Computational Biology Research Group University of Oxford
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FAQ: Bioinformatics


Welcome to the CBRG

The Computational Biology Research Group (CBRG) provides computing support for bioinformatics analysis at the University of Oxford. We have expertise in many aspects of bioinformatics (sequence analysis, microarrays, proteomics and integration). We especially encourage collaborations that require writing custom software, bioinformatics tools and databases.

An account with the CBRG has many benefits and gives automatic access to a large number of molecular biology computing packages and to numerous biological databases.

We are based at the Sir William Dunn School of Pathology and at the Weatherall Institute of Molecular Medicine. Full details can be found on the contact details page.

Bioinformatics analysis tools online:

A wide range of bioinformatics programs are available online via EMBOSS Explorer.
You will need a molbiol username and password to use these tools.

Other web tools available include: BLAST, MIG, Mir-CRISPR, MASCOT and CRISPRscreen   (see full list).

Recent Papers:

------------ 2016

Twigg SR, Hufnagel RB, Miller KA, Zhou Y, McGowan SJ, Taylor J, Craft J, Taylor JC, Santoro SL, Huang T, Hopkin RJ, Brady AF, Clayton-Smith J, Clericuzio CL, Grange DK, Groesser L, Hafner C, Horn D, Temple IK, Dobyns WB, Curry CJ, Jones MC, Wilkie AO
A Recurrent Mosaic Mutation in SMO, Encoding the Hedgehog Signal Transducer Smoothened, Is the Major Cause of Curry-Jones Syndrome.
Am J Hum Genet (2016) 98: 1256-65
  » View abstract

Dolatshad H, Pellagatti A, Liberante FG, Llorian M, Repapi E, Steeples V, Roy S, Scifo L, Armstrong RN, Shaw J, Yip BH, Killick S, Kušec R, Taylor S, Mills KI, Savage KI, Smith CW, Boultwood J
Cryptic splicing events in the iron transporter ABCB7 and other key target genes in SF3B1-mutant myelodysplastic syndromes.
Leukemia (2016) :
  » View abstract

Bannard O, McGowan SJ, Ersching J, Ishido S, Victora GD, Shin JS, Cyster JG
Ubiquitin-mediated fluctuations in MHC class II facilitate efficient germinal center B cell responses.
J Exp Med (2016) 213: 993-1009
  » View abstract

Goos JA, Fenwick AL, Swagemakers SM, McGowan SJ, Knight SJ, Twigg SR, Hoogeboom AJ, van Dooren MF, Magielsen FJ, Wall SA, Mathijssen IM, Wilkie AO, van der Spek PJ, van den Ouweland AM
Identification of Intragenic Exon Deletions and Duplication of TCF12 by Whole Genome or Targeted Sequencing as a Cause of TCF12-Related Craniosynostosis.
Hum Mutat (2016) 37: 732-6
  » View abstract

Maher GJ, McGowan SJ, Giannoulatou E, Verrill C, Goriely A, Wilkie AO
Visualizing the origins of selfish de novo mutations in individual seminiferous tubules of human testes.
Proc Natl Acad Sci U S A (2016) 113: 2454-9
  » View abstract

------------ 2015

Davies JO, Telenius JM, McGowan SJ, Roberts NA, Taylor S, Higgs DR, Hughes JR
Multiplexed analysis of chromosome conformation at vastly improved sensitivity.
Nat Methods (2015) 13: 74-80
  » View abstract

Ramcharan R, Aleksic T, Kamdoum WP, Gao S, Pfister SX, Tanner J, Bridges E, Asher R, Watson AJ, Margison GP, Woodcock M, Repapi E, Li JL, Middleton MR, Macaulay VM
IGF-1R inhibition induces schedule-dependent sensitization of human melanoma to temozolomide.
Oncotarget (2015) 6: 39877-90
  » View abstract

Twigg SR, Forecki J, Goos JA, Richardson IC, Hoogeboom AJ, van den Ouweland AM, Swagemakers SM, Lequin MH, Van Antwerp D, McGowan SJ, Westbury I, Miller KA, Wall SA, van der Spek PJ, Mathijssen IM, Pauws E, Merzdorf CS, Wilkie AO
Gain-of-Function Mutations in ZIC1 Are Associated with Coronal Craniosynostosis and Learning Disability.
Am J Hum Genet (2015) 97: 378-88
  » View abstract

Ledaki I, McIntyre A, Wigfield S, Buffa F, McGowan S, Baban D, Li JL, Harris AL
Carbonic anhydrase IX induction defines a heterogeneous cancer cell response to hypoxia and mediates stem cell-like properties and sensitivity to HDAC inhibition.
Oncotarget (2015) 6: 19413-27
  » View abstract

Clynes D, Jelinska C, Xella B, Ayyub H, Scott C, Mitson M, Taylor S, Higgs DR, Gibbons RJ
Suppression of the alternative lengthening of telomere pathway by the chromatin remodelling factor ATRX.
Nat Commun (2015) 6: 7538
  » View abstract

Belaya K, Rodrguez Cruz PM, Liu WW, Maxwell S, McGowan S, Farrugia ME, Petty R, Walls TJ, Sedghi M, Basiri K, Yue WW, Sarkozy A, Bertoli M, Pitt M, Kennett R, Schaefer A, Bushby K, Parton M, Lochmller H, Palace J, Muntoni F, Beeson D
Mutations in GMPPB cause congenital myasthenic syndrome and bridge myasthenic disorders with dystroglycanopathies.
Brain (2015) 138: 2493-504
  » View abstract

Taylor JC, Martin HC, Lise S, Broxholme J, Cazier JB, Rimmer A, Kanapin A, Lunter G, Fiddy S, Allan C, Aricescu AR, Attar M, Babbs C, Becq J, Beeson D, Bento C, Bignell P, Blair E, Buckle VJ, Bull K, Cais O, Cario H, Chapel H, Copley RR, Cornall R, Craft J, Dahan K, Davenport EE, Dendrou C, Devuyst O, Fenwick AL, Flint J, Fugger L, Gilbert RD, Goriely A, Green A, Greger IH, Grocock R, Gruszczyk AV, Hastings R, Hatton E, Higgs D, Hill A, Holmes C, Howard M, Hughes L, Humburg P, Johnson D, Karpe F, Kingsbury Z, Kini U, Knight JC, Krohn J, Lamble S, Langman C, Lonie L, Luck J, McCarthy D, McGowan SJ, McMullin MF, Miller KA, Murray L, Nmeth AH, Nesbit MA, Nutt D, Ormondroyd E, Oturai AB, Pagnamenta A, Patel SY, Percy M, Petousi N, Piazza P, Piret SE, Polanco-Echeverry G, Popitsch N, Powrie F, Pugh C, Quek L, Robbins PA, Robson K, Russo A, Sahgal N, van Schouwenburg PA, Schuh A, Silverman E, Simmons A, Srensen PS, Sweeney E, Taylor J, Thakker RV, Tomlinson I, Trebes A, Twigg SR, Uhlig HH, Vyas P, Vyse T, Wall SA, Watkins H, Whyte MP, Witty L, Wright B, Yau C, Buck D, Humphray S, Ratcliffe PJ, Bell JI, Wilkie AO, Bentley D, Donnelly P, McVean G
Factors influencing success of clinical genome sequencing across a broad spectrum of disorders.
Nat Genet (2015) 47: 717-26
  » View abstract

Zhang Y, Makvandi-Nejad S, Qin L, Zhao Y, Zhang T, Wang L, Repapi E, Taylor S, McMichael A, Li N, Dong T, Wu H
Interferon-induced transmembrane protein-3 rs12252-C is associated with rapid progression of acute HIV-1 infection in Chinese MSM cohort.
AIDS (2015) 29: 889-94
  » View abstract

French A, Yang CT, Taylor S, Watt SM, Carpenter L
Human induced pluripotent stem cell-derived B lymphocytes express sIgM and can be generated via a hemogenic endothelium intermediate.
Stem Cells Dev (2015) 24: 1082-95
  » View abstract

------------ 2014

Babbs C, Lloyd D, Pagnamenta AT, Twigg SR, Green J, McGowan SJ, Mirza G, Naples R, Sharma VP, Volpi EV, Buckle VJ, Wall SA, Knight SJ, Parr JR, Wilkie AO
De novo and rare inherited mutations implicate the transcriptional coregulator TCF20/SPBP in autism spectrum disorder.
J Med Genet (2014) 51: 737-47
  » View abstract

see more...

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This file last modified Monday February 02, 2015