Lincoln Stein

Lincoln Stein

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Lincoln Stein

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Visualization of drug target interactions in the contexts of pathways and networks with ReactomeFIViz.

F1000Res 2019 20;8:908. Epub 2019 Jun 20.

Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, 97239, USA.

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http://dx.doi.org/10.12688/f1000research.19592.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6644836PMC
June 2020

Metabolic Regulation of the Epigenome Drives Lethal Infantile Ependymoma.

Cell 2020 Jun 22;181(6):1329-1345.e24. Epub 2020 May 22.

The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Division of Neurosurgery, The Hospital for Sick Children, Toronto, ON M5G 1L7, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2020.04.047DOI Listing
June 2020

Using Reactome to build an autophagy mechanism knowledgebase.

Autophagy 2020 Jun 2:1-12. Epub 2020 Jun 2.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus , Cambridge, UK.

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http://dx.doi.org/10.1080/15548627.2020.1761659DOI Listing
June 2020

Vennter - An interactive analysis tool for WormBase interaction data using Venn diagrams.

MicroPubl Biol 2020 May 25;2020. Epub 2020 May 25.

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.17912/micropub.biology.000258DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7251783PMC
May 2020

Candidate Cancer Driver Mutations in Distal Regulatory Elements and Long-Range Chromatin Interaction Networks.

Mol Cell 2020 03 17;77(6):1307-1321.e10. Epub 2020 Jan 17.

Computational Biology Program, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada; Department of Medical Biophysics, University of Toronto, 101 College Street Suite 15-701, Toronto, ON M5G 1L7, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2019.12.027DOI Listing
March 2020

Combined burden and functional impact tests for cancer driver discovery using DriverPower.

Nat Commun 2020 02 5;11(1):734. Epub 2020 Feb 5.

Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada, M5S 1A8.

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http://dx.doi.org/10.1038/s41467-019-13929-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7002750PMC
February 2020

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.

Nature 2020 02 5;578(7793):102-111. Epub 2020 Feb 5.

The Broad Institute of MIT and Harvard, Cambridge, MA, USA.

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http://dx.doi.org/10.1038/s41586-020-1965-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7054214PMC
February 2020

The U1 spliceosomal RNA is recurrently mutated in multiple cancers.

Nature 2019 10 9;574(7780):712-716. Epub 2019 Oct 9.

Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1038/s41586-019-1651-zDOI Listing
October 2019

Recurrent noncoding U1 snRNA mutations drive cryptic splicing in SHH medulloblastoma.

Nature 2019 10 9;574(7780):707-711. Epub 2019 Oct 9.

The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1038/s41586-019-1650-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7141958PMC
October 2019

Quantifying immune-based counterselection of somatic mutations.

PLoS Genet 2019 07 25;15(7):e1008227. Epub 2019 Jul 25.

Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1371/journal.pgen.1008227DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6657826PMC
July 2019

The International Cancer Genome Consortium Data Portal.

Nat Biotechnol 2019 04;37(4):367-369

Ontario Institute for Cancer Research, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1038/s41587-019-0055-9DOI Listing
April 2019

Reactome and ORCID-fine-grained credit attribution for community curation.

Database (Oxford) 2019 01;2019

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.

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http://dx.doi.org/10.1093/database/baz123DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6892999PMC
January 2019

Aberrant expression impacts the pan-cancer genomic landscape.

Genome Res 2018 11 19;28(11):1611-1620. Epub 2018 Oct 19.

Ontario Institute for Cancer Research, Department of Computational Biology, Toronto, Ontario M5G 0A3, Canada.

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http://genome.cshlp.org/lookup/doi/10.1101/gr.231696.117
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http://dx.doi.org/10.1101/gr.231696.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211651PMC
November 2018

Mutations in Mitochondrial DNA From Pancreatic Ductal Adenocarcinomas Associate With Survival Times of Patients and Accumulate as Tumors Progress.

Gastroenterology 2018 05 29;154(6):1620-1624.e5. Epub 2018 Mar 29.

Informatics Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, Canada. Electronic address:

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http://dx.doi.org/10.1053/j.gastro.2018.01.029DOI Listing
May 2018

Reactome diagram viewer: data structures and strategies to boost performance.

Bioinformatics 2018 04;34(7):1208-1214

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK.

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http://dx.doi.org/10.1093/bioinformatics/btx752DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6030826PMC
April 2018

Interleukins and their signaling pathways in the Reactome biological pathway database.

J Allergy Clin Immunol 2018 04 21;141(4):1411-1416. Epub 2018 Feb 21.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, United Kingdom; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Radiation Medicine, Beijing, China. Electronic address:

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http://dx.doi.org/10.1016/j.jaci.2017.12.992DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5927619PMC
April 2018

Reactome graph database: Efficient access to complex pathway data.

PLoS Comput Biol 2018 01 29;14(1):e1005968. Epub 2018 Jan 29.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, United Kingdom.

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http://dx.plos.org/10.1371/journal.pcbi.1005968
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http://dx.doi.org/10.1371/journal.pcbi.1005968DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5805351PMC
January 2018

ISOWN: accurate somatic mutation identification in the absence of normal tissue controls.

Genome Med 2017 06 29;9(1):59. Epub 2017 Jun 29.

Informatics and Bio-computing, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1186/s13073-017-0446-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5490163PMC
June 2017

Simple multiplexed PCR-based barcoding of DNA for ultrasensitive mutation detection by next-generation sequencing.

Nat Protoc 2017 04 2;12(4):664-682. Epub 2017 Mar 2.

Department of Surgery, Boston University School of Medicine, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/nprot.2017.006DOI Listing
April 2017

Reactome pathway analysis: a high-performance in-memory approach.

BMC Bioinformatics 2017 Mar 2;18(1):142. Epub 2017 Mar 2.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK.

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http://dx.doi.org/10.1186/s12859-017-1559-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5333408PMC
March 2017

A Metastatic Mouse Model Identifies Genes That Regulate Neuroblastoma Metastasis.

Cancer Res 2017 02 29;77(3):696-706. Epub 2016 Nov 29.

Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, Canada.

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http://dx.doi.org/10.1158/0008-5472.CAN-16-1502DOI Listing
February 2017

Insights into cancer severity from biomolecular interaction mechanisms.

Sci Rep 2016 10 4;6:34490. Epub 2016 Oct 4.

CellNetworks, Bioquant, Im Neuenheimer Feld 267, University of Heidelberg, 69120 Heidelberg, Germany.

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http://dx.doi.org/10.1038/srep34490DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5048291PMC
October 2016

Impact of outdated gene annotations on pathway enrichment analysis.

Nat Methods 2016 08;13(9):705-6

Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1038/nmeth.3963DOI Listing
August 2016

Simple, multiplexed, PCR-based barcoding of DNA enables sensitive mutation detection in liquid biopsies using sequencing.

Nucleic Acids Res 2016 06 7;44(11):e105. Epub 2016 Apr 7.

Department of Surgery, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118, USA

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http://dx.doi.org/10.1093/nar/gkw224DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4914102PMC
June 2016

Candidate DNA repair susceptibility genes identified by exome sequencing in high-risk pancreatic cancer.

Cancer Lett 2016 Jan 3;370(2):302-12. Epub 2015 Nov 3.

Research Institute of the McGill University Health Centre, 1001 Décarie Boulevard, Montreal, QC, Canada H4A 3J1; Goodman Cancer Research Centre, McGill University, 1160 Pine Avenue West, Montreal, QC, Canada H3A 1A3; Program in Cancer Genetics, Departments of Oncology and Human Genetics, Sir Mortimer B. Davis-Jewish General Hospital, McGill University, 3755 Côte-Ste-Catherine Road, Montreal, QC, Canada H3T 1E2. Electronic address:

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http://dx.doi.org/10.1016/j.canlet.2015.10.030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5725760PMC
January 2016

Surveillance in Patients With Barrett's Esophagus for Early Detection of Esophageal Adenocarcinoma: A Systematic Review and Meta-Analysis.

Clin Transl Gastroenterol 2015 Dec 10;6:e131. Epub 2015 Dec 10.

Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1038/ctg.2015.58DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4816094PMC
December 2015

RNASequel: accurate and repeat tolerant realignment of RNA-seq reads.

Nucleic Acids Res 2015 Oct 16;43(18):e122. Epub 2015 Jun 16.

Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada, M5S 1A8 Informatics and Biocomputing, Ontario Institute for Cancer Research, Toronto, Ontario, Canada, M5G 0A3

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http://dx.doi.org/10.1093/nar/gkv594DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4605292PMC
October 2015

Unix Survival Guide.

Authors:
Lincoln D Stein

Curr Protoc Bioinformatics 2015 Sep 3;51:A1.C.1-A1.C.27. Epub 2015 Sep 3.

Ontario Institute for Cancer Research, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1002/0471250953.bia01cs51DOI Listing
September 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

Data analysis: Create a cloud commons.

Nature 2015 Jul;523(7559):149-51

European Molecular Biology Laboratory, Heidelberg, Germany.

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http://dx.doi.org/10.1038/523149aDOI Listing
July 2015

Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis.

Genome Res 2015 May 17;25(5):667-78. Epub 2015 Mar 17.

Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada, M5S 3B2; Center for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada, M5S 3B2.

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http://dx.doi.org/10.1101/gr.187237.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4417115PMC
May 2015

Glucocorticoid-induced reversal of interleukin-1β-stimulated inflammatory gene expression in human oviductal cells.

PLoS One 2014 21;9(5):e97997. Epub 2014 May 21.

Department of Obstetrics and Gynecology, University of Toronto, Toronto, Ontario, Canada; Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, Ontario, Canada.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0097997PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4029821PMC
January 2015

TDP-1, the Caenorhabditis elegans ortholog of TDP-43, limits the accumulation of double-stranded RNA.

EMBO J 2014 Dec 12;33(24):2947-66. Epub 2014 Nov 12.

Institute for Behavioral Genetics University of Colorado, Boulder, CO, USA Integrative Physiology, University of Colorado, Boulder, CO, USA.

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http://dx.doi.org/10.15252/embj.201488740DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4282642PMC
December 2014

Redefining genomic privacy: trust and empowerment.

PLoS Biol 2014 Nov 4;12(11):e1001983. Epub 2014 Nov 4.

Illumina Inc., San Diego, California, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.1001983DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4219652PMC
November 2014

ReactomeFIViz: a Cytoscape app for pathway and network-based data analysis.

F1000Res 2014 1;3:146. Epub 2014 Jul 1.

Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada ; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4184317PMC
http://dx.doi.org/10.12688/f1000research.4431.2DOI Listing
October 2014

Next-generation sequencing identifies rare variants associated with Noonan syndrome.

Proc Natl Acad Sci U S A 2014 Aug 21;111(31):11473-8. Epub 2014 Jul 21.

Department of Genetics, Harvard Medical School, Boston, MA 02115;Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115;

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http://dx.doi.org/10.1073/pnas.1324128111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4128129PMC
August 2014

Pathprinting: An integrative approach to understand the functional basis of disease.

Genome Med 2013 26;5(7):68. Epub 2013 Jul 26.

Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA ; Bioinformatics Core, Harvard School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA ; Harvard Stem Cell Institute, 1350 Massachusetts Ave, Cambridge, MA 02138.

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http://dx.doi.org/10.1186/gm472DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3971351PMC
May 2014

Inferring clonal evolution of tumors from single nucleotide somatic mutations.

BMC Bioinformatics 2014 Feb 1;15:35. Epub 2014 Feb 1.

Department of Molecular Genetics, University of Toronto, Toronto, Canada.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-15-35DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3922638PMC
February 2014

WormBase 2014: new views of curated biology.

Nucleic Acids Res 2014 Jan 4;42(Database issue):D789-93. Epub 2013 Nov 4.

Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada, Genome Sequencing Center, Washington University, School of Medicine, St Louis, MO 63108, USA, Division of Biology and Biological Engineering 156-29, California Institute of Technology, Pasadena, CA 91125, USA, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Department of Genetics Campus, Washington University School of Medicine, St. Louis, MO 63110, USA, Genetics Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1093/nar/gkt1063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965043PMC
January 2014

Gramene 2013: comparative plant genomics resources.

Nucleic Acids Res 2014 Jan 11;42(Database issue):D1193-9. Epub 2013 Nov 11.

Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA, Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA, EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, Informatics and Bio-computing Program, Ontario Institute of Cancer Research, Toronto M5G 1L7, Canada, Department of Biochemistry & Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA and NAA Plant, Soil & Nutrition Laboratory Research Unit, USDA-ARS, Ithaca, NY 14853, USA.

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http://dx.doi.org/10.1093/nar/gkt1110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3964986PMC
January 2014

The Reactome pathway knowledgebase.

Nucleic Acids Res 2014 Jan 15;42(Database issue):D472-7. Epub 2013 Nov 15.

European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada, College of Pharmacy and Health Sciences, St. John's University, Queens, NY 11439, USA, NYU School of Medicine, New York, NY 10016, USA, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA and Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A1, Canada.

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http://dx.doi.org/10.1093/nar/gkt1102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965010PMC
January 2014

Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE.

BMC Genomics 2013 Jul 22;14:494. Epub 2013 Jul 22.

Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Suite 800, Toronto, ON, M5G 0A3, Canada.

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http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2164-14-494DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734164PMC
July 2013

Creating databases for biological information: an introduction.

Authors:
Lincoln Stein

Curr Protoc Bioinformatics 2013 Jun;Chapter 9:Unit9.1

Ontario Institute for Cancer Research, Toronto, Ontario, Canada.

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http://doi.wiley.com/10.1002/0471250953.bi0901s42
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http://dx.doi.org/10.1002/0471250953.bi0901s42DOI Listing
June 2013

Using GBrowse 2.0 to visualize and share next-generation sequence data.

Authors:
Lincoln D Stein

Brief Bioinform 2013 Mar 1;14(2):162-71. Epub 2013 Feb 1.

Ontario Institute for Cancer Research, 101 College Street, Suite 800, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1093/bib/bbt001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3603216PMC
March 2013

Modeling the evolution dynamics of exon-intron structure with a general random fragmentation process.

BMC Evol Biol 2013 Feb 28;13:57. Epub 2013 Feb 28.

Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.

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http://dx.doi.org/10.1186/1471-2148-13-57DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3732091PMC
February 2013

Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes.

Authors:
Andrew V Biankin Nicola Waddell Karin S Kassahn Marie-Claude Gingras Lakshmi B Muthuswamy Amber L Johns David K Miller Peter J Wilson Ann-Marie Patch Jianmin Wu David K Chang Mark J Cowley Brooke B Gardiner Sarah Song Ivon Harliwong Senel Idrisoglu Craig Nourse Ehsan Nourbakhsh Suzanne Manning Shivangi Wani Milena Gongora Marina Pajic Christopher J Scarlett Anthony J Gill Andreia V Pinho Ilse Rooman Matthew Anderson Oliver Holmes Conrad Leonard Darrin Taylor Scott Wood Qinying Xu Katia Nones J Lynn Fink Angelika Christ Tim Bruxner Nicole Cloonan Gabriel Kolle Felicity Newell Mark Pinese R Scott Mead Jeremy L Humphris Warren Kaplan Marc D Jones Emily K Colvin Adnan M Nagrial Emily S Humphrey Angela Chou Venessa T Chin Lorraine A Chantrill Amanda Mawson Jaswinder S Samra James G Kench Jessica A Lovell Roger J Daly Neil D Merrett Christopher Toon Krishna Epari Nam Q Nguyen Andrew Barbour Nikolajs Zeps Nipun Kakkar Fengmei Zhao Yuan Qing Wu Min Wang Donna M Muzny William E Fisher F Charles Brunicardi Sally E Hodges Jeffrey G Reid Jennifer Drummond Kyle Chang Yi Han Lora R Lewis Huyen Dinh Christian J Buhay Timothy Beck Lee Timms Michelle Sam Kimberly Begley Andrew Brown Deepa Pai Ami Panchal Nicholas Buchner Richard De Borja Robert E Denroche Christina K Yung Stefano Serra Nicole Onetto Debabrata Mukhopadhyay Ming-Sound Tsao Patricia A Shaw Gloria M Petersen Steven Gallinger Ralph H Hruban Anirban Maitra Christine A Iacobuzio-Donahue Richard D Schulick Christopher L Wolfgang Richard A Morgan Rita T Lawlor Paola Capelli Vincenzo Corbo Maria Scardoni Giampaolo Tortora Margaret A Tempero Karen M Mann Nancy A Jenkins Pedro A Perez-Mancera David J Adams David A Largaespada Lodewyk F A Wessels Alistair G Rust Lincoln D Stein David A Tuveson Neal G Copeland Elizabeth A Musgrove Aldo Scarpa James R Eshleman Thomas J Hudson Robert L Sutherland David A Wheeler John V Pearson John D McPherson Richard A Gibbs Sean M Grimmond

Nature 2012 Nov 24;491(7424):399-405. Epub 2012 Oct 24.

The Kinghorn Cancer Centre, 370 Victoria Street, Darlinghurst, Sydney, New South Wales 2010, Australia.

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http://dx.doi.org/10.1038/nature11547DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530898PMC
November 2012

Novel loci for adiponectin levels and their influence on type 2 diabetes and metabolic traits: a multi-ethnic meta-analysis of 45,891 individuals.

Authors:
Zari Dastani Marie-France Hivert Nicholas Timpson John R B Perry Xin Yuan Robert A Scott Peter Henneman Iris M Heid Jorge R Kizer Leo-Pekka Lyytikäinen Christian Fuchsberger Toshiko Tanaka Andrew P Morris Kerrin Small Aaron Isaacs Marian Beekman Stefan Coassin Kurt Lohman Lu Qi Stavroula Kanoni James S Pankow Hae-Won Uh Ying Wu Aurelian Bidulescu Laura J Rasmussen-Torvik Celia M T Greenwood Martin Ladouceur Jonna Grimsby Alisa K Manning Ching-Ti Liu Jaspal Kooner Vincent E Mooser Peter Vollenweider Karen A Kapur John Chambers Nicholas J Wareham Claudia Langenberg Rune Frants Ko Willems-Vandijk Ben A Oostra Sara M Willems Claudia Lamina Thomas W Winkler Bruce M Psaty Russell P Tracy Jennifer Brody Ida Chen Jorma Viikari Mika Kähönen Peter P Pramstaller David M Evans Beate St Pourcain Naveed Sattar Andrew R Wood Stefania Bandinelli Olga D Carlson Josephine M Egan Stefan Böhringer Diana van Heemst Lyudmyla Kedenko Kati Kristiansson Marja-Liisa Nuotio Britt-Marie Loo Tamara Harris Melissa Garcia Alka Kanaya Margot Haun Norman Klopp H-Erich Wichmann Panos Deloukas Efi Katsareli David J Couper Bruce B Duncan Margreet Kloppenburg Linda S Adair Judith B Borja James G Wilson Solomon Musani Xiuqing Guo Toby Johnson Robert Semple Tanya M Teslovich Matthew A Allison Susan Redline Sarah G Buxbaum Karen L Mohlke Ingrid Meulenbelt Christie M Ballantyne George V Dedoussis Frank B Hu Yongmei Liu Bernhard Paulweber Timothy D Spector P Eline Slagboom Luigi Ferrucci Antti Jula Markus Perola Olli Raitakari Jose C Florez Veikko Salomaa Johan G Eriksson Timothy M Frayling Andrew A Hicks Terho Lehtimäki George Davey Smith David S Siscovick Florian Kronenberg Cornelia van Duijn Ruth J F Loos Dawn M Waterworth James B Meigs Josee Dupuis J Brent Richards Benjamin F Voight Laura J Scott Valgerdur Steinthorsdottir Christian Dina Ryan P Welch Eleftheria Zeggini Cornelia Huth Yurii S Aulchenko Gudmar Thorleifsson Laura J McCulloch Teresa Ferreira Harald Grallert Najaf Amin Guanming Wu Cristen J Willer Soumya Raychaudhuri Steve A McCarroll Oliver M Hofmann Ayellet V Segrè Mandy van Hoek Pau Navarro Kristin Ardlie Beverley Balkau Rafn Benediktsson Amanda J Bennett Roza Blagieva Eric Boerwinkle Lori L Bonnycastle Kristina Bengtsson Boström Bert Bravenboer Suzannah Bumpstead Noël P Burtt Guillaume Charpentier Peter S Chines Marilyn Cornelis Gabe Crawford Alex S F Doney Katherine S Elliott Amanda L Elliott Michael R Erdos Caroline S Fox Christopher S Franklin Martha Ganser Christian Gieger Niels Grarup Todd Green Simon Griffin Christopher J Groves Candace Guiducci Samy Hadjadj Neelam Hassanali Christian Herder Bo Isomaa Anne U Jackson Paul R V Johnson Torben Jørgensen Wen H L Kao Augustine Kong Peter Kraft Johanna Kuusisto Torsten Lauritzen Man Li Aloysius Lieverse Cecilia M Lindgren Valeriya Lyssenko Michel Marre Thomas Meitinger Kristian Midthjell Mario A Morken Narisu Narisu Peter Nilsson Katharine R Owen Felicity Payne Ann-Kristin Petersen Carl Platou Christine Proença Inga Prokopenko Wolfgang Rathmann N William Rayner Neil R Robertson Ghislain Rocheleau Michael Roden Michael J Sampson Richa Saxena Beverley M Shields Peter Shrader Gunnar Sigurdsson Thomas Sparsø Klaus Strassburger Heather M Stringham Qi Sun Amy J Swift Barbara Thorand Jean Tichet Tiinamaija Tuomi Rob M van Dam Timon W van Haeften Thijs van Herpt Jana V van Vliet-Ostaptchouk G Bragi Walters Michael N Weedon Cisca Wijmenga Jacqueline Witteman Richard N Bergman Stephane Cauchi Francis S Collins Anna L Gloyn Ulf Gyllensten Torben Hansen Winston A Hide Graham A Hitman Albert Hofman David J Hunter Kristian Hveem Markku Laakso Andrew D Morris Colin N A Palmer Igor Rudan Eric Sijbrands Lincoln D Stein Jaakko Tuomilehto Andre Uitterlinden Mark Walker Richard M Watanabe Goncalo R Abecasis Bernhard O Boehm Harry Campbell Mark J Daly Andrew T Hattersley Oluf Pedersen Inês Barroso Leif Groop Rob Sladek Unnur Thorsteinsdottir James F Wilson Thomas Illig Philippe Froguel Cornelia M van Duijn Kari Stefansson David Altshuler Michael Boehnke Mark I McCarthy Nicole Soranzo Eleanor Wheeler Nicole L Glazer Nabila Bouatia-Naji Reedik Mägi Joshua Randall Paul Elliott Denis Rybin Abbas Dehghan Jouke Jan Hottenga Kijoung Song Anuj Goel Taina Lajunen Alex Doney Christine Cavalcanti-Proença Meena Kumari Nicholas J Timpson Carina Zabena Erik Ingelsson Ping An Jeffrey O'Connell Jian'an Luan Amanda Elliott Steven A McCarroll Rosa Maria Roccasecca François Pattou Praveen Sethupathy Yavuz Ariyurek Philip Barter John P Beilby Yoav Ben-Shlomo Sven Bergmann Murielle Bochud Amélie Bonnefond Knut Borch-Johnsen Yvonne Böttcher Eric Brunner Suzannah J Bumpstead Yii-Der Ida Chen Peter Chines Robert Clarke Lachlan J M Coin Matthew N Cooper Laura Crisponi Ian N M Day Eco J C de Geus Jerome Delplanque Annette C Fedson Antje Fischer-Rosinsky Nita G Forouhi Maria Grazia Franzosi Pilar Galan Mark O Goodarzi Jürgen Graessler Scott Grundy Rhian Gwilliam Göran Hallmans Naomi Hammond Xijing Han Anna-Liisa Hartikainen Caroline Hayward Simon C Heath Serge Hercberg David R Hillman Aroon D Hingorani Jennie Hui Joe Hung Marika Kaakinen Jaakko Kaprio Y Antero Kesaniemi Mika Kivimaki Beatrice Knight Seppo Koskinen Peter Kovacs Kirsten Ohm Kyvik G Mark Lathrop Debbie A Lawlor Olivier Le Bacquer Cécile Lecoeur Yun Li Robert Mahley Massimo Mangino María Teresa Martínez-Larrad Jarred B McAteer Ruth McPherson Christa Meisinger David Melzer David Meyre Braxton D Mitchell Sutapa Mukherjee Silvia Naitza Matthew J Neville Marco Orrù Ruth Pakyz Giuseppe Paolisso Cristian Pattaro Daniel Pearson John F Peden Nancy L Pedersen Andreas F H Pfeiffer Irene Pichler Ozren Polasek Danielle Posthuma Simon C Potter Anneli Pouta Michael A Province Nigel W Rayner Kenneth Rice Samuli Ripatti Fernando Rivadeneira Olov Rolandsson Annelli Sandbaek Manjinder Sandhu Serena Sanna Avan Aihie Sayer Paul Scheet Udo Seedorf Stephen J Sharp Beverley Shields Gunnar Sigurðsson Eric J G Sijbrands Angela Silveira Laila Simpson Andrew Singleton Nicholas L Smith Ulla Sovio Amy Swift Holly Syddall Ann-Christine Syvänen Anke Tönjes André G Uitterlinden Ko Willems van Dijk Dhiraj Varma Sophie Visvikis-Siest Veronique Vitart Nicole Vogelzangs Gérard Waeber Peter J Wagner Andrew Walley Kim L Ward Hugh Watkins Sarah H Wild Gonneke Willemsen Jaqueline C M Witteman John W G Yarnell Diana Zelenika Björn Zethelius Guangju Zhai Jing Hua Zhao M Carola Zillikens Ingrid B Borecki Pierre Meneton Patrik K E Magnusson David M Nathan Gordon H Williams Kaisa Silander Stefan R Bornstein Peter Schwarz Joachim Spranger Fredrik Karpe Alan R Shuldiner Cyrus Cooper Manuel Serrano-Ríos Lars Lind Lyle J Palmer Frank B Hu Paul W Franks Shah Ebrahim Michael Marmot W H Linda Kao Peter Paul Pramstaller Alan F Wright Michael Stumvoll Anders Hamsten Thomas A Buchanan Timo T Valle Jerome I Rotter Brenda W J H Penninx Dorret I Boomsma Antonio Cao Angelo Scuteri David Schlessinger Manuela Uda Aimo Ruokonen Marjo-Riitta Jarvelin Leena Peltonen Vincent Mooser Robert Sladek Kiran Musunuru Albert V Smith Andrew C Edmondson Ioannis M Stylianou Masahiro Koseki James P Pirruccello Daniel I Chasman Christopher T Johansen Sigrid W Fouchier Gina M Peloso Maja Barbalic Sally L Ricketts Joshua C Bis Mary F Feitosa Marju Orho-Melander Olle Melander Xiaohui Li Mingyao Li Yoon Shin Cho Min Jin Go Young Jin Kim Jong-Young Lee Taesung Park Kyunga Kim Xueling Sim Rick Twee-Hee Ong Damien C Croteau-Chonka Leslie A Lange Joshua D Smith Andreas Ziegler Weihua Zhang Robert Y L Zee John B Whitfield John R Thompson Ida Surakka Tim D Spector Johannes H Smit Juha Sinisalo James Scott Juha Saharinen Chiara Sabatti Lynda M Rose Robert Roberts Mark Rieder Alex N Parker Guillaume Pare Christopher J O'Donnell Markku S Nieminen Deborah A Nickerson Grant W Montgomery Wendy McArdle David Masson Nicholas G Martin Fabio Marroni Gavin Lucas Robert Luben Marja-Liisa Lokki Guillaume Lettre Lenore J Launer Edward G Lakatta Reijo Laaksonen Kirsten O Kyvik Inke R König Kay-Tee Khaw Lee M Kaplan Åsa Johansson A Cecile J W Janssens Wilmar Igl G Kees Hovingh Christian Hengstenberg Aki S Havulinna Nicholas D Hastie Tamara B Harris Talin Haritunians Alistair S Hall Leif C Groop Elena Gonzalez Nelson B Freimer Jeanette Erdmann Kenechi G Ejebe Angela Döring Anna F Dominiczak Serkalem Demissie Panagiotis Deloukas Ulf de Faire Gabriel Crawford Yii-der I Chen Mark J Caulfield S Matthijs Boekholdt Themistocles L Assimes Thomas Quertermous Mark Seielstad Tien Y Wong E-Shyong Tai Alan B Feranil Christopher W Kuzawa Herman A Taylor Stacey B Gabriel Hilma Holm Vilmundur Gudnason Ronald M Krauss Jose M Ordovas Patricia B Munroe Jaspal S Kooner Alan R Tall Robert A Hegele John J P Kastelein Eric E Schadt David P Strachan Muredach P Reilly Nilesh J Samani Heribert Schunkert L Adrienne Cupples Manjinder S Sandhu Paul M Ridker Daniel J Rader Sekar Kathiresan

PLoS Genet 2012 29;8(3):e1002607. Epub 2012 Mar 29.

Department of Epidemiology, Biostatistics, and Occupational Health, Jewish General Hospital, Lady Davis Institute, McGill University, Montreal, Canada.

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September 2012

Using the reactome database.

Curr Protoc Bioinformatics 2012 Jun;Chapter 8:Unit8.7

Ontario Institute for Cancer Research, Toronto, Ontario, Canada.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427849PMC
June 2012

A genome-wide association search for type 2 diabetes genes in African Americans.

Authors:
Nicholette D Palmer Caitrin W McDonough Pamela J Hicks Bong H Roh Maria R Wing S Sandy An Jessica M Hester Jessica N Cooke Meredith A Bostrom Megan E Rudock Matthew E Talbert Joshua P Lewis Assiamira Ferrara Lingyi Lu Julie T Ziegler Michele M Sale Jasmin Divers Daniel Shriner Adebowale Adeyemo Charles N Rotimi Maggie C Y Ng Carl D Langefeld Barry I Freedman Donald W Bowden Benjamin F Voight Laura J Scott Valgerdur Steinthorsdottir Andrew P Morris Christian Dina Ryan P Welch Eleftheria Zeggini Cornelia Huth Yurii S Aulchenko Gudmar Thorleifsson Laura J McCulloch Teresa Ferreira Harald Grallert Najaf Amin Guanming Wu Cristen J Willer Soumya Raychaudhuri Steve A McCarroll Claudia Langenberg Oliver M Hofmann Josée Dupuis Lu Qi Ayellet V Segrè Mandy van Hoek Pau Navarro Kristin Ardlie Beverley Balkau Rafn Benediktsson Amanda J Bennett Roza Blagieva Eric Boerwinkle Lori L Bonnycastle Kristina Bengtsson Boström Bert Bravenboer Suzannah Bumpstead Noël P Burtt Guillaume Charpentier Peter S Chines Marilyn Cornelis David J Couper Gabe Crawford Alex S F Doney Katherine S Elliott Amanda L Elliott Michael R Erdos Caroline S Fox Christopher S Franklin Martha Ganser Christian Gieger Niels Grarup Todd Green Simon Griffin Christopher J Groves Candace Guiducci Samy Hadjadj Neelam Hassanali Christian Herder Bo Isomaa Anne U Jackson Paul R V Johnson Torben Jørgensen Wen H L Kao Norman Klopp Augustine Kong Peter Kraft Johanna Kuusisto Torsten Lauritzen Man Li Aloysius Lieverse Cecilia M Lindgren Valeriya Lyssenko Michel Marre Thomas Meitinger Kristian Midthjell Mario A Morken Narisu Narisu Peter Nilsson Katharine R Owen Felicity Payne John R B Perry Ann-Kristin Petersen Carl Platou Christine Proença Inga Prokopenko Wolfgang Rathmann N William Rayner Neil R Robertson Ghislain Rocheleau Michael Roden Michael J Sampson Richa Saxena Beverley M Shields Peter Shrader Gunnar Sigurdsson Thomas Sparsø Klaus Strassburger Heather M Stringham Qi Sun Amy J Swift Barbara Thorand Jean Tichet Tiinamaija Tuomi Rob M van Dam Timon W van Haeften Thijs van Herpt Jana V van Vliet-Ostaptchouk G Bragi Walters Michael N Weedon Cisca Wijmenga Jacqueline Witteman Richard N Bergman Stephane Cauchi Francis S Collins Anna L Gloyn Ulf Gyllensten Torben Hansen Winston A Hide Graham A Hitman Albert Hofman David J Hunter Kristian Hveem Markku Laakso Karen L Mohlke Andrew D Morris Colin N A Palmer Peter P Pramstaller Igor Rudan Eric Sijbrands Lincoln D Stein Jaakko Tuomilehto Andre Uitterlinden Mark Walker Nicholas J Wareham Richard M Watanabe Goncalo R Abecasis Bernhard O Boehm Harry Campbell Mark J Daly Andrew T Hattersley Frank B Hu James B Meigs James S Pankow Oluf Pedersen H-Erich Wichmann Inês Barroso Jose C Florez Timothy M Frayling Leif Groop Rob Sladek Unnur Thorsteinsdottir James F Wilson Thomas Illig Philippe Froguel Cornelia M van Duijn Kari Stefansson David Altshuler Michael Boehnke Mark I McCarthy Nicole Soranzo Eleanor Wheeler Nicole L Glazer Nabila Bouatia-Naji Reedik Mägi Joshua Randall Toby Johnson Paul Elliott Denis Rybin Peter Henneman Abbas Dehghan Jouke Jan Hottenga Kijoung Song Anuj Goel Josephine M Egan Taina Lajunen Alex Doney Stavroula Kanoni Christine Cavalcanti-Proença Meena Kumari Nicholas J Timpson Carina Zabena Erik Ingelsson Ping An Jeffrey O'Connell Jian'an Luan Amanda Elliott Steven A McCarroll Rosa Maria Roccasecca François Pattou Praveen Sethupathy Yavuz Ariyurek Philip Barter John P Beilby Yoav Ben-Shlomo Sven Bergmann Murielle Bochud Amélie Bonnefond Knut Borch-Johnsen Yvonne Böttcher Eric Brunner Suzannah J Bumpstead Yii-Der Ida Chen Peter Chines Robert Clarke Lachlan J M Coin Matthew N Cooper Laura Crisponi Ian N M Day Eco J C de Geus Jerome Delplanque Annette C Fedson Antje Fischer-Rosinsky Nita G Forouhi Rune Frants Maria Grazia Franzosi Pilar Galan Mark O Goodarzi Jürgen Graessler Scott Grundy Rhian Gwilliam Göran Hallmans Naomi Hammond Xijing Han Anna-Liisa Hartikainen Caroline Hayward Simon C Heath Serge Hercberg Andrew A Hicks David R Hillman Aroon D Hingorani Jennie Hui Joe Hung Antti Jula Marika Kaakinen Jaakko Kaprio Y Antero Kesaniemi Mika Kivimaki Beatrice Knight Seppo Koskinen Peter Kovacs Kirsten Ohm Kyvik G Mark Lathrop Debbie A Lawlor Olivier Le Bacquer Cécile Lecoeur Yun Li Robert Mahley Massimo Mangino Alisa K Manning María Teresa Martínez-Larrad Jarred B McAteer Ruth McPherson Christa Meisinger David Melzer David Meyre Braxton D Mitchell Sutapa Mukherjee Silvia Naitza Matthew J Neville Ben A Oostra Marco Orrù Ruth Pakyz Giuseppe Paolisso Cristian Pattaro Daniel Pearson John F Peden Nancy L Pedersen Markus Perola Andreas F H Pfeiffer Irene Pichler Ozren Polasek Danielle Posthuma Simon C Potter Anneli Pouta Michael A Province Bruce M Psaty Nigel W Rayner Kenneth Rice Samuli Ripatti Fernando Rivadeneira Olov Rolandsson Annelli Sandbaek Manjinder Sandhu Serena Sanna Avan Aihie Sayer Paul Scheet Udo Seedorf Stephen J Sharp Beverley Shields Eric J G Sijbrands Angela Silveira Laila Simpson Andrew Singleton Nicholas L Smith Ulla Sovio Amy Swift Holly Syddall Ann-Christine Syvänen Toshiko Tanaka Anke Tönjes André G Uitterlinden Ko Willems van Dijk Dhiraj Varma Sophie Visvikis-Siest Veronique Vitart Nicole Vogelzangs Gérard Waeber Peter J Wagner Andrew Walley Kim L Ward Hugh Watkins Sarah H Wild Gonneke Willemsen Jaqueline C M Witteman John W G Yarnell Diana Zelenika Björn Zethelius Guangju Zhai Jing Hua Zhao M Carola Zillikens Ingrid B Borecki Ruth J F Loos Pierre Meneton Patrik K E Magnusson David M Nathan Gordon H Williams Kaisa Silander Veikko Salomaa George Davey Smith Stefan R Bornstein Peter Schwarz Joachim Spranger Fredrik Karpe Alan R Shuldiner Cyrus Cooper George V Dedoussis Manuel Serrano-Ríos Lars Lind Lyle J Palmer Paul W Franks Shah Ebrahim Michael Marmot W H Linda Kao Peter Paul Pramstaller Alan F Wright Michael Stumvoll Anders Hamsten Thomas A Buchanan Timo T Valle Jerome I Rotter David S Siscovick Brenda W J H Penninx Dorret I Boomsma Panos Deloukas Timothy D Spector Luigi Ferrucci Antonio Cao Angelo Scuteri David Schlessinger Manuela Uda Aimo Ruokonen Marjo-Riitta Jarvelin Dawn M Waterworth Peter Vollenweider Leena Peltonen Vincent Mooser Robert Sladek

PLoS One 2012 4;7(1):e29202. Epub 2012 Jan 4.

Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States of America.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3251563PMC
May 2012

Cancer genomics: technology, discovery, and translation.

J Clin Oncol 2012 Feb 23;30(6):647-60. Epub 2012 Jan 23.

FRCPC, Princess Margaret Hospital, Drug Development Program, 610 University Ave, Ste 5-718, Toronto, Ontario, M5G 2M9, Canada.

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http://dx.doi.org/10.1200/JCO.2011.39.2316DOI Listing
February 2012