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:

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

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, Németh 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, Sørensen 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

Bassett AR, Azzam G, Wheatley L, Tibbit C, Rajakumar T, McGowan S, Stanger N, Ewels PA, Taylor S, Ponting CP, Liu JL, Sauka-Spengler T, Fulga TA
Understanding functional miRNA-target interactions in vivo by site-specific genome engineering.
Nat Commun (2014) 5: 4640
  » View abstract

Armitage AE, Stacey AR, Giannoulatou E, Marshall E, Sturges P, Chatha K, Smith NM, Huang X, Xu X, Pasricha SR, Li N, Wu H, Webster C, Prentice AM, Pellegrino P, Williams I, Norris PJ, Drakesmith H, Borrow P
Distinct patterns of hepcidin and iron regulation during HIV-1, HBV, and HCV infections.
Proc Natl Acad Sci U S A (2014) 111: 12187-92
  » View abstract

Taylor S, Noble R
HTML5 PivotViewer: high-throughput visualization and querying of image data on the web.
Bioinformatics (2014) 30: 2691-2
  » View abstract

Woll PS, Kjällquist U, Chowdhury O, Doolittle H, Wedge DC, Thongjuea S, Erlandsson R, Ngara M, Anderson K, Deng Q, Mead AJ, Stenson L, Giustacchini A, Duarte S, Giannoulatou E, Taylor S, Karimi M, Scharenberg C, Mortera-Blanco T, Macaulay IC, Clark SA, Dybedal I, Josefsen D, Fenaux P, Hokland P, Holm MS, Cazzola M, Malcovati L, Tauro S, Bowen D, Boultwood J, Pellagatti A, Pimanda JE, Unnikrishnan A, Vyas P, Göhring G, Schlegelberger B, Tobiasson M, Kvalheim G, Constantinescu SN, Nerlov C, Nilsson L, Campbell PJ, Sandberg R, Papaemmanuil E, Hellström-Lindberg E, Linnarsson S, Jacobsen SE
Myelodysplastic syndromes are propagated by rare and distinct human cancer stem cells in vivo.
Cancer Cell (2014) 25: 794-808
  » View abstract

Clynes D, Jelinska C, Xella B, Ayyub H, Taylor S, Mitson M, Bachrati CZ, Higgs DR, Gibbons RJ
ATRX dysfunction induces replication defects in primary mouse cells.
PLoS One (2014) 9: e92915
  » View abstract

Hay AS, Pieper B, Cooke E, Mandáková T, Cartolano M, Tattersall AD, Ioio RD, McGowan SJ, Barkoulas M, Galinha C, Rast MI, Hofhuis H, Then C, Plieske J, Ganal M, Mott R, Martinez-Garcia JF, Carine MA, Scotland RW, Gan X, Filatov DA, Lysak MA, Tsiantis M
Cardamine hirsuta: a versatile genetic system for comparative studies.
Plant J (2014) 78: 1-15
  » View abstract

Gutowska-Owsiak D, Selvakumar TA, Salimi M, Taylor S, Ogg GS
Histamine enhances keratinocyte-mediated resolution of inflammation by promoting wound healing and response to infection.
Clin Exp Dermatol (2014) 39: 187-95
  » View abstract

Hughes JR, Roberts N, McGowan S, Hay D, Giannoulatou E, Lynch M, De Gobbi M, Taylor S, Gibbons R, Higgs DR
Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment.
Nat Genet (2014) 46: 205-12
  » View abstract

Favaro FP, Alvizi L, Zechi-Ceide RM, Bertola D, Felix TM, de Souza J, Raskin S, Twigg SR, Weiner AM, Armas P, Margarit E, Calcaterra NB, Andersen GR, McGowan SJ, Wilkie AO, Richieri-Costa A, de Almeida ML, Passos-Bueno MR
A noncoding expansion in EIF4A3 causes Richieri-Costa-Pereira syndrome, a craniofacial disorder associated with limb defects.
Am J Hum Genet (2014) 94: 120-8
  » View abstract

Pan X, Huang LC, Dong T, Peng Y, Cerundolo V, McGowan S, Ogg G
Combinatorial HLA-peptide bead libraries for high throughput identification of CD8⁺ T cell specificity.
J Immunol Methods (2014) 403: 72-8
  » View abstract

------------ 2013

Swiers G, Baumann C, O'Rourke J, Giannoulatou E, Taylor S, Joshi A, Moignard V, Pina C, Bee T, Kokkaliaris KD, Yoshimoto M, Yoder MC, Frampton J, Schroeder T, Enver T, Göttgens B, de Bruijn MF
Early dynamic fate changes in haemogenic endothelium characterized at the single-cell level.
Nat Commun (2013) 4: 2924
  » View abstract

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This file last modified Monday February 02, 2015