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.
2013
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, 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.
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, 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.
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.