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Items: 31

1.

Author Correction: WWP2 regulates pathological cardiac fibrosis by modulating SMAD2 signaling.

Chen H, Moreno-Moral A, Pesce F, Devapragash N, Mancini M, Heng EL, Rotival M, Srivastava PK, Harmston N, Shkura K, Rackham OJL, Yu WP, Sun XM, Tee NGZ, Tan ELS, Barton PJR, Felkin LE, Lara-Pezzi E, Angelini G, Beltrami C, Pravenec M, Schafer S, Bottolo L, Hubner N, Emanueli C, Cook SA, Petretto E.

Nat Commun. 2019 Sep 9;10(1):4085. doi: 10.1038/s41467-019-12060-5.

2.

WWP2 regulates pathological cardiac fibrosis by modulating SMAD2 signaling.

Chen H, Moreno-Moral A, Pesce F, Devapragash N, Mancini M, Heng EL, Rotival M, Srivastava PK, Harmston N, Shkura K, Rackham OJL, Yu WP, Sun XM, Tee NGZ, Tan ELS, Barton PJR, Felkin LE, Lara-Pezzi E, Angelini G, Beltrami C, Pravenec M, Schafer S, Bottolo L, Hubner N, Emanueli C, Cook SA, Petretto E.

Nat Commun. 2019 Aug 9;10(1):3616. doi: 10.1038/s41467-019-11551-9. Erratum in: Nat Commun. 2019 Sep 9;10(1):4085.

3.

MethylCal: Bayesian calibration of methylation levels.

Ochoa E, Zuber V, Fernandez-Jimenez N, Bilbao JR, Clark GR, Maher ER, Bottolo L.

Nucleic Acids Res. 2019 Aug 22;47(14):e81. doi: 10.1093/nar/gkz325.

4.

Genotype, extrapyramidal features, and severity of variant ataxia-telangiectasia.

Schon K, van Os NJH, Oscroft N, Baxendale H, Scoffings D, Ray J, Suri M, Whitehouse WP, Mehta PR, Everett N, Bottolo L, van de Warrenburg BP, Byrd PJ, Weemaes C, Willemsen MA, Tischkowitz M, Taylor AM, Hensiek AE.

Ann Neurol. 2019 Feb;85(2):170-180. doi: 10.1002/ana.25394.

5.

The chromosome 6q22.33 region is associated with age at diagnosis of type 1 diabetes and disease risk in those diagnosed under 5 years of age.

Inshaw JRJ, Walker NM, Wallace C, Bottolo L, Todd JA.

Diabetologia. 2018 Jan;61(1):147-157. doi: 10.1007/s00125-017-4440-y. Epub 2017 Oct 5.

6.

Particle MCMC algorithms and architectures for accelerating inference in state-space models.

Mingas G, Bottolo L, Bouganis CS.

Int J Approx Reason. 2017 Apr;83:413-433. doi: 10.1016/j.ijar.2016.10.011.

7.

A Bayesian Approach for Analysis of Whole-Genome Bisulfite Sequencing Data Identifies Disease-Associated Changes in DNA Methylation.

Rackham OJ, Langley SR, Oates T, Vradi E, Harmston N, Srivastava PK, Behmoaras J, Dellaportas P, Bottolo L, Petretto E.

Genetics. 2017 Apr;205(4):1443-1458. doi: 10.1534/genetics.116.195008. Epub 2017 Feb 17.

8.

Expression QTLs Mapping and Analysis: A Bayesian Perspective.

Imprialou M, Petretto E, Bottolo L.

Methods Mol Biol. 2017;1488:189-215. Review.

PMID:
27933525
9.

Wars2 is a determinant of angiogenesis.

Wang M, Sips P, Khin E, Rotival M, Sun X, Ahmed R, Widjaja AA, Schafer S, Yusoff P, Choksi PK, Ko NS, Singh MK, Epstein D, Guan Y, Houštěk J, Mracek T, Nuskova H, Mikell B, Tan J, Pesce F, Kolar F, Bottolo L, Mancini M, Hubner N, Pravenec M, Petretto E, MacRae C, Cook SA.

Nat Commun. 2016 Jul 8;7:12061. doi: 10.1038/ncomms12061.

10.

R2GUESS: A Graphics Processing Unit-Based R Package for Bayesian Variable Selection Regression of Multivariate Responses.

Liquet B, Bottolo L, Campanella G, Richardson S, Chadeau-Hyam M.

J Stat Softw. 2016 Jan 29;69(2). doi: 10.18637/jss.v069.i02.

11.

Systems genetics identifies a convergent gene network for cognition and neurodevelopmental disease.

Johnson MR, Shkura K, Langley SR, Delahaye-Duriez A, Srivastava P, Hill WD, Rackham OJ, Davies G, Harris SE, Moreno-Moral A, Rotival M, Speed D, Petrovski S, Katz A, Hayward C, Porteous DJ, Smith BH, Padmanabhan S, Hocking LJ, Starr JM, Liewald DC, Visconti A, Falchi M, Bottolo L, Rossetti T, Danis B, Mazzuferi M, Foerch P, Grote A, Helmstaedter C, Becker AJ, Kaminski RM, Deary IJ, Petretto E.

Nat Neurosci. 2016 Feb;19(2):223-32. doi: 10.1038/nn.4205. Epub 2015 Dec 21.

12.

MT-HESS: an efficient Bayesian approach for simultaneous association detection in OMICS datasets, with application to eQTL mapping in multiple tissues.

Lewin A, Saadi H, Peters JE, Moreno-Moral A, Lee JC, Smith KG, Petretto E, Bottolo L, Richardson S.

Bioinformatics. 2016 Feb 15;32(4):523-32. doi: 10.1093/bioinformatics/btv568. Epub 2015 Oct 26.

13.

WGBSSuite: simulating whole-genome bisulphite sequencing data and benchmarking differential DNA methylation analysis tools.

Rackham OJ, Dellaportas P, Petretto E, Bottolo L.

Bioinformatics. 2015 Jul 15;31(14):2371-3. doi: 10.1093/bioinformatics/btv114. Epub 2015 Mar 15.

14.

Systems genetics identifies Sestrin 3 as a regulator of a proconvulsant gene network in human epileptic hippocampus.

Johnson MR, Behmoaras J, Bottolo L, Krishnan ML, Pernhorst K, Santoscoy PLM, Rossetti T, Speed D, Srivastava PK, Chadeau-Hyam M, Hajji N, Dabrowska A, Rotival M, Razzaghi B, Kovac S, Wanisch K, Grillo FW, Slaviero A, Langley SR, Shkura K, Roncon P, De T, Mattheisen M, Niehusmann P, O'Brien TJ, Petrovski S, von Lehe M, Hoffmann P, Eriksson J, Coffey AJ, Cichon S, Walker M, Simonato M, Danis B, Mazzuferi M, Foerch P, Schoch S, De Paola V, Kaminski RM, Cunliffe VT, Becker AJ, Petretto E.

Nat Commun. 2015 Jan 23;6:6031. doi: 10.1038/ncomms7031.

15.

Low copy number of the salivary amylase gene predisposes to obesity.

Falchi M, El-Sayed Moustafa JS, Takousis P, Pesce F, Bonnefond A, Andersson-Assarsson JC, Sudmant PH, Dorajoo R, Al-Shafai MN, Bottolo L, Ozdemir E, So HC, Davies RW, Patrice A, Dent R, Mangino M, Hysi PG, Dechaume A, Huyvaert M, Skinner J, Pigeyre M, Caiazzo R, Raverdy V, Vaillant E, Field S, Balkau B, Marre M, Visvikis-Siest S, Weill J, Poulain-Godefroy O, Jacobson P, Sjostrom L, Hammond CJ, Deloukas P, Sham PC, McPherson R, Lee J, Tai ES, Sladek R, Carlsson LM, Walley A, Eichler EE, Pattou F, Spector TD, Froguel P.

Nat Genet. 2014 May;46(5):492-7. doi: 10.1038/ng.2939. Epub 2014 Mar 30.

16.

Multi-tissue analysis of co-expression networks by higher-order generalized singular value decomposition identifies functionally coherent transcriptional modules.

Xiao X, Moreno-Moral A, Rotival M, Bottolo L, Petretto E.

PLoS Genet. 2014 Jan;10(1):e1004006. doi: 10.1371/journal.pgen.1004006. Epub 2014 Jan 2.

17.

GUESS-ing polygenic associations with multiple phenotypes using a GPU-based evolutionary stochastic search algorithm.

Bottolo L, Chadeau-Hyam M, Hastie DI, Zeller T, Liquet B, Newcombe P, Yengo L, Wild PS, Schillert A, Ziegler A, Nielsen SF, Butterworth AS, Ho WK, Castagné R, Munzel T, Tregouet D, Falchi M, Cambien F, Nordestgaard BG, Fumeron F, Tybjærg-Hansen A, Froguel P, Danesh J, Petretto E, Blankenberg S, Tiret L, Richardson S.

PLoS Genet. 2013;9(8):e1003657. doi: 10.1371/journal.pgen.1003657. Epub 2013 Aug 8.

18.

Deciphering the complex: methodological overview of statistical models to derive OMICS-based biomarkers.

Chadeau-Hyam M, Campanella G, Jombart T, Bottolo L, Portengen L, Vineis P, Liquet B, Vermeulen RC.

Environ Mol Mutagen. 2013 Aug;54(7):542-57. doi: 10.1002/em.21797. Epub 2013 Aug 5. Review.

PMID:
23918146
19.

Systems-level approaches reveal conservation of trans-regulated genes in the rat and genetic determinants of blood pressure in humans.

Langley SR, Bottolo L, Kunes J, Zicha J, Zidek V, Hubner N, Cook SA, Pravenec M, Aitman TJ, Petretto E.

Cardiovasc Res. 2013 Mar 15;97(4):653-65. doi: 10.1093/cvr/cvs329. Epub 2012 Oct 31.

20.

Novel association approach for variable number tandem repeats (VNTRs) identifies DOCK5 as a susceptibility gene for severe obesity.

El-Sayed Moustafa JS, Eleftherohorinou H, de Smith AJ, Andersson-Assarsson JC, Alves AC, Hadjigeorgiou E, Walters RG, Asher JE, Bottolo L, Buxton JL, Sladek R, Meyre D, Dina C, Visvikis-Siest S, Jacobson P, Sjöström L, Carlsson LM, Walley A, Falchi M, Froguel P, Blakemore AI, Coin LJ.

Hum Mol Genet. 2012 Aug 15;21(16):3727-38. doi: 10.1093/hmg/dds187. Epub 2012 May 16.

21.

A genome-wide association study identifies rs2000999 as a strong genetic determinant of circulating haptoglobin levels.

Froguel P, Ndiaye NC, Bonnefond A, Bouatia-Naji N, Dechaume A, Siest G, Herbeth B, Falchi M, Bottolo L, Guéant-Rodriguez RM, Lecoeur C, Langlois MR, Labrune Y, Ruokonen A, El Shamieh S, Stathopoulou MG, Morandi A, Maffeis C, Meyre D, Delanghe JR, Jacobson P, Sjöström L, Carlsson LM, Walley A, Elliott P, Jarvelin MR, Dedoussis GV, Visvikis-Siest S.

PLoS One. 2012;7(3):e32327. doi: 10.1371/journal.pone.0032327. Epub 2012 Mar 5.

22.

Endonuclease G is a novel determinant of cardiac hypertrophy and mitochondrial function.

McDermott-Roe C, Ye J, Ahmed R, Sun XM, Serafín A, Ware J, Bottolo L, Muckett P, Cañas X, Zhang J, Rowe GC, Buchan R, Lu H, Braithwaite A, Mancini M, Hauton D, Martí R, García-Arumí E, Hubner N, Jacob H, Serikawa T, Zidek V, Papousek F, Kolar F, Cardona M, Ruiz-Meana M, García-Dorado D, Comella JX, Felkin LE, Barton PJ, Arany Z, Pravenec M, Petretto E, Sanchis D, Cook SA.

Nature. 2011 Oct 5;478(7367):114-8. doi: 10.1038/nature10490.

23.

Bayesian detection of expression quantitative trait loci hot spots.

Bottolo L, Petretto E, Blankenberg S, Cambien F, Cook SA, Tiret L, Richardson S.

Genetics. 2011 Dec;189(4):1449-59. doi: 10.1534/genetics.111.131425. Epub 2011 Sep 16.

24.

Differential coexpression analysis of obesity-associated networks in human subcutaneous adipose tissue.

Walley AJ, Jacobson P, Falchi M, Bottolo L, Andersson JC, Petretto E, Bonnefond A, Vaillant E, Lecoeur C, Vatin V, Jernas M, Balding D, Petteni M, Park YS, Aitman T, Richardson S, Sjostrom L, Carlsson LM, Froguel P.

Int J Obes (Lond). 2012 Jan;36(1):137-47. doi: 10.1038/ijo.2011.22. Epub 2011 Mar 22.

25.

ESS++: a C++ objected-oriented algorithm for Bayesian stochastic search model exploration.

Bottolo L, Chadeau-Hyam M, Hastie DI, Langley SR, Petretto E, Tiret L, Tregouet D, Richardson S.

Bioinformatics. 2011 Feb 15;27(4):587-8. doi: 10.1093/bioinformatics/btq684. Epub 2011 Jan 13.

26.

A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk.

Heinig M, Petretto E, Wallace C, Bottolo L, Rotival M, Lu H, Li Y, Sarwar R, Langley SR, Bauerfeind A, Hummel O, Lee YA, Paskas S, Rintisch C, Saar K, Cooper J, Buchan R, Gray EE, Cyster JG; Cardiogenics Consortium, Erdmann J, Hengstenberg C, Maouche S, Ouwehand WH, Rice CM, Samani NJ, Schunkert H, Goodall AH, Schulz H, Roider HG, Vingron M, Blankenberg S, Münzel T, Zeller T, Szymczak S, Ziegler A, Tiret L, Smyth DJ, Pravenec M, Aitman TJ, Cambien F, Clayton D, Todd JA, Hubner N, Cook SA.

Nature. 2010 Sep 23;467(7314):460-4. doi: 10.1038/nature09386. Epub 2010 Sep 8.

27.

New insights into the genetic control of gene expression using a Bayesian multi-tissue approach.

Petretto E, Bottolo L, Langley SR, Heinig M, McDermott-Roe C, Sarwar R, Pravenec M, Hübner N, Aitman TJ, Cook SA, Richardson S.

PLoS Comput Biol. 2010 Apr 8;6(4):e1000737. doi: 10.1371/journal.pcbi.1000737.

28.

Genome-wide detection and characterization of positive selection in human populations.

Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, Cotsapas C, Xie X, Byrne EH, McCarroll SA, Gaudet R, Schaffner SF, Lander ES; International HapMap Consortium, Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, Gibbs RA, Belmont JW, Boudreau A, Hardenbol P, Leal SM, Pasternak S, Wheeler DA, Willis TD, Yu F, Yang H, Zeng C, Gao Y, Hu H, Hu W, Li C, Lin W, Liu S, Pan H, Tang X, Wang J, Wang W, Yu J, Zhang B, Zhang Q, Zhao H, Zhao H, Zhou J, Gabriel SB, Barry R, Blumenstiel B, Camargo A, Defelice M, Faggart M, Goyette M, Gupta S, Moore J, Nguyen H, Onofrio RC, Parkin M, Roy J, Stahl E, Winchester E, Ziaugra L, Altshuler D, Shen Y, Yao Z, Huang W, Chu X, He Y, Jin L, Liu Y, Shen Y, Sun W, Wang H, Wang Y, Wang Y, Xiong X, Xu L, Waye MM, Tsui SK, Xue H, Wong JT, Galver LM, Fan JB, Gunderson K, Murray SS, Oliphant AR, Chee MS, Montpetit A, Chagnon F, Ferretti V, Leboeuf M, Olivier JF, Phillips MS, Roumy S, Sallée C, Verner A, Hudson TJ, Kwok PY, Cai D, Koboldt DC, Miller RD, Pawlikowska L, Taillon-Miller P, Xiao M, Tsui LC, Mak W, Song YQ, Tam PK, Nakamura Y, Kawaguchi T, Kitamoto T, Morizono T, Nagashima A, Ohnishi Y, Sekine A, Tanaka T, Tsunoda T, Deloukas P, Bird CP, Delgado M, Dermitzakis ET, Gwilliam R, Hunt S, Morrison J, Powell D, Stranger BE, Whittaker P, Bentley DR, Daly MJ, de Bakker PI, Barrett J, Chretien YR, Maller J, McCarroll S, Patterson N, Pe'er I, Price A, Purcell S, Richter DJ, Sabeti P, Saxena R, Schaffner SF, Sham PC, Varilly P, Altshuler D, Stein LD, Krishnan L, Smith AV, Tello-Ruiz MK, Thorisson GA, Chakravarti A, Chen PE, Cutler DJ, Kashuk CS, Lin S, Abecasis GR, Guan W, Li Y, Munro HM, Qin ZS, Thomas DJ, McVean G, Auton A, Bottolo L, Cardin N, Eyheramendy S, Freeman C, Marchini J, Myers S, Spencer C, Stephens M, Donnelly P, Cardon LR, Clarke G, Evans DM, Morris AP, Weir BS, Tsunoda T, Johnson TA, Mullikin JC, Sherry ST, Feolo M, Skol A, Zhang H, Zeng C, Zhao H, Matsuda I, Fukushima Y, Macer DR, Suda E, Rotimi CN, Adebamowo CA, Ajayi I, Aniagwu T, Marshall PA, Nkwodimmah C, Royal CD, Leppert MF, Dixon M, Peiffer A, Qiu R, Kent A, Kato K, Niikawa N, Adewole IF, Knoppers BM, Foster MW, Clayton EW, Watkin J, Gibbs RA, Belmont JW, Muzny D, Nazareth L, Sodergren E, Weinstock GM, Wheeler DA, Yakub I, Gabriel SB, Onofrio RC, Richter DJ, Ziaugra L, Birren BW, Daly MJ, Altshuler D, Wilson RK, Fulton LL, Rogers J, Burton J, Carter NP, Clee CM, Griffiths M, Jones MC, McLay K, Plumb RW, Ross MT, Sims SK, Willey DL, Chen Z, Han H, Kang L, Godbout M, Wallenburg JC, L'Archevêque P, Bellemare G, Saeki K, Wang H, An D, Fu H, Li Q, Wang Z, Wang R, Holden AL, Brooks LD, McEwen JE, Guyer MS, Wang VO, Peterson JL, Shi M, Spiegel J, Sung LM, Zacharia LF, Collins FS, Kennedy K, Jamieson R, Stewart J.

Nature. 2007 Oct 18;449(7164):913-8.

29.

A second generation human haplotype map of over 3.1 million SNPs.

International HapMap Consortium, Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, Gibbs RA, Belmont JW, Boudreau A, Hardenbol P, Leal SM, Pasternak S, Wheeler DA, Willis TD, Yu F, Yang H, Zeng C, Gao Y, Hu H, Hu W, Li C, Lin W, Liu S, Pan H, Tang X, Wang J, Wang W, Yu J, Zhang B, Zhang Q, Zhao H, Zhao H, Zhou J, Gabriel SB, Barry R, Blumenstiel B, Camargo A, Defelice M, Faggart M, Goyette M, Gupta S, Moore J, Nguyen H, Onofrio RC, Parkin M, Roy J, Stahl E, Winchester E, Ziaugra L, Altshuler D, Shen Y, Yao Z, Huang W, Chu X, He Y, Jin L, Liu Y, Shen Y, Sun W, Wang H, Wang Y, Wang Y, Xiong X, Xu L, Waye MM, Tsui SK, Xue H, Wong JT, Galver LM, Fan JB, Gunderson K, Murray SS, Oliphant AR, Chee MS, Montpetit A, Chagnon F, Ferretti V, Leboeuf M, Olivier JF, Phillips MS, Roumy S, Sallée C, Verner A, Hudson TJ, Kwok PY, Cai D, Koboldt DC, Miller RD, Pawlikowska L, Taillon-Miller P, Xiao M, Tsui LC, Mak W, Song YQ, Tam PK, Nakamura Y, Kawaguchi T, Kitamoto T, Morizono T, Nagashima A, Ohnishi Y, Sekine A, Tanaka T, Tsunoda T, Deloukas P, Bird CP, Delgado M, Dermitzakis ET, Gwilliam R, Hunt S, Morrison J, Powell D, Stranger BE, Whittaker P, Bentley DR, Daly MJ, de Bakker PI, Barrett J, Chretien YR, Maller J, McCarroll S, Patterson N, Pe'er I, Price A, Purcell S, Richter DJ, Sabeti P, Saxena R, Schaffner SF, Sham PC, Varilly P, Altshuler D, Stein LD, Krishnan L, Smith AV, Tello-Ruiz MK, Thorisson GA, Chakravarti A, Chen PE, Cutler DJ, Kashuk CS, Lin S, Abecasis GR, Guan W, Li Y, Munro HM, Qin ZS, Thomas DJ, McVean G, Auton A, Bottolo L, Cardin N, Eyheramendy S, Freeman C, Marchini J, Myers S, Spencer C, Stephens M, Donnelly P, Cardon LR, Clarke G, Evans DM, Morris AP, Weir BS, Tsunoda T, Mullikin JC, Sherry ST, Feolo M, Skol A, Zhang H, Zeng C, Zhao H, Matsuda I, Fukushima Y, Macer DR, Suda E, Rotimi CN, Adebamowo CA, Ajayi I, Aniagwu T, Marshall PA, Nkwodimmah C, Royal CD, Leppert MF, Dixon M, Peiffer A, Qiu R, Kent A, Kato K, Niikawa N, Adewole IF, Knoppers BM, Foster MW, Clayton EW, Watkin J, Gibbs RA, Belmont JW, Muzny D, Nazareth L, Sodergren E, Weinstock GM, Wheeler DA, Yakub I, Gabriel SB, Onofrio RC, Richter DJ, Ziaugra L, Birren BW, Daly MJ, Altshuler D, Wilson RK, Fulton LL, Rogers J, Burton J, Carter NP, Clee CM, Griffiths M, Jones MC, McLay K, Plumb RW, Ross MT, Sims SK, Willey DL, Chen Z, Han H, Kang L, Godbout M, Wallenburg JC, L'Archevêque P, Bellemare G, Saeki K, Wang H, An D, Fu H, Li Q, Wang Z, Wang R, Holden AL, Brooks LD, McEwen JE, Guyer MS, Wang VO, Peterson JL, Shi M, Spiegel J, Sung LM, Zacharia LF, Collins FS, Kennedy K, Jamieson R, Stewart J.

Nature. 2007 Oct 18;449(7164):851-61.

30.

The distribution and causes of meiotic recombination in the human genome.

Myers S, Spencer CC, Auton A, Bottolo L, Freeman C, Donnelly P, McVean G.

Biochem Soc Trans. 2006 Aug;34(Pt 4):526-30.

PMID:
16856851
31.

A fine-scale map of recombination rates and hotspots across the human genome.

Myers S, Bottolo L, Freeman C, McVean G, Donnelly P.

Science. 2005 Oct 14;310(5746):321-4.

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