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CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data J Cairns, P Freire-Pritchett, SW Wingett, C Várnai, A Dimond, V Plagnol, ... Genome biology 17, 1-17, 2016 | 393 | 2016 |
Lineage-specific dynamic and pre-established enhancer–promoter contacts cooperate in terminal differentiation AJ Rubin, BC Barajas, M Furlan-Magaril, V Lopez-Pajares, MR Mumbach, ... Nature genetics 49 (10), 1522-1528, 2017 | 287 | 2017 |
AZD7648 is a potent and selective DNA-PK inhibitor that enhances radiation, chemotherapy and olaparib activity JHL Fok, A Ramos-Montoya, M Vazquez-Chantada, PWG Wijnhoven, ... Nature communications 10 (1), 5065, 2019 | 231 | 2019 |
Dynamic rewiring of promoter-anchored chromatin loops during adipocyte differentiation R Siersbæk, JGS Madsen, BM Javierre, R Nielsen, EK Bagge, J Cairns, ... Molecular cell 66 (3), 420-435. e5, 2017 | 205 | 2017 |
Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells P Freire-Pritchett, S Schoenfelder, C Várnai, SW Wingett, J Cairns, ... Elife 6, e21926, 2017 | 152 | 2017 |
Long-range enhancer interactions are prevalent in mouse embryonic stem cells and are reorganized upon pluripotent state transition CL Novo, BM Javierre, J Cairns, A Segonds-Pichon, SW Wingett, ... Cell reports 22 (10), 2615-2627, 2018 | 103 | 2018 |
Integrated in vitro models for hepatic safety and metabolism: evaluation of a human Liver-Chip and liver spheroid AJ Foster, B Chouhan, SL Regan, H Rollison, S Amberntsson, ... Archives of toxicology 93 (4), 1021-1037, 2019 | 89 | 2019 |
Chromosome contacts in activated T cells identify autoimmune disease candidate genes OS Burren, A Rubio García, BM Javierre, DB Rainbow, J Cairns, ... Genome biology 18, 1-19, 2017 | 85 | 2017 |
BASH: a tool for managing BeadArray spatial artefacts JM Cairns, MJ Dunning, ME Ritchie, R Russell, AG Lynch Bioinformatics 24 (24), 2921-2922, 2008 | 82 | 2008 |
Platelet function is modified by common sequence variation in megakaryocyte super enhancers R Petersen, JJ Lambourne, BM Javierre, L Grassi, R Kreuzhuber, ... Nature communications 8 (1), 16058, 2017 | 62 | 2017 |
Phenotype specific analyses reveal distinct regulatory mechanism for chronically activated p53 K Kirschner, SA Samarajiwa, JM Cairns, S Menon, PA Pérez-Mancera, ... PLoS genetics 11 (3), e1005053, 2015 | 62 | 2015 |
BayesPeak—an R package for analysing ChIP-seq data J Cairns, C Spyrou, R Stark, ML Smith, AG Lynch, S Tavaré Bioinformatics 27 (5), 713-714, 2011 | 54 | 2011 |
The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle M Furlan-Magaril, M Ando-Kuri, RG Arzate-Mejía, J Morf, J Cairns, ... Genome biology 22 (1), 162, 2021 | 28 | 2021 |
RNA proximity sequencing reveals the spatial organization of the transcriptome in the nucleus J Morf, SW Wingett, I Farabella, J Cairns, M Furlan-Magaril, ... Nature biotechnology 37 (7), 793-802, 2019 | 28 | 2019 |
Chicdiff: a computational pipeline for detecting differential chromosomal interactions in Capture Hi-C data J Cairns, WR Orchard, V Malysheva, M Spivakov Bioinformatics 35 (22), 4764-4766, 2019 | 24 | 2019 |
Single‐cell study of neural stem cells derived from human iPSCs reveals distinct progenitor populations with neurogenic and gliogenic potential M Lam, T Sanosaka, A Lundin, K Imaizumi, D Etal, FH Karlsson, ... Genes to Cells 24 (12), 836-847, 2019 | 22 | 2019 |
Detecting chromosomal interactions in Capture Hi-C data with CHiCAGO and companion tools P Freire-Pritchett, H Ray-Jones, M Della Rosa, CQ Eijsbouts, WR Orchard, ... Nature protocols 16 (9), 4144-4176, 2021 | 21 | 2021 |
Consortium B, Stunnenberg HG, Todd JA, Zerbino DR, Stegle O, Ouwehand WH, Frontini M, Wallace C, Spivakov M, Fraser P. Lineage-specific genome architecture links enhancers and … BM Javierre, OS Burren, SP Wilder, R Kreuzhuber, SM Hill, S Sewitz, ... Cell 167 (5), 1369-138419, 2016 | 15 | 2016 |
Radiopotentiation profiling of multiple inhibitors of the DNA damage response for early clinical development SJ Gill, PWG Wijnhoven, JHL Fok, RL Lloyd, J Cairns, J Armenia, J Nikkilä, ... Molecular cancer therapeutics 20 (9), 1614-1626, 2021 | 13 | 2021 |