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Items: 46

1.

A Bayesian framework for the analysis of systems biology models of the brain.

Russell-Buckland J, Barnes CP, Tachtsidis I.

PLoS Comput Biol. 2019 Apr 26;15(4):e1006631. doi: 10.1371/journal.pcbi.1006631. eCollection 2019 Apr.

2.

Two New Plasmid Post-segregational Killing Mechanisms for the Implementation of Synthetic Gene Networks in Escherichia coli.

Fedorec AJH, Ozdemir T, Doshi A, Ho YK, Rosa L, Rutter J, Velazquez O, Pinheiro VB, Danino T, Barnes CP.

iScience. 2019 Apr 26;14:323-334. doi: 10.1016/j.isci.2019.03.019. Epub 2019 Mar 22.

3.

Modelling microbiome recovery after antibiotics using a stability landscape framework.

Shaw LP, Bassam H, Barnes CP, Walker AS, Klein N, Balloux F.

ISME J. 2019 Jul;13(7):1845-1856. doi: 10.1038/s41396-019-0392-1. Epub 2019 Mar 15.

4.

Crypt fusion as a homeostatic mechanism in the human colon.

Baker AM, Gabbutt C, Williams MJ, Cereser B, Jawad N, Rodriguez-Justo M, Jansen M, Barnes CP, Simons BD, McDonald SA, Graham TA, Wright NA.

Gut. 2019 Mar 14. pii: gutjnl-2018-317540. doi: 10.1136/gutjnl-2018-317540. [Epub ahead of print]

5.

Towards an Aspect-Oriented Design and Modelling Framework for Synthetic Biology.

Boeing P, Leon M, Nesbeth DN, Finkelstein A, Barnes CP.

Processes (Basel). 2018 Sep 15;6(9):167. doi: 10.3390/pr6090167.

6.

Computing with biological switches and clocks.

Dalchau N, Szép G, Hernansaiz-Ballesteros R, Barnes CP, Cardelli L, Phillips A, Csikász-Nagy A.

Nat Comput. 2018;17(4):761-779. doi: 10.1007/s11047-018-9686-x. Epub 2018 Jun 1.

7.

Reply to 'Neutral tumor evolution?'

Heide T, Zapata L, Williams MJ, Werner B, Caravagna G, Barnes CP, Graham TA, Sottoriva A.

Nat Genet. 2018 Dec;50(12):1633-1637. doi: 10.1038/s41588-018-0256-z. No abstract available.

PMID:
30374073
8.

Reply to 'Currently available bulk sequencing data do not necessarily support a model of neutral tumor evolution'.

Werner B, Williams MJ, Barnes CP, Graham TA, Sottoriva A.

Nat Genet. 2018 Dec;50(12):1624-1626. doi: 10.1038/s41588-018-0235-4. No abstract available.

PMID:
30374070
9.

Reply to 'Revisiting signatures of neutral tumor evolution in the light of complexity of cancer genomic data'.

Williams MJ, Werner B, Heide T, Barnes CP, Graham TA, Sottoriva A.

Nat Genet. 2018 Dec;50(12):1628-1630. doi: 10.1038/s41588-018-0210-0. No abstract available.

PMID:
30250125
10.

Synthetic Biology and Engineered Live Biotherapeutics: Toward Increasing System Complexity.

Ozdemir T, Fedorec AJH, Danino T, Barnes CP.

Cell Syst. 2018 Jul 25;7(1):5-16. doi: 10.1016/j.cels.2018.06.008. Review.

11.

Author Correction: Quantification of subclonal selection in cancer from bulk sequencing data.

Williams MJ, Werner B, Heide T, Curtis C, Barnes CP, Sottoriva A, Graham TA.

Nat Genet. 2018 Sep;50(9):1342. doi: 10.1038/s41588-018-0169-x.

PMID:
30022114
12.

Quantification of subclonal selection in cancer from bulk sequencing data.

Williams MJ, Werner B, Heide T, Curtis C, Barnes CP, Sottoriva A, Graham TA.

Nat Genet. 2018 Jun;50(6):895-903. doi: 10.1038/s41588-018-0128-6. Epub 2018 May 28. Erratum in: Nat Genet. 2018 Sep;50(9):1342.

13.

Combining a Toggle Switch and a Repressilator within the AC-DC Circuit Generates Distinct Dynamical Behaviors.

Perez-Carrasco R, Barnes CP, Schaerli Y, Isalan M, Briscoe J, Page KM.

Cell Syst. 2018 Apr 25;6(4):521-530.e3. doi: 10.1016/j.cels.2018.02.008. Epub 2018 Mar 21.

14.

Reply: Uncertainties in tumor allele frequencies limit power to infer evolutionary pressures.

Williams MJ, Werner B, Barnes CP, Graham TA, Sottoriva A.

Nat Genet. 2017 Aug 30;49(9):1289-1291. doi: 10.1038/ng.3877. No abstract available.

PMID:
28854180
15.

Catch my drift? Making sense of genomic intra-tumour heterogeneity.

Sottoriva A, Barnes CP, Graham TA.

Biochim Biophys Acta Rev Cancer. 2017 Apr;1867(2):95-100. doi: 10.1016/j.bbcan.2016.12.003. Epub 2017 Jan 7. Review.

16.
17.

Mechanistic Modelling and Bayesian Inference Elucidates the Variable Dynamics of Double-Strand Break Repair.

Woods ML, Barnes CP.

PLoS Comput Biol. 2016 Oct 14;12(10):e1005131. doi: 10.1371/journal.pcbi.1005131. eCollection 2016 Oct.

18.

Robustness of MEK-ERK Dynamics and Origins of Cell-to-Cell Variability in MAPK Signaling.

Filippi S, Barnes CP, Kirk PD, Kudo T, Kunida K, McMahon SS, Tsuchiya T, Wada T, Kuroda S, Stumpf MP.

Cell Rep. 2016 Jun 14;15(11):2524-35. doi: 10.1016/j.celrep.2016.05.024. Epub 2016 Jun 2.

19.

Mathematical models help explain experimental data. Response to 'Transcriptional interpretation of Shh morphogen signaling: computational modeling validates empirically established models'.

Cohen M, Page KM, Perez-Carrasco R, Barnes CP, Briscoe J.

Development. 2016 May 15;143(10):1640-3. doi: 10.1242/dev.138461. No abstract available.

20.

Short-term outcomes after arthroscopic capsular release for adhesive capsulitis.

Barnes CP, Lam PH, Murrell GA.

J Shoulder Elbow Surg. 2016 Sep;25(9):e256-64. doi: 10.1016/j.jse.2015.12.025. Epub 2016 Mar 8.

PMID:
26968090
21.

A Statistical Approach Reveals Designs for the Most Robust Stochastic Gene Oscillators.

Woods ML, Leon M, Perez-Carrasco R, Barnes CP.

ACS Synth Biol. 2016 Jun 17;5(6):459-70. doi: 10.1021/acssynbio.5b00179. Epub 2016 Feb 17.

22.

Identification of neutral tumor evolution across cancer types.

Williams MJ, Werner B, Barnes CP, Graham TA, Sottoriva A.

Nat Genet. 2016 Mar;48(3):238-244. doi: 10.1038/ng.3489. Epub 2016 Jan 18.

23.

Ptch1 and Gli regulate Shh signalling dynamics via multiple mechanisms.

Cohen M, Kicheva A, Ribeiro A, Blassberg R, Page KM, Barnes CP, Briscoe J.

Nat Commun. 2015 Apr 2;6:6709. doi: 10.1038/ncomms7709.

24.

A theoretical framework for the regulation of Shh morphogen-controlled gene expression.

Cohen M, Page KM, Perez-Carrasco R, Barnes CP, Briscoe J.

Development. 2014 Oct;141(20):3868-78. doi: 10.1242/dev.112573.

25.

Seven rules to live by: accommodations in social work education and the field.

Neely-Barnes SL, McCabe HA, Barnes CP.

J Soc Work Disabil Rehabil. 2014;13(4):279-96. doi: 10.1080/1536710X.2014.961113. Epub 2014 Oct 21. Review.

PMID:
25221960
26.

Directional collective cell migration emerges as a property of cell interactions.

Woods ML, Carmona-Fontaine C, Barnes CP, Couzin ID, Mayor R, Page KM.

PLoS One. 2014 Sep 2;9(9):e104969. doi: 10.1371/journal.pone.0104969. eCollection 2014.

27.

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.

28.

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.

29.

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
30.

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.

31.

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
32.

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.

33.

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.

34.

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 MPH.

Integr Biol (Camb). 2012 Mar;4(3):335-345. doi: 10.1039/c2ib00175f. Epub 2012 Feb 10.

35.

SMN1 gene duplications are associated with sporadic ALS.

Blauw HM, Barnes CP, van Vught PW, van Rheenen W, Verheul M, Cuppen E, Veldink JH, van den Berg LH.

Neurology. 2012 Mar 13;78(11):776-80. doi: 10.1212/WNL.0b013e318249f697. Epub 2012 Feb 8.

36.

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.

37.

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.

38.

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.

39.

Electrospun polydioxanone-elastin blends: potential for bioresorbable vascular grafts.

Sell SA, McClure MJ, Barnes CP, Knapp DC, Walpoth BH, Simpson DG, Bowlin GL.

Biomed Mater. 2006 Jun;1(2):72-80. doi: 10.1088/1748-6041/1/2/004. Epub 2006 May 4.

PMID:
18460759
40.

Nanofiber technology: designing the next generation of tissue engineering scaffolds.

Barnes CP, Sell SA, Boland ED, Simpson DG, Bowlin GL.

Adv Drug Deliv Rev. 2007 Dec 10;59(14):1413-33. Epub 2007 Aug 25. Review.

PMID:
17916396
41.

Suture-reinforced electrospun polydioxanone-elastin small-diameter tubes for use in vascular tissue engineering: a feasibility study.

Smith MJ, McClure MJ, Sell SA, Barnes CP, Walpoth BH, Simpson DG, Bowlin GL.

Acta Biomater. 2008 Jan;4(1):58-66. Epub 2007 Aug 17.

PMID:
17897890
42.

Cross-linking electrospun type II collagen tissue engineering scaffolds with carbodiimide in ethanol.

Barnes CP, Pemble CW, Brand DD, Simpson DG, Bowlin GL.

Tissue Eng. 2007 Jul;13(7):1593-605.

PMID:
17523878
43.

Electrospun fibrinogen: feasibility as a tissue engineering scaffold in a rat cell culture model.

McManus MC, Boland ED, Simpson DG, Barnes CP, Bowlin GL.

J Biomed Mater Res A. 2007 May;81(2):299-309.

PMID:
17120217
44.

Mechanical properties of electrospun fibrinogen structures.

McManus MC, Boland ED, Koo HP, Barnes CP, Pawlowski KJ, Wnek GE, Simpson DG, Bowlin GL.

Acta Biomater. 2006 Jan;2(1):19-28. Epub 2005 Nov 22.

PMID:
16701855
45.

Electrospinning polydioxanone for biomedical applications.

Boland ED, Coleman BD, Barnes CP, Simpson DG, Wnek GE, Bowlin GL.

Acta Biomater. 2005 Jan;1(1):115-23.

PMID:
16701785
46.

Substance abuse attitudes and policies in US rehabilitation training programs: a comparison of 1985 and 2000.

Basford JR, Rohe DE, Barnes CP, DePompolo RW.

Arch Phys Med Rehabil. 2002 Apr;83(4):517-22.

PMID:
11932854

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