Publications by authors named "Levi Waldron"

78Publications

"Stoma or no stoma": First report of intestinal transplantation without stoma.

Am J Transplant 2020 May 20. Epub 2020 May 20.

Department of Surgery, Icahn School of Medicine at Mount Sinai, Recanati Miller Transplantation Institute, New York, New York, USA.

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http://dx.doi.org/10.1111/ajt.16065DOI Listing
May 2020

Reliable Analysis of Clinical Tumor-Only Whole-Exome Sequencing Data.

JCO Clin Cancer Inform 2020 04;4:321-335

Novartis Institutes for BioMedical Research, Cambridge, MA.

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http://dx.doi.org/10.1200/CCI.19.00130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7259876PMC
April 2020

Toward a gold standard for benchmarking gene set enrichment analysis.

Brief Bioinform 2020 Feb 6. Epub 2020 Feb 6.

Graduate School of Public Health and Health Policy, City University of New York, New York, NY 10027, USA.

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http://dx.doi.org/10.1093/bib/bbz158DOI Listing
February 2020

CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes.

Bioinformatics 2020 02;36(3):972-973

Department of Epidemiology and Biostatistics, Graduate School of Public Health and Health Policy, City University of New York, New York, NY 10027, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz632DOI Listing
February 2020

Sociodemographic variation in the oral microbiome.

Ann Epidemiol 2019 07 8;35:73-80.e2. Epub 2019 May 8.

Department of Epidemiology and Biostatistics, Graduate School of Public Health and Health Policy, City University of New York, New York, NY; Department of Global Health and Social Medicine, King's College London, London, UK.

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http://dx.doi.org/10.1016/j.annepidem.2019.03.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6626698PMC
July 2019

Tobacco exposure associated with oral microbiota oxygen utilization in the New York City Health and Nutrition Examination Study.

Ann Epidemiol 2019 06 28;34:18-25.e3. Epub 2019 Mar 28.

Department of Epidemiology and Biostatistics, City University of New York (CUNY), Graduate School of Public Health and Health Policy, New York; Institute for Implementation Science in Population Health, City University of New York, New York.

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http://dx.doi.org/10.1016/j.annepidem.2019.03.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6548637PMC
June 2019

restfulSE: A semantically rich interface for cloud-scale genomics with Bioconductor.

F1000Res 2019 7;8:21. Epub 2019 Jan 7.

Channing Division of Network Medicine, Harvard Medical School, Boston, Massachusetts, 02115, USA.

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http://dx.doi.org/10.12688/f1000research.17518.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6392152PMC
June 2020

Waldron et al. Reply to "Commentary on the HMP16SData Bioconductor Package".

Am J Epidemiol 2019 06;188(6):1031-1032

the Centre for Integrative Biology, University of Trento, Trento, Italy.

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http://dx.doi.org/10.1093/aje/kwz008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6545274PMC
June 2019

HMP16SData: Efficient Access to the Human Microbiome Project Through Bioconductor.

Am J Epidemiol 2019 06;188(6):1023-1026

Graduate School of Public Health and Health Policy, City University of New York, New York, New York.

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http://dx.doi.org/10.1093/aje/kwz006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6545282PMC
June 2019

Orchestrating a community-developed computational workshop and accompanying training materials.

F1000Res 2018 17;7:1656. Epub 2018 Oct 17.

Graduate School of Public Health and Health Policy and the Institute for Implementation Science in Population Health, City University of New York, New York, NY, 10027, USA.

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https://f1000research.com/articles/7-1656/v1
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http://dx.doi.org/10.12688/f1000research.16516.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6234736PMC
September 2019

Impact of an HIV Care Coordination Program on Durable Viral Suppression.

J Acquir Immune Defic Syndr 2019 01;80(1):46-55

Institute for Implementation Science in Population Health (ISPH), City University of New York (CUNY), New York City, New York.

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http://Insights.ovid.com/crossref?an=00126334-201901010-0001
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http://dx.doi.org/10.1097/QAI.0000000000001877DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6289598PMC
January 2019

The impact of different sources of heterogeneity on loss of accuracy from genomic prediction models.

Biostatistics 2020 04;21(2):253-268

Graduate School of Public Health and Health Policy, Institute for Implementation Science in Population Health, City University of New York, 55 W 125th St, New York, NY, USA.

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http://dx.doi.org/10.1093/biostatistics/kxy044DOI Listing
April 2020

Using Registry Data to Construct a Comparison Group for Programmatic Effectiveness Evaluation: The New York City HIV Care Coordination Program.

Am J Epidemiol 2018 09;187(9):1980-1989

Institute for Implementation Science in Population Health, Graduate School of Public Health and Health Policy, City University of New York, New York, New York.

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http://dx.doi.org/10.1093/aje/kwy103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6118060PMC
September 2018

Data and Statistical Methods To Analyze the Human Microbiome.

Authors:
Levi Waldron

mSystems 2018 Mar-Apr;3(2). Epub 2018 Mar 13.

Graduate School of Public Health and Health Policy, City University of New York, New York, New York, USA.

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http://dx.doi.org/10.1128/mSystems.00194-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5850081PMC
March 2018

Widespread modulation of gene expression by copy number variation in skeletal muscle.

Sci Rep 2018 01 23;8(1):1399. Epub 2018 Jan 23.

Animal Biotechnology Laboratory, Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, CEP 13418-900, Brazil.

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http://dx.doi.org/10.1038/s41598-018-19782-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5780461PMC
January 2018

bioBakery: a meta'omic analysis environment.

Bioinformatics 2018 04;34(7):1235-1237

Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA.

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http://dx.doi.org/10.1093/bioinformatics/btx754DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6030947PMC
April 2018

Meta-analysis and commentary: Preemptive correction of arteriovenous access stenosis.

Hemodial Int 2018 04 3;22(2):279-280. Epub 2017 Oct 3.

Renal Research Institute, New York, New York, USA.

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http://dx.doi.org/10.1111/hdi.12614DOI Listing
April 2018

Multiparametric Quantitative Ultrasound Imaging in Assessment of Chronic Kidney Disease.

J Ultrasound Med 2017 Nov 13;36(11):2245-2256. Epub 2017 Apr 13.

Rogosin Institute, New York Presbyterian Hospital, Weill Cornell Medicine, New York, New York, USA.

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http://dx.doi.org/10.1002/jum.14209DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5640470PMC
November 2017

Control of Gene Expression by RNA Binding Protein Action on Alternative Translation Initiation Sites.

PLoS Comput Biol 2016 12 6;12(12):e1005198. Epub 2016 Dec 6.

Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Polo Scientifico e Tecnologico Fabio Ferrari, Trento, Italy.

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http://dx.plos.org/10.1371/journal.pcbi.1005198
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http://dx.doi.org/10.1371/journal.pcbi.1005198DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5140048PMC
December 2016

Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights.

PLoS Comput Biol 2016 07 11;12(7):e1004977. Epub 2016 Jul 11.

Centre for Integrative Biology, University of Trento, Trento, Italy.

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http://dx.doi.org/10.1371/journal.pcbi.1004977DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4939962PMC
July 2016

The Doppelgänger Effect: Hidden Duplicates in Databases of Transcriptome Profiles.

J Natl Cancer Inst 2016 11 5;108(11). Epub 2016 Jul 5.

Affiliations of authors: City University of New York School of Public Health, New York, NY (LW, MRa); Novartis Institutes for BioMedical Research, Cambridge, MA (MRi); Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute/Harvard Medical School, Boston, MA (GP); Center for Cancer Research, Massachusetts General Hospital, Boston, MA (MB).

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http://dx.doi.org/10.1093/jnci/djw146DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5241903PMC
November 2016

Racial/Ethnic Disparities in Genomic Sequencing.

JAMA Oncol 2016 Aug;2(8):1070-4

Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York.

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http://dx.doi.org/10.1001/jamaoncol.2016.1854DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5123755PMC
August 2016

Shear Wave Elastography of the Spleen for Monitoring Transjugular Intrahepatic Portosystemic Shunt Function: A Pilot Study.

J Ultrasound Med 2016 May 1;35(5):951-8. Epub 2016 Apr 1.

Institute of Ultrasound Imaging, Second Affiliated Hospital, Chongqing Medical University, Chongqing, China.

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http://dx.doi.org/10.7863/ultra.15.07009DOI Listing
May 2016

Meta-Analysis in Gene Expression Studies.

Methods Mol Biol 2016 ;1418:161-76

Novartis Institutes for BioMedical Research (NIBR), 250 Massachusetts Avenue, Cambridge, MA, 02139, USA.

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http://dx.doi.org/10.1007/978-1-4939-3578-9_8DOI Listing
December 2016

Creation of a Human Secretome: A Novel Composite Library of Human Secreted Proteins: Validation Using Ovarian Cancer Gene Expression Data and a Virtual Secretome Array.

Clin Cancer Res 2015 Nov 5;21(21):4960-9. Epub 2015 May 5.

Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts. Harvard Medical School, Boston, Massachusetts.

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http://dx.doi.org/10.1158/1078-0432.CCR-14-3173DOI Listing
November 2015

Molecular subtypes of high-grade serous ovarian cancer: the holy grail?

J Natl Cancer Inst 2014 Oct 30;106(10). Epub 2014 Sep 30.

City University of New York School of Public Health, Hunter College, New York, NY (LW); Novartis Institutes for BioMedical Research, Cambridge, MA (MR); Center for Cancer Research, Massachusetts General Hospital, Boston, MA (MB).

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http://dx.doi.org/10.1093/jnci/dju297DOI Listing
October 2014

Lineage-specific interface proteins match up the cell cycle and differentiation in embryo stem cells.

Stem Cell Res 2014 Sep 4;13(2):316-28. Epub 2014 Aug 4.

Center for Biological Sequence Analysis, Technical University of Denmark, Kemitorvet, DK2800 Lyngby, Denmark; Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, DK2200 Copenhagen, Denmark. Electronic address:

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http://orbit.dtu.dk/files/101390945/elsevier_9_.pdf
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http://linkinghub.elsevier.com/retrieve/pii/S187350611400089
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http://dx.doi.org/10.1016/j.scr.2014.07.008DOI Listing
September 2014

Más-o-menos: a simple sign averaging method for discrimination in genomic data analysis.

Bioinformatics 2014 Nov 23;30(21):3062-9. Epub 2014 Jul 23.

Department of Statistics, University of Illinois at Urbana-Champaign, Champaign, IL 61820, Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115, City University of New York School of Public Health, Hunter College, New York, NY 10035, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu488DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4201155PMC
November 2014

Cross-study validation for the assessment of prediction algorithms.

Bioinformatics 2014 Jun;30(12):i105-12

Leibniz Supercomputing Center, Garching, Department for Medical Informatics, Biometry and Epidemiology, Munich, Germany, Cambridge, MA, Dana-Farber Cancer Institute, Boston, Harvard School of Public Health, Boston, USA and City University of New York School of Public Health, Hunter College, New York, USALeibniz Supercomputing Center, Garching, Department for Medical Informatics, Biometry and Epidemiology, Munich, Germany, Cambridge, MA, Dana-Farber Cancer Institute, Boston, Harvard School of Public Health, Boston, USA and City University of New York School of Public Health, Hunter College, New York, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu279DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4058929PMC
June 2014

Risk prediction for late-stage ovarian cancer by meta-analysis of 1525 patient samples.

J Natl Cancer Inst 2014 Apr 3;106(5). Epub 2014 Apr 3.

Affiliations of authors: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (MR, ACC, LT, FM, CH, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (MR, ACC, LT, FM, CH, GP); Center for Cancer Research (WW, S-hK, MB) and Department of Pathology (EO), Massachusetts General Hospital, Boston, MA; City University of New York School of Public Health, Hunter College, New York, NY (LW); Sung-hoon Kim, Yonsei University College of Medicine, Seoul, Korea (S-HK).

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http://dx.doi.org/10.1093/jnci/dju048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4580556PMC
April 2014

Comparative meta-analysis of prognostic gene signatures for late-stage ovarian cancer.

J Natl Cancer Inst 2014 Apr 3;106(5). Epub 2014 Apr 3.

Affiliations of authors: City University of New York School of Public Health, Hunter College, New York, NY (LW); Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (LW, AC, MR, JD, XVW, ST, TR, BG, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (LW, AC, CH, GP); Center for Cancer Research, Massachusetts General Hospital, Boston, MA (MB); Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada (BH); Medical Biophysics Department, University of Toronto, Toronto, Ontario, Canada (BH);Institute for Medical Information Sciences, Biometry, and Epidemiology, LMU Munich, Munich, Germany (CB).

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http://dx.doi.org/10.1093/jnci/dju049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4580554PMC
April 2014

Two-stage microbial community experimental design.

ISME J 2013 Dec 15;7(12):2330-9. Epub 2013 Aug 15.

1] Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA [2] The Broad Institute of MIT and Harvard, Cambridge, MA, USA.

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http://dx.doi.org/10.1038/ismej.2013.139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3834858PMC
December 2013

Potentially prognostic miRNAs in HPV-associated oropharyngeal carcinoma.

Clin Cancer Res 2013 Apr 4;19(8):2154-62. Epub 2013 Mar 4.

Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1158/1078-0432.CCR-12-3572DOI Listing
April 2013

A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets.

PLoS Comput Biol 2013 10;9(1):e1002863. Epub 2013 Jan 10.

Department of Microbiology, Cornell University, Ithaca, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1002863DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3542080PMC
June 2013

Metagenomic microbial community profiling using unique clade-specific marker genes.

Nat Methods 2012 Jun 10;9(8):811-4. Epub 2012 Jun 10.

Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/nmeth.2066DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3443552PMC
June 2012

Report on emerging technologies for translational bioinformatics: a symposium on gene expression profiling for archival tissues.

BMC Cancer 2012 Mar 29;12:124. Epub 2012 Mar 29.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA.

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http://dx.doi.org/10.1186/1471-2407-12-124DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3342119PMC
March 2012

The murine caecal microRNA signature depends on the presence of the endogenous microbiota.

Int J Biol Sci 2012 19;8(2):171-86. Epub 2011 Dec 19.

Department of Nutritional Sciences, University of Toronto, Ontario, Canada.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3248702PMC
http://dx.doi.org/10.7150/ijbs.8.171DOI Listing
September 2012

Optimized application of penalized regression methods to diverse genomic data.

Bioinformatics 2011 Dec;27(24):3399-406

Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr591DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232376PMC
December 2011

Integrative approaches for microarray data analysis.

Methods Mol Biol 2012 ;802:157-82

Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA.

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http://dx.doi.org/10.1007/978-1-61779-400-1_11DOI Listing
April 2012

Stem cell gene expression programs influence clinical outcome in human leukemia.

Nat Med 2011 Aug 28;17(9):1086-93. Epub 2011 Aug 28.

Division of Stem Cell and Developmental Biology, Campbell Family Institute for Cancer Research, Ontario Cancer Institute, University Health Network and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.

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http://www.nature.com/articles/nm.2415
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http://dx.doi.org/10.1038/nm.2415DOI Listing
August 2011

Metagenomic biomarker discovery and explanation.

Genome Biol 2011 Jun 24;12(6):R60. Epub 2011 Jun 24.

Department of Biostatistics, 677 Huntington Avenue, Harvard School of Public Health, Boston, MA 02115, USA.

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http://www.researchgate.net/profile/Dirk_Gevers/publication/
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http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
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http://dx.doi.org/10.1186/gb-2011-12-6-r60DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218848PMC
June 2011

MicroRNA-301 mediates proliferation and invasion in human breast cancer.

Cancer Res 2011 Apr 10;71(8):2926-37. Epub 2011 Mar 10.

Department of Medical Biophysics, Ontario Cancer Institute, University Health Network, University of Toronto, Toronto, Canada.

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http://dx.doi.org/10.1158/0008-5472.CAN-10-3369DOI Listing
April 2011

Comprehensive MicroRNA profiling for head and neck squamous cell carcinomas.

Clin Cancer Res 2010 Feb 9;16(4):1129-39. Epub 2010 Feb 9.

Division of Applied Molecular Oncology, Ontario Cancer Institute, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1158/1078-0432.CCR-09-2166DOI Listing
February 2010

Genotype and time of day shape the Populus drought response.

Plant J 2009 Nov 8;60(4):703-15. Epub 2009 Aug 8.

Department of Cell & Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada.

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http://dx.doi.org/10.1111/j.1365-313X.2009.03993.xDOI Listing
November 2009

Robust global micro-RNA profiling with formalin-fixed paraffin-embedded breast cancer tissues.

Lab Invest 2009 May 16;89(5):597-606. Epub 2009 Mar 16.

Division of Applied Molecular Oncology, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada.

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http://dx.doi.org/10.1038/labinvest.2009.12DOI Listing
May 2009