Benjamin Haibe-Kains

Benjamin Haibe-Kains

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Benjamin Haibe-Kains

Benjamin Haibe-Kains

Publications by authors named "Benjamin Haibe-Kains"

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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

Integrative Pharmacogenomics Analysis of Patient-Derived Xenografts.

Cancer Res 2019 Sep 29;79(17):4539-4550. Epub 2019 May 29.

Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1158/0008-5472.CAN-19-0349DOI Listing
September 2019

Creating reproducible pharmacogenomic analysis pipelines.

Sci Data 2019 09 3;6(1):166. Epub 2019 Sep 3.

Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1038/s41597-019-0174-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6722117PMC
September 2019

SIGN: Similarity identification in gene expression.

Bioinformatics 2019 Jun 14. Epub 2019 Jun 14.

Princess Margaret Cancer Centre, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btz485DOI Listing
June 2019

Why imaging data alone is not enough: AI-based integration of imaging, omics, and clinical data.

Eur J Nucl Med Mol Imaging 2019 Jun 15. Epub 2019 Jun 15.

Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, Canada.

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http://dx.doi.org/10.1007/s00259-019-04382-9DOI Listing
June 2019

Network-based approach to identify principal isoforms among four cancer types.

Mol Omics 2019 04 5;15(2):117-129. Epub 2019 Feb 5.

National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, P. R. China.

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http://dx.doi.org/10.1039/c8mo00234gDOI Listing
April 2019

Dr.VAE: Improving drug response prediction via modeling of drug perturbation effects.

Bioinformatics 2019 Mar 8. Epub 2019 Mar 8.

Department of Computer Science,University of Toronto, Toronto, ON, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btz158DOI Listing
March 2019

A Comparative Study of Cluster Detection Algorithms in Protein-Protein Interaction for Drug Target Discovery and Drug Repurposing.

Front Pharmacol 2019 19;10:109. Epub 2019 Feb 19.

National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, China.

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http://dx.doi.org/10.3389/fphar.2019.00109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6389713PMC
February 2019

Vulnerabilities of radiomic signature development: The need for safeguards.

Radiother Oncol 2019 Jan 8;130:2-9. Epub 2018 Nov 8.

Department of Medical Biophysics, University of Toronto, Canada; Department of Radiation Oncology, University of Toronto, Canada; IBBME, University of Toronto, Canada; Radiation Medicine Program, Princess Margaret Cancer Centre, Toronto, Canada; The Techna Institute for the Advancement of Technology for Health, Toronto, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.radonc.2018.10.027DOI Listing
January 2019

Radiomic Biomarkers to Refine Risk Models for Distant Metastasis in HPV-related Oropharyngeal Carcinoma.

Int J Radiat Oncol Biol Phys 2018 11 1;102(4):1107-1116. Epub 2018 Feb 1.

Department of Radiation Oncology, Princess Margaret Cancer Centre/University of Toronto, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.ijrobp.2018.01.057DOI Listing
November 2018

Network science in clinical trials: A patient-centered approach.

Semin Cancer Biol 2018 10 24;52(Pt 2):135-150. Epub 2017 Dec 24.

Bioinformatics and Computational Genomics Laboratory, Princess Margaret Cancer Center, Toronto, ON, Canada; Department of Computer Science, University of Toronto, Toronto, ON, Canada; Ontario Institute of Cancer Research, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.semcancer.2017.12.006DOI Listing
October 2018

MYC Interacts with the G9a Histone Methyltransferase to Drive Transcriptional Repression and Tumorigenesis.

Cancer Cell 2018 10;34(4):579-595.e8

Princess Margaret Cancer Centre, Toronto, ON M5G1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G1L7, Canada. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S15356108183041
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http://dx.doi.org/10.1016/j.ccell.2018.09.001DOI Listing
October 2018

A review of connectivity map and computational approaches in pharmacogenomics.

Brief Bioinform 2018 05;19(3):506-523

Predictive Medicine and Analytics Lab, Department of Signal Processing, Tampere University of Technology, Tampere, Finland.

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http://dx.doi.org/10.1093/bib/bbw112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5952941PMC
May 2018

Rational design and identification of immuno-oncology drug combinations.

Eur J Cancer 2018 05 7;95:38-51. Epub 2018 Apr 7.

Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, 610 University Ave, Toronto, Ontario, M5G 2M9, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.ejca.2018.02.027DOI Listing
May 2018

CrosstalkNet: A Visualization Tool for Differential Co-expression Networks and Communities.

Cancer Res 2018 04 19;78(8):2140-2143. Epub 2018 Feb 19.

Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1158/0008-5472.CAN-17-1383DOI Listing
April 2018

Gene Expression Analyses in Breast Cancer: Sample Matters.

JNCI Cancer Spectr 2018 Apr 22;2(2):pky019. Epub 2018 May 22.

Campbell Family Institute for Breast Cancer Research, Department of Research, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.

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http://dx.doi.org/10.1093/jncics/pky019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6649719PMC
April 2018

Predictive approaches for drug combination discovery in cancer.

Brief Bioinform 2018 03;19(2):263-276

Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.

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https://academic.oup.com/bib/article/19/2/263/2562643
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http://dx.doi.org/10.1093/bib/bbw104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6018991PMC
March 2018

AutoDock and AutoDockTools for Protein-Ligand Docking: Beta-Site Amyloid Precursor Protein Cleaving Enzyme 1(BACE1) as a Case Study.

Methods Mol Biol 2017 ;1598:391-403

Department of Biochemistry and Molecular Genetics, American University of Beirut, DTS4-19A, Bliss Street, Riad El Solh, Beirut, 1107 2020, Lebanon.

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http://dx.doi.org/10.1007/978-1-4939-6952-4_20DOI Listing
March 2018

Statin-Induced Cancer Cell Death Can Be Mechanistically Uncoupled from Prenylation of RAS Family Proteins.

Cancer Res 2018 03 11;78(5):1347-1357. Epub 2017 Dec 11.

Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1158/0008-5472.CAN-17-1231DOI Listing
March 2018

The international MAQC Society launches to enhance reproducibility of high-throughput technologies.

Nat Biotechnol 2017 12;35(12):1127-1128

National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas, USA.

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http://dx.doi.org/10.1038/nbt.4029DOI Listing
December 2017

Integrative cancer pharmacogenomics to establish drug mechanism of action: drug repurposing.

Pharmacogenomics 2017 11 23;18(16):1469-1472. Epub 2017 Oct 23.

Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.

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http://dx.doi.org/10.2217/pgs-2017-0132DOI Listing
November 2017

Gene isoforms as expression-based biomarkers predictive of drug response in vitro.

Nat Commun 2017 10 24;8(1):1126. Epub 2017 Oct 24.

Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, ON, Canada, M5G1L7.

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http://dx.doi.org/10.1038/s41467-017-01153-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5655668PMC
October 2017

Defining the biological basis of radiomic phenotypes in lung cancer.

Elife 2017 07 21;6. Epub 2017 Jul 21.

Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, United States.

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http://dx.doi.org/10.7554/eLife.23421DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5590809PMC
July 2017

Integrative Cancer Pharmacogenomics to Infer Large-Scale Drug Taxonomy.

Cancer Res 2017 06 17;77(11):3057-3069. Epub 2017 Mar 17.

Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1158/0008-5472.CAN-17-0096DOI Listing
June 2017

Bidirectional terminators in Saccharomyces cerevisiae prevent cryptic transcription from invading neighboring genes.

Nucleic Acids Res 2017 Jun;45(11):6417-6426

Institut de recherches cliniques de Montréal, Montréal, Québec H2W 1R7, Canada.

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http://dx.doi.org/10.1093/nar/gkx242DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5499651PMC
June 2017

Transcriptome Analysis of Human Reninomas as an Approach to Understanding Juxtaglomerular Cell Biology.

Hypertension 2017 06 10;69(6):1145-1155. Epub 2017 Apr 10.

From the Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands (A.G.M., E.C.H.F., A.H.v.d.M., A.H.J.D.); Laboratory of Molecular Biochemistry of Hypertension (L.K.X., M.-J.L., C.M., T.L.R.) and Laboratory of Bioinformatics and Computational Genomics (A.B.-C., B.H.-K.), Institut de Recherches Cliniques de Montréal (IRCM), Quebec, Canada; Division of Experimental Medicine, Faculty of Medicine, McGill University, Montréal, Quebec, Canada (L.K.X., T.L.R.); Department of Biochemistry (B.H.-K., T.L.R.) and Department of Medicine (T.L.R.), Université de Montréal, Quebec, Canada; Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY (K.W.G.); Hôpital Européen Georges Pompidou, Centre d'Investigations Cliniques 1418, Paris, France (M.A.); Collège de France, Center for Interdisciplinary Research in Biology (CIRB), Paris, France (P.C., G.N.); and INSERM, U1050, Paris, France (G.N.).

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https://www.ahajournals.org/doi/10.1161/HYPERTENSIONAHA.117.
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http://dx.doi.org/10.1161/HYPERTENSIONAHA.117.09179DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5426967PMC
June 2017

Study of Meta-analysis strategies for network inference using information-theoretic approaches.

BioData Min 2017 6;10:15. Epub 2017 May 6.

Bioinformatics and Systems Biology (BioSys) Lab, Université de Liège, Liège, Belgium.

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http://dx.doi.org/10.1186/s13040-017-0136-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5420410PMC
May 2017

Genomic biomarkers for precision radiation medicine.

Lancet Oncol 2017 05;18(5):e238

Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Department of Computer Science, University of Toronto, Toronto, ON, Canada; Ontario Institute of Cancer Research, Toronto, ON, Canada.

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http://dx.doi.org/10.1016/S1470-2045(17)30263-2DOI Listing
May 2017

Safikhani et al. reply.

Nature 2016 11;540(7631):E6-E8

Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada.

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http://dx.doi.org/10.1038/nature20172DOI Listing
November 2016

Safikhani et al. reply.

Nature 2016 11;540(7631):E11-E12

Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada.email:

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http://dx.doi.org/10.1038/nature20581DOI Listing
November 2016

Safikhani et al. reply.

Nature 2016 11;540(7631):E2-E4

Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada.

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http://dx.doi.org/10.1038/nature19839DOI Listing
November 2016

DNA replication stress: a source of APOBEC3B expression in breast cancer.

Genome Biol 2016 09 30;17(1):202. Epub 2016 Sep 30.

Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.

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http://dx.doi.org/10.1186/s13059-016-1069-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5045630PMC
September 2016

Adenosine 2B Receptor Expression on Cancer Cells Promotes Metastasis.

Cancer Res 2016 08 24;76(15):4372-82. Epub 2016 May 24.

Immunology in Cancer and Infection Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia. School of Medicine, The University of Queensland, Herston, Queensland, Australia.

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http://dx.doi.org/10.1158/0008-5472.CAN-16-0544DOI Listing
August 2016

Assessment of pharmacogenomic agreement.

F1000Res 2016 9;5:825. Epub 2016 May 9.

Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 1L7, Canada; Department of Computer Science, University of Toronto, Toronto, Ontario, M5S 2E4, Canada.

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http://dx.doi.org/10.12688/f1000research.8705.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4926729PMC
July 2016

PharmacoGx: an R package for analysis of large pharmacogenomic datasets.

Bioinformatics 2016 04 9;32(8):1244-6. Epub 2015 Dec 9.

Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada, Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btv723DOI Listing
April 2016

MM2S: personalized diagnosis of medulloblastoma patients and model systems.

Source Code Biol Med 2016 11;11. Epub 2016 Apr 11.

Bioinformatics and Computational Genomics Laboratory, Princess Margaret Cancer Center, University Health Network, Toronto, Ontario Canada ; Department of Medical Biophysics, University of Toronto, Toronto, Ontario Canada ; Department of Computer Science, University of Toronto, Toronto, Ontario Canada.

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http://dx.doi.org/10.1186/s13029-016-0053-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4827218PMC
April 2016

Characterization of Conserved Toxicogenomic Responses in Chemically Exposed Hepatocytes across Species and Platforms.

Environ Health Perspect 2016 Mar 14;124(3):313-20. Epub 2015 Jul 14.

Integrative systems biology, Institut de Recherches Cliniques de Montréal, Montreal, Quebec, Canada.

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http://dx.doi.org/10.1289/ehp.1409157DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4786983PMC
March 2016

CD73 is associated with poor prognosis in high-grade serous ovarian cancer.

Cancer Res 2015 Nov 11;75(21):4494-503. Epub 2015 Sep 11.

Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Québec, Canada. Institut du Cancer de Montréal, Montréal, Québec, Canada. Faculté de Pharmacie, Université de Montréal, Québec, Canada.

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http://dx.doi.org/10.1158/0008-5472.CAN-14-3569DOI Listing
November 2015

ABC: a tool to identify SNVs causing allele-specific transcription factor binding from ChIP-Seq experiments.

Bioinformatics 2015 Sep 20;31(18):3057-9. Epub 2015 May 20.

Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada, Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada and Ontario Institute for Cancer Research, Toronto, ON, Canada Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada, Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada and Ontario Institute for Cancer Research, Toronto, ON, Canada Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada, Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada and Ontario Institute for Cancer Research, Toronto, ON, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btv321DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4668780PMC
September 2015

Personalized diagnosis of medulloblastoma subtypes across patients and model systems.

Genomics 2015 Aug 12;106(2):96-106. Epub 2015 May 12.

Bioinformatics and Computational Genomics Laboratory, Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada; Medical Biophysics Department, University of Toronto, Toronto, Ontario, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.ygeno.2015.05.002DOI Listing
August 2015

Test set bias affects reproducibility of gene signatures.

Bioinformatics 2015 Jul 18;31(14):2318-23. Epub 2015 Mar 18.

Department of Biostatistics, Johns Hopkins School of Public Health, Baltimore, MD, USA.

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http://dx.doi.org/10.1093/bioinformatics/btv157DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4495301PMC
July 2015

Radiomic feature clusters and prognostic signatures specific for Lung and Head & Neck cancer.

Sci Rep 2015 Jun 5;5:11044. Epub 2015 Jun 5.

1] Departments of Radiation Oncology [2] Radiology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA [3] Department of Biostatistics &Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA.

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http://dx.doi.org/10.1038/srep11044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937496PMC
June 2015

Using shRNA experiments to validate gene regulatory networks.

Genom Data 2015 Jun 1;4:123-6. Epub 2015 Apr 1.

Bioinformatics and Computational Genomics Laboratory, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada ; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1016/j.gdata.2015.03.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4535466PMC
June 2015

A network model for angiogenesis in ovarian cancer.

BMC Bioinformatics 2015 Apr 11;16:115. Epub 2015 Apr 11.

Dana-Farber Cancer Institute, Boston, MA, USA.

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http://dx.doi.org/10.1186/s12859-015-0551-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4408593PMC
April 2015

Robust Radiomics feature quantification using semiautomatic volumetric segmentation.

PLoS One 2014 15;9(7):e102107. Epub 2014 Jul 15.

Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America; Department of Radiation Oncology (MAASTRO), Maastricht University, Maastricht, The Netherlands; Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0102107PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4098900PMC
March 2015

APOBEC3B expression in breast cancer reflects cellular proliferation, while a deletion polymorphism is associated with immune activation.

Proc Natl Acad Sci U S A 2015 Mar 17;112(9):2841-6. Epub 2015 Feb 17.

Princess Margaret Cancer Centre, University Health Network, M5G 2M9 Toronto, Canada; Campbell Family Institute for Breast Cancer Research, M5G 2M9 Toronto, Canada; Department of Medical Biophysics, University of Toronto, M5G 1L7 Toronto, Canada; and

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http://dx.doi.org/10.1073/pnas.1424869112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4352793PMC
March 2015

CT-based radiomic signature predicts distant metastasis in lung adenocarcinoma.

Radiother Oncol 2015 Mar 4;114(3):345-50. Epub 2015 Mar 4.

Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, USA; Department of Radiology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, USA; Department of Radiation Oncology (MAASTRO), GROW Research Institute, Maastricht University, The Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.radonc.2015.02.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4400248PMC
March 2015

ZNF143 provides sequence specificity to secure chromatin interactions at gene promoters.

Nat Commun 2015 Feb 3;2:6186. Epub 2015 Feb 3.

1] The Princess Margaret Cancer Centre-University Health Network, Toronto, Ontario, Canada M5G 1L7 [2] Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada M5G 1L7 [3] Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 1L7.

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http://dx.doi.org/10.1038/ncomms7186DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4431651PMC
February 2015

Inference and validation of predictive gene networks from biomedical literature and gene expression data.

Genomics 2014 May-Jun;103(5-6):329-36. Epub 2014 Mar 29.

Computational Biology and Functional Genomics Laboratory, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ygeno.2014.03.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4119824PMC
January 2015

Gene regulatory networks and their applications: understanding biological and medical problems in terms of networks.

Front Cell Dev Biol 2014 19;2:38. Epub 2014 Aug 19.

Bioinformatics and Computational Genomics Laboratory, Department of Medical Biophysics, Princess Margaret Cancer Centre, University of Toronto Canada.

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http://dx.doi.org/10.3389/fcell.2014.00038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4207011PMC
November 2014

Exploiting high-throughput cell line drug screening studies to identify candidate therapeutic agents in head and neck cancer.

BMC Pharmacol Toxicol 2014 Nov 27;15:66. Epub 2014 Nov 27.

Department of Otolaryngology Head & Neck Surgery, Western University, London, Ontario, Canada.

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http://dx.doi.org/10.1186/2050-6511-15-66DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4258049PMC
November 2014

Untangling statistical and biological models to understand network inference: the need for a genomics network ontology.

Front Genet 2014 29;5:299. Epub 2014 Aug 29.

Bioinformatics and Computational Genomics Laboratory, Princess Margaret Cancer Centre, University Health Network Toronto, ON, Canada.

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http://dx.doi.org/10.3389/fgene.2014.00299DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4148777PMC
September 2014

Enhancing reproducibility in cancer drug screening: how do we move forward?

Cancer Res 2014 Aug 11;74(15):4016-23. Epub 2014 Jul 11.

Princess Margaret Cancer Centre, University Health Network; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada;

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http://dx.doi.org/10.1158/0008-5472.CAN-14-0725DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4119520PMC
August 2014

Relevance of different prior knowledge sources for inferring gene interaction networks.

Front Genet 2014 24;5:177. Epub 2014 Jun 24.

Bioinformatics and Computational Genomics, Princess Margaret Cancer Centre, University Health Network Toronto, ON, Canada ; Medical Biophysics Department, University of Toronto Toronto, ON, Canada.

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http://dx.doi.org/10.3389/fgene.2014.00177DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4067568PMC
July 2014

Quantitative assessment and validation of network inference methods in bioinformatics.

Front Genet 2014 16;5:221. Epub 2014 Jul 16.

Computational Biology and Machine Learning Laboratory, Center for Cancer Research and Cell Biology, Queen's University Belfast Belfast, UK.

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http://dx.doi.org/10.3389/fgene.2014.00221DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4099936PMC
July 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

A genome-wide aberrant RNA splicing in patients with acute myeloid leukemia identifies novel potential disease markers and therapeutic targets.

Clin Cancer Res 2014 Mar 27;20(5):1135-45. Epub 2013 Nov 27.

Authors' Affiliations: Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts; Bioinformatics and Computational Genomics Laboratory, Institut de Recherches Cliniques de Montréal, Montreal, Quebec, Canada; Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada; Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts; Dana-Farber Cancer Institute, Center for Cancer Systems Biology and Department of Genetics, Harvard Medical School, Boston University School of Medicine and Biomedical Engineering Department, Boston University, Boston, Massachusetts; Unité de Génomique du Myélome, Laboratoire UGM, University Hospital, CHU Rangueil, Toulouse, France; Hematology Laboratory, University Hospital; and INSERM U892, Nantes, France; Molecular Diagnostics Laboratory, Dana Farber Cancer Institute, Boston, Massachusetts; Biotique Systems Inc., www.biotiquesystems.com; Adult Leukemia Program, Dana Farber Cancer Institute, Boston, Massachusetts; Brigham and Women's Hospital, Boston, Massachusetts; Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.

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http://dx.doi.org/10.1158/1078-0432.CCR-13-0956DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4458245PMC
March 2014

Similarity network fusion for aggregating data types on a genomic scale.

Nat Methods 2014 Mar 26;11(3):333-7. Epub 2014 Jan 26.

1] Genetics and Genome Biology, SickKids Research Institute, Toronto, Ontario, Canada. [2] Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1038/nmeth.2810DOI Listing
March 2014

Importance of collection in gene set enrichment analysis of drug response in cancer cell lines.

Sci Rep 2014 Feb 13;4:4092. Epub 2014 Feb 13.

1] Bioinformatics and Computational Genomics Laboratory, Institut de Recherches Cliniques de Montréal, University of Montreal, Montreal, Quebec, Canada [2] Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1038/srep04092DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3923229PMC
February 2014

The gene regulatory network for breast cancer: integrated regulatory landscape of cancer hallmarks.

Front Genet 2014 3;5:15. Epub 2014 Feb 3.

Institute for Bioinformatics and Translational Research, UMIT, Eduard Wallnoefer Zentrum 1 Hall in Tyrol, Austria.

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http://journal.frontiersin.org/article/10.3389/fgene.2014.00
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http://dx.doi.org/10.3389/fgene.2014.00015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3909882PMC
February 2014

Network statistics of genetically-driven gene co-expression modules in mouse crosses.

Front Genet 2013 26;4:291. Epub 2013 Dec 26.

Cardiovascular Biology Research Unit, Institut de Recherches Cliniques de Montréal Montreál, QC, Canada.

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http://dx.doi.org/10.3389/fgene.2013.00291DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3872724PMC
January 2014

Novel effects of chromosome Y on cardiac regulation, chromatin remodeling, and neonatal programming in male mice.

Endocrinology 2013 Dec 8;154(12):4746-56. Epub 2013 Oct 8.

Institut de Recherches Cliniques de Montréal, 110 Pine Avenue West, Montréal, Québec, Canada H2W 1R7.

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http://dx.doi.org/10.1210/en.2013-1699DOI Listing
December 2013

Inconsistency in large pharmacogenomic studies.

Nature 2013 Dec 27;504(7480):389-93. Epub 2013 Nov 27.

1] Department of Biostatistics and Computational Biology and Center for Cancer Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [3].

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http://dx.doi.org/10.1038/nature12831DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4237165PMC
December 2013