Swain, T., Pflueger, C., Lloyd, J. P. B., Secco, D., Small, I., Kidd, B. & Lister, R., 2022, bioRxiv.Research output: Working paper › Preprint
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Epigenome plasticity in plants
Lloyd, J. P. B. & Lister, R., Jan 2022, In: Nature Reviews-Genetics. 23, 1, p. 55-68 14 p.Research output: Contribution to journal › Review article › peer-review
77 Citations (Web of Science) -
Human prefrontal cortex gene regulatory dynamics from gestation to adulthood at single-cell resolution
Herring, C. A., Simmons, R. K., Freytag, S., Poppe, D., Moffet, J. J. D., Pflueger, J., Buckberry, S., Vargas Landin, D., Clement, O., Goni Echeverria, E., Sutton, G. J., Alvarez Franco, A., Hou, R., Pflueger, C., McDonald, K., Polo, J. M., Forrest, A. R. R., Nowak, A. K., Voineagu, I., Martelotto, L., & 1 others, 10 Nov 2022, In: Cell. 185, 23, p. 4428-4447.e28 20 p.Research output: Contribution to journal › Article › peer-review
Open Access46 Citations (Scopus) -
Intestinal stem cell aging signature reveals a reprogramming strategy to enhance regenerative potential
Nefzger, C. M., Jardé, T., Srivastava, A., Schroeder, J., Rossello, F. J., Horvay, K., Prasko, M., Paynter, J. M., Chen, J., Weng, C. F., Sun, Y. B. Y., Liu, X., Chan, E., Deshpande, N., Chen, X., Li, Y. J., Pflueger, J., Engel, R. M., Knaupp, A. S., Tsyganov, K., & 5 others, Dec 2022, In: npj Regenerative Medicine. 7, 1, 31.Research output: Contribution to journal › Article › peer-review
Open Access5 Citations (Scopus) -
Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability
de Mendoza, A., Nguyen, T. V., Ford, E., Poppe, D., Buckberry, S., Pflueger, J., Grimmer, M. R., Stolzenburg, S., Bogdanovic, O., Oshlack, A., Farnham, P. J., Blancafort, P. & Lister, R., Dec 2022, In: Genome Biology. 23, 1, p. 1-31 32 p., 163.Research output: Contribution to journal › Article › peer-review
Open Access35 Citations (Scopus) -
Protoplast isolation and transfection in a 96-well plate
Khan, A., Lloyd, J. P. B., Kidd, B. & Lister, R., 2022, protocols.io.Research output: Book/Report › Other output
Open Access -
Retrotransposon instability dominates the acquired mutation landscape of mouse induced pluripotent stem cells
Gerdes, P., Lim, S. M., Ewing, A. D., Larcombe, M. R., Chan, D., Sanchez-Luque, F. J., Walker, L., Carleton, A. L., James, C., Knaupp, A. S., Carreira, P. E., Nefzger, C. M., Lister, R., Richardson, S. R., Polo, J. M. & Faulkner, G. J., Dec 2022, In: Nature Communications. 13, 1, 18 p., 7470.Research output: Contribution to journal › Article › peer-review
Open Access9 Citations (Scopus) -
Single Nucleus RNA Sequencing of Pre-Malignant Liver Reveals Disease-Associated Hepatocyte State with HCC Prognostic Potential
Carlessi, R., Denisenko, E., Boslem, E., Koehn-Galone, J., Main, N., Abu Bakar, N. D. B., Shirolkar, G. D., Jones, M., Poppe, D., Dwyer, B. J., Jackaman, C., Tjiam, C., Lister, R., Karin, M., Fallowfield, J. A., Kendall, T. J., Forbes, S. J., Olyny, J. K., Yeoh, G., Forrest, A., & 3 others, 27 Mar 2022, bioRxiv, 30 p.Research output: Working paper › Preprint
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Synthetic memory circuits for stable cell reprogramming in plants
Lloyd, J. P. B., Ly, F., Gong, P., Pflueger, J., Swain, T., Pflueger, C., Fourie, E., Khan, M. A., Kidd, B. N. & Lister, R., Dec 2022, In: Nature Biotechnology. 40, 12, p. 1862-1872 11 p.Research output: Contribution to journal › Article › peer-review
Open AccessFile41 Citations (Scopus)209 Downloads (Pure) -
2021
Cerebrospinal fluid liquid biopsy for detecting somatic mosaicism in brain
Ye, Z., Chatterton, Z., Pflueger, J., Damiano, J. A., McQuillan, L., Harvey, A. S., Malone, S., Do, H., Maixner, W., Schneider, A., Nolan, B., Wood, M., Lee, W. S., Gillies, G., Pope, K., Wilson, M., Lockhart, P. J., Dobrovic, A., Scheffer, I. E., Bahlo, M., & 4 others, 2021, In: Brain communications. 3, 1, fcaa235.Research output: Contribution to journal › Article › peer-review
Open Access48 Citations (Scopus) -
Comprehensive evaluation of deconvolution methods for human brain gene expression
Sutton, G. J., Poppe, D., Simmons, R., Walsh, K., Nawaz, U., Lister, R., Gagnon-Bartsch, J. A. & Voineagu, I., 27 Oct 2021, bioRxiv, 42 p. (bioRxiv).Research output: Working paper › Preprint
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Genomic Targeting of TET Activity for Targeted Demethylation Using CRISPR/Cas9
Nguyen, T. V. & Lister, R., 2021, TET Proteins and DNA Demethylation: Methods and Protocols. Bogdanovic, O. & Vermeulen, M. (eds.). Humana Press Inc., Vol. 2272. p. 181-194 14 p. (Methods in Molecular Biology; vol. 2272).Research output: Chapter in Book/Conference paper › Chapter › peer-review
9 Citations (Scopus) -
Modelling human blastocysts by reprogramming fibroblasts into iBlastoids
Liu, X., Tan, J. P., Schröder, J., Aberkane, A., Ouyang, J. F., Mohenska, M., Lim, S. M., Sun, Y. B. Y., Chen, J., Sun, G., Zhou, Y., Poppe, D., Lister, R., Clark, A. T., Rackham, O. J. L., Zenker, J. & Polo, J. M., 25 Mar 2021, In: Nature. 591, 7851, p. 627-632 6 p.Research output: Contribution to journal › Article › peer-review
215 Citations (Scopus) -
The emergence of the brain non-CpG methylation system in vertebrates
de Mendoza, A., Poppe, D., Buckberry, S., Pflueger, J., Albertin, C. B., Daish, T., Bertrand, S., de la Calle-Mustienes, E., Gómez-Skarmeta, J. L., Nery, J. R., Ecker, J. R., Baer, B., Ragsdale, C. W., Grützner, F., Escriva, H., Venkatesh, B., Bogdanovic, O. & Lister, R., Mar 2021, In: Nature Ecology and Evolution. 5, 3, p. 369-378 10 p.Research output: Contribution to journal › Article › peer-review
Open AccessFile60 Citations (Scopus)156 Downloads (Pure) -
Transcriptional signature in microglia associated with Aβ plaque phagocytosis
Grubman, A., Choo, X. Y., Chew, G., Ouyang, J. F., Sun, G., Croft, N. P., Rossello, F. J., Simmons, R., Buckberry, S., Landin, D. V., Pflueger, J., Vandekolk, T. H., Abay, Z., Zhou, Y., Liu, X., Chen, J., Larcombe, M., Haynes, J. M., McLean, C., Williams, S., & 8 others, 1 Dec 2021, In: Nature Communications. 12, 1, 3015.Research output: Contribution to journal › Article › peer-review
Open Access135 Citations (Scopus) -
2020
Conserved and divergent features of DNA methylation in embryonic stem cell-derived neurons
Martin, S., Poppe, D., Olova, N., O'Leary, C., Ivanova, E., Pflueger, J., Dechka, J., Simmons, R. K., Cooper, H. M., Reik, W., Lister, R. & Wolvetang, E., 9 Jan 2020, bioRxiv, 61 p. (bioRxiv).Research output: Working paper › Preprint
Open Access -
Depletion of Foxk transcription factors causes genome-wide transcriptional misregulation and developmental arrest in zebrafish embryos
Geng, F-S., de la Calle-Mustienes, E., Gómez-Skarmeta, J. L., Lister, R. & Bogdanovic, O., 8 Dec 2020, microPublication biology, 2020.Research output: Contribution to specialist publication › Article in specialist publication › peer-review
Open Access -
Evolution of DNA methylome diversity in eukaryotes
de Mendoza, A., Lister, R. & Bogdanovic, O., 13 Mar 2020, In: Journal of Molecular Biology. 432, 6, p. 1687-1705 19 p.Research output: Contribution to journal › Review article › peer-review
75 Citations (Scopus) -
Genomic adaptations to aquatic and aerial life in mayflies and the origin of insect wings
Almudi, I., Vizueta, J., Wyatt, C. D. R., de Mendoza, A., Marlétaz, F., Firbas, P. N., Feuda, R., Masiero, G., Medina, P., Alcaina-Caro, A., Cruz, F., Gómez-Garrido, J., Gut, M., Alioto, T. S., Vargas-Chavez, C., Davie, K., Misof, B., González, J., Aerts, S., Lister, R., & 6 others, 1 Dec 2020, In: Nature Communications. 11, 1, 2631.Research output: Contribution to journal › Article › peer-review
Open Access49 Citations (Web of Science) -
Mitochondrial CLPP2 Assists Coordination and Homeostasis of Respiratory Complexes
Petereit, J., Duncan, O., Murcha, M. W., Fenske, R., Cincu, E., Cahn, J., Pruzinska, A., Ivanova, A., Kollipara, L., Wortelkamp, S., Sickmann, A., Lee, J., Lister, R., Millar, A. H. & Huang, S., 8 Sept 2020, In: Plant Physiology. 184, 1, p. 148-164 17 p.Research output: Contribution to journal › Article › peer-review
Open Access22 Citations (Scopus) -
Reprogramming roadmap reveals route to human induced trophoblast stem cells
Liu, X., Ouyang, J. F., Rossello, F. J., Tan, J. P., Davidson, K. C., Valdes, D. S., Schröder, J., Sun, Y. B. Y., Chen, J., Knaupp, A. S., Sun, G., Chy, H. S., Huang, Z., Pflueger, J., Firas, J., Tano, V., Buckberry, S., Paynter, J. M., Larcombe, M. R., Poppe, D., & 19 others, 1 Oct 2020, In: Nature. 586, 7827, p. 101-107 7 p.Research output: Contribution to journal › Article › peer-review
Open AccessFile124 Citations (Scopus)315 Downloads (Pure) -
Schex avoids overplotting for large single cell RNA-sequencing datasets
Freytag, S. & Lister, R., 1 Apr 2020, In: Bioinformatics (Oxford, England). 36, 7, p. 2291-2292 2 p.Research output: Contribution to journal › Article › peer-review
5 Citations (Scopus) -
Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows
Denisenko, E., Guo, B. B., Jones, M., Hou, R., de Kock, L., Lassmann, T., Poppe, D., Clément, O., Simmons, R. K., Lister, R. & Forrest, A. R. R., 2 Jun 2020, In: Genome Biology. 21, 1, p. 130 130.Research output: Contribution to journal › Article › peer-review
Open Access301 Citations (Scopus) -
Systematic bias assessment in solid tissue 10x scRNA-seq workflows
Denisenko, E., Guo, B., Jones, M., Hou, R., De Kock, L., Lassmann, T., Poppe, D., Clement, O., Simmons, R. K., Lister, R. & Forrest, A., 2020, bioRxiv, p. 1-47, 47 p. (bioRxiv).Research output: Working paper › Preprint
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TINC— A Method to Dissect Regulatory Complexes at Single-Locus Resolution— Reveals an Extensive Protein Complex at the Nanog Promoter
Knaupp, A. S., Mohenska, M., Larcombe, M. R., Ford, E., Lim, S. M., Wong, K., Chen, J., Firas, J., Huang, C., Liu, X., Nguyen, T., Sun, Y. B. Y., Holmes, M. L., Tripathi, P., Pflueger, J., Rossello, F. J., Schröder, J., Davidson, K. C., Nefzger, C. M., Das, P. P., & 4 others, 8 Dec 2020, In: Stem Cell Reports. 15, 6, p. 1246-1259 14 p.Research output: Contribution to journal › Article › peer-review
Open Access10 Citations (Scopus) -
Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri
Kenny, N. J., Francis, W. R., Rivera-Vicéns, R. E., Juravel, K., de Mendoza, A., Díez-Vives, C., Lister, R., Bezares-Calderón, L. A., Grombacher, L., Roller, M., Barlow, L. D., Camilli, S., Ryan, J. F., Wörheide, G., Hill, A. L., Riesgo, A. & Leys, S. P., 1 Dec 2020, In: Nature Communications. 11, 1, 3676.Research output: Contribution to journal › Article › peer-review
Open Access68 Citations (Scopus) -
2019
A single-cell atlas of entorhinal cortex from individuals with Alzheimer's disease reveals cell-type-specific gene expression regulation
Grubman, A., Chew, G., Ouyang, J. F., Sun, G., Choo, X. Y., McLean, C., Simmons, R. K., Buckberry, S., Vargas-Landin, D. B., Poppe, D., Pflueger, J., Lister, R., Rackham, O. J. L., Petretto, E. & Polo, J. M., 1 Dec 2019, In: Nature Neuroscience. 22, 12, p. 2087-2097 11 p.Research output: Contribution to journal › Article › peer-review
505 Citations (Scopus) -
Capture of a functionally active methyl-CpG binding domain by an arthropod retrotransposon family
de Mendoza, A., Pflueger, J. & Lister, R., Aug 2019, In: Genome Research. 29, 8, p. 1277-1286 10 p.Research output: Contribution to journal › Article › peer-review
Open AccessFile15 Citations (Scopus)350 Downloads (Pure) -
Convergent evolution of a vertebrate-like methylome in a marine sponge
de Mendoza, A., Hatleberg, W. L., Pang, K., Leininger, S., Bogdanovic, O., Pflueger, J., Buckberry, S., Technau, U., Hejnol, A., Adamska, M., Degnan, B. M., Degnan, S. M. & Lister, R., 1 Oct 2019, In: Nature Ecology and Evolution. 3, 10, p. 1464-1473 10 p.Research output: Contribution to journal › Article › peer-review
Open AccessFile45 Citations (Scopus)73 Downloads (Pure) -
Harnessing targeted DNA methylation and demethylation using dCas9
Pflueger, C., Swain, T. & Lister, R., 20 Dec 2019, In: Essays in Biochemistry. 63, 6, p. 813-825 13 p.Research output: Contribution to journal › Article › peer-review
Open Access9 Citations (Scopus)