Publications from Babraham Bioinformatics
The Babraham Bioinformatics group is not a research group
and as such we do not generally produce our own papers -
however in the course of our work some groups are kind
enough to put members of the group as authors on their
publications.
Rather than try to produce a comprehensive and ever changing list of the areas of science in which we have experience this list of publications, along with our publicly released projects probably provides a reasonable reflection of the types of work we undertake.
2023
Mielczarek O, Rogers CH, Zhan Y, Matheson LS, Stubbington MJT, Schoenfelder S, Bolland DJ, Javierre BM, Wingett SW, Varnai C, Segonds-Pichon A, Conn SJ, Krueger F, Andrews S, Fraser P, Giorgetti L, Corcoran AE. Intra- and interchromosomal contact mapping reveals the Igh locus has extensive conformational heterogeneity and interacts with B-lineage genes. Cell Rep. 2023 Sep 6;42(9):113074
Chetwynd SA, Andrews S, Inglesfield S, Delon C, Ktistakis NT, Welch HCE. Functions and mechanisms of the GPCR adaptor protein Norbin. Biochem Soc Trans. 2023 Aug 31;51(4):1545-1558
Chessa TAM, Jung P, Anwar A, Suire S, Anderson KE, Barneda D, Kielkowska A, Sadiq BA, Lai IW, Felisbino S, Turnham DJ, Pearson HB, Phillips WA, Sasaki J, Sasaki T, Oxley D, Spensberger D, Segonds-Pichon A, Wilson M, Walker S, Okkenhaug H, Cosulich S, Hawkins PT, Stephens LR. PLEKHS1 drives PI3Ks and remodels pathway homeostasis in PTEN-null prostate. Mol Cell. 2023 Aug 17;83(16):2991-3009.e13
Machin PA, Johnsson AE, Massey EJ, Pantarelli C, Chetwynd SA, Chu JY, Okkenhaug H, Segonds-Pichon A, Walker S, Malliri A, Fukui Y, Welch HCE. Dock2 generates characteristic spatiotemporal patterns of Rac activity to regulate neutrophil polarisation, migration and phagocytosis. Front Immunol. 2023 Jun 13;14:1180886
Saucedo-Cuevas L, Ivanova E, Herta AC, Krueger F, Billooye K, Smitz J, Kelsey G, Anckaert E. Genome-wide assessment of DNA methylation alterations induced by superovulation, sexual immaturity and in vitro follicle growth in mouse blastocysts. Clin Epigenetics. 2023 Jan 16;15(1):9
Maskalenka K, Alagz G, Krueger F, Wright J, Rostovskaya M, Nakhuda A, Bendall A, Krueger C, Walker S, Scally A, Rugg-Gunn PJ. NANOGP1, a tandem duplicate of NANOG, exhibits partial functional conservation in human nave pluripotent stem cells. Development. 2023 Jan 15;150(2):dev201155
Demond H, Hanna CW, Castillo-Fernandez J, Santos F, Papachristou EK, Segonds-Pichon A, Kishore K, Andrews S, D'Santos CS, Kelsey G. Multi-omics analyses demonstrate a critical role for EHMT1 methyltransferase in transcriptional repression during oogenesis. Genome Res. 2023 Jan;33(1):18-31.
Samant RS, Batista S, Larance M, Ozer B, Milton CI, Bludau I, Wu E, Biggins L, Andrews S, Hervieu A, Johnston HE, Al-Lazikhani B, Lamond AI, Clarke PA, Workman P. Native Size-Exclusion Chromatography-Based Mass Spectrometry Reveals New Components of the Early Heat Shock Protein 90 Inhibition Response Among Limited Global Changes. Mol Cell Proteomics. 2023 Feb;22(2):100485.
Andrews S, Krueger C, Mellado-Lopez M, Hemberger M, Dean W, Perez-Garcia V, Hanna CW. Mechanisms and function of de novo DNA methylation in placental development reveals an essential role for DNMT3B. Nat Commun. 2023 Jan 23;14(1):371.
2022
Channathodiyil P, May K, Segonds-Pichon A, Smith PD, Cook SJ, Houseley J. Escape from G1 arrest during acute MEK inhibition drives the acquisition of drug resistance. NAR Cancer. 2022 Oct 17;4(4):zcac032.
Hornigold K, Chu JY, Chetwynd SA, Machin PA, Crossland L, Pantarelli C, Anderson KE, Hawkins PT, Segonds-Pichon A, Oxley D, Welch HCE. Age-related decline in the resistance of mice to bacterial infection and in LPS/TLR4 pathway-dependent neutrophil responses. Front Immunol. 2022 Aug 24;13:888415.
Lopes JS, Ivanova E, Ruiz S, Andrews S, Kelsey G, Coy P. Effect of Superovulation Treatment on Oocyte's DNA Methylation. Int J Mol Sci. 2022 Dec 18;23(24):16158.
Lawson CD, Hornigold K, Pan D, Niewczas I, Andrews S, Clark J, Welch H.~ Small-molecule inhibitors of P-Rex guanine-nucleotide exchange factors. Small GTPases. 2022 Jan;13(1):307-326.
Vashishtha K, Gaud C, Andrews S, Krueger C. Librarian: A quality control tool to analyse sequencing library compositions. F1000Res. 2022 Sep 29;11:1122.
Nunes C, Depestel L, Mus L, Keller KM, Delhaye L, Louwagie A, Rishfi M, Whale A, Kara N, Andrews SR, Dela Cruz F, You D, Siddiquee A, Cologna CT, De Craemer S, Dolman E, Bartenhagen C, De Vloed F, Sanders E, Eggermont A, Bekaert SL, Van Loocke W, Bek JW, Dewyn G, Loontiens S, Van Isterdael G, Decaesteker B, Tilleman L, Van Nieuwerburgh F, Vermeirssen V, Van Neste C, Ghesquiere B, Goossens S, Eyckerman S, De Preter K, Fischer M, Houseley J, Molenaar J, De Wilde B, Roberts SS, Durinck K, Speleman F. RRM2 enhances MYCN-driven neuroblastoma formation and acts as a synergistic target with CHK1 inhibition. Sci Adv. 2022 Jul 15;8(28):eabn1382.
Rostovskaya M, Andrews S, Reik W, Rugg-Gunn PJ. Amniogenesis occurs in two independent waves in primates. Cell Stem Cell. 2022 May 5;29(5):744-759.e6 2021 Oct;22(10):1245-1255.
Hanna CW, Huang J, Belton C, Reinhardt S, Dahl A, Andrews S, Stewart AF, Kranz A, Kelsey G. Loss of histone methyltransferase SETD1B in oogenesis results in the redistribution of genomic histone 3 lysine 4 trimethylation. Nucleic Acids Res. 2022 Feb 28;50(4):1993-2004
Zijlmans DW, Talon I, Verhelst S, Bendall A, Van Nerum K, Javali A, Malcolm AA, van Knippenberg SSFA, Biggins L, To SK, Janiszewski A, Admiraal D, Knops R, Corthout N, Balaton BP, Georgolopoulos G, Panda A, Bhanu NV, Collier AJ, Fabian C, Allsop RN, Chappell J, Pham TXA, Oberhuemer M, Ertekin C, Vanheer L, Athanasouli P, Lluis F, Deforce D, Jansen JH, Garcia BA, Vermeulen M, Rivron N, Dhaenens M, Marks H, Rugg-Gunn PJ, Pasque V. Integrated multi-omics reveal polycomb repressive complex 2 restricts human trophoblast induction. Nat Cell Biol. 2022 Jun;24(6):858-871
Rodriguez-Ubreva J, Arutyunyan A, Bonder MJ, Del Pino-Molina L, Clark SJ, de la Calle-Fabregat C, Garcia-Alonso L, Handfield LF, Ciudad L, Andres-Leon E, Krueger F, Catala-Moll F, Rodriguez-Cortez VC, Polanski K, Mamanova L, van Dongen S, Kiselev VY, Martinez-Saavedra MT, Heyn H, Martin J, Warnatz K, Lopez-Granados E, Rodriguez-Gallego C, Stegle O, Kelsey G, Vento-Tormo R, Ballestar E. Single-cell Atlas of common variable immunodeficiency shows germinal center-associated epigenetic dysregulation in B-cell responses. Nat Commun. 2022 Apr 1;13(1):1779.
Taubenschmid-Stowers J, Rostovskaya M, Santos F, Ljung S, Argelaguet R, Krueger F, Nichols J, Reik W. 8C-like cells capture the human zygotic genome activation program in vitro. Cell Stem Cell. 2022 Mar 3;29(3):449-459.e6
2021
Suriyalaksh M, Raimondi C, Mains A, Segonds-Pichon A, Mukhtar S, Murdoch S, Aldunate R, Krueger F, Guimera R, Andrews S, Sales-Pardo M, Casanueva O. Gene regulatory network inference in long-lived C. elegans reveals modular properties that are predictive of novel aging genes. iScience.2021 Dec 20;25(1):103663.
Fiancette R, Finlay CM, Willis C, Bevington SL, Soley J, Ng STH, Baker SM, Andrews S, Hepworth MR, Withers DR. Reciprocal transcription factor networks govern tissue-resident ILC3 subset function and identity Nat Immunol. 2021 Oct;22(10):1245-1255.
Osnato A, Brown S, Krueger C, Andrews S, Collier AJ, Nakanoh S, Quiroga Londono M, Wesley BT, Muraro D, Brumm AS, Niakan KK, Vallier L, Ortmann D, Rugg-Gunn PJ. TGF-beta signalling is required to maintain pluripotency of human naive pluripotent stem cells. Elife. 2021 Aug 31;10:e67259
Baizan-Edge A, Stubbs BA, Stubbington MJT, Bolland DJ, Tabbada K, Andrews S, Corcoran AE. IL-7R signaling activates widespread VH and DH gene usage to drive antibody diversity in bone marrow B cells. Cell Rep. 2021 Jul 13;36(2):109349
Gaud C, C Sousa B, Nguyen A, Fedorova M, Ni Z, O'Donnell VB, Wakelam MJO, Andrews S, Lopez-Clavijo AF. BioPAN: a web-based tool to explore mammalian lipidome metabolic pathways on LIPID MAPS F1000Res. 2021 Jan 6;10:4
Furlan-Magaril M, Ando-Kuri M, Arzate-Mejia RG, Morf J, Cairns J, Roman-Figueroa A, Tenorio-Hernandez L, Poot-Hernandez AC, Andrews S, Varnai C, Virk B, Wingett SW, Fraser P. The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle. Genome Biol. 2021 Jun 8;22(1):162
Dolezalova N, Gruszczyk A, Barkan K, Gamble JA, Galvin S, Moreth T, O'Holleran K, Mahbubani KT, Higgins JA, Gribble FM, Reimann F, Surmacki J, Andrews S, Casey JJ, Pampaloni F, Murphy MP, Ladds G, Slater NKH, Saeb-Parsy K. Accelerating cryoprotectant diffusion kinetics improves cryopreservation of pancreatic islets. Sci Rep. 2021 May 17;11(1):10418
Halsall JA, Andrews S, Krueger F, Rutledge CE, Ficz G, Reik W, Turner BM. Histone modifications form a cell-type-specific chromosomal bar code that persists through the cell cycle. Sci Rep. 2021 Feb 4;11(1):3009
Kara N, Krueger F, Rugg-Gunn P, Houseley J. Genome-wide analysis of DNA replication and DNA double-strand breaks using TrAEL-seq. PLoS Biol. 2021 Mar 24;19(3):e3000886
Pantarelli C, Pan D, Chetwynd S, Stark AK, Hornigold K, Machin P, Crossland L, Cleary SJ, Baker MJ, Hampson E, Mandel A, Segonds-Pichon A, Walker R, van 't Veer C, Riffo-Vasquez Y, Okkenhaug K, Pitchford S, Welch HCE. The GPCR adaptor protein norbin suppresses the neutrophil-mediated immunity of mice to pneumococcal infection Blood Adv. 2021 Aug 24;5(16):3076-309
Panta P, Reddy P, Misra SR, Segonds-Pichon A, Patil S. Impact of COVID-19 Lockdown on Oral Oncology-related Outpatient Volume at Indian Dental Institutions J Contemp Dent Pract. 2021 May 1;22(5):501-505.
Young KA, Biggins L, Sharpe HJ Protein tyrosine phosphatases in cell adhesion Biochem J. 2021 Mar 12;478(5):1061-1083
Freire-Pritchett P, Ray-Jones H, Della Rosa M, Eijsbouts CQ, Orchard WR, Wingett SW, Wallace C, Cairns J, Spivakov M, Malysheva V. Detecting chromosomal interactions in Capture Hi-C data with CHiCAGO and companion tools. Nat Protoc. 2021 Sep;16(9):4144-4176.
2020
Bevan S, Schoenfelder S, Young RJ, Zhang L, Andrews S, Fraser P, O'Callaghan PM. High-resolution three-dimensional chromatin profiling of the Chinese hamster ovary cell genome Biotechnol Bioeng. 2020 Oct 23. doi: 10.1002/bit.27607
Alvarez-Jarreta J, Rodrigues PRS, Fahy E, O'Connor A, Price A, Gaud C, Andrews S, Benton P, Siuzdak G, Hawksworth JI, Valdivia-Garcia M, Allen SM, O'Donnell VB. LipidFinder 2.0: advanced informatics pipeline for lipidomics discovery applications. Bioinformatics.2020 Oct 7:btaa856. doi: 10.1093/bioinformatics/btaa856
Chauve L, Le Pen J, Hodge F, Todtenhaupt P, Biggins L, Miska EA, Andrews S, Casanueva O. High-Throughput Quantitative RT-PCR in Single and Bulk C. elegans Samples Using Nanofluidic Technology J Vis Exp.2020 May 28;(159). doi: 10.3791/61132
Nasrallah R, Imianowski CJ, Bossini-Castillo L, Grant FM, Dogan M, Placek L, Kozhaya L, Kuo P, Sadiyah F, Whiteside SK, Mumbach MR, Glinos D, Vardaka P, Whyte CE, Lozano T, Fujita T, Fujii H, Liston A, Andrews S, Cozzani A, Yang J, Mitra S, Lugli E, Chang HY, Unutmaz D, Trynka G, Roychoudhuri R A distal enhancer at risk locus 11q13.5 promotes suppression of colitis by Treg cells. Nature.2020 Jul;583(7816):447-452. doi: 10.1038/s41586-020-2296-7
Ivanova E, Canovas S, Garcia-Martínez S, Romar R, Lopes JS, Rizos D, Sanchez-Calabuig MJ, Krueger F, Andrews S, Perez-Sanz F, Kelsey G, Coy P. DNA methylation changes during preimplantation development reveal inter-species differences and reprogramming events at imprinted genes. Clin Epigenetics. 2020 May 11;12(1):64. doi: 10.1186/s13148-020-00857-x
Thompson O, von Meyenn F, Hewitt Z, Alexander J, Wood A, Weightman R, Gregory S, Krueger F, Andrews S, Barbaric I, Gokhale PJ, Moore HD, Reik W, Milo M, Nik-Zainal S, Yusa K, Andrews PW. Low rates of mutation in clinical grade human pluripotent stem cells under different culture conditions. Nat Commun.2020 Mar 23;11(1):1528. doi: 10.1038/s41467-020-15271-3
Wingett SW, Andrews S, Fraser P, Morf J. RNA proximity sequencing data and analysis pipeline from a human neuroblastoma nuclear transcriptome. Sci Data.2020 Jan 28;7(1):35. doi: 10.1038/s41597-020-0372-3
Klobučar T, Kreibich E, Krueger F, Arez M, Pólvora-Brandão D, von Meyenn F, da Rocha ST, Eckersley-Maslin M. IMPLICON: an ultra-deep sequencing method to uncover DNA methylation at imprinted regions. Nucleic Acids Res.2020 Sep 18;48(16):e92. doi: 10.1093/nar/gkaa567
Wojdyla K, Collier AJ, Fabian C, Nisi PS, Biggins L, Oxley D, Rugg-Gunn PJ. Cell-Surface Proteomics Identifies Differences in Signaling and Adhesion Protein Expression between Naive and Primed Human Pluripotent Stem Cells Stem Cell Reports.2020 May 12;14(5):972-988. doi: 10.1016/j.stemcr.2020.03.017
Stammers M, Niewczas IS, Segonds-Pichon A, Clark J. Mechanical stretching changes crosslinking and glycation levels in the collagen of mouse tail tendon. J Biol Chem.2020 Jul 31;295(31):10572-10580. doi: 10.1074/jbc.RA119.012067
Stammers M, Ivanova IM, Niewczas IS, Segonds-Pichon A, Streeter M, Spiegel DA, Clark J Age-related changes in the physical properties, cross-linking, and glycation of collagen from mouse tail tendon J Biol Chem. 2020 Jul 31;295(31):10562-10571
2019
Demond H, Anvar Z, Jahromi BN, Sparago A, Verma A, Davari M, Calzari L, Russo S, Jahromi MA, Monk D, Andrews S, Riccio A, Kelsey G. A KHDC3L mutation resulting in recurrent hydatidiform mole causes genome-wide DNA methylation loss in oocytes and persistent imprinting defects post-fertilisation. Genome Med.2019 Dec 17;11(1):84. doi: 10.1186/s13073-019-0694-y
Gambardella L, McManus SA, Moignard V, Sebukhan D, Delaune A, Andrews S, Bernard WG, Morrison MA, Riley PR, Göttgens B, Gambardella Le Novère N, Sinha S. BNC1 regulates cell heterogeneity in human pluripotent stem cell-derived epicardium. Development. 2019 Dec 13;146(24):dev174441. doi: 10.1242/dev.174441
Hanna CW, Pérez-Palacios R, Gahurova L, Schubert M, Krueger F, Biggins L, Andrews S, Colomé-Tatché M, Bourc'his D, Dean W, Kelsey G. Endogenous retroviral insertions drive non-canonical imprinting in extra-embryonic tissues. Genome Biol.2019 Oct 29;20(1):225. doi: 10.1186/s13059-019-1833-x
Hernando-Herraez I, Evano B, Stubbs T, Commere PH, Jan Bonder M, Clark S, Andrews S, Tajbakhsh S, Reik W. Ageing affects DNA methylation drift and transcriptional cell-to-cell variability in mouse muscle stem cells. Nat Commun.2019 Sep 25;10(1):4361. doi: 10.1038/s41467-019-12293-4
Saenz-de-Juano MD, Ivanova E, Romero S, Lolicato F, Sánchez F, Van Ranst H, Krueger F, Segonds-Pichon A, De Vos M, Andrews S, Smitz J, Kelsey G, Anckaert E. DNA methylation and mRNA expression of imprinted genes in blastocysts derived from an improved in vitro maturation method for oocytes from small antral follicles in polycystic ovary syndrome patients. Hum Reprod.2019 Sep 29;34(9):1640-1649. doi: 10.1093/humrep/dez121. PMID: 31398248
Morf J, Wingett SW, Farabella I, Cairns J, Furlan-Magaril M, Jiménez-García LF, Liu X, Craig FF, Walker S, Segonds-Pichon A, Andrews S, Marti-Renom MA, Fraser P. RNA proximity sequencing reveals the spatial organization of the transcriptome in the nucleus. Nat Biotechnol.2019 Jul;37(7):793-802. doi: 10.1038/s41587-019-0166-3
Arbore G, Henley T, Biggins L, Andrews S, Vigorito E, Turner M, Leyland R. MicroRNA-155 is essential for the optimal proliferation and survival of plasmablast B cells. Life Sci Alliance.2019 May 16;2(3):e201800244. doi: 10.26508/lsa.201800244
Argelaguet R, Clark SJ, Mohammed H, Stapel LC, Krueger C, Kapourani CA, Imaz-Rosshandler I, Lohoff T, Xiang Y, Hanna CW, Smallwood S, Ibarra-Soria X, Buettner F, Sanguinetti G, Xie W, Krueger F, Göttgens B, Rugg-Gunn PJ, Kelsey G, Dean W, Nichols J, Stegle O, Marioni JC, Reik W. Multi-omics profiling of mouse gastrulation at single-cell resolution. Nature.2019 Dec;576(7787):487-491. doi: 10.1038/s41586-019-1825-8
Hull RM, King M, Pizza G, Krueger F, Vergara X, Houseley J. Transcription-induced formation of extrachromosomal DNA during yeast ageing. PLoS Biol.2019 Dec 3;17(12):e3000471. doi: 10.1371/journal.pbio.3000471
Gdula MR, Nesterova TB, Pintacuda G, Godwin J, Zhan Y, Ozadam H, McClellan M, Moralli D, Krueger F, Green CM, Reik W, Kriaucionis S, Heard E, Dekker J, Brockdorff N. The non-canonical SMC protein SmcHD1 antagonises TAD formation and compartmentalisation on the inactive X chromosome. Nat Commun.2019 Jan 3;10(1):30. doi: 10.1038/s41467-018-07907-2
Suire S, Baltanas FC, Segonds-Pichon A, Davidson K, Santos E, Hawkins PT, Stephens LR. Frontline Science: TNF-α and GM-CSF1 priming augments the role of SOS1/2 in driving activation of Ras, PI3K-γ, and neutrophil proinflammatory responses J Leukoc Biol.2019 Oct;106(4):815-822. doi: 10.1002/JLB.2HI0918-359RR
Morf J, Wingett SW. Proximity RNA-seq: A Sequencing Method to Identify Co-localization of RNA. Methods Mol Biol.2020;2161:175-194. doi: 10.1007/978-1-0716-0680-3_13
Nützmann HW, Doerr D, Ramírez-Colmenero A, Sotelo-Fonseca JE, Wegel E, Di Stefano M, Wingett SW, Fraser P, Hurst L, Fernandez-Valverde SL, Osbourn A. Active and repressed biosynthetic gene clusters have spatially distinct chromosome states Proc Natl Acad Sci U S A.2020 Jun 16;117(24):13800-13809. doi: 10.1073/pnas.1920474117
Hill DL, Pierson W, Bolland DJ, Mkindi C, Carr EJ, Wang J, Houard S, Wingett SW, Audran R, Wallin EF, Jongo SA, Kamaka K, Zand M, Spertini F, Daubenberger C, Corcoran AE, Linterman MA The adjuvant GLA-SE promotes human Tfh cell expansion and emergence of public TCRβ clonotypes J Exp Med.2019 Aug 5;216(8):1857-1873. doi: 10.1084/jem.20190301
Gdula MR, Nesterova TB, Pintacuda G, Godwin J, Zhan Y, Ozadam H, McClellan M, Moralli D, Krueger F, Green CM, Reik W, Kriaucionis S, Heard E, Dekker J, Brockdorff N. The non-canonical SMC protein SmcHD1 antagonises TAD formation and compartmentalisation on the inactive X chromosome Nat Commun. 2019 Jan 3;10(1):30. doi: 10.1038/s41467-018-07907-2
2018
Koohy H, Bolland DJ, Matheson LS, Schoenfelder S, Stellato C, Dimond A, Varnai C, Chovanec P, Chessa T, Denizot J, Manzano Garcia R, Wingett SW, Freire-Pritchett P, Nagano T, Hawkins P, Stephens L, Elderkin S, Spivakov M, Fraser P, Corcoran AE, Varga-Weisz PD. Genome organization and chromatin analysis identify transcriptional downregulation of insulin-like growth factor signaling as a hallmark of aging in developing B cells. Genome Biol. 2018 Sep 5;19(1):126. doi: 10.1186/s13059-018-1489-y.
Wingett SW, Andrews S. FastQ Screen: A tool for multi-genome mapping and quality control. F1000Res. 2018 Aug 24 [revised 2018 Jan 1];7:1338. doi: 10.12688/f1000research.15931.2. eCollection
White MA, Kim E, Duffy A, Adalbert R, Phillips BU, Peters OM, Stephenson J, Yang S, Massenzio F, Lin Z, Andrews S, Segonds-Pichon A, Metterville J, Saksida LM, Mead R, Ribchester RR, Barhomi Y, Serre T, Coleman MP, Fallon JR, Bussey TJ, Brown RH Jr, Sreedharan J. TDP-43 gains function due to perturbed autoregulation in a Tardbp knock-in mouse model of ALS-FTD. Nat Neurosci. 2018 Aug;21(8):1138. doi: 10.1038/s41593-018-0160-y.
Rulands S, Lee HJ, Clark SJ, Angermueller C, Smallwood SA, Krueger F, Mohammed H, Dean W, Nichols J, Rugg-Gunn P, Kelsey G, Stegle O, Simons BD, Reik W. Genome-Scale Oscillations in DNA Methylation during Exit from Pluripotency. Cell Syst. 2018 Jul 25;7(1):63-76.e12. doi: 10.1016/j.cels.2018.06.012.
Schoenfelder S, Javierre BM, Furlan-Magaril M, Wingett SW, Fraser P. Promoter interactome of human embryonic stem cell-derived cardiomyocytes connects GWAS regions to cardiac gene networks. Nat Commun. 2018 Jun 28;9(1):2526. doi: 10.1038/s41467-018-04931-0
Beekman R, Chapaprieta V, Russinol N, Vilarrasa-Blasi R, Verdaguer-Dot N, Martens JHA, Duran-Ferrer M, Kulis M, Serra F, Javierre BM, Wingett SW, Clot G, Queiros AC, Castellano G, Blanc J, Gut M, Merkel A, Heath S, Vlasova A, Ullrich S, Palumbo E, Enjuanes A, Martin-Garcia D, Bea S, Pinyol M, Aymerich M, Royo R, Puiggros M, Torrents D, Datta A, Lowy E, Kostadima M, Roller M, Clarke L, Flicek P, Agirre X, Prosper F, Baumann T, Delgado J, Lopez-Guillermo A, Fraser P, Yaspo ML, Guigo R, Siebert R, Marti-Renom MA, Puente XS, Lopez-Otin C, Gut I, Stunnenberg HG, Campo E, Martin-Subero JI. The reference epigenome and regulatory chromatin landscape of chronic lymphocytic leukemia. Nat Med. 2018 Jun;24(6):868-880. doi: 10.1038/s41591-018-0028-4.
Choy MK, Javierre BM, Williams SG, Baross SL, Liu Y, Wingett SW, Akbarov A, Wallace C, Freire-Pritchett P, Rugg-Gunn PJ, Spivakov M, Fraser P, Keavney BD. Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions. J Vis Exp. 2018 Jun 28;(136). doi: 10.3791/57320
Chovanec P, Bolland DJ, Matheson LS, Wood AL, Krueger F, Andrews S, Corcoran AE. Unbiased quantification of immunoglobulin diversity at the DNA level with VDJ-seq Nat Protoc. 2018 Jun;13(6):1232-1252. doi: 10.1038/nprot.2018.021
Smyrnias I, Goodwin N, Wachten D, Skogestad J, Aronsen JM, Robinson EL, Demydenko K, Segonds-Pichon A, Oxley D, Sadayappan S, Sipido K, Bootman MD, Roderick HL. Contractile responses to endothelin-1 are regulated by PKC phosphorylation of cardiac myosin binding protein-C in rat ventricular myocytes. J Mol Cell Cardiol. 2018 Apr;117:1-18. doi: 10.1016/j.yjmcc.2018.02.012.
Olova N, Krueger F, Andrews S, Oxley D, Berrens RV, Branco MR, Reik W. Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data Genome Biol. 2018 Mar 15;19(1):33. doi: 10.1186/s13059-018-1408-2.
Baxter JS, Leavy OC, Dryden NH, Maguire S, Johnson N, Fedele V, Simigdala N, Martin LA, Andrews S, Wingett SW, Assiotis I, Fenwick K, Chauhan R, Rust AG, Orr N, Dudbridge F, Haider S, Fletcher O. Capture Hi-C identifies putative target genes at 33 breast cancer risk loci. Nat Commun. 2018 Mar 12;9(1):1028. doi: 10.1038/s41467-018-03411-9.
Novo CL, Javierre BM, Cairns J, Segonds-Pichon A, Wingett SW, Freire-Pritchett P, Furlan-Magaril M, Schoenfelder S, Fraser P, Rugg-Gunn PJ. Long-Range Enhancer Interactions Are Prevalent in Mouse Embryonic Stem Cells and Are Reorganized upon Pluripotent State Transition. Cell Rep. 2018 Mar 6;22(10):2615-2627. doi: 10.1016/j.celrep.2018.02.040.
Clark SJ, Argelaguet R, Kapourani CA, Stubbs TM, Lee HJ, Alda-Catalinas C, Krueger F, Sanguinetti G, Kelsey G, Marioni JC, Stegle O, Reik W. scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells. Nat Commun. 2018 Feb 22;9(1):781. doi: 10.1038/s41467-018-03149-4.
Kirschner K, Krueger F, Green AR, Chandra T. Multiplexing for Oxidative Bisulfite Sequencing (oxBS-seq). Methods Mol Biol. 2018;1708:665-678. doi: 10.1007/978-1-4939-7481-8_34.
Hanna CW, Taudt A, Huang J, Gahurova L, Kranz A, Andrews S, Dean W, Stewart AF, Colome-Tatche M, Kelsey G. MLL2 conveys transcription-independent H3K4 trimethylation in oocytes. Nat Struct Mol Biol. 2018 Jan;25(1):73-82. doi: 10.1038/s41594-017-0013-5.
2017
Matheson LS, Bolland DJ, Chovanec P, Krueger F, Andrews S, Koohy H, Corcoran AE. Local Chromatin Features Including PU.1 and IKAROS Binding and H3K4 Methylation Shape the Repertoire of Immunoglobulin Kappa Genes Chosen for V(D)J Recombination Front Immunol. 2017 Nov 17;8:1550. doi: 10.3389/fimmu.2017.01550
Berrens RV, Andrews S, Spensberger D, Santos F, Dean W, Gould P, Sharif J, Olova N, Chandra T, Koseki H, von Meyenn F, Reik W. An endosiRNA-Based Repression Mechanism Counteracts Transposon Activation during Global DNA Demethylation in Embryonic Stem Cells. Cell Stem Cell. 2017 Nov 2;21(5):694-703.e7. doi: 10.1016/j.stem.2017.10.004.
Martin-Herranz DE, Ribeiro AJM, Krueger F, Thornton JM, Reik W, Stubbs TM. cuRRBS: simple and robust evaluation of enzyme combinations for reduced representation approaches. Nucleic Acids Res. 2017 Sep 19. doi: 10.1093/nar/gkx814
Gahurova L, Tomizawa SI, Smallwood SA, Stewart-Morgan KR, Saadeh H, Kim J, Andrews SR, Chen T, Kelsey G. Transcription and chromatin determinants of de novo DNA methylation timing in oocytes. Epigenetics Chromatin. 2017 May 12;10:25.
Stubbs TM, Bonder MJ, Stark AK, Krueger F; BI Ageing Clock Team., von Meyenn F, Stegle O, Reik W. Multi-tissue DNA methylation age predictor in mouse. Genome Biol.2017 Apr 11;18(1):68.
Hahn O, Grönke S, Stubbs TM, Ficz G, Hendrich O, Krueger F, Andrews S, Zhang Q, Wakelam MJ, Beyer A, Reik W, Partridge L. Dietary restriction protects from age-associated DNA methylation and induces epigenetic reprogramming of lipid metabolism. Genome Biology. 2017 Mar 18;18(1):56.
Milagre I, Stubbs TM, King MR, Spindel J, Santos F, Krueger F, Bachman M, Segonds-Pichon A, Balasubramanian S, Andrews SR, Dean W, Reik W. Gender Differences in Global but Not Targeted Demethylation in iPSC Reprogramming. Cell Rep. 2017 Jan 31;18(5):1079-1089.
Clark SJ, Smallwood SA, Lee HJ, Krueger F, Reik W, Kelsey G. Genome-wide base-resolution mapping of DNA methylation in single cells using single-cell bisulfite sequencing (scBS-seq). Nat Protoc. 2017 Mar;12(3):534-547
Stepper P, Kungulovski G, Jurkowska RZ, Chandra T, Krueger F, Reinhardt R, Reik W, Jeltsch A, Jurkowski TP. Efficient targeted DNA methylation with chimeric dCas9-Dnmt3a-Dnmt3L methyltransferase. Nucleic Acids Res 2017 Feb 28;45(4):1703-1713.
Canovas S, Ivanova E, Romar R, Garci-Martinez S, Soriano-Ubeda C, Garcia Vazquez FA, Saadeh H, Andrews S, Kelsey G, Coy P. DNA methylation and gene expression changes derived from assisted reproductive technologies can be decreased by reproductive fluids. Elife. 2017 Feb 1;6.
2016
Natisvili T, Yandim C, Silva R, Emanuelli G, Krueger F, Nageshwaran S, Festenstein R.
Transcriptional Activation of Pericentromeric Satellite Repeats and Disruption of Centromeric Clustering upon Proteasome Inhibition.
Ewels P, Krueger F, Kaler M, Andrews S. Cluster Flow: A user-friendly bioinformatics workflow tool. F1000Res 2016 Dec 6;5:2824.
Collinson A, Collier AJ, Morgan NP, Sienerth AR, Chandra T, Andrews S, Rugg-Gunn PJ. Deletion of the Polycomb-Group Protein EZH2 Leads to Compromised Self-Renewal and Differentiation Defects in Human Embryonic Stem Cells. Cell Rep. 2016 Dec 6;17(10):2700-2714.
Stepper P, Kungulovski G, Jurkowska RZ, Chandra T, Krueger F, Reinhardt R, Reik W, Jeltsch A, Jurkowski TP Efficient targeted DNA methylation with chimeric dCas9-Dnmt3a-Dnmt3L methyltransferase. Nucleic Acids Res. 2016 Nov 29. pii: gkw1112
von Meyenn F, Berrens RV, Andrews S, Santos F, Collier AJ, Krueger F, Osorno R, Dean W, Rugg-Gunn PJ, Reik W. Comparative Principles of DNA Methylation Reprogramming during Human and Mouse In Vitro Primordial Germ Cell Specification. Dev Cell. 2016 Oct 10;39(1):104-115.
Vermeren MM, Zhang Q, Smethurst E, Segonds-Pichon A, Schrewe H, Wakelam MJ. The Phospholipase D2 Knock Out Mouse Has Ectopic Purkinje Cells and Suffers from Early Adult-Onset Anosmia. PLoS One. 2016 Sep 22;11(9):e0162814
Eckersley-Maslin MA, Svensson V, Krueger C, Stubbs TM, Giehr P, Krueger F, Miragaia RJ, Kyriakopoulos C, Berrens RV, Milagre I, Walter J, Teichmann SA, Reik W. MERVL/Zscan4 Network Activation Results in Transient Genome-wide DNA Demethylation of mESCs Cell Rep. 2016 Sep 27;17(1):179-92
Wood CD, Veenstra H, Khasnis S, Gunnell A, Webb HM, Shannon-Lowe C, Andrews S, Osborne CS, West MJ. MYC activation and BCL2L11 silencing by a tumour virus through the large-scale reconfiguration of enhancer-promoter hubs.Elife. 2016 Aug 4;5. pii: e18270. doi: 10.7554/eLife.18270
Tschurtschenthaler M, Kachroo P, Heinsen FA, Adolph TE, Rühlemann MC, Klughammer J, Offner FA, Ammerpohl O, Krueger F, Smallwood S, Szymczak S, Kaser A, Franke A. Paternal chronic colitis causes epigenetic inheritance of susceptibility to colitis. Sci Rep. 2016 Aug 19;6:31640
Krueger F, Andrews SR. SNPsplit: Allele-specific splitting of alignments between genomes with known SNP genotypes. F1000Res. 2016 Jun 23;5:1479. doi: 10.12688/f1000research.9037.1
Bolland DJ, Koohy H, Wood AL, Matheson LS, Krueger F, Stubbington MJ, Baizan-Edge A, Chovanec P, Stubbs BA, Tabbada K, Andrews SR, Spivakov M, Corcoran AE. Two Mutually Exclusive Local Chromatin States Drive Efficient V(D)J Recombination. Cell Rep. 2016 Jun 14;15(11):2475-87. doi: 10.1016/j.celrep.2016.05.020
Galloway A, Saveliev A, Åukasiak S, Hodson DJ, Bolland D, Balmanno K, Ahlfors H, Monzón-Casanova E, Mannurita SC, Bell LS, Andrews S, DÃaz-Muñoz MD, Cook SJ, Corcoran A, Turner M. RNA-binding proteins ZFP36L1 and ZFP36L2 promote cell quiescence. Science. 2016 Apr 22;352(6284):453-9. doi: 10.1126/science.aad5978.
Hanna CW, Penaherrera MS, Saadeh H, Andrews S, McFadden DE, Kelsey G, Robinson WP. Pervasive polymorphic imprinted methylation in the human placenta. Genome Res. 2016 Jan 14. pii: gr.196139.115.
Sandovici I, Hammerle CM, Cooper WN, Smith NH, Tarry-Adkins JL, Dunmore BJ, Bauer J, Andrews SR, Yeo GS, Ozanne SE, Constancia M. Ageing is associated with molecular signatures of inflammation and type 2 diabetes in rat pancreatic islets. Diabetologia. 2016 Mar;59(3):502-11.
Norton L, Lindsay Y, Deladeriere A, Chessa T, Guillou H, Suire S, Lucocq J, Walker S, Andrews S, Segonds-Pichon A, Rausch O, Finan P, Sasaki T, Du CJ, Bretschneider T, Ferguson GJ, Hawkins PT, Stephens L. Localizing the lipid products of PI3Kó in neutrophils. Adv Biol Regul. 2016 Jan;60:36-45.
Angermueller C, Clark SJ, Lee HJ, Macaulay IC, Teng MJ, Hu TX, Krueger F, Smallwood SA, Ponting CP, Voet T, Kelsey G, Stegle O, Reik W. Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity. Nat Methods. 2016 Jan 11.
2015
Wingett S, Ewels P, Furlan-Magaril M, Nagano T, Schoenfelder S, Fraser P, Andrews S. HiCUP: pipeline for mapping and processing Hi-C data F1000Res. 2015 Nov 20;4:1310
Patalano S, Vlasova A, Wyatt C, Ewels P, Camara F, Ferreira PG, Asher CL, Jurkowski TP, Segonds-Pichon A, Bachman M, González-Navarrete I, Minoche AE, Krueger F, Lowy E, Marcet-Houben M, Rodriguez-Ales JL, Nascimento FS, Balasubramanian S, Gabaldon T, Tarver JE, Andrews S, Himmelbauer H, Hughes WO, Guigó R, Reik W, Sumner S. Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies. Proc Natl Acad Sci USA. 2015 Oct 19
Schoenfelder S, Sugar R, Dimond A, Javierre BM, Armstrong H, Mifsud B, Dimitrova E, Matheson L, Tavares-Cadete F, Furlan-Magaril M, Segonds-Pichon A, Jurkowski W, Wingett SW, Tabbada K, Andrews S, Herman B, LeProust E, Osborne CS, Koseki H, Fraser P, Luscombe NM, Elderkin S Polycomb repressive complex PRC1 spatially constrains the mouse embryonic stem cell genome Nature Genetics 2015 Oct;47(10):1179-1186. doi: 10.1038/ng.3393
Veselovska L, Smallwood SA, Saadeh H, Stewart KR, Krueger F, Maupetit-Méhouas S, Arnaud P, Tomizawa S, Andrews S, Kelsey G Deep sequencing and de novo assembly of the mouse oocyte transcriptome define the contribution of transcription to the DNA methylation landscape Genome Biology 2015 Sep 25;16(1):209. doi: 10.1186/s13059-015-0769-z
Sun H, Damez-Werno DM, Scobie KN, Shao NY, Dias C, Rabkin J, Koo JW, Korb E, Bagot RC, Ahn FH, Cahill ME, Labonté B, Mouzon E, Heller EA, Cates H, Golden SA, Gleason K, Russo SJ, Andrews S, Neve R, Kennedy PJ, Maze I, Dietz DM, Allis CD, Turecki G, Varga-Weisz P, Tamminga C, Shen L, Nestler EJ ACF chromatin-remodeling complex mediates stress-induced depressive-like behavior Nature Medicine 2015 Sep 21. doi: 10.1038/nm.3939
Mifsud B, Tavares-Cadete F, Young AN, Sugar R, Schoenfelder S, Ferreira L, Wingett SW, Andrews S, Grey W, Ewels PA, Herman B, Happe S, Higgs A, LeProust E, Follows GA, Fraser P, Luscombe NM, Osborne CS Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C Nature Genetics 2015 Jun;47(6):598-606. doi: 10.1038/ng.3286. Epub 2015 May 4
Strogantsev R, Krueger F, Yamazawa K, Shi H, Gould P, Goldman-Roberts M, McEwen K, Sun B, Pedersen R, Ferguson-Smith AC Allele-specific binding of ZFP57 in the epigenetic regulation of imprinted and non-imprinted monoallelic expression Genome Biology 2015 May 30;16(1):112
Schoenfelder S, Furlan-Magaril M, Mifsud B, Tavares-Cadete F, Sugar R, Javierre BM, Nagano T, Katsman Y, Sakthidevi M, Wingett SW, Dimitrova E, Dimond A, Edelman LB, Elderkin S, Tabbada K, Darbo E, Andrews S, Herman B, Higgs A, LeProust E, Osborne CS, Mitchell JA, Luscombe NM, Fraser P. The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements Genome Research 2015 Apr;25(4):582-97. doi: 10.1101/gr.185272.114. Epub 2015 Mar 9.
Diaz-Munoz MD, Bell SE, Fairfax K, Monzon-Casanova E, Cunningham AF, Gonzalez-Porta M, Andrews SR, Bunik VI, Zarnack K, Curk T, Heggermont WA, Heymans S, Gibson GE, Kontoyiannis DL, Ule J, Turner M. The RNA-binding protein HuR is essential for the B cell antibody response Nature Immunology 2015 Apr;16(4):415-25. doi: 10.1038/ni.3115. Epub 2015 Feb 23
Uribe-Lewis S, Stark R, Carroll T, Dunning MJ, Bachman M, Ito Y, Stojic L, Halim S, Vowler SL, Lynch AG, Delatte B, de Bony EJ, Colin L, Defrance M, Krueger F, Silva AL, Ten Hoopen R, Ibrahim AE, Fuks F, Murrell A 5-hydroxymethylcytosine marks promoters in colon that resist DNA hypermethylation in cancer Genome Biology 2015 Apr 1;16:69. doi: 10.1186/s13059-015-0605-5
Chandra T, Ewels PA, Schoenfelder S, Furlan-Magaril M, Wingett SW, Kirschner K, Thuret JY, Andrews S, Fraser P, Reik W. Global reorganization of the nuclear landscape in senescent cells Cell Reports 2015 Feb 3;10(4):471-83. doi: 10.1016/j.celrep.2014.12.055. Epub 2015 Jan 29
Cini A, Patalano S, Segonds-Pichon A, Busby GB, Cervo R, Sumner S. Social parasitism and the molecular basis of phenotypic evolution Front Genet. 2015 Feb 18;6:32. doi: 10.3389/fgene.2015.00032. eCollection 2015
Nicol AU, Segonds-Pichon A, Magnusson MS Complex spike patterns in olfactory bulb neuronal networks J Neurosci Methods 2015 Jan 15;239:11-7. doi: 10.1016/j.jneumeth.2014.09.016. Epub 2014 Sep 26
2014
Smallwood SA, Lee HJ, Angermueller C, Krueger F, Saadeh H, Peat J, Andrews SR, Stegle O, Reik W, Kelsey G. Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity Nature Methods 2014;11(8):817-820.
Nicol AU, Sanchez-Andrade G, Collado P, Segonds-Pichon A, Kendrick KM. Olfactory bulb encoding during learning under anesthesia. Front Behav Neurosci. 2014 Jun 5;8:193
Johnsson AK, Dai Y, Nobis M, Baker MJ, McGhee EJ, Walker S, Schwarz JP, Kadir S, Morton JP, Myant KB, Huels DJ, Segonds-Pichon A, Sansom OJ, Anderson KI, Timpson P, Welch HC. The Rac-FRET mouse reveals tight spatiotemporal control of Rac activity in primary cells and tissues. Cell Reports 2014 Mar 27;6(6):1153-64.
Dryden NH, Broome LR, Dudbridge F, Johnson N, Orr N, Schoenfelder S, Nagano T, Andrews S, Wingett S, Kozarewa I, Assiotis I, Fenwick K, Maguire SL, Campbell J, Natrajan R, Lambros M, Perrakis E, Ashworth A, Fraser P, Fletcher O. Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C Genome Research 2014 Nov;24(11):1854-68. doi: 10.1101/gr.175034.114. Epub 2014 Aug 13
Takashima Y, Guo G, Loos R, Nichols J, Ficz G, Krueger F, Oxley D, Santos F, Clarke J, Mansfield W, Reik W, Bertone P, Smith A. Resetting transcription factor control circuitry toward ground-state pluripotency in human Cell 2014 Sep 11;158(6):1254-69. doi: 10.1016/j.cell.2014.08.029
Cambuli F, Murray A, Dean W, Dudzinska D, Krueger F, Andrews S, Senner CE, Cook SJ, Hemberger M. Epigenetic memory of the first cell fate decision prevents complete ES cell reprogramming into trophoblast Nature Communications 2014 Nov 26;5:5538. doi: 10.1038/ncomms6538.
Peat JR, Dean W, Clark SJ, Krueger F, Smallwood SA, Ficz G, Kim JK, Marioni JC, Hore TA, Reik W. Genome-wide bisulfite sequencing in zygotes identifies demethylation targets and maps the contribution of TET3 oxidation Cell Reports 2014 Dec 24;9(6):1990-2000. doi: 10.1016/j.celrep.2014.11.034. Epub 2014 Dec 12
2013
Iurlaro M, Ficz G, Oxley D, Raiber EA, Bachman M, Booth MJ, Andrews S, Balasubramanian S, Reik W. A screen for hydroxymethylcytosine and formylcytosine binding proteins suggests functions in transcription and chromatin regulation. Genome Biol. 2013;14(10):R119.
Conte N, Varela I, Grove C, Manes N, Yusa K, Moreno T, Segonds-Pichon A, Bench A, Gudgin E, Herman B, Bolli N, Ellis P, Haddad D, Costeas P, Rad R, Scott M, Huntly B, Bradley A, Vassiliou GS. Detailed molecular characterisation of acute myeloid leukaemia with a normal karyotype using targeted DNA capture. Leukemia 2013 Sep;27(9):1820-5
Ficz G, Hore TA, Santos F, Lee HJ, Dean W, Arand J, Krueger F, Oxley D, Paul YL, Walter J, Cook SJ, Andrews S, Branco MR, Reik W FGF Signaling Inhibition in ESCs Drives Rapid Genome-wide Demethylation to the Epigenetic Ground State of Pluripotency. Cell Stem Cell 2013 Sep 5;13(3):351-9.
Chandra A, van Maldegem F, Andrews S, Neuberger MS, Rada C. Deficiency in spliceosome-associated factor CTNNBL1 does not affect ongoing cell cycling but delays exit from quiescence and results in embryonic lethality in mice. Cell Cycle. 2013 Jan 23;12(5).
Kreck B, Richter J, Ammerpohl O, Barann M, Esser D, Petersen BS, Vater I, Penas EM, Chung CB, Seisenberger S, Boyd VL, Smallwood S, Drexler HG, Macleod RA, Hummel M, Krueger F, Häsler R, Schreiber S, Rosenstiel P, Franke A, Siebert R. Base-pair-resolution DNA methylome of the EBV-positive endemic burkitt lymphoma cell line DAUDI determined by SOLiD⢠bisulfite-sequencing. Leukemia. 2013 Jan 11. doi: 10.1038/leu.2013.4.
2012
Pichon B, Ladhani SN, Slack MP, Segonds-Pichon A, Andrews NJ, Waight PA, Miller E, George R. Changes in the molecular epidemiology of Streptococcus pneumoniae causing meningitis following the introduction of pneumococcal conjugate vaccination in England and Wales. J Clin Microbiol. 2012 Dec 26.
Seisenberger S, Andrews S, Krueger F, Arand J, Walter J, Santos F, Popp C, Thienpont B, Dean W, Reik W. The Dynamics of Genome-wide DNA Methylation Reprogramming in Mouse Primordial Germ Cells Mol. Cell 2012 Dec 6.
Drawnel FM, Wachten D, Molkentin JD, Maillet M, Aronsen JM, Swift F, Sjaastad I, Liu N, Catalucci D, Mikoshiba K, Hisatsune C, Okkenhaug H, Andrews SR, Bootman MD, Roderick HL. Mutual antagonism between IP3RII and miRNA-133a regulates calcium signals and cardiac hypertrophy. J. Cell Biol. 2012 Nov 26;199(5):783-98.
Senner CE, Krueger F, Oxley D, Andrews S, Hemberger M. DNA Methylation Profiles Define Stem Cell Identity and Reveal a Tight Embryonic-Extraembryonic Lineage Boundary. Stem Cells 2012 Oct 3. doi: 10.1002/stem.1249.
Ivanova E, Chen JH, Segonds-Pichon A, Ozanne SE, Kelsey G. DNA methylation at differentially methylated regions of imprinted genes are resistant to developmental programming by maternal nutrition. Epigenetics. 2012 Sep 11;7(10).
Durand-Dubief M, Will WR, Petrini E, Theodorou D, Harris RR, Crawford MR, Paszkiewicz K, Krueger F, Correra RM, Vetter AT, Miller JR, Kent NA, Varga-Weisz P. SWI/SNF-Like Chromatin Remodeling Factor Fun30 Supports Point Centromere Function in S. cerevisiae. PLoS Genet. 2012 Sep;8(9):e1002974. doi: 10.1371/journal.pgen.1002974.
Chell V, Balmanno K, Little AS, Wilson M, Andrews S, Blockley L, Hampson M, Gavine PR, Cook SJ. Tumour cell responses to new fibroblast growth factor receptor tyrosine kinase inhibitors and identification of a gatekeeper mutation in FGFR3 as a mechanism of acquired resistance.Oncogene. 2012 Aug 6. doi: 10.1038/onc.2012.319.
Karp NA, Segonds-Pichon A, Gerdin AK, RamÃÂrez-Solis R, White JK. The fallacy of ratio correction to address confounding factors. Lab Anim. 2012 Jul;46(3):245-52.
Krueger C, King MR, Krueger F, Branco MR, Osborne CS, Niakan KK, Higgins MJ, Reik W. Pairing of homologous regions in the mouse genome is associated with transcription but not imprinting status. PLoS One. 2012;7(7):e38983. Epub 2012 Jul 3.
Radford EJ, Isganaitis E, Jimenez-Chillaron J, Schroeder J, Molla M, Andrews S, Didier N, Charalambous M, McEwen K, Marazzi G, Sassoon D, Patti ME, Ferguson-Smith AC. An unbiased assessment of the role of imprinted genes in an intergenerational model of developmental programming.PLoS Genet. 2012 Apr;8(4):e1002605.
Booth MJ, Branco MR, Ficz G, Oxley D, Krueger F, Reik W, Balasubramanian S. Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution. Science. 2012 May 18;336(6083):934-7.
Kreck B, Marnellos G, Richter J, Krueger F, Siebert R, Franke A. B-SOLANA: an approach for the analysis of two-base encoding bisulfite sequencing data.Bioinformatics. 2012 Feb 1;28(3):428-9
Krueger F, Kreck B, Franke A, Andrews SR. DNA methylome analysis using short bisulfite sequencing data.Nat Methods. 2012 Jan 30;9(2):145-51. doi: 10.1038/nmeth.1828.
2011
James LR, Andrews S, Walker S, de Sousa PR, Ray A, Russell NA, Bellamy TC. High-throughput analysis of calcium signalling kinetics in astrocytes stimulated with different neurotransmitters.PLoS One. 2011;6(10):e26889. Epub 2011 Oct 25.
Macaulay EC, Weeks RJ, Andrews S, Morison IM. Hypomethylation of functional retrotransposon-derived genes in the human placenta.Mamm Genome. 2011 Aug 27.
Smallwood SA, Tomizawa SI, Krueger F, Ruf N, Carli N, Segonds-Pichon A, Sato S, Hata K, Andrews SR, Kelsey G. Dynamic CpG island methylation landscape in oocytes and preimplantation embryos.Nat Genet. 2011 Jun 26. doi: 10.1038/ng.864
Krueger F, Andrews SR. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications.Bioinformatics. 2011 Jun 1;27(11):1571-2
Gilley J, Seereeram A, Ando K, Mosely S, Andrews S, Kerschensteiner M, Misgeld T, Brion JP, Anderton B, Hanger DP, Coleman MP. Age-dependent axonal transport and locomotor changes and tau hypophosphorylation in a "P301L" tau knockin mouse.Neurobiol Aging. 2011 Apr 13.
Gambardella L, Anderson KE, Nussbaum C, Segonds-Pichon A, Margarido T, Norton L, Ludwig T, Sperandio M, Hawkins PT, Stephens L, Vermeren S. The GTPase activating protein ARAP3 regulates chemotaxis and adhesion-dependent processes in neutrophils.Blood. 2011 Apr 13.
Kulkarni S, Sitaru C, Jakus Z, Anderson KE, Damoulakis G, Davidson K, Hirose M, Juss J, Oxley D, Chessa TA, Ramadani F, Guillou H, Segonds-Pichon A, Fritsch A, Jarvis GE, Okkenhaug K, Ludwig R, Zillikens D, Mocsai A, Vanhaesebroeck B, Stephens LR, Hawkins PT. PI3K beta plays a critical role in neutrophil activation by immune complexes.Sci Signal. 2011 Apr 12;4(168):ra23.
Ficz G, Branco MR, Seisenberger S, Santos F, Krueger F, Hore TA, Marques CJ, Andrews S, Reik W. Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation. Nature. 2011 Apr 3.
Krueger F, Andrews SR, Osborne CS Large Scale Loss of Data in Low-Diversity Illumina Sequencing Libraries Can Be Recovered by Deferred Cluster Calling PLoS One. 6(1): e16607.
Tomizawa SI, Kobayashi H, Watanabe T, Andrews S, Hata K, Kelsey G, Sasaki H. Dynamic stage-specific changes in imprinted differentially methylated regions during early mammalian development and prevalence of non-CpG methylation in oocytes. Development. 2011 Jan 19.
Ktistakis NT, Andrews S, Long J. What is the advantage of a transient precursor in autophagosome biogenesis? Autophagy. 2011 Jan;7(1):118-22. Epub 2011 Jan 1.
2010
Gambardella L, Hemberger M, Hughes B, Zudaire E, Andrews S, Vermeren S. PI3K signaling through the dual GTPase-activating protein ARAP3 is essential for developmental angiogenesis. Sci Signal. 2010 Oct 26;3(145):ra76.
Andrews S, Gilley J, Coleman MP. Difference Tracker: ImageJ plugins for fully automated analysis of multiple axonal transport parameters. J Neurosci Methods. 2010 Nov 30;193(2):281-7. Epub 2010 Sep 24
Hodson DJ, Janas ML, Galloway A, Bell SE, Andrews S, Li CM, Pannell R, Siebel CW, MacDonald HR, De Keersmaecker K, Ferrando AA, Grutz G, Turner M. Deletion of the RNA-binding proteins ZFP36L1 and ZFP36L2 leads to perturbed thymic development and T lymphoblastic leukemia.Nat Immunol. 2010 Aug;11(8):717-24. Epub 2010 Jul 11.
Ktistaki E, Garefalaki A, Williams A, Andrews SR, Bell DM, Foster KE, Spilianakis CG, Flavell RA, Kosyakova N, Trifonov V, Liehr T, Kioussis D. CD8 locus nuclear dynamics during thymocyte development. J Immunol. 2010 May 15;184(10):5686-95. Epub 2010 Apr 19.
Popp C, Dean W, Feng S, Cokus SJ, Andrews S, Pellegrini M, Jacobsen SE, Reik W. Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency Nature 2010 Feb 25;463(7284):1101-5
Craig HE, Coadwell J, Guillou H, Vermeren S ARAP3 binding to phosphatidylinositol-(3,4,5)-trisphosphate depends on N-terminal tandem PH domains and adjacent sequences Cell Signal 2010 Feb;22(2):257-64. Epub 2009 Sep 25
Schoenfelder S, Sexton T, Chakalova L, Cope NF, Horton A, Andrews S, Kurukuti S, Mitchell JA, Umlauf D, Dimitrova DS, Eskiw CH, Luo Y, Wei CL, Ruan Y, Bieker JJ, Fraser P Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells Nat Genet 2010 Jan;42(1):53-61. Epub 2009 Dec 13
2009
Matheson LS, Osborn MJ, Smith JA, Corcos D, Hamon M, Chaouaf R, Coadwell J, Morgan G, Oxley D, Brüggemann M Light chain-deficient mice produce novel multimeric heavy-chain-only IgA by faulty class switching. Int Immunol. 2009 Aug;21(8):957-66. Epub 2009 Jun 26.
Raghu P, Manifava M, Coadwell J, Ktistakis NT Emerging findings from studies of phospholipase D in model organisms (and a short update on phosphatidic acid effectors). Biochim Biophys Acta. 2009 Apr 2.
Saudemont A, Garçon F, Yadi H, Roche-Molina M, Kim N, Segonds-Pichon A, MartÃÂn-Fontecha A, Okkenhaug K, Colucci F p110gamma and p110delta isoforms of phosphoinositide 3-kinase differentially regulate natural killer cell migration in health and disease Proc Natl Acad Sci USA.. 2009 Apr 7;106(14):5795-800.
Morreale G, Conforti L, Coadwell J, Wilbrey AL, Coleman MP Evolutionary divergence of valosin-containing protein/cell division cycle protein 48 binding interactions among endoplasmic reticulum-associated degradation proteins. FEBS J. 2009 Mar;276(5):1208-20.
2008
Walters E, Segonds-Pichon A, Nicol AU. The correlation determinant in tests for synchronization in neuronal spike data. J Neurosci Methods. 2008 Jul 15;172(1):60-6. Epub 2008 Apr 11.
Farthing CR, Ficz G, Ng RK, Chan CF, Andrews S, Dean W, Hemberger M, Reik W. Global mapping of DNA methylation in mouse promoters reveals epigenetic reprogramming of pluripotency genes.PLoS Genet. 2008 Jun 27;4(6):e1000116.
Jones R, James PS, Oxley D, Coadwell J, Suzuki-Toyota F, Howes EA. The Equatorial Subsegment in Mammalian Spermatozoa Is Enriched in Tyrosine Phosphorylated Proteins. Biol Reprod. 2008 Apr 30.
Donald S, Humby T, Fyfe I, Segonds-Pichon A, Walker SA, Andrews SR, Coadwell WJ, Emson P, Wilkinson LS, Welch HC. P-Rex2 regulates Purkinje cell dendrite morphology and motor coordination. Proc Natl Acad Sci USA. 2008 Mar 18;105(11):4483-8. Epub 2008 Mar 11.
2007
Stace C, Manifava M, Delon C, Coadwell J, Cockcroft S, Ktistakis NT. PA binding of phosphatidylinositol 4-phosphate 5-kinase. Adv Enzyme Regul. 2007 Nov 26.
Andrews S, Stephens LR, Hawkins PT. PI3K class IB pathway in neutrophils. Science STKE. 2007 Oct 9;2007(407):cm3. Review.
Andrews S, Stephens LR, Hawkins PT. PI3K class IB pathway. Science STKE. 2007 Oct 9;2007(407):cm2. Review.
Carter C, Dion C, Schnell S, Coadwell WJ, Graham M, Hepburn L, Morgan G, Hutchings A, Pascall JC, Jacobs H, Miller JR, Butcher GW. A natural hypomorphic variant of the apoptosis regulator Gimap4/IAN1. J Immunol. 2007 Aug 1;179(3):1784-95.
Burman C, Maqueira B, Coadwell J, Evans PD. Eleven new putative aminergic G-protein coupled receptors from Amphioxus (Branchiostoma floridae): identification, sequence analysis and phylogenetic relationship. Invert Neurosci. 2007 Jun;7(2):87-98. Epub 2007 Jan 16.
Ferguson GJ, Milne L, Kulkarni S, Sasaki T, Walker S, Andrews S, Crabbe T, Finan P, Jones G, Jackson S, Camps M, Rommel C, Wymann M, Hirsch E, Hawkins P, Stephens L. PI(3)Kgamma has an important context-dependent role in neutrophil chemokinesis. Nat Cell Biol. 2007 Jan;9(1):86-91. Epub 2006 Dec 17.
2006
Suire S, Condliffe AM, Ferguson GJ, Ellson CD, Guillou H, Davidson K, Welch H, Coadwell J, Turner M, Chilvers ER, Hawkins PT, Stephens L. Gbetagammas and the Ras binding domain of p110gamma are both important regulators of PI(3)Kgamma signalling in neutrophils. Nat Cell Biol. 2006 Nov;8(11):1303-9. Epub 2006 Oct 15.
Krugmann S, Andrews S, Stephens L, Hawkins PT. ARAP3 is essential for formation of lamellipodia after growth factor stimulation. J Cell Sci. 2006 Feb 1;119(Pt 3):425-32. Epub 2006 Jan 17.
2005
Welch HC, Condliffe AM, Milne LJ, Ferguson GJ, Hill K, Webb LM, Okkenhaug K, Coadwell WJ, Andrews SR, Thelen M, Jones GE, Hawkins PT, Stephens LR. P-Rex1 regulates neutrophil function. Curr Biol. 2005 Oct 25;15(20):1867-73.
Pugh N, Mead-Savery FC, Coadwell WJ, Rossi D, Sorrentino V, Williams AJ. Probing luminal negative charge in the type 3 ryanodine receptor. Biochem Biophys Res Commun. 2005 Dec 2;337(4):1072-9. Epub 2005 Oct 5.
Dion C, Carter C, Hepburn L, Coadwell WJ, Morgan G, Graham M, Pugh N, Anderson G, Butcher GW, Miller JR. Expression of the Ian family of putative GTPases during T cell development and description of an Ian with three sets of GTP/GDP-binding motifs. Int Immunol. 2005 Sep;17(9):1257-68. Epub 2005 Aug 15.
Raha-Chowdhury R, Andrews SR, Gruen JR. CAT 53: a protein phosphatase 1 nuclear targeting subunit encoded in the MHC Class I region strongly expressed in regions of the brain involved in memory, learning, and Alzheimer's disease. Brain Res Mol Brain Res. 2005 Jul 29;138(1):70-83.
Suire S, Coadwell J, Ferguson GJ, Davidson K, Hawkins P, Stephens L. p84, a new Gbetagamma-activated regulatory subunit of the type IB phosphoinositide 3-kinase p110gamma. Curr Biol. 2005 Mar 29;15(6):566-70.
Hill K, Krugmann S, Andrews SR, Coadwell WJ, Finan P, Welch HC, Hawkins PT, Stephens LR. Regulation of P-Rex1 by phosphatidylinositol (3,4,5)-trisphosphate and Gbetagamma subunits. J Biol Chem. 2005 Feb 11;280(6):4166-73. Epub 2004 Nov 15.