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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.


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.


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. PLoS One. 2016 Nov 2;11(11)

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, Łukasiak S, Hodson DJ, Bolland D, Balmanno K, Ahlfors H, Monzón-Casanova E, Mannurita SC, Bell LS, Andrews S, Díaz-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 PI3Kγ 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.


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


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


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.


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, Ramírez-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.


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.


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


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, Martín-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.


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.


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.


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.


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.