Publications by authors named "Sam Aparicio"

13Publications

Correction to: ReMixT: clone-specific genomic structure estimation in cancer.

Authors:

Andrew W McPherson Andrew Roth Gavin Ha Cedric Chauve Adi Steif Camila P E de Souza Peter Eirew Alexandre Bouchard-Côté Sam Aparicio S Cenk Sahinalp Sohrab P Shah

Genome Biol 2017 10 6;18(1):188. Epub 2017 Oct 6.

Department of Molecular Oncology, BC Cancer Agency, Vancouver, Canada.

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October 2017

ReMixT: clone-specific genomic structure estimation in cancer.

Authors:

Andrew W McPherson Andrew Roth Gavin Ha Cedric Chauve Adi Steif Camila P E de Souza Peter Eirew Alexandre Bouchard-Côté Sam Aparicio S Cenk Sahinalp Sohrab P Shah

Genome Biol 2017 07 27;18(1):140. Epub 2017 Jul 27.

Department of Molecular Oncology, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, Canada.

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July 2017

BCL11A is a triple-negative breast cancer gene with critical functions in stem and progenitor cells.

Authors:

Walid T Khaled Song Choon Lee John Stingl Xiongfeng Chen H Raza Ali Oscar M Rueda Fazal Hadi Juexuan Wang Yong Yu Suet-Feung Chin Mike Stratton Andy Futreal Nancy A Jenkins Sam Aparicio Neal G Copeland Christine J Watson Carlos Caldas Pentao Liu

Nat Commun 2015 Jan 9;6:5987. Epub 2015 Jan 9.

Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK.

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January 2015

Mobile DNA in cancer. Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes.

Authors:

Jose M C Tubio Yilong Li Young Seok Ju Inigo Martincorena Susanna L Cooke Marta Tojo Gunes Gundem Christodoulos P Pipinikas Jorge Zamora Keiran Raine Andrew Menzies Pablo Roman-Garcia Anthony Fullam Moritz Gerstung Adam Shlien Patrick S Tarpey Elli Papaemmanuil Stian Knappskog Peter Van Loo Manasa Ramakrishna Helen R Davies John Marshall David C Wedge Jon W Teague Adam P Butler Serena Nik-Zainal Ludmil Alexandrov Sam Behjati Lucy R Yates Niccolo Bolli Laura Mudie Claire Hardy Sancha Martin Stuart McLaren Sarah O'Meara Elizabeth Anderson Mark Maddison Stephen Gamble Christopher Foster Anne Y Warren Hayley Whitaker Daniel Brewer Rosalind Eeles Colin Cooper David Neal Andy G Lynch Tapio Visakorpi William B Isaacs Laura Van't Veer Carlos Caldas Christine Desmedt Christos Sotiriou Sam Aparicio John A Foekens Jórunn Erla Eyfjörd Sunil R Lakhani Gilles Thomas Ola Myklebost Paul N Span Anne-Lise Børresen-Dale Andrea L Richardson Marc Van de Vijver Anne Vincent-Salomon Gert G Van den Eynden Adrienne M Flanagan P Andrew Futreal Sam M Janes G Steven Bova Michael R Stratton Ultan McDermott Peter J Campbell

Science 2014 Aug;345(6196):1251343

Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK.

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August 2014

Ordering of mutations in preinvasive disease stages of esophageal carcinogenesis.

Nat Genet 2014 Aug 22;46(8):837-843. Epub 2014 Jun 22.

MRC Cancer Unit, University of Cambridge, Cambridge, UK.

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August 2014

The shaping and functional consequences of the microRNA landscape in breast cancer.

Authors:

Heidi Dvinge Anna Git Stefan Gräf Mali Salmon-Divon Christina Curtis Andrea Sottoriva Yongjun Zhao Martin Hirst Javier Armisen Eric A Miska Suet-Feung Chin Elena Provenzano Gulisa Turashvili Andrew Green Ian Ellis Sam Aparicio Carlos Caldas

Nature 2013 May 5;497(7449):378-82. Epub 2013 May 5.

Cancer Research UK Cambridge Institute and Department of Oncology, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.

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May 2013

iReckon: simultaneous isoform discovery and abundance estimation from RNA-seq data.

Authors:

Aziz M Mezlini Eric J M Smith Marc Fiume Orion Buske Gleb L Savich Sohrab Shah Sam Aparicio Derek Y Chiang Anna Goldenberg Michael Brudno

Genome Res 2013 Mar 29;23(3):519-29. Epub 2012 Nov 29.

Department of Computer Science, University of Toronto, Ontario M5S 2E4, Canada.

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March 2013

Quantitative image analysis of cellular heterogeneity in breast tumors complements genomic profiling.

Authors:

Yinyin Yuan Henrik Failmezger Oscar M Rueda H Raza Ali Stefan Gräf Suet-Feung Chin Roland F Schwarz Christina Curtis Mark J Dunning Helen Bardwell Nicola Johnson Sarah Doyle Gulisa Turashvili Elena Provenzano Sam Aparicio Carlos Caldas Florian Markowetz

Sci Transl Med 2012 Oct;4(157):157ra143

Cancer Research UK Cambridge Research Institute, Cambridge CB2 0RE, UK.

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October 2012

Mutation discovery in regions of segmental cancer genome amplifications with CoNAn-SNV: a mixture model for next generation sequencing of tumors.

Authors:

Anamaria Crisan Rodrigo Goya Gavin Ha Jiarui Ding Leah M Prentice Arusha Oloumi Janine Senz Thomas Zeng Kane Tse Allen Delaney Marco A Marra David G Huntsman Martin Hirst Sam Aparicio Sohrab Shah

PLoS One 2012 16;7(8):e41551. Epub 2012 Aug 16.

Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada.

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May 2013

Functional proteomics can define prognosis and predict pathologic complete response in patients with breast cancer.

Clin Proteomics 2011 Jul 8;8(1):11. Epub 2011 Jul 8.

Departments of Breast Medical Oncology and Systems Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA.

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July 2011

SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors.

Authors:

Rodrigo Goya Mark G F Sun Ryan D Morin Gillian Leung Gavin Ha Kimberley C Wiegand Janine Senz Anamaria Crisan Marco A Marra Martin Hirst David Huntsman Kevin P Murphy Sam Aparicio Sohrab P Shah

Bioinformatics 2010 Mar 3;26(6):730-6. Epub 2010 Feb 3.

Department of Molecular Oncology Breast Cancer Research Program, British Columbia Cancer Research Centre, Vancouver, BC, Canada.

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March 2010

A consensus prognostic gene expression classifier for ER positive breast cancer.

Authors:

Andrew E Teschendorff Ali Naderi Nuno L Barbosa-Morais Sarah E Pinder Ian O Ellis Sam Aparicio James D Brenton Carlos Caldas

Genome Biol 2006 31;7(10):R101. Epub 2006 Oct 31.

Cancer Genomics Program, Department of Oncology, University of Cambridge, Hutchison/MRC Research Center, Hills Road, Cambridge CB2 2XZ, UK.

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March 2007

The link between nutritional status and insulin sensitivity is dependent on the adipocyte-specific peroxisome proliferator-activated receptor-gamma2 isoform.

Diabetes 2005 Jun;54(6):1706-16

Department of Clinical Biochemistry, University of Cambridge/Addenbrooke's Hospital, Hills Road, Cambridge CB2 2QR, UK.

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June 2005