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Items: 19

1.

A Method for Checking Genomic Integrity in Cultured Cell Lines from SNP Genotyping Data.

Danecek P, McCarthy SA; HipSci Consortium, Durbin R.

PLoS One. 2016 May 13;11(5):e0155014. doi: 10.1371/journal.pone.0155014. eCollection 2016.

2.

BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data.

Narasimhan V, Danecek P, Scally A, Xue Y, Tyler-Smith C, Durbin R.

Bioinformatics. 2016 Jun 1;32(11):1749-51. doi: 10.1093/bioinformatics/btw044. Epub 2016 Jan 30.

3.

Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel.

Huang J, Howie B, McCarthy S, Memari Y, Walter K, Min JL, Danecek P, Malerba G, Trabetti E, Zheng HF; UK10K Consortium, Gambaro G, Richards JB, Durbin R, Timpson NJ, Marchini J, Soranzo N.

Nat Commun. 2015 Sep 14;6:8111. doi: 10.1038/ncomms9111.

4.

The UK10K project identifies rare variants in health and disease.

UK10K Consortium, Walter K, Min JL, Huang J, Crooks L, Memari Y, McCarthy S, Perry JR, Xu C, Futema M, Lawson D, Iotchkova V, Schiffels S, Hendricks AE, Danecek P, Li R, Floyd J, Wain LV, Barroso I, Humphries SE, Hurles ME, Zeggini E, Barrett JC, Plagnol V, Richards JB, Greenwood CM, Timpson NJ, Durbin R, Soranzo N.

Nature. 2015 Oct 1;526(7571):82-90. doi: 10.1038/nature14962. Epub 2015 Sep 14.

5.

Whole-genome sequencing identifies EN1 as a determinant of bone density and fracture.

Zheng HF, Forgetta V, Hsu YH, Estrada K, Rosello-Diez A, Leo PJ, Dahia CL, Park-Min KH, Tobias JH, Kooperberg C, Kleinman A, Styrkarsdottir U, Liu CT, Uggla C, Evans DS, Nielson CM, Walter K, Pettersson-Kymmer U, McCarthy S, Eriksson J, Kwan T, Jhamai M, Trajanoska K, Memari Y, Min J, Huang J, Danecek P, Wilmot B, Li R, Chou WC, Mokry LE, Moayyeri A, Claussnitzer M, Cheng CH, Cheung W, Medina-Gómez C, Ge B, Chen SH, Choi K, Oei L, Fraser J, Kraaij R, Hibbs MA, Gregson CL, Paquette D, Hofman A, Wibom C, Tranah GJ, Marshall M, Gardiner BB, Cremin K, Auer P, Hsu L, Ring S, Tung JY, Thorleifsson G, Enneman AW, van Schoor NM, de Groot LC, van der Velde N, Melin B, Kemp JP, Christiansen C, Sayers A, Zhou Y, Calderari S, van Rooij J, Carlson C, Peters U, Berlivet S, Dostie J, Uitterlinden AG, Williams SR, Farber C, Grinberg D, LaCroix AZ, Haessler J, Chasman DI, Giulianini F, Rose LM, Ridker PM, Eisman JA, Nguyen TV, Center JR, Nogues X, Garcia-Giralt N, Launer LL, Gudnason V, Mellström D, Vandenput L, Amin N, van Duijn CM, Karlsson MK, Ljunggren Ö, Svensson O, Hallmans G, Rousseau F, Giroux S, Bussière J, Arp PP, Koromani F, Prince RL, Lewis JR, Langdahl BL, Hermann AP, Jensen JE, Kaptoge S, Khaw KT, Reeve J, Formosa MM, Xuereb-Anastasi A, Åkesson K, McGuigan FE, Garg G, Olmos JM, Zarrabeitia MT, Riancho JA, Ralston SH, Alonso N, Jiang X, Goltzman D, Pastinen T, Grundberg E, Gauguier D, Orwoll ES, Karasik D, Davey-Smith G; AOGC Consortium, Smith AV, Siggeirsdottir K, Harris TB, Zillikens MC, van Meurs JB, Thorsteinsdottir U, Maurano MT, Timpson NJ, Soranzo N, Durbin R, Wilson SG, Ntzani EE, Brown MA, Stefansson K, Hinds DA, Spector T, Cupples LA, Ohlsson C, Greenwood CM; UK10K Consortium, Jackson RD, Rowe DW, Loomis CA, Evans DM, Ackert-Bicknell CL, Joyner AL, Duncan EL, Kiel DP, Rivadeneira F, Richards JB.

Nature. 2015 Oct 1;526(7571):112-7. doi: 10.1038/nature14878. Epub 2015 Sep 14.

6.

Tracing the route of modern humans out of Africa by using 225 human genome sequences from Ethiopians and Egyptians.

Pagani L, Schiffels S, Gurdasani D, Danecek P, Scally A, Chen Y, Xue Y, Haber M, Ekong R, Oljira T, Mekonnen E, Luiselli D, Bradman N, Bekele E, Zalloua P, Durbin R, Kivisild T, Tyler-Smith C.

Am J Hum Genet. 2015 Jun 4;96(6):986-91. doi: 10.1016/j.ajhg.2015.04.019. Epub 2015 May 28.

7.

Erratum: Whole-genome sequence-based analysis of thyroid function.

Taylor PN, Porcu E, Chew S, Campbell PJ, Traglia M, Brown SJ, Mullin BH, Shihab HA, Min J, Walter K, Memari Y, Huang J, Barnes MR, Beilby JP, Charoen P, Danecek P, Dudbridge F, Forgetta V, Greenwood C, Grundberg E, Johnson AD, Hui J, Lim EM, McCarthy S, Muddyman D, Panicker V, Perry JR, Bell JT, Yuan W, Relton C, Gaunt T, Schlessinger D, Abecasis G, Cucca F, Surdulescu GL, Woltersdorf W, Zeggini E, Zheng HF, Toniolo D, Dayan CM, Naitza S, Walsh JP, Spector T, Smith GD, Durbin R, Richards JB, Sanna S, Soranzo N, Timpson NJ, Wilson SG; UK10K Consortium.

Nat Commun. 2015 May 20;6:7172. doi: 10.1038/ncomms8172. No abstract available.

8.

Erratum: A rare variant in APOC3 is associated with plasma triglyceride and VLDL levels in Europeans.

Timpson NJ, Walter K, Min JL, Tachmazidou I, Malerba G, Shin SY, Chen L, Futema M, Southam L, Iotchkova V, Cocca M, Huang J, Memari Y, McCarthy S, Danecek P, Muddyman D, Mangino M, Menni C, Perry JR, Ring SM, Gaye A, Dedoussis G, Farmaki AE, Burton P, Talmud PJ, Gambaro G, Spector TD, Smith GD, Durbin R, Richards JB, Humphries SE, Zeggini E, Soranzo N; UK10K Consortium.

Nat Commun. 2015 May 12;6:7171. doi: 10.1038/ncomms8171. No abstract available.

9.

Whole-genome sequence-based analysis of thyroid function.

Taylor PN, Porcu E, Chew S, Campbell PJ, Traglia M, Brown SJ, Mullin BH, Shihab HA, Min J, Walter K, Memari Y, Huang J, Barnes MR, Beilby JP, Charoen P, Danecek P, Dudbridge F, Forgetta V, Greenwood C, Grundberg E, Johnson AD, Hui J, Lim EM, McCarthy S, Muddyman D, Panicker V, Perry JR, Bell JT, Yuan W, Relton C, Gaunt T, Schlessinger D, Abecasis G, Cucca F, Surdulescu GL, Woltersdorf W, Zeggini E, Zheng HF, Toniolo D, Dayan CM, Naitza S, Walsh JP, Spector T, Davey Smith G, Durbin R, Richards JB, Sanna S, Soranzo N, Timpson NJ, Wilson SG; UK0K Consortium.

Nat Commun. 2015 Mar 6;6:5681. doi: 10.1038/ncomms6681. Erratum in: Nat Commun. 2015;6:7172. Lotchkova, Valentina [corrected to Iotchkova, Valentina]; Quai, Michael A [corrected to Quail, Michael].

10.

A rare variant in APOC3 is associated with plasma triglyceride and VLDL levels in Europeans.

Timpson NJ, Walter K, Min JL, Tachmazidou I, Malerba G, Shin SY, Chen L, Futema M, Southam L, Iotchkova V, Cocca M, Huang J, Memari Y, McCarthy S, Danecek P, Muddyman D, Mangino M, Menni C, Perry JR, Ring SM, Gaye A, Dedoussis G, Farmaki AE, Burton P, Talmud PJ, Gambaro G, Spector TD, Smith GD, Durbin R, Richards JB, Humphries SE, Zeggini E, Soranzo N; UK1OK Consortium Members; UK1OK Consortium Members.

Nat Commun. 2014 Sep 16;5:4871. doi: 10.1038/ncomms5871. Erratum in: Nat Commun. 2015;6:7171.

11.

A comparative phenotypic and genomic analysis of C57BL/6J and C57BL/6N mouse strains.

Simon MM, Greenaway S, White JK, Fuchs H, Gailus-Durner V, Wells S, Sorg T, Wong K, Bedu E, Cartwright EJ, Dacquin R, Djebali S, Estabel J, Graw J, Ingham NJ, Jackson IJ, Lengeling A, Mandillo S, Marvel J, Meziane H, Preitner F, Puk O, Roux M, Adams DJ, Atkins S, Ayadi A, Becker L, Blake A, Brooker D, Cater H, Champy MF, Combe R, Danecek P, di Fenza A, Gates H, Gerdin AK, Golini E, Hancock JM, Hans W, Hölter SM, Hough T, Jurdic P, Keane TM, Morgan H, Müller W, Neff F, Nicholson G, Pasche B, Roberson LA, Rozman J, Sanderson M, Santos L, Selloum M, Shannon C, Southwell A, Tocchini-Valentini GP, Vancollie VE, Westerberg H, Wurst W, Zi M, Yalcin B, Ramirez-Solis R, Steel KP, Mallon AM, de Angelis MH, Herault Y, Brown SD.

Genome Biol. 2013 Jul 31;14(7):R82. doi: 10.1186/gb-2013-14-7-r82.

12.

High levels of RNA-editing site conservation amongst 15 laboratory mouse strains.

Danecek P, Nellåker C, McIntyre RE, Buendia-Buendia JE, Bumpstead S, Ponting CP, Flint J, Durbin R, Keane TM, Adams DJ.

Genome Biol. 2012 Apr 23;13(4):26. doi: 10.1186/gb-2012-13-4-r26.

13.

Mouse genomic variation and its effect on phenotypes and gene regulation.

Keane TM, Goodstadt L, Danecek P, White MA, Wong K, Yalcin B, Heger A, Agam A, Slater G, Goodson M, Furlotte NA, Eskin E, Nellåker C, Whitley H, Cleak J, Janowitz D, Hernandez-Pliego P, Edwards A, Belgard TG, Oliver PL, McIntyre RE, Bhomra A, Nicod J, Gan X, Yuan W, van der Weyden L, Steward CA, Bala S, Stalker J, Mott R, Durbin R, Jackson IJ, Czechanski A, Guerra-Assunção JA, Donahue LR, Reinholdt LG, Payseur BA, Ponting CP, Birney E, Flint J, Adams DJ.

Nature. 2011 Sep 14;477(7364):289-94. doi: 10.1038/nature10413.

14.

The variant call format and VCFtools.

Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R; 1000 Genomes Project Analysis Group.

Bioinformatics. 2011 Aug 1;27(15):2156-8. doi: 10.1093/bioinformatics/btr330. Epub 2011 Jun 7.

15.

Flavitrack analysis of the structure and function of West Nile non-structural proteins.

Danecek P, Schein CH.

Int J Bioinform Res Appl. 2010;6(2):134-46.

16.

PCP consensus sequences of flaviviruses: correlating variance with vector competence and disease phenotype.

Danecek P, Lu W, Schein CH.

J Mol Biol. 2010 Feb 26;396(3):550-63. doi: 10.1016/j.jmb.2009.11.070. Epub 2009 Dec 4.

17.

Comparison of quantitative conformer analyses by nuclear magnetic resonance and Raman optical activity spectra for model dipeptides.

Budesínský M, Danecek P, Bednárová L, Kapitán J, Baumruk V, Bour P.

J Phys Chem A. 2008 Sep 18;112(37):8633-40. doi: 10.1021/jp806181q. Epub 2008 Aug 27.

PMID:
18729424
18.

Anharmonic effects in IR, Raman, and Raman optical activity spectra of alanine and proline zwitterions.

Danecek P, Kapitán J, Baumruk V, Bednárová L, Kopecký V Jr, Bour P.

J Chem Phys. 2007 Jun 14;126(22):224513.

PMID:
17581069
19.
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