Works matching AU Lister, Ryan

Results: 48

STAR: an integrated solution to management and visualization of sequencing data.

Published in:

Bioinformatics, 2013, v. 29, n. 24, p. 3204, doi. 10.1093/bioinformatics/btt558

By:

Wang, Tao;
Liu, Jie;
Shen, Li;
Tonti-Filippini, Julian;
Zhu, Yun;
Jia, Haiyang;
Lister, Ryan;
Whitaker, John W.;
Ecker, Joseph R.;
Millar, A. Harvey;
Ren, Bing;
Wang, Wei

Publication type:

Article

Synthetic Epigenetic Reprogramming of Mesenchymal to Epithelial States Using the CRISPR/dCas9 Platform in Triple Negative Breast Cancer.

Published in:

Advanced Science, 2023, v. 10, n. 22, p. 1, doi. 10.1002/advs.202301802

By:

Waryah, Charlene;
Cursons, Joseph;
Foroutan, Momeneh;
Pflueger, Christian;
Wang, Edina;
Molania, Ramyar;
Woodward, Eleanor;
Sorolla, Anabel;
Wallis, Christopher;
Moses, Colette;
Glas, Irina;
Magalhães, Leandro;
Thompson, Erik W.;
Fearnley, Liam G.;
Chaffer, Christine L.;
Davis, Melissa;
Papenfuss, Anthony T.;
Redfern, Andrew;
Lister, Ryan;
Esteller, Manel

Publication type:

Article

Rapid Recovery Gene Downregulation during Excess-Light Stress and Recovery in Arabidopsis.

Published in:

Plant Cell, 2017, v. 29, n. 8, p. 1836, doi. 10.1105/tpc.16.00828

By:

Crisp, Peter A.;
Ganguly, Diep R.;
Smith, Aaron B.;
Murray, Kevin D.;
Estavillo, Gonzalo M.;
Searle, Iain;
Ford, Ethan;
Bogdanović, Ozren;
Lister, Ryan;
Borevitz, Justin O.;
Eichten, Steven R.;
Pogson, Barry J.

Publication type:

Article

The switch‐liker's guide to plant synthetic gene circuits.

Published in:

Plant Journal, 2025, v. 121, n. 5, p. 1, doi. 10.1111/tpj.70090

By:

Lloyd, James P. B.;
Khan, Adil;
Lister, Ryan

Publication type:

Article

Embryonic Stem Cell-Derived Neurons as a Model System for Epigenome Maturation during Development.

Published in:

Genes, 2023, v. 14, n. 5, p. 957, doi. 10.3390/genes14050957

By:

Martin, Sally;
Poppe, Daniel;
Olova, Nelly;
O'Leary, Conor;
Ivanova, Elena;
Pflueger, Jahnvi;
Dechka, Jennifer;
Simmons, Rebecca K.;
Cooper, Helen M.;
Reik, Wolf;
Lister, Ryan;
Wolvetang, Ernst J.

Publication type:

Article

Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows.

Published in:

Genome Biology, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s13059-020-02048-6

By:

Denisenko, Elena;
Guo, Belinda B.;
Jones, Matthew;
Hou, Rui;
de Kock, Leanne;
Lassmann, Timo;
Poppe, Daniel;
Clément, Olivier;
Simmons, Rebecca K.;
Lister, Ryan;
Forrest, Alistair R. R.

Publication type:

Article

Comprehensive evaluation of deconvolution methods for human brain gene expression.

Published in:

Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-28655-4

By:

Sutton, Gavin J.;
Poppe, Daniel;
Simmons, Rebecca K.;
Walsh, Kieran;
Nawaz, Urwah;
Lister, Ryan;
Gagnon-Bartsch, Johann A.;
Voineagu, Irina

Publication type:

Article

Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02728-5

By:

de Mendoza, Alex;
Nguyen, Trung Viet;
Ford, Ethan;
Poppe, Daniel;
Buckberry, Sam;
Pflueger, Jahnvi;
Grimmer, Matthew R.;
Stolzenburg, Sabine;
Bogdanovic, Ozren;
Oshlack, Alicia;
Farnham, Peggy J.;
Blancafort, Pilar;
Lister, Ryan

Publication type:

Article

Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02728-5

By:

de Mendoza, Alex;
Nguyen, Trung Viet;
Ford, Ethan;
Poppe, Daniel;
Buckberry, Sam;
Pflueger, Jahnvi;
Grimmer, Matthew R.;
Stolzenburg, Sabine;
Bogdanovic, Ozren;
Oshlack, Alicia;
Farnham, Peggy J.;
Blancafort, Pilar;
Lister, Ryan

Publication type:

Article

Turning over DNA methylation in the mind.

Published in:

Frontiers in Neuroscience, 2015, p. 1, doi. 10.3389/fnins.2015.00252

By:

Lister, Ryan;
Mukamel, Eran A.

Publication type:

Article

Exploring the identity of individual plant cells in space and time.

Published in:

New Phytologist, 2023, v. 240, n. 1, p. 61, doi. 10.1111/nph.19153

By:

Oliva, Marina;
Lister, Ryan

Publication type:

Article

Retrotransposon instability dominates the acquired mutation landscape of mouse induced pluripotent stem cells.

Published in:

Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-35180-x

By:

Gerdes, Patricia;
Lim, Sue Mei;
Ewing, Adam D.;
Larcombe, Michael R.;
Chan, Dorothy;
Sanchez-Luque, Francisco J.;
Walker, Lucinda;
Carleton, Alexander L.;
James, Cini;
Knaupp, Anja S.;
Carreira, Patricia E.;
Nefzger, Christian M.;
Lister, Ryan;
Richardson, Sandra R.;
Polo, Jose M.;
Faulkner, Geoffrey J.

Publication type:

Article

Comprehensive evaluation of deconvolution methods for human brain gene expression.

Published in:

Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-28655-4

By:

Sutton, Gavin J.;
Poppe, Daniel;
Simmons, Rebecca K.;
Walsh, Kieran;
Nawaz, Urwah;
Lister, Ryan;
Gagnon-Bartsch, Johann A.;
Voineagu, Irina

Publication type:

Article

methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data.

Published in:

BMC Bioinformatics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12859-015-0742-6

By:

Kishore, Kamal;
de Pretis, Stefano;
Lister, Ryan;
Morelli, Marco J.;
Bianchi, Valerio;
Amati, Bruno;
Ecker, Joseph R.;
Pelizzola, Mattia

Publication type:

Article

methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data.

Published in:

BMC Bioinformatics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12859-015-0742-6

By:

Kishore, Kamal;
de Pretis, Stefano;
Lister, Ryan;
Morelli, Marco J.;
Bianchi, Valerio;
Amati, Bruno;
Ecker, Joseph R.;
Pelizzola, Mattia

Publication type:

Article

Dynamic and rapid changes in the transcriptome and epigenome during germination and in developing rice ( Oryza sativa) coleoptiles under anoxia and re-oxygenation.

Published in:

Plant Journal, 2017, v. 89, n. 4, p. 805, doi. 10.1111/tpj.13418

By:

Narsai, Reena;
Secco, David;
Schultz, Matthew D.;
Ecker, Joseph R.;
Lister, Ryan;
Whelan, James

Publication type:

Article

Retrograde signalling caused by heritable mitochondrial dysfunction is partially mediated by ANAC017 and improves plant performance.

Published in:

Plant Journal, 2016, v. 88, n. 4, p. 542, doi. 10.1111/tpj.13276

By:

Van Aken, Olivier;
Ford, Ethan;
Lister, Ryan;
Huang, Shaobai;
Millar, A.Harvey

Publication type:

Article

The Arabidopsis glutathione transferase gene family displays complex stress regulation and co-silencing multiple genes results in altered metabolic sensitivity to oxidative stress.

Published in:

Plant Journal, 2009, v. 58, n. 1, p. 53, doi. 10.1111/j.1365-313X.2008.03761.x

By:

Sappl, Pia G.;
Carroll, Adam J.;
Clifton, Rachael;
Lister, Ryan;
Whelan, James;
Harvey Millar, A.;
Singh, Karam B.

Publication type:

Article

Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons.

Published in:

Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-03724-9

By:

de Mendoza, Alex;
Bonnet, Amandine;
Vargas-Landin, Dulce B.;
Nanjing Ji;
Hongfei Li;
Feng Yang;
Ling Li;
Koichi Hori;
Pflueger, Jahnvi;
Buckberry, Sam;
Hiroyuki Ohta;
Rosic, Nedeljka;
Lesage, Pascale;
Senjie Lin;
Lister, Ryan

Publication type:

Article

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.

Published in:

Nature Biotechnology, 2010, v. 28, n. 10, p. 1097, doi. 10.1038/nbt.1682

By:

Harris, R. Alan;
Ting Wang;
Coarfa, Cristian;
Nagarajan, Raman P.;
Hong, Chibo;
Downey, Sara L.;
Johnson, Brett E.;
Fouse, Shaun D.;
Delaney, Allen;
Yongjun Zhao;
Olshen, Adam;
Ballinger, Tracy;
Xin Zhou;
Forsberg, Kevin J.;
Junchen Gu;
Echipare, Lorigail;
O'Geen, Henriette;
Lister, Ryan;
Pelizzola, Mattia;
Yuanxin Xi

Publication type:

Article

A plant outer mitochondrial membrane protein with high amino acid sequence identity to a chloroplast protein import receptor

Published in:

FEBS Letters, 2004, v. 557, n. 1-3, p. 109, doi. 10.1016/S0014-5793(03)01457-1

By:

Chew, Orinda;
Lister, Ryan;
Qbadou, Soumya;
Heazlewood, Joshua L.;
Soll, Jurgen;
Schleiff, Enrico;
Millar, A. Harvey;
Whelan, James

Publication type:

Article

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

Published in:

Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-17397-w

By:

Kenny, Nathan J.;
Francis, Warren R.;
Rivera-Vicéns, Ramón E.;
Juravel, Ksenia;
de Mendoza, Alex;
Díez-Vives, Cristina;
Lister, Ryan;
Bezares-Calderón, Luis A.;
Grombacher, Lauren;
Roller, Maša;
Barlow, Lael D.;
Camilli, Sara;
Ryan, Joseph F.;
Wörheide, Gert;
Hill, April L.;
Riesgo, Ana;
Leys, Sally P.

Publication type:

Article

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

Published in:

Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-16284-8

By:

Almudi, Isabel;
Vizueta, Joel;
Wyatt, Christopher D. R.;
de Mendoza, Alex;
Marlétaz, Ferdinand;
Firbas, Panos N.;
Feuda, Roberto;
Masiero, Giulio;
Medina, Patricia;
Alcaina-Caro, Ana;
Cruz, Fernando;
Gómez-Garrido, Jessica;
Gut, Marta;
Alioto, Tyler S.;
Vargas-Chavez, Carlos;
Davie, Kristofer;
Misof, Bernhard;
González, Josefa;
Aerts, Stein;
Lister, Ryan

Publication type:

Article

Zinc-dependent intermembrane space proteins stimulate import of carrier proteins into plant mitochondria.

Published in:

Plant Journal, 2002, v. 30, n. 5, p. 555, doi. 10.1046/j.1365-313X.2002.01316.x

By:

Lister, Ryan;
Mowday, Brett;
Whelan, James;
Millar, A. Harvey

Publication type:

Article

A modular dCas9-based recruitment platform for combinatorial epigenome editing.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 1, p. 474, doi. 10.1093/nar/gkad1108

By:

Swain, Tessa;
Pflueger, Christian;
Freytag, Saskia;
Poppe, Daniel;
Pflueger, Jahnvi;
Nguyen, Trung Viet;
Li, Ji Kevin;
Lister, Ryan

Publication type:

Article

Erratum: Embryonic transcription is controlled by maternally defined chromatin state.

Published in:

Nature Communications, 2016, v. 7, n. 7, p. 12208, doi. 10.1038/ncomms12208

By:

Hontelez, Saartje;
van Kruijsbergen, Ila;
Georgiou, Georgios;
van Heeringen, Simon J.;
Bogdanovic, Ozren;
Lister, Ryan;
Veenstra, Gert Jan C.

Publication type:

Article

Embryonic transcription is controlled by maternally defined chromatin state.

Published in:

Nature Communications, 2015, v. 6, n. 12, p. 10148, doi. 10.1038/ncomms10148

By:

Hontelez, Saartje;
van Kruijsbergen, Ila;
Georgiou, Georgios;
van Heeringen, Simon J.;
Bogdanovic, Ozren;
Lister, Ryan;
Veenstra, Gert Jan C.

Publication type:

Article

Human DNA methylomes at base resolution show widespread epigenomic differences.

Published in:

Nature, 2009, v. 462, n. 7271, p. 315, doi. 10.1038/nature08514

By:

Lister, Ryan;
Pelizzola, Mattia;
Dowen, Robert H.;
Hawkins, R. David;
Hon, Gary;
Tonti-Filippini, Julian;
Nery, Joseph R.;
Lee, Leonard;
Zhen Ye;
Que-Minh Ngo;
Edsall, Lee;
Antosiewicz-Bourget, Jessica;
Stewart, Ron;
Ruotti, Victor;
Millar, A. Harvey;
Thomson, James A.;
Ren, Bing;
Ecker, Joseph R.

Publication type:

Article

The Mitochondrial Protein Import Machinery of Plants (MPIMP) database.

Published in:

Nucleic Acids Research, 2003, v. 31, n. 1, p. 325, doi. 10.1093/nar/gkg055

By:

Lister, Ryan;
Murcha, Monika W.;
Whelan, James

Publication type:

Article

Retention of paternal DNA methylome in the developing zebrafish germline.

Published in:

Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-10895-6

By:

Skvortsova, Ksenia;
Tarbashevich, Katsiaryna;
Stehling, Martin;
Lister, Ryan;
Irimia, Manuel;
Raz, Erez;
Bogdanovic, Ozren

Publication type:

Article

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

Published in:

Tree Physiology, 2023, v. 43, n. 4, p. 675, doi. 10.1093/treephys/tpac146

By:

Hermawaty, Dina;
Cahn, Jonathan;
Lister, Ryan;
Considine, Michael J

Publication type:

Article

schex avoids overplotting for large single-cell RNA-sequencing datasets.

Published in:

Bioinformatics, 2020, v. 36, n. 7, p. 2291, doi. 10.1093/bioinformatics/btz907

By:

Freytag, Saskia;
Lister, Ryan

Publication type:

Article

Early moderate prenatal alcohol exposure and maternal diet impact offspring DNA methylation across species.

Published in:

eLife, 2024, p. 1, doi. 10.7554/eLife.92135

By:

Bestry, Mitchell;
Larcombe, Alexander N.;
Kresoje, Nina;
Chivers, Emily K.;
Bakker, Chloe;
Fitzpatrick, James P.;
Elliott, Elizabeth J.;
Craig, Jeffrey M.;
Muggli, Evelyne;
Halliday, Jane;
Hutchinson, Delyse;
Buckberry, Sam;
Lister, Ryan;
Symons, Martyn;
Martino, David

Publication type:

Article

Regulatory remodeling in the allo-tetraploid frog Xenopus laevis.

Published in:

Genome Biology, 2017, v. 18, p. 1, doi. 10.1186/s13059-017-1335-7

By:

Elurbe, Dei M.;
Paranjpe, Sarita S.;
Georgiou, Georgios;
van Kruijsbergen, Ila;
Bogdanovic, Ozren;
Gibeaux, Romain;
Heald, Rebecca;
Lister, Ryan;
Huynen, Martijn A.;
van Heeringen, Simon J.;
Veenstra, Gert Jan C.

Publication type:

Article

Extensive transcriptomic and epigenomic remodelling occurs during Arabidopsis thaliana germination.

Published in:

Genome Biology, 2017, v. 18, p. 1, doi. 10.1186/s13059-017-1302-3

By:

Narsai, Reena;
Gouil, Quentin;
Secco, David;
Srivastava, Akanksha;
Karpievitch, Yuliya V.;
Lim Chee Liew;
Lister, Ryan;
Lewsey, Mathew G.;
Whelan, James

Publication type:

Article

MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing.

Published in:

Nature Protocols, 2015, v. 10, n. 3, p. 475, doi. 10.1038/nprot.2014.114

By:

Urich, Mark A.;
Nery, Joseph R.;
Lister, Ryan;
Schmitz, Robert J.;
Ecker, Joseph R.

Publication type:

Article

Harnessing targeted DNA methylation and demethylation using dCas9.

Published in:

Essays in Biochemistry, 2019, v. 63, n. 6, p. 813, doi. 10.1042/EBC20190029

By:

Pflueger, Christian;
Swain, Tessa;
Lister, Ryan

Publication type:

Article

HOME: a histogram based machine learning approach for effective identification of differentially methylated regions.

Published in:

BMC Bioinformatics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12859-019-2845-y

By:

Srivastava, Akanksha;
Karpievitch, Yuliya V.;
Eichten, Steven R.;
Borevitz, Justin O.;
Lister, Ryan

Publication type:

Article

Corrigendum: Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells.

Published in:

Nature, 2014, v. 514, n. 7520, p. 126, doi. 10.1038/nature13843

By:

Lister, Ryan;
Pelizzola, Mattia;
Kida, Yasuyuki S.;
Hawkins, R. David;
Nery, Joseph R.;
Hon, Gary;
Antosiewicz-Bourget, Jessica;
O'Malley, Ronan;
Castanon, Rosa;
Klugman, Sarit;
Downes, Michael;
Yu, Ruth;
Stewart, Ron;
Ren, Bing;
Thomson, James A.;
Evans, Ronald M.;
Ecker, Joseph R.

Publication type:

Article

Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells.

Published in:

Nature, 2011, v. 473, n. 7347, p. 394, doi. 10.1038/nature10102

By:

Pastor, William A.;
Pape, Utz J.;
Huang, Yun;
Henderson, Hope R.;
Lister, Ryan;
Myunggon Ko;
McLoughlin, Erin M.;
Brudno, Yevgeny;
Mahapatra, Sahasransu;
Kapranov, Philipp;
Tahiliani, Mamta;
Daley, George Q.;
Liu, X. Shirley;
Ecker, Joseph R.;
Milos, Patrice M.;
Agarwal, Suneet;
Rao, Anjana

Publication type:

Article

Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells.

Published in:

Nature, 2011, v. 471, n. 7336, p. 68, doi. 10.1038/nature09798

By:

Lister, Ryan;
Pelizzola, Mattia;
Kida, Yasuyuki S.;
Hawkins, R. David;
Nery, Joseph R.;
Hon, Gary;
Antosiewicz-Bourget, Jessica;
O'Malley, Ronan;
Castanon, Rosa;
Klugman, Sarit;
Downes, Michael;
Yu, Ruth;
Stewart, Ron;
Ren, Bing;
Thomson, James A.;
Evans, Ronald M.;
Ecker, Joseph R.

Publication type:

Article

Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation.

Published in:

eLife, 2016, p. 1, doi. 10.7554/eLife.20777

By:

Stuart, Tim;
Eichten, Steven R.;
Cahn, Jonathan;
Karpievitch, Yuliya V.;
Borevitz, Justin O.;
Lister, Ryan

Publication type:

Article

Epigenomic landscapes of retinal rods and cones.

Published in:

eLife, 2016, p. 1, doi. 10.7554/eLife.11613

By:

Mo, Alisa;
Chongyuan Luo;
Davis, Fred P.;
Mukamel, Eran A.;
Henry, Gilbert L.;
Nery, Joseph R.;
Urich, Mark A.;
Picard, Serge;
Lister, Ryan;
Eddy, Sean R.;
Beer, Michael A.;
Ecker, Joseph R.;
Nathans, Jeremy

Publication type:

Article

Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements.

Published in:

eLife, 2015, p. 1, doi. 10.7554/eLife.09343

By:

Secco, David;
Chuang Wang;
Huixia Shou;
Schultz, Matthew D.;
Chiarenza, Serge;
Nussaume, Laurent;
Ecker, Joseph R.;
Whelan, James;
Lister, Ryan

Publication type:

Article

Analysis of an artificial zinc finger epigenetic modulator: widespread binding but limited regulation.

Published in:

Nucleic Acids Research, 2014, v. 42, n. 16, p. 10856, doi. 10.1093/nar/gku708

By:

Grimmer, Matthew R.;
Stolzenburg, Sabine;
Ford, Ethan;
Lister, Ryan;
Blancafort, Pilar;
Farnham, Peggy J.

Publication type:

Article

Mitochondrial CLPP2 Assists Coordination and Homeostasis of Respiratory Complexes.

Published in:

Plant Physiology, 2020, v. 184, n. 1, p. 148, doi. 10.1104/pp.20.00136

By:

Petereit, Jakob;
Duncan, Owen;
Murcha, Monika W.;
Fenske, Ricarda;
Cincu, Emilia;
Cahn, Jonathan;
PruÅinskÃ¡, Adriana;
Ivanova, Aneta;
Kollipara, Laxmikanth;
Wortelkamp, Stefanie;
Sickmann, Albert;
Lee, Jiwon;
Lister, Ryan;
Millar, A. Harvey;
Huang, Shaobai

Publication type:

Article

CRISPRi-based circuits to control gene expression in plants.

Published in:

Nature Biotechnology, 2025, v. 43, n. 3, p. 416, doi. 10.1038/s41587-024-02236-w

By:

Khan, Muhammad Adil;
Herring, Gabrielle;
Zhu, Jia Yuan;
Oliva, Marina;
Fourie, Elliott;
Johnston, Benjamin;
Zhang, Zhining;
Potter, Jarred;
Pineda, Luke;
Pflueger, Jahnvi;
Swain, Tessa;
Pflueger, Christian;
Lloyd, James P. B.;
Secco, David;
Small, Ian;
Kidd, Brendan N.;
Lister, Ryan

Publication type:

Article

Synthetic memory circuits for stable cell reprogramming in plants.

Published in:

Nature Biotechnology, 2022, v. 40, n. 12, p. 1862, doi. 10.1038/s41587-022-01383-2

By:

Lloyd, James P. B.;
Ly, Florence;
Gong, Patrick;
Pflueger, Jahnvi;
Swain, Tessa;
Pflueger, Christian;
Fourie, Elliott;
Khan, Muhammad Adil;
Kidd, Brendan N.;
Lister, Ryan

Publication type:

Article