Sohrab P Shah

Sohrab P Shah

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Sohrab P Shah

Publications by authors named "Sohrab P Shah"

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Regulation of pH by Carbonic Anhydrase 9 Mediates Survival of Pancreatic Cancer Cells With Activated KRAS in Response to Hypoxia.

Gastroenterology 2019 09 9;157(3):823-837. Epub 2019 May 9.

Department of Integrative Oncology, BC Cancer Research Centre, Vancouver, British Columbia, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada. Electronic address:

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http://dx.doi.org/10.1053/j.gastro.2019.05.004DOI Listing
September 2019

Integrated structural variation and point mutation signatures in cancer genomes using correlated topic models.

PLoS Comput Biol 2019 02 22;15(2):e1006799. Epub 2019 Feb 22.

Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1006799DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6402697PMC
February 2019

Somatic mutation detection and classification through probabilistic integration of clonal population information.

Commun Biol 2019 31;2:44. Epub 2019 Jan 31.

4Department of Molecular Oncology, University of British Columbia, 675 West 10th Avenue, V5Z 1L3 Vancouver, Canada.

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http://dx.doi.org/10.1038/s42003-019-0291-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6355807PMC
January 2019

Copy number signatures in ovarian cancer.

Authors:
Sohrab P Shah

Nat Genet 2018 09;50(9):1208-1209

Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.

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http://dx.doi.org/10.1038/s41588-018-0212-yDOI Listing
September 2018

Interpretable dimensionality reduction of single cell transcriptome data with deep generative models.

Nat Commun 2018 05 21;9(1):2002. Epub 2018 May 21.

Department of Computer Science, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.

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http://dx.doi.org/10.1038/s41467-018-04368-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5962608PMC
May 2018

Observing Clonal Dynamics across Spatiotemporal Axes: A Prelude to Quantitative Fitness Models for Cancer.

Cold Spring Harb Perspect Med 2018 02 1;8(2). Epub 2018 Feb 1.

Department of Molecular Oncology, BC Cancer Agency, Vancouver V5Z 1L3, Canada.

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http://dx.doi.org/10.1101/cshperspect.a029603DOI Listing
February 2018

LINE-1 retrotransposon-mediated DNA transductions in endometriosis associated ovarian cancers.

Gynecol Oncol 2017 12 9;147(3):642-647. Epub 2017 Oct 9.

Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada; Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC, Canada. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00908258173135
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http://dx.doi.org/10.1016/j.ygyno.2017.09.032DOI Listing
December 2017

Prognostic Model to Predict Post-Autologous Stem-Cell Transplantation Outcomes in Classical Hodgkin Lymphoma.

J Clin Oncol 2017 Nov 12;35(32):3722-3733. Epub 2017 Sep 12.

Fong Chun Chan, Anja Mottok, Alina S. Gerrie, Maryse Power, Kerry J. Savage, Sohrab P. Shah, Joseph M. Connors, Randy D. Gascoyne, David W. Scott, and Christian Steidl, British Columbia Cancer Agency; Fong Chun Chan, Anja Mottok, Sohrab P. Shah, and Christian Steidl, University of British Columbia, Canada; Marcel Nijland, Arjan Diepstra, and Anke van den Berg, University Medical Center Groningen, Groningen, the Netherlands; and Peter Kamper, Francesco d'Amore, Alexander Lindholm d'Amore, and Stephen Hamilton-Dutoit, Aarhus University Hospital, Aarhus, Denmark.

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http://dx.doi.org/10.1200/JCO.2017.72.7925DOI Listing
November 2017

Kronos: a workflow assembler for genome analytics and informatics.

Gigascience 2017 07;6(7):1-10

Department of Molecular Oncology, British Columbia Cancer Agency, 675 West 10th Ave, V5Z 1L3 Vancouver, BC, Canada.

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http://dx.doi.org/10.1093/gigascience/gix042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5569921PMC
July 2017

E-scape: interactive visualization of single-cell phylogenetics and cancer evolution.

Nat Methods 2017 05;14(6):549-550

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

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http://dx.doi.org/10.1038/nmeth.4303DOI Listing
May 2017

ddClone: joint statistical inference of clonal populations from single cell and bulk tumour sequencing data.

Genome Biol 2017 03 1;18(1):44. Epub 2017 Mar 1.

Bioinformatics Graduate Program, University of British Columbia, 570 West 7th Avenue, Vancouver, V5Z 4S6, BC, Canada.

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http://dx.doi.org/10.1186/s13059-017-1169-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5333399PMC
March 2017

Scalable whole-genome single-cell library preparation without preamplification.

Nat Methods 2017 02 9;14(2):167-173. Epub 2017 Jan 9.

Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada.

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http://www.nature.com/articles/nmeth.4140
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http://dx.doi.org/10.1038/nmeth.4140DOI Listing
February 2017

Overexpression screens identify conserved dosage chromosome instability genes in yeast and human cancer.

Proc Natl Acad Sci U S A 2016 09 22;113(36):9967-76. Epub 2016 Aug 22.

Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z4; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada V6T 1Z3;

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http://dx.doi.org/10.1073/pnas.1611839113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5018746PMC
September 2016

Clonal genotype and population structure inference from single-cell tumor sequencing.

Nat Methods 2016 07 16;13(7):573-6. Epub 2016 May 16.

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

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http://dx.doi.org/10.1038/nmeth.3867DOI Listing
July 2016

Robust high-performance nanoliter-volume single-cell multiple displacement amplification on planar substrates.

Proc Natl Acad Sci U S A 2016 07 13;113(30):8484-9. Epub 2016 Jul 13.

Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z4; Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, Canada V6T 1Z4

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http://dx.doi.org/10.1073/pnas.1520964113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4968760PMC
July 2016

Synchronous Endometrial and Ovarian Carcinomas: Evidence of Clonality.

J Natl Cancer Inst 2016 Jun 1;108(6):djv428. Epub 2016 Feb 1.

Department of Pathology and Laboratory Medicine, (MSA, HMH, JS, HLC, ANK, BSS, MKM, CBG, SK, DGH) and Department of Obstetrics and Gynaecology (MSA, DGH), University of British Columbia, Vancouver, Canada; Department of Molecular Oncology, British Columbia Cancer Agency Cancer Research Centre, Vancouver, Canada (YKW, AB, RM, DSG, SPS); Department of Women's Health, University Hospital Tuebingen, Tuebingen, Germany (MM, FAT, DW, SB, SK); Division of Anatomic Pathology, Synlab MVZ, Institute of Pathology, Mannheim, Germany (FK); Division of Gynecologic Pathology, Institute of Pathology and Neuropathology, University Hospital Tuebingen, Tuebingen, Germany (AS); Department of Anatomical Pathology, Vancouver General Hospital, Vancouver, Canada (CBG).

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http://dx.doi.org/10.1093/jnci/djv428DOI Listing
June 2016

Identification of the epigenetic reader CBX2 as a potential drug target in advanced prostate cancer.

Clin Epigenetics 2016 12;8:16. Epub 2016 Feb 12.

Department of Experimental Therapeutics, British Columbia Cancer Research Centre, 675 W 10th Avenue, Vancouver, British Columbia V5Z 1L3 Canada ; Department of Surgery, University of British Columbia, 910 W 10th Avenue, Vancouver, British Columbia V5Z 4E3 Canada.

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http://dx.doi.org/10.1186/s13148-016-0182-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4751702PMC
April 2016

The genomic landscape of epithelioid sarcoma cell lines and tumours.

J Pathol 2016 Jan 19;238(1):63-73. Epub 2015 Oct 19.

Genetic Pathology Evaluation Centre, Vancouver, BC, Canada.

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http://dx.doi.org/10.1002/path.4636DOI Listing
January 2016

Systematic analysis of somatic mutations impacting gene expression in 12 tumour types.

Nat Commun 2015 Oct 5;6:8554. Epub 2015 Oct 5.

Department of Molecular Oncology, BC Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3.

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http://dx.doi.org/10.1038/ncomms9554DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4600750PMC
October 2015

Spatial genomic heterogeneity within localized, multifocal prostate cancer.

Nat Genet 2015 Jul 25;47(7):736-45. Epub 2015 May 25.

1] Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada. [2] Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada. [3] Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1038/ng.3315DOI Listing
July 2015

Using Somatic Mutations to Guide Treatment Decisions: Context Matters.

JAMA Oncol 2015 Jun;1(3):275-6

Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada2Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada4Department of Obstetrics and Gynecol.

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http://dx.doi.org/10.1001/jamaoncol.2015.35DOI Listing
June 2015

Cis-regulatory somatic mutations and gene-expression alteration in B-cell lymphomas.

Genome Biol 2015 Apr 23;16:84. Epub 2015 Apr 23.

Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, V5Z 1L3, BC, Canada.

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http://dx.doi.org/10.1186/s13059-015-0648-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4467049PMC
April 2015

Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution.

Nature 2015 Feb 26;518(7539):422-6. Epub 2014 Nov 26.

1] Department of Molecular Oncology, BC Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada [2] Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada [3] Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 1L3, Canada [4] Centre for Translational and Applied Genomics, BC Cancer Agency, 600 West 10th Avenue, Vancouver, British Columbia V5Z 4E6, Canada.

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http://dx.doi.org/10.1038/nature13952DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4864027PMC
February 2015

TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data.

Genome Res 2014 Nov 24;24(11):1881-93. Epub 2014 Jul 24.

Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada; Department of Computer Science, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada;

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http://dx.doi.org/10.1101/gr.180281.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4216928PMC
November 2014

Recurrent somatic mutations of PTPN1 in primary mediastinal B cell lymphoma and Hodgkin lymphoma.

Nat Genet 2014 Apr 16;46(4):329-35. Epub 2014 Feb 16.

1] Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada. [2] Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.

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http://dx.doi.org/10.1038/ng.2900DOI Listing
April 2014

PyClone: statistical inference of clonal population structure in cancer.

Nat Methods 2014 Apr 16;11(4):396-8. Epub 2014 Mar 16.

1] Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada. [2] Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.

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http://dx.doi.org/10.1038/nmeth.2883DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4864026PMC
April 2014

Ovarian and endometrial endometrioid carcinomas have distinct CTNNB1 and PTEN mutation profiles.

Mod Pathol 2014 Jan 14;27(1):128-34. Epub 2013 Jun 14.

1] Department of Pathology and Laboratory Medicine, University of British Columbia, BC Cancer Agency, Centre for Translational and Applied Genomics, Vancouver, BC, Canada [2] Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC, Canada.

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http://dx.doi.org/10.1038/modpathol.2013.107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3915240PMC
January 2014

BRCA1 and BRCA2 mutations correlate with TP53 abnormalities and presence of immune cell infiltrates in ovarian high-grade serous carcinoma.

Mod Pathol 2012 May 27;25(5):740-50. Epub 2012 Jan 27.

Department of Gynecology and Obstetrics, Division of Gynecologic Oncology, University of British Columbia, Vancouver, BC, Canada.

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http://dx.doi.org/10.1038/modpathol.2011.211DOI Listing
May 2012

Subtype-specific mutation of PPP2R1A in endometrial and ovarian carcinomas.

J Pathol 2011 Apr 7;223(5):567-73. Epub 2011 Mar 7.

Department of Pathology and Laboratory Medicine, University of British Columbia, British Columbia Cancer Agency, 3427-600 West 10th Avenue, Vancouver, BC, Canada.

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http://dx.doi.org/10.1002/path.2848DOI Listing
April 2011

Genome-wide copy number analysis of Hodgkin Reed-Sternberg cells identifies recurrent imbalances with correlations to treatment outcome.

Blood 2010 Jul 25;116(3):418-27. Epub 2010 Mar 25.

Department of Pathology and Laboratory Medicine, Centre for Translational and Applied Genomics, BC Cancer Agency, University of British Columbia, Vancouver, BC, Canada.

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http://dx.doi.org/10.1182/blood-2009-12-257345DOI Listing
July 2010

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

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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http://dx.doi.org/10.1093/bioinformatics/btq040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832826PMC
March 2010

Model-based clustering of array CGH data.

Bioinformatics 2009 Jun;25(12):i30-8

Department of Computer Science, University of British Columbia, Vancouver, BC, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btp205DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2687959PMC
June 2009

Modeling recurrent DNA copy number alterations in array CGH data.

Bioinformatics 2007 Jul;23(13):i450-8

Department of Computer Science, University of British Columbia, 201-2366 Main Mall Vancouver, BC V6T 1Z4 Canada.

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http://dx.doi.org/10.1093/bioinformatics/btm221DOI Listing
July 2007

Integrating copy number polymorphisms into array CGH analysis using a robust HMM.

Bioinformatics 2006 Jul;22(14):e431-9

Department of Computer Science, University of British Columbia, 201-2366 Main Mall Vancouver, BC V6T 1Z4 Canada.

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http://dx.doi.org/10.1093/bioinformatics/btl238DOI Listing
July 2006

Atlas - a data warehouse for integrative bioinformatics.

BMC Bioinformatics 2005 Feb 21;6:34. Epub 2005 Feb 21.

UBC Bioinformatics Centre, University of British Columbia, Vancouver, BC, Canada.

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http://dx.doi.org/10.1186/1471-2105-6-34DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC554782PMC
February 2005

GeneComber: combining outputs of gene prediction programs for improved results.

Bioinformatics 2003 Jul;19(10):1296-7

UBC Bioinformatics Centre, University of British Columbia, 950 28th Ave W, Vancouver, BC V5Z4H4 Canada.

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http://dx.doi.org/10.1093/bioinformatics/btg139DOI Listing
July 2003