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Items: 22

1.

The Genomic and Immune Landscapes of Lethal Metastatic Breast Cancer.

De Mattos-Arruda L, Sammut SJ, Ross EM, Bashford-Rogers R, Greenstein E, Markus H, Morganella S, Teng Y, Maruvka Y, Pereira B, Rueda OM, Chin SF, Contente-Cuomo T, Mayor R, Arias A, Ali HR, Cope W, Tiezzi D, Dariush A, Dias Amarante T, Reshef D, Ciriaco N, Martinez-Saez E, Peg V, Ramon Y Cajal S, Cortes J, Vassiliou G, Getz G, Nik-Zainal S, Murtaza M, Friedman N, Markowetz F, Seoane J, Caldas C.

Cell Rep. 2019 May 28;27(9):2690-2708.e10. doi: 10.1016/j.celrep.2019.04.098.

2.

Partially methylated domains are hypervariable in breast cancer and fuel widespread CpG island hypermethylation.

Brinkman AB, Nik-Zainal S, Simmer F, Rodríguez-González FG, Smid M, Alexandrov LB, Butler A, Martin S, Davies H, Glodzik D, Zou X, Ramakrishna M, Staaf J, Ringnér M, Sieuwerts A, Ferrari A, Morganella S, Fleischer T, Kristensen V, Gut M, van de Vijver MJ, Børresen-Dale AL, Richardson AL, Thomas G, Gut IG, Martens JWM, Foekens JA, Stratton MR, Stunnenberg HG.

Nat Commun. 2019 Apr 15;10(1):1749. doi: 10.1038/s41467-019-09828-0.

3.

A Compendium of Mutational Signatures of Environmental Agents.

Kucab JE, Zou X, Morganella S, Joel M, Nanda AS, Nagy E, Gomez C, Degasperi A, Harris R, Jackson SP, Arlt VM, Phillips DH, Nik-Zainal S.

Cell. 2019 May 2;177(4):821-836.e16. doi: 10.1016/j.cell.2019.03.001. Epub 2019 Apr 11.

4.

GARFIELD classifies disease-relevant genomic features through integration of functional annotations with association signals.

Iotchkova V, Ritchie GRS, Geihs M, Morganella S, Min JL, Walter K, Timpson NJ; UK10K Consortium, Dunham I, Birney E, Soranzo N.

Nat Genet. 2019 Feb;51(2):343-353. doi: 10.1038/s41588-018-0322-6. Epub 2019 Jan 28.

PMID:
30692680
5.

Author Correction: Landscape of somatic mutations in 560 breast cancer whole-genome sequences.

Nik-Zainal S, Davies H, Staaf J, Ramakrishna M, Glodzik D, Zou X, Martincorena I, Alexandrov LB, Martin S, Wedge DC, Van Loo P, Ju YS, Smid M, Brinkman AB, Morganella S, Aure MR, Lingjærde OC, Langerød A, Ringnér M, Ahn SM, Boyault S, Brock JE, Broeks A, Butler A, Desmedt C, Dirix L, Dronov S, Fatima A, Foekens JA, Gerstung M, Hooijer GKJ, Jang SJ, Jones DR, Kim HY, King TA, Krishnamurthy S, Lee HJ, Lee JY, Li Y, McLaren S, Menzies A, Mustonen V, O'Meara S, Pauporté I, Pivot X, Purdie CA, Raine K, Ramakrishnan K, Rodríguez-González FG, Romieu G, Sieuwerts AM, Simpson PT, Shepherd R, Stebbings L, Stefansson OA, Teague J, Tommasi S, Treilleux I, Van den Eynden GG, Vermeulen P, Vincent-Salomon A, Yates L, Caldas C, Van't Veer L, Tutt A, Knappskog S, Tan BKT, Jonkers J, Borg Å, Ueno NT, Sotiriou C, Viari A, Futreal PA, Campbell PJ, Span PN, Van Laere S, Lakhani SR, Eyfjord JE, Thompson AM, Birney E, Stunnenberg HG, van de Vijver MJ, Martens JWM, Børresen-Dale AL, Richardson AL, Kong G, Thomas G, Stratton MR.

Nature. 2019 Feb;566(7742):E1. doi: 10.1038/s41586-019-0883-2.

PMID:
30659290
6.

Noncanonical secondary structures arising from non-B DNA motifs are determinants of mutagenesis.

Georgakopoulos-Soares I, Morganella S, Jain N, Hemberg M, Nik-Zainal S.

Genome Res. 2018 Sep;28(9):1264-1271. doi: 10.1101/gr.231688.117. Epub 2018 Aug 13.

7.

ChromoTrace: Computational reconstruction of 3D chromosome configurations for super-resolution microscopy.

Barton C, Morganella S, Ødegård-Fougner Ø, Alexander S, Ries J, Fitzgerald T, Ellenberg J, Birney E.

PLoS Comput Biol. 2018 Mar 9;14(3):e1006002. doi: 10.1371/journal.pcbi.1006002. eCollection 2018 Mar.

8.

Corrigendum: A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers.

Glodzik D, Morganella S, Davies H, Simpson PT, Li Y, Zou X, Diez-Perez J, Staaf J, Alexandrov LB, Smid M, Brinkman AB, Rye IH, Russnes H, Raine K, Purdie CA, Lakhani SR, Thompson AM, Birney E, Stunnenberg HG, van de Vijver MJ, Martens JWM, Børresen-Dale AL, Richardson AL, Kong G, Viari A, Easton D, Evan G, Campbell PJ, Stratton MR, Nik-Zainal S.

Nat Genet. 2017 Oct 27;49(11):1661. doi: 10.1038/ng1117-1661a.

PMID:
29074948
9.

Short inverted repeats contribute to localized mutability in human somatic cells.

Zou X, Morganella S, Glodzik D, Davies H, Li Y, Stratton MR, Nik-Zainal S.

Nucleic Acids Res. 2017 Nov 2;45(19):11213-11221. doi: 10.1093/nar/gkx731.

10.

Whole-Genome Sequencing Reveals Breast Cancers with Mismatch Repair Deficiency.

Davies H, Morganella S, Purdie CA, Jang SJ, Borgen E, Russnes H, Glodzik D, Zou X, Viari A, Richardson AL, Børresen-Dale AL, Thompson A, Eyfjord JE, Kong G, Stratton MR, Nik-Zainal S.

Cancer Res. 2017 Sep 15;77(18):4755-4762. doi: 10.1158/0008-5472.CAN-17-1083.

11.

Mutational Signatures in Breast Cancer: The Problem at the DNA Level.

Nik-Zainal S, Morganella S.

Clin Cancer Res. 2017 Jun 1;23(11):2617-2629. doi: 10.1158/1078-0432.CCR-16-2810.

12.

HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures.

Davies H, Glodzik D, Morganella S, Yates LR, Staaf J, Zou X, Ramakrishna M, Martin S, Boyault S, Sieuwerts AM, Simpson PT, King TA, Raine K, Eyfjord JE, Kong G, Borg Å, Birney E, Stunnenberg HG, van de Vijver MJ, Børresen-Dale AL, Martens JW, Span PN, Lakhani SR, Vincent-Salomon A, Sotiriou C, Tutt A, Thompson AM, Van Laere S, Richardson AL, Viari A, Campbell PJ, Stratton MR, Nik-Zainal S.

Nat Med. 2017 Apr;23(4):517-525. doi: 10.1038/nm.4292. Epub 2017 Mar 13.

13.

A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers.

Glodzik D, Morganella S, Davies H, Simpson PT, Li Y, Zou X, Diez-Perez J, Staaf J, Alexandrov LB, Smid M, Brinkman AB, Rye IH, Russnes H, Raine K, Purdie CA, Lakhani SR, Thompson AM, Birney E, Stunnenberg HG, van de Vijver MJ, Martens JW, Børresen-Dale AL, Richardson AL, Kong G, Viari A, Easton D, Evan G, Campbell PJ, Stratton MR, Nik-Zainal S.

Nat Genet. 2017 Mar;49(3):341-348. doi: 10.1038/ng.3771. Epub 2017 Jan 23. Erratum in: Nat Genet. 2017 Oct 27;49(11):1661.

14.

The topography of mutational processes in breast cancer genomes.

Morganella S, Alexandrov LB, Glodzik D, Zou X, Davies H, Staaf J, Sieuwerts AM, Brinkman AB, Martin S, Ramakrishna M, Butler A, Kim HY, Borg Å, Sotiriou C, Futreal PA, Campbell PJ, Span PN, Van Laere S, Lakhani SR, Eyfjord JE, Thompson AM, Stunnenberg HG, van de Vijver MJ, Martens JW, Børresen-Dale AL, Richardson AL, Kong G, Thomas G, Sale J, Rada C, Stratton MR, Birney E, Nik-Zainal S.

Nat Commun. 2016 May 2;7:11383. doi: 10.1038/ncomms11383.

15.

Landscape of somatic mutations in 560 breast cancer whole-genome sequences.

Nik-Zainal S, Davies H, Staaf J, Ramakrishna M, Glodzik D, Zou X, Martincorena I, Alexandrov LB, Martin S, Wedge DC, Van Loo P, Ju YS, Smid M, Brinkman AB, Morganella S, Aure MR, Lingjærde OC, Langerød A, Ringnér M, Ahn SM, Boyault S, Brock JE, Broeks A, Butler A, Desmedt C, Dirix L, Dronov S, Fatima A, Foekens JA, Gerstung M, Hooijer GK, Jang SJ, Jones DR, Kim HY, King TA, Krishnamurthy S, Lee HJ, Lee JY, Li Y, McLaren S, Menzies A, Mustonen V, O'Meara S, Pauporté I, Pivot X, Purdie CA, Raine K, Ramakrishnan K, Rodríguez-González FG, Romieu G, Sieuwerts AM, Simpson PT, Shepherd R, Stebbings L, Stefansson OA, Teague J, Tommasi S, Treilleux I, Van den Eynden GG, Vermeulen P, Vincent-Salomon A, Yates L, Caldas C, van't Veer L, Tutt A, Knappskog S, Tan BK, Jonkers J, Borg Å, Ueno NT, Sotiriou C, Viari A, Futreal PA, Campbell PJ, Span PN, Van Laere S, Lakhani SR, Eyfjord JE, Thompson AM, Birney E, Stunnenberg HG, van de Vijver MJ, Martens JW, Børresen-Dale AL, Richardson AL, Kong G, Thomas G, Stratton MR.

Nature. 2016 Jun 2;534(7605):47-54. doi: 10.1038/nature17676. Epub 2016 May 2. Erratum in: Nature. 2019 Feb;566(7742):E1.

16.

The genome as a record of environmental exposure.

Nik-Zainal S, Kucab JE, Morganella S, Glodzik D, Alexandrov LB, Arlt VM, Weninger A, Hollstein M, Stratton MR, Phillips DH.

Mutagenesis. 2015 Nov;30(6):763-70. doi: 10.1093/mutage/gev073. Epub 2015 Oct 6.

17.

VEGAWES: variational segmentation on whole exome sequencing for copy number detection.

Anjum S, Morganella S, D'Angelo F, Iavarone A, Ceccarelli M.

BMC Bioinformatics. 2015 Sep 29;16:315. doi: 10.1186/s12859-015-0748-0.

18.

VegaMC: a R/bioconductor package for fast downstream analysis of large array comparative genomic hybridization datasets.

Morganella S, Ceccarelli M.

Bioinformatics. 2012 Oct 1;28(19):2512-4. Epub 2012 Jul 18.

PMID:
22815357
19.

Finding recurrent copy number alterations preserving within-sample homogeneity.

Morganella S, Pagnotta SM, Ceccarelli M.

Bioinformatics. 2011 Nov 1;27(21):2949-56. doi: 10.1093/bioinformatics/btr488. Epub 2011 Aug 25.

PMID:
21873327
20.

VEGA: variational segmentation for copy number detection.

Morganella S, Cerulo L, Viglietto G, Ceccarelli M.

Bioinformatics. 2010 Dec 15;26(24):3020-7. doi: 10.1093/bioinformatics/btq586. Epub 2010 Oct 19.

PMID:
20959380
21.

TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach.

Zoppoli P, Morganella S, Ceccarelli M.

BMC Bioinformatics. 2010 Mar 25;11:154. doi: 10.1186/1471-2105-11-154.

22.

IRIS: a method for reverse engineering of regulatory relations in gene networks.

Morganella S, Zoppoli P, Ceccarelli M.

BMC Bioinformatics. 2009 Dec 23;10:444. doi: 10.1186/1471-2105-10-444.

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