Works by Cairns, Jonathan

Results: 18

BayesPeak—an R package for analysing ChIP-seq data.

Published in:

Bioinformatics, 2011, v. 27, n. 5, p. 713, doi. 10.1093/bioinformatics/btq685

By:

Cairns, Jonathan;
Spyrou, Christiana;
Stark, Rory;
Smith, Mike L.;
Lynch, Andy G.;
Tavaré, Simon

Publication type:

Article

The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02374-3

By:

Furlan-Magaril, Mayra;
Ando-Kuri, Masami;
Arzate-Mejía, Rodrigo G.;
Morf, Jörg;
Cairns, Jonathan;
Román-Figueroa, Abraham;
Tenorio-Hernández, Luis;
Poot-Hernández, A. César;
Andrews, Simon;
Várnai, Csilla;
Virk, Boo;
Wingett, Steven W.;
Fraser, Peter

Publication type:

Article

Integrated in vitro models for hepatic safety and metabolism: evaluation of a human Liver-Chip and liver spheroid.

Published in:

Archives of Toxicology, 2019, v. 93, n. 4, p. 1021, doi. 10.1007/s00204-019-02427-4

By:

Foster, Alison J.;
Regan, Sophie L.;
Rollison, Helen;
Srivastava, Abhishek;
Williams, Dominic;
Ewart, Lorna;
Morgan, Paul;
Chouhan, Bhavik;
Amberntsson, Sara;
Andersson, Linda C.;
Darnell, Malin;
Cairns, Jonathan;
Lazic, Stanley E.;
Jang, Kyung-Jin;
Petropolis, Debora B.;
Kodella, Konstantia;
Rubins, Jonathan E.;
Hamilton, Geraldine A.

Publication type:

Article

Quantifying the impact of inter-site heterogeneity on the distribution of ChIP-seq data.

Published in:

Frontiers in Genetics, 2014, v. 5, p. 1, doi. 10.3389/fgene.2014.00399

By:

Cairns, Jonathan;
Lynch, Andy G.;
Tavaré, Simon

Publication type:

Article

Single‐cell study of neural stem cells derived from human iPSCs reveals distinct progenitor populations with neurogenic and gliogenic potential.

Published in:

Genes to Cells, 2019, v. 24, n. 12, p. 836, doi. 10.1111/gtc.12731

By:

Lam, Matti;
Sanosaka, Tsukasa;
Lundin, Anders;
Imaizumi, Kent;
Etal, Damla;
Karlsson, Fredrik H.;
Clausen, Maryam;
Cairns, Jonathan;
Hicks, Ryan;
Kohyama, Jun;
Kele, Malin;
Okano, Hideyuki;
Falk, Anna

Publication type:

Article

Normoglycemia and physiological cortisone level maintain glucose homeostasis in a pancreas-liver microphysiological system.

Published in:

Communications Biology, 2024, p. 1, doi. 10.1038/s42003-024-06514-w

By:

Rigal, Sophie;
Casas, Belén;
Kanebratt, Kajsa P.;
Wennberg Huldt, Charlotte;
Magnusson, Lisa U.;
Müllers, Erik;
Karlsson, Fredrik;
Clausen, Maryam;
Hansson, Sara F.;
Leonard, Louise;
Cairns, Jonathan;
Jansson Löfmark, Rasmus;
Ämmälä, Carina;
Marx, Uwe;
Gennemark, Peter;
Cedersund, Gunnar;
Andersson, Tommy B.;
Vilén, Liisa K.

Publication type:

Article

Optimal experimental design for efficient toxicity testing in microphysiological systems: A bone marrow application.

Published in:

Frontiers in Pharmacology, 2023, v. 14, p. 1, doi. 10.3389/fphar.2023.1142581

By:

Cairns, Jonathan;
Leonard, Emilyanne;
Khan, Kainat;
Parks, Conor;
Maglennon, Gareth;
Bairu Zhang;
Lazic, Stanley E.;
Ewart, Lorna;
David, Rhiannon

Publication type:

Article

Correction: A statistical simulation model to guide the choices of analytical methods in arrayed CRISPR screen experiments.

Published in:

2025

By:

Kim, Chang Sik;
Cairns, Jonathan;
Quarantotti, Valentina;
Kaczkowski, Bogumil;
Wang, Yinhai;
Konings, Peter;
Zhang, Xiang

Publication type:

Correction Notice

A statistical simulation model to guide the choices of analytical methods in arrayed CRISPR screen experiments.

Published in:

PLoS ONE, 2024, v. 19, n. 8, p. 1, doi. 10.1371/journal.pone.0307445

By:

Kim, Chang Sik;
Cairns, Jonathan;
Quarantotti, Valentina;
Kaczkowski, Bogumil;
Wang, Yinhai;
Konings, Peter;
Zhang, Xiang

Publication type:

Article

Platelet function is modified by common sequence variation in megakaryocyte super enhancers.

Published in:

Nature Communications, 2017, v. 8, n. 7, p. 16058, doi. 10.1038/ncomms16058

By:

Petersen, Romina;
Lambourne, John J.;
Javierre, Biola M.;
Grassi, Luigi;
Kreuzhuber, Roman;
Ruklisa, Dace;
Rosa, Isabel M.;
Tomé, Ana R.;
Elding, Heather;
van Geffen, Johanna P.;
Jiang, Tao;
Farrow, Samantha;
Cairns, Jonathan;
Al-Subaie, Abeer M.;
Ashford, Sofie;
Attwood, Antony;
Batista, Joana;
Bouman, Heleen;
Burden, Frances;
Choudry, Fizzah A.

Publication type:

Article

AZD7648 is a potent and selective DNA-PK inhibitor that enhances radiation, chemotherapy and olaparib activity.

Published in:

Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-12836-9

By:

Fok, Jacqueline H. L.;
Ramos-Montoya, Antonio;
Vazquez-Chantada, Mercedes;
Wijnhoven, Paul W. G.;
Follia, Valeria;
James, Neil;
Farrington, Paul M.;
Karmokar, Ankur;
Willis, Sophie E.;
Cairns, Jonathan;
Nikkilä, Jenni;
Beattie, David;
Lamont, Gillian M.;
Finlay, M. Raymond V.;
Wilson, Joanne;
Smith, Aaron;
O'Connor, Lenka Oplustil;
Ling, Stephanie;
Fawell, Stephen E.;
O'Connor, Mark J.

Publication type:

Article

Chicdiff: a computational pipeline for detecting differential chromosomal interactions in Capture Hi-C data.

Published in:

Bioinformatics, 2019, v. 35, n. 22, p. 4764, doi. 10.1093/bioinformatics/btz450

By:

Cairns, Jonathan;
Orchard, William R;
Malysheva, Valeriya;
Spivakov, Mikhail

Publication type:

Article

Chromosome contacts in activated T cells identify autoimmune disease candidate genes.

Published in:

Genome Biology, 2017, v. 18, p. 1, doi. 10.1186/s13059-017-1285-0

By:

Burren, Oliver S.;
García, Arcadio Rubio;
Javierre, Biola-Maria;
Rainbow, Daniel B.;
Cairns, Jonathan;
Cooper, Nicholas J.;
Lambourne, John J.;
Schofield, Ellen;
Xaquin Castro Dopico;
Ferreira, Ricardo C.;
Coulson, Richard;
Burden, Frances;
Rowlston, Sophia P.;
Downes, Kate;
Wingett, Steven W.;
Frontini, Mattia;
Ouwehand, Willem H.;
Fraser, Peter;
Spivakov, Mikhail;
Todd, John A.

Publication type:

Article

CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data.

Published in:

Genome Biology, 2016, v. 17, p. 1, doi. 10.1186/s13059-016-0992-2

By:

Cairns, Jonathan;
Freire-Pritchett, Paula;
Wingett, Steven W.;
Várnai, Csilla;
Dimond, Andrew;
Plagnol, Vincent;
Zerbino, Daniel;
Schoenfelder, Stefan;
Javierre, Biola-Maria;
Osborne, Cameron;
Fraser, Peter;
Spivakov, Mikhail

Publication type:

Article

Detecting chromosomal interactions in Capture Hi-C data with CHiCAGO and companion tools.

Published in:

Nature Protocols, 2021, v. 16, n. 9, p. 4144, doi. 10.1038/s41596-021-00567-5

By:

Freire-Pritchett, Paula;
Ray-Jones, Helen;
Della Rosa, Monica;
Eijsbouts, Chris Q.;
Orchard, William R.;
Wingett, Steven W.;
Wallace, Chris;
Cairns, Jonathan;
Spivakov, Mikhail;
Malysheva, Valeriya

Publication type:

Article

Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells.

Published in:

eLife, 2017, p. 1, doi. 10.7554/eLife.21926

By:

Freire-Pritchett, Paula;
Schoenfelder, Stefan;
Vá Rnai, Csilla;
Wingett, Steven W.;
Cairns, Jonathan;
Collier, Amanda J.;
García-Vílchez, Raquel;
Furlan-Magaril, Mayra;
Osborne, Cameron S.;
Fraser, Peter;
Rugg-Gunn, Peter J.;
Spivakov, Mikhail

Publication type:

Article

RNA proximity sequencing reveals the spatial organization of the transcriptome in the nucleus.

Published in:

Nature Biotechnology, 2019, v. 37, n. 7, p. 793, doi. 10.1038/s41587-019-0166-3

By:

Morf, Jörg;
Wingett, Steven W.;
Farabella, Irene;
Cairns, Jonathan;
Furlan-Magaril, Mayra;
Jiménez-García, Luis F.;
Liu, Xin;
Craig, Frank F.;
Walker, Simon;
Segonds-Pichon, Anne;
Andrews, Simon;
Marti-Renom, Marc A.;
Fraser, Peter

Publication type:

Article

Phenotype Specific Analyses Reveal Distinct Regulatory Mechanism for Chronically Activated p53.

Published in:

PLoS Genetics, 2015, v. 11, n. 3, p. 1, doi. 10.1371/journal.pgen.1005053

By:

Kirschner, Kristina;
Samarajiwa, Shamith A.;
Cairns, Jonathan M.;
Menon, Suraj;
Pérez-Mancera, Pedro A.;
Tomimatsu, Kosuke;
Bermejo-Rodriguez, Camino;
Ito, Yoko;
Chandra, Tamir;
Narita, Masako;
Lyons, Scott K.;
Lynch, Andy G.;
Kimura, Hiroshi;
Ohbayashi, Tetsuya;
Tavaré, Simon;
Narita, Masashi

Publication type:

Article