Chris Barnes

NOTE: Chris Barnes Left the lab in 2012

I completed my PhD in experimental high energy physics at Imperial College / Fermilab in 2005. I worked for a short time at CERN and then moved to the Wellcome Trust Sanger Institute in 2006 to work in statistical genetics and Copy Number Variation (CNV). There I developed tools to perform robust association studies using CNV (called CNVtools). In 2009 I moved to the Theoretical Systems Biology Group at Imperial to work on inference in systems and synthetic biology models, Approximate Bayesian Computation (ABC) and stochastic modelling. In 2012 I moved to the Department of Cell and Developmental Biology at University College London to start my own research group in the area of computational systems and synthetic biology.

 

Research interests

The three main themes of my research all utilise mathematical modelling and statistical methods to gain insights into biological processes and their relation to disease.

  • Modelling mutational processes in the genome
  • Reverse engineering of signalling systems
  • Design of synthetic biological systems for therapeutic applications

Software projects

cuda-sim
A python package for simulation of deterministic and stochastic dynamical systems using CUDA on Nvidia Graphics Processing Units.
abc-sysbio
Approximate Bayesian computation in Python with GPU support.
cnv-tools
Robust case-control and quantitative trait association using Copy Number Variants. Now also available in bioconductor

Recent talks

CRISM : GPUs in computational Statistics, Warwick, UK
Jstar ’11, Rennes, France
ICMSB, Lleida, Spain
Graphical models for reasoning on biological systems, a satellite meeting of ECCS’10, Lisbon, Portugal slides video
Learning and Inference in Computational Systems Biology 2010, Warwick, UK slides+video

Recent publications

Model selection in systems biology depends on experimental design.

Silk D, Kirk PD, Barnes CP, Toni T, Stumpf MP.

PLoS Comput Biol. 2014 Jun 12;10(6):e1003650. doi: 10.1371/journal.pcbi.1003650. eCollection 2014 Jun.

PMID:
24922483
[PubMed - in process]

Free PMC Article

A framework for parameter estimation and model selection from experimental data in systems biology using approximate Bayesian computation.

Liepe J, Kirk P, Filippi S, Toni T, Barnes CP, Stumpf MP.

Nat Protoc. 2014 Feb;9(2):439-56. doi: 10.1038/nprot.2014.025. Epub 2014 Jan 23.

PMID:
24457334
[PubMed - in process]

Reduced burden of very large and rare CNVs in bipolar affective disorder.

Grozeva D, Kirov G, Conrad DF, Barnes CP, Hurles M, Owen MJ, O’Donovan MC, Craddock N.

Bipolar Disord. 2013 Dec;15(8):893-8. doi: 10.1111/bdi.12125. Epub 2013 Oct 16.

PMID:
24127788
[PubMed - indexed for MEDLINE]

Reciprocal duplication of the Williams-Beuren syndrome deletion on chromosome 7q11.23 is associated with schizophrenia.

Mulle JG, Pulver AE, McGrath JA, Wolyniec PS, Dodd AF, Cutler DJ, Sebat J, Malhotra D, Nestadt G, Conrad DF, Hurles M, Barnes CP, Ikeda M, Iwata N, Levinson DF, Gejman PV, Sanders AR, Duan J, Mitchell AA, Peter I, Sklar P, O’Dushlaine CT, Grozeva D, O’Donovan MC, Owen MJ, Hultman CM, Kähler AK, Sullivan PF; Molecular Genetics of Schizophrenia Consortium, Kirov G, Warren ST.

Biol Psychiatry. 2014 Mar 1;75(5):371-7. doi: 10.1016/j.biopsych.2013.05.040. Epub 2013 Jul 17.

PMID:
23871472
[PubMed - in process]

On optimality of kernels for approximate Bayesian computation using sequential Monte Carlo.

Filippi S, Barnes CP, Cornebise J, Stumpf MP.

Stat Appl Genet Mol Biol. 2013 Mar 26;12(1):87-107. doi: 10.1515/sagmb-2012-0069.

PMID:
23502346
[PubMed - indexed for MEDLINE]

Bayesian design strategies for synthetic biology.

Barnes CP, Silk D, Stumpf MP.

Interface Focus. 2011 Dec 6;1(6):895-908. doi: 10.1098/rsfs.2011.0056. Epub 2011 Oct 5.

PMID:
23226588
[PubMed]

Free PMC Article

Clinical drug resistance linked to interconvertible phenotypic and functional states of tumor-propagating cells in multiple myeloma.

Chaidos A, Barnes CP, Cowan G, May PC, Melo V, Hatjiharissi E, Papaioannou M, Harrington H, Doolittle H, Terpos E, Dimopoulos M, Abdalla S, Yarranton H, Naresh K, Foroni L, Reid A, Rahemtulla A, Stumpf M, Roberts I, Karadimitris A.

Blood. 2013 Jan 10;121(2):318-28. doi: 10.1182/blood-2012-06-436220. Epub 2012 Nov 20.

PMID:
23169779
[PubMed - indexed for MEDLINE]

Free Article

Genome-wide screen for metabolic syndrome susceptibility Loci reveals strong lipid gene contribution but no evidence for common genetic basis for clustering of metabolic syndrome traits.

Kristiansson K, Perola M, Tikkanen E, Kettunen J, Surakka I, Havulinna AS, Stancáková A, Barnes C, Widen E, Kajantie E, Eriksson JG, Viikari J, Kähönen M, Lehtimäki T, Raitakari OT, Hartikainen AL, Ruokonen A, Pouta A, Jula A, Kangas AJ, Soininen P, Ala-Korpela M, Männistö S, Jousilahti P, Bonnycastle LL, Järvelin MR, Kuusisto J, Collins FS, Laakso M, Hurles ME, Palotie A, Peltonen L, Ripatti S, Salomaa V.

Circ Cardiovasc Genet. 2012 Apr 1;5(2):242-9. doi: 10.1161/CIRCGENETICS.111.961482. Epub 2012 Mar 7.

PMID:
22399527
[PubMed - indexed for MEDLINE]

Free PMC Article

Calibrating spatio-temporal models of leukocyte dynamics against in vivo live-imaging data using approximate Bayesian computation.

Liepe J, Taylor H, Barnes CP, Huvet M, Bugeon L, Thorne T, Lamb JR, Dallman MJ, Stumpf MP.

Integr Biol (Camb). 2012 Mar;4(3):335-45. doi: 10.1039/c2ib00175f. Epub 2012 Feb 10.

PMID:
22327539
[PubMed - indexed for MEDLINE]

Independent estimation of the frequency of rare CNVs in the UK population confirms their role in schizophrenia.

Grozeva D, Conrad DF, Barnes CP, Hurles M, Owen MJ, O’Donovan MC, Craddock N, Kirov G; WTCCC.

Schizophr Res. 2012 Mar;135(1-3):1-7. doi: 10.1016/j.schres.2011.11.004. Epub 2011 Nov 29.

PMID:
22130109
[PubMed - indexed for MEDLINE]

Free PMC Article

Designing attractive models via automated identification of chaotic and oscillatory dynamical regimes.

Silk D, Kirk PD, Barnes CP, Toni T, Rose A, Moon S, Dallman MJ, Stumpf MP.

Nat Commun. 2011 Oct 4;2:489. doi: 10.1038/ncomms1496.

PMID:
21971504
[PubMed - indexed for MEDLINE]

Free PMC Article

Bayesian design of synthetic biological systems.

Barnes CP, Silk D, Sheng X, Stumpf MP.

Proc Natl Acad Sci U S A. 2011 Sep 13;108(37):15190-5. doi: 10.1073/pnas.1017972108. Epub 2011 Aug 29.

PMID:
21876136
[PubMed - indexed for MEDLINE]

Free PMC Article

Computational design approaches and tools for synthetic biology.

MacDonald JT, Barnes C, Kitney RI, Freemont PS, Stan GB.

Integr Biol (Camb). 2011 Feb;3(2):97-108. doi: 10.1039/c0ib00077a. Epub 2011 Jan 24. Review.

PMID:
21258712
[PubMed - indexed for MEDLINE]

GPU accelerated biochemical network simulation.

Zhou Y, Liepe J, Sheng X, Stumpf MP, Barnes C.

Bioinformatics. 2011 Mar 15;27(6):874-6. doi: 10.1093/bioinformatics/btr015. Epub 2011 Jan 11.

PMID:
21224286
[PubMed - indexed for MEDLINE]

Free PMC Article

Integrating common and rare genetic variation in diverse human populations.

International HapMap 3 Consortium, Altshuler DM, Gibbs RA, Peltonen L, Altshuler DM, Gibbs RA, Peltonen L, Dermitzakis E, Schaffner SF, Yu F, Peltonen L, Dermitzakis E, Bonnen PE, Altshuler DM, Gibbs RA, de Bakker PI, Deloukas P, Gabriel SB, Gwilliam R, Hunt S, Inouye M, Jia X, Palotie A, Parkin M, Whittaker P, Yu F, Chang K, Hawes A, Lewis LR, Ren Y, Wheeler D, Gibbs RA, Muzny DM, Barnes C, Darvishi K, Hurles M, Korn JM, Kristiansson K, Lee C, McCarrol SA, Nemesh J, Dermitzakis E, Keinan A, Montgomery SB, Pollack S, Price AL, Soranzo N, Bonnen PE, Gibbs RA, Gonzaga-Jauregui C, Keinan A, Price AL, Yu F, Anttila V, Brodeur W, Daly MJ, Leslie S, McVean G, Moutsianas L, Nguyen H, Schaffner SF, Zhang Q, Ghori MJ, McGinnis R, McLaren W, Pollack S, Price AL, Schaffner SF, Takeuchi F, Grossman SR, Shlyakhter I, Hostetter EB, Sabeti PC, Adebamowo CA, Foster MW, Gordon DR, Licinio J, Manca MC, Marshall PA, Matsuda I, Ngare D, Wang VO, Reddy D, Rotimi CN, Royal CD, Sharp RR, Zeng C, Brooks LD, McEwen JE.

Nature. 2010 Sep 2;467(7311):52-8. doi: 10.1038/nature09298.

PMID:
20811451
[PubMed - indexed for MEDLINE]

Free PMC Article

Founder population-specific HapMap panel increases power in GWA studies through improved imputation accuracy and CNV tagging.

Surakka I, Kristiansson K, Anttila V, Inouye M, Barnes C, Moutsianas L, Salomaa V, Daly M, Palotie A, Peltonen L, Ripatti S.

Genome Res. 2010 Oct;20(10):1344-51. doi: 10.1101/gr.106534.110. Epub 2010 Sep 1.

PMID:
20810666
[PubMed - indexed for MEDLINE]

Free PMC Article

ABC-SysBio–approximate Bayesian computation in Python with GPU support.

Liepe J, Barnes C, Cule E, Erguler K, Kirk P, Toni T, Stumpf MP.

Bioinformatics. 2010 Jul 15;26(14):1797-9. doi: 10.1093/bioinformatics/btq278.

PMID:
20591907
[PubMed - indexed for MEDLINE]

Free PMC Article

Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls.

Wellcome Trust Case Control Consortium, Craddock N, Hurles ME, Cardin N, Pearson RD, Plagnol V, Robson S, Vukcevic D, Barnes C, Conrad DF, Giannoulatou E, Holmes C, Marchini JL, Stirrups K, Tobin MD, Wain LV, Yau C, Aerts J, Ahmad T, Andrews TD, Arbury H, Attwood A, Auton A, Ball SG, Balmforth AJ, Barrett JC, Barroso I, Barton A, Bennett AJ, Bhaskar S, Blaszczyk K, Bowes J, Brand OJ, Braund PS, Bredin F, Breen G, Brown MJ, Bruce IN, Bull J, Burren OS, Burton J, Byrnes J, Caesar S, Clee CM, Coffey AJ, Connell JM, Cooper JD, Dominiczak AF, Downes K, Drummond HE, Dudakia D, Dunham A, Ebbs B, Eccles D, Edkins S, Edwards C, Elliot A, Emery P, Evans DM, Evans G, Eyre S, Farmer A, Ferrier IN, Feuk L, Fitzgerald T, Flynn E, Forbes A, Forty L, Franklyn JA, Freathy RM, Gibbs P, Gilbert P, Gokumen O, Gordon-Smith K, Gray E, Green E, Groves CJ, Grozeva D, Gwilliam R, Hall A, Hammond N, Hardy M, Harrison P, Hassanali N, Hebaishi H, Hines S, Hinks A, Hitman GA, Hocking L, Howard E, Howard P, Howson JM, Hughes D, Hunt S, Isaacs JD, Jain M, Jewell DP, Johnson T, Jolley JD, Jones IR, Jones LA, Kirov G, Langford CF, Lango-Allen H, Lathrop GM, Lee J, Lee KL, Lees C, Lewis K, Lindgren CM, Maisuria-Armer M, Maller J, Mansfield J, Martin P, Massey DC, McArdle WL, McGuffin P, McLay KE, Mentzer A, Mimmack ML, Morgan AE, Morris AP, Mowat C, Myers S, Newman W, Nimmo ER, O’Donovan MC, Onipinla A, Onyiah I, Ovington NR, Owen MJ, Palin K, Parnell K, Pernet D, Perry JR, Phillips A, Pinto D, Prescott NJ, Prokopenko I, Quail MA, Rafelt S, Rayner NW, Redon R, Reid DM, Renwick, Ring SM, Robertson N, Russell E, St Clair D, Sambrook JG, Sanderson JD, Schuilenburg H, Scott CE, Scott R, Seal S, Shaw-Hawkins S, Shields BM, Simmonds MJ, Smyth DJ, Somaskantharajah E, Spanova K, Steer S, Stephens J, Stevens HE, Stone MA, Su Z, Symmons DP, Thompson JR, Thomson W, Travers ME, Turnbull C, Valsesia A, Walker M, Walker NM, Wallace C, Warren-Perry M, Watkins NA, Webster J, Weedon MN, Wilson AG, Woodburn M, Wordsworth BP, Young AH, Zeggini E, Carter NP, Frayling TM, Lee C, McVean G, Munroe PB, Palotie A, Sawcer SJ, Scherer SW, Strachan DP, Tyler-Smith C, Brown MA, Burton PR, Caulfield MJ, Compston A, Farrall M, Gough SC, Hall AS, Hattersley AT, Hill AV, Mathew CG, Pembrey M, Satsangi J, Stratton MR, Worthington J, Deloukas P, Duncanson A, Kwiatkowski DP, McCarthy MI, Ouwehand W, Parkes M, Rahman N, Todd JA, Samani NJ, Donnelly P.

Nature. 2010 Apr 1;464(7289):713-20. doi: 10.1038/nature08979.

PMID:
20360734
[PubMed - indexed for MEDLINE]

Free PMC Article

Origins and functional impact of copy number variation in the human genome.

Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y, Aerts J, Andrews TD, Barnes C, Campbell P, Fitzgerald T, Hu M, Ihm CH, Kristiansson K, Macarthur DG, Macdonald JR, Onyiah I, Pang AW, Robson S, Stirrups K, Valsesia A, Walter K, Wei J; Wellcome Trust Case Control Consortium, Tyler-Smith C, Carter NP, Lee C, Scherer SW, Hurles ME.

Nature. 2010 Apr 1;464(7289):704-12. doi: 10.1038/nature08516. Epub 2009 Oct 7.

PMID:
19812545
[PubMed - indexed for MEDLINE]

Free PMC Article

A genome-wide association study confirms VKORC1, CYP2C9, and CYP4F2 as principal genetic determinants of warfarin dose.

Takeuchi F, McGinnis R, Bourgeois S, Barnes C, Eriksson N, Soranzo N, Whittaker P, Ranganath V, Kumanduri V, McLaren W, Holm L, Lindh J, Rane A, Wadelius M, Deloukas P.

PLoS Genet. 2009 Mar;5(3):e1000433. doi: 10.1371/journal.pgen.1000433. Epub 2009 Mar 20.

PMID:
19300499
[PubMed - indexed for MEDLINE]

Free PMC Article

A robust statistical method for case-control association testing with copy number variation.

Barnes C, Plagnol V, Fitzgerald T, Redon R, Marchini J, Clayton D, Hurles ME.

Nat Genet. 2008 Oct;40(10):1245-52. doi: 10.1038/ng.206. Epub 2008 Sep 7.

PMID:
18776912
[PubMed - indexed for MEDLINE]

Free PMC Article