Johnson, Rory Baldwin

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2021

Bosch-Guiteras, Núria; Uroda, Tina; Guillen-Ramirez, Hugo A.; Riedo, Rahel; Gazdhar, Amiq; Esposito, Roberta; Pulido-Quetglas, Carlos; Zimmer, Yitzhak; Medová, Michaela; Johnson, Rory (2021). Enhancing CRISPR deletion via pharmacological delay of DNA-PKcs. Genome research, 31(3), pp. 461-471. Cold Spring Harbor, N.Y 10.1101/gr.265736.120

Frankish, Adam; Diekhans, Mark; Jungreis, Irwin; Lagarde, Julien; Loveland, Jane E; Mudge, Jonathan M; Sisu, Cristina; Wright, James C; Armstrong, Joel; Barnes, If; Berry, Andrew; Bignell, Alexandra; Boix, Carles; Carbonell Sala, Silvia; Cunningham, Fiona; Di Domenico, Tomás; Donaldson, Sarah; Fiddes, Ian T; García Girón, Carlos; Gonzalez, Jose Manuel; ... (2021). GENCODE 2021. Nucleic acids research, 49(D1), D916-D923. Oxford University Press 10.1093/nar/gkaa1087

Carbonell Sala, Sílvia; Uszczyńska-Ratajczak, Barbara; Lagarde, Julien; Johnson, Rory; Guigó, Roderic (2021). Annotation of Full-Length Long Noncoding RNAs with Capture Long-Read Sequencing (CLS). Methods in molecular biology, 2254, pp. 133-159. Springer 10.1007/978-1-0716-1158-6_9

2020

Bracher, Lisamaria; Ferro, Iolanda; Pulido-Quetglas, Carlos; Ruepp, Marc-David; Johnson, Rory; Polacek, Norbert (2020). Human vtRNA1-1 Levels Modulate Signaling Pathways and Regulate Apoptosis in Human Cancer Cells. Biomolecules, 10(4), p. 614. MDPI 10.3390/biom10040614

Bergada Pijuan, Judith; Pulido Quetglas, Carlos; Vancura, Adrienne; Johnson, Rory (2020). CASPR, an analysis pipeline for single and paired guide RNA CRISPR screens, reveals optimal target selection for long noncoding RNAs. Bioinformatics, 36(6), pp. 1673-1680. Oxford University Press 10.1093/bioinformatics/btz811

Carlevaro Fita, Joana; Lanzós, Andrés; Feuerbach, Lars; Hong, Chen; Mas-Ponte, David; Pedersen, Jakob Skou; Johnson, Rory (2020). Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis. Communications biology, 3(1), p. 56. Springer Nature 10.1038/s42003-019-0741-7

Reyna, Matthew A; Haan, David; Paczkowska, Marta; Verbeke, Lieven P C; Vazquez, Miguel; Kahraman, Abdullah; Pulido-Tamayo, Sergio; Barenboim, Jonathan; Wadi, Lina; Dhingra, Priyanka; Shrestha, Raunak; Getz, Gad; Lawrence, Michael S; Pedersen, Jakob Skou; Rubin, Mark Andrew; Wheeler, David A; Brunak, Søren; Izarzugaza, Jose M G; Khurana, Ekta; Marchal, Kathleen; ... (2020). Pathway and network analysis of more than 2500 whole cancer genomes. Nature communications, 11(1), p. 729. Nature Publishing Group 10.1038/s41467-020-14367-0

Rheinbay, Esther; Nielsen, Morten Muhlig; Abascal, Federico; Wala, Jeremiah A; Shapira, Ofer; Tiao, Grace; Hornshøj, Henrik; Hess, Julian M; Juul, Randi Istrup; Lin, Ziao; Feuerbach, Lars; Sabarinathan, Radhakrishnan; Madsen, Tobias; Kim, Jaegil; Mularoni, Loris; Shuai, Shimin; Lanzos, Andrés; Herrmann, Carl; Maruvka, Yosef E; Shen, Ciyue; ... (2020). Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature, 578(7793), pp. 102-111. Springer Nature 10.1038/s41586-020-1965-x

2019

Carlevaro-Fita, Joana; Liu, Leibo; Zhou, Yuan; Zhang, Shan; Chouvardas, Panagiotis; Johnson, Rory; Li, Jianwei (2019). LnCompare: gene set feature analysis for human long non-coding RNAs. Nucleic acids research, 47(W1), W523-W529. Oxford University Press 10.1093/nar/gkz410

Carlevaro-Fita, Joana; Johnson, Rory (2019). Global Positioning System: Understanding Long Noncoding RNAs through Subcellular Localization. Molecular cell, 73(5), pp. 869-883. Cell Press 10.1016/j.molcel.2019.02.008

Carlevaro-Fita, Joana; Polidori, Taisia; Das, Monalisa; Navarro, Carmen; Zoller, Tatjana I.; Johnson, Rory (2019). Ancient exapted transposable elements promote nuclear enrichment of human long noncoding RNAs. Genome research, 29(2), pp. 208-222. Cold Spring Harbor, N.Y 10.1101/gr.229922.117

Frankish, Adam; Diekhans, Mark; Ferreira, Anne-Maud; Johnson, Rory Baldwin; Jungreis, Irwin; Loveland, Jane; Mudge, Jonathan M; Sisu, Cristina; Wright, James; Armstrong, Joel; Barnes, If; Berry, Andrew; Bignell, Alexandra; Carbonell Sala, Silvia; Chrast, Jacqueline; Cunningham, Fiona; Di Domenico, Tomás; Donaldson, Sarah; Fiddes, Ian T; García Girón, Carlos; ... (2019). GENCODE reference annotation for the human and mouse genomes. Nucleic acids research, 47(D1), D766-D773. Oxford University Press 10.1093/nar/gky955

Esposito, Roberta; Bosch, Núria; Lanzos Camaioni, Andrés Arturo; Polidori, Taisia; Pulido-Quetglas, Carlos; Johnson, Rory (2019). Hacking the Cancer Genome: Profiling Therapeutically Actionable Long Non-coding RNAs Using CRISPR-Cas9 Screening. Cancer cell, 35(4), pp. 545-557. Cell Press 10.1016/j.ccell.2019.01.019

2018

Uszczynska-Ratajczak, Barbara; Lagarde, Julien; Frankish, Adam; Guigó, Roderic; Johnson, Rory Baldwin (2018). Towards a complete map of the human long non-coding RNA transcriptome. Nature Reviews. Genetics, 19(9), pp. 535-548. Natue Publishing Group 10.1038/s41576-018-0017-y

Lagarde, Julien; Johnson, Rory Baldwin (2018). Capturing a Long Look at Our Genetic Library. Cell systems, 6(2), pp. 153-155. Elsevier 10.1016/j.cels.2018.02.003

2017

Lagarde, Julien; Uszczynska-Ratajczak, Barbara; Carbonell, Silvia; Pérez-Lluch, Sílvia; Abad, Amaya; Davis, Carrie; Gingeras, Thomas R; Frankish, Adam; Harrow, Jennifer; Guigo, Roderic; Johnson, Rory (2017). High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing. Nature genetics, 49(12), pp. 1731-1740. Nature America 10.1038/ng.3988

Mas-Ponte, David; Carlevaro Fita, Joana; Palumbo, Emilio; Hermoso Pulido, Toni; Guigo, Roderic; Johnson, Rory (2017). LncATLAS database for subcellular localization of long noncoding RNAs. RNA - a publication of the RNA Society, 23(7), pp. 1080-1087. Cold Spring Harbor Laboratory Press 10.1261/rna.060814.117

Pulido-Quetglas, Carlos; Aparicio-Prat, Estel; Arnan, Carme; Polidori, Taisia; Hermoso, Toni; Palumbo, Emilio; Ponomarenko, Julia; Guigo, Roderic; Johnson, Rory Baldwin (2017). Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion. PLoS computational biology, 13(3), e1005341. Public Library of Science 10.1371/journal.pcbi.1005341

Lanzós, Andrés; Carlevaro-Fita, Joana; Mularoni, Loris; Reverter, Ferran; Palumbo, Emilio; Guigó, Roderic; Johnson, Rory (2017). Discovery of Cancer Driver Long Noncoding RNAs across 1112 Tumour Genomes: New Candidates and Distinguishing Features. Scientific Reports, 7(41544), p. 41544. Nature Publishing Group 10.1038/srep41544

2016

Carlevaro Fita, Joana; Rahim, Anisa; Guigó, Roderic; Vardy, Leah A; Johnson, Rory Baldwin (2016). Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells. RNA - a publication of the RNA Society, 22(6), pp. 867-882. Cold Spring Harbor Laboratory Press 10.1261/rna.053561.115

Aparicio-Prat, Estel; Arnan, Carme; Sala, Ilaria; Bosch, Núria; Guigó, Roderic; Johnson, Rory Baldwin (2016). Erratum to: 'DECKO: Single-oligo, dual-CRISPR deletion of genomic elements including long non-coding RNAs'. BMC Genomics, 17(215), p. 215. BioMed Central 10.1186/s12864-016-2544-2

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