Presentations

All the slides and posters are listed here

2017

Reproducible Research in Genome Biology and Bioinformatics. The Collaborative Graduate Program in Genome Biology and Bioinformatics, University of Toronto, 2017 Oct 17, Toronto, Ontario, Canada. Presenters: Zhaleh Safikhani and Benjamin Haibe-Kains. Slides; Exercises: Rmd, PDF




Integration of pharmacogenomic data for biomarker discovery and drug classification. 3rd DIA China Drug Discovery Innovation Conference, 2017 September 26, Shanghai, China. Presenter: Benjamin Haibe-Kains. Slides




Drug taxonomy via integrative analysis of pharmacogenomic data. Cancer Research UK Manchester Institute, 2017 June 21, Manchester, UK. Presenter: Benjamin Haibe-Kains. Slides




Distance Metric Learning on Gene Expression Data. James Lepock Memorial Symposium, 2017 June 6, Toronto, Canada. Presenter: Ian Smith. Poster




Near-global copy-neutral loss of heterozygosity is a defining feature of pancreatic neuroendocrine tumours. Great Lakes Chromosome Conference, 2017 May 17, Toronto, Canada. Presenter: Rene Quevedo. Slides




Data-driven re-annotation of patient tumors and derived model systems. Great Lakes Chromosome Conference, 2017 May 17, Toronto, Canada. Presenter: Rene Quevedo. Slides




Exploiting Bimodality of Gene Expression for the Enhancement of Drug Sensitivity Prediction. Toronto Bioinformatics Users Group (TorBUG), 2017 April 26, Toronto, Canada. Presenter: Wail Ba-alawi. Slides




Integrative biomarker discovery in cancer precision medicine. Biomedicum Helsinki Seminar Series, Biomedicum Helsinki Research Center, 2017 April 24, Helsinki, Finland. Presenter: Benjamin Haibe-Kains. Slides




Integrative Analysis and Applications of Large-Scale Drug Screening. Stanford Center for Cancer Systems Biology (CCSB) Seminar Series, Stanford University, 2017 April 21, Stanford, California, USA. Presenter: Benjamin Haibe-Kains. Slides



The Importance of Data and Code Sharing and Transparent Pre- and Post-Publication Review: A Case Study in Pharmacogenomics. The MAQC 2017 Conference: Reproducible Genomics, 2017 April 12, North Carolina, USA. Presenter: Benjamin Haibe-Kains. Slides



Integrative cancer pharmacogenomics to infer large-scale drug taxonomy. Statistical and Computational Challenges in Large Scale Molecular Biology, Banff International Research Station for Mathematical Innovation and Discovery, 2017 March 30, Banff, Alberta, Canada. Presenter: Benjamin Haibe-Kains. Slides



Large-scale in vitro Drug Screening and Applications. Distinguished Scientist Lecture Series, Institute for Research in Immunology and Cancer, Université de Montréal, 2017 March 6, Montreal, Quebec, Canada. Presenter: Benjamin Haibe-Kains. Slides



PharmacoGx: R/Bioconductor package for computational pharmacogenomicsR/Bioconductor for Pharmacogenomics, 2017 March 2, Boston, USA. Presenter: Benjamin Haibe-Kains. Slides




A systems biology approach to investigating tumor microenvironmental interactions in TNBC patients. Personalizing Cancer Medicine Conference, 2017 February, Toronto, Canada. Presenter: Venkata Manem. Poster




Integrative Analysis and Applications of Large-Scale Drug Screening. Cancer and the Immune System, 16th Annual BCI-McGill Workshop, 2017 January 24, Holetown, Barbados. Presenter: Benjamin Haibe-Kains. Slides




Network-based discovery of drug target isoforms. 2017 International Conference on Bioinformatics and Computing Technologies, 2017 January 6-8, Hong Kong, China. Presenter: Jun Ma. Slides

2016

Tissue specificity of in vitro drug sensitivity. The 6th Translational Bioinformatics Conference, 2016 October 16, Jeju Island, South Korea. Presenter: Benjamin Haibe-Kains. Slides




Reproducibility in large in vitro drug screening: where do we stand?. The 6th Translational Bioinformatics Conference, 2016 October 16, Jeju Island, South Korea. Presenter: Benjamin Haibe-Kains. Slides




em>Inference and validation of large­-scale causal gene regulatory networks from transcriptomic data. Workshop on Models for Oncogenesis, Clonality and Tumor Progression, Mathematical Biosciences Institute. 2016 September 29, Columbus, Ohio, USA. Presenter: Benjamin Haibe-Kains. Slides



Bioinformatics challenges in meta-analysis of large-scale pharmacogenomic datasets.Sequencing Quality Control Project (SEQC2) Workshop, 2016 September 13, National Institutes of Health, Maryland, USA. Presenter: Benjamin Haibe-Kains. Slides



Open data science for biomarker discovery in precision medicine. Trends and future in data science and bioinformatics, Machine Learning Group Workshop, 2016 July 18, Université Libre de Bruxelles, Brussels, Belgium. Presenter: Benjamin Haibe-Kains. Slides



PharmacoGx: Data Sharing and Research Reproducibility in Pharmacogenomics. Bioconductor 2016 Conference, Stanford University, 2016 June 24, Stanford, California, USA. Presenter: Benjamin Haibe-Kains. Slides




Reproducible research, algorithms, and data. Bioconductor 2016 Conference, Stanford University, 2016 June 23, Stanford, California, USA. Presenter: Benjamin Haibe-Kains. Slides




Using networks to identify key players in breast cancer microenvironment interactions. The GLBIO/CCBC Great Lakes Bioinformatics and the Canadian Computational Biology Conference, 2016 May, Toronto, Canada. Presenter: Venkata Manem. Poster



Tumor-specific isoforms as expression-based biomarkers predictive of drug response. The GLBIO/CCBC Great Lakes Bioinformatics and the Canadian Computational Biology Conference, 2016 May 15. Presenter: Zhaleh Safikhani. Slides



Decoding compound mechanism of action using integrative pharmacogenomics. The GLBIO/CCBC Great Lakes Bioinformatics and the Canadian Computational Biology Conference, 2016 May 15. Presenter: Nehme El-Hachem. Slides




Data/Code Sharing and Research Reproducibility: Why, How and When? 5th Annual Canadian Human and Statistical Genetics Meeting, 2016 April 16, Halifax, Nova Scotia, Canada. Presenter: Benjamin Haibe-Kains. Slides




Integration of GTEx with Pharmacogenomic Datasets Enables Identification of Novel Biomarkers Predictive of Drug Response. Applied Bioinformatics in Life Sciences, 2016 March 17, Leuven, Belgium. Presenter: Benjamin Haibe-Kains. Slides



PharmacoGx: An R package for analysis of large pharmacogenomic datasetsé.Personalizing Cancer Medicine Conference, March 2016, Toronto, Canada. Presenter: Zhaleh Safikhani. Poster




Investigating key interactions in breast tumor microenvironment. Personalizing Cancer Medicine Conference, 2016 March, Toronto, Canada. Presenter: Venkata Manem. Poster




Computational biology to link radiomics and genomics. Adaptive Genomics Symposium, RMP Personalized Cancer Program, 2016 March 11, Toronto, Ontario, Canada. Presenter: Benjamin Haibe-Kains. Slides




Reproducibility in Large Pharmacogenomics Studies: Will We Reach Consensus? The 17th MAQC Project Meeting, MAQC and JMAC Joint Workshop on Sequencing Quality Control Phase II (SEQC2), 2016 February 11, Tokyo, Japan. Presenter: Benjamin Haibe-Kains. Slides




2015

Revisiting inconsistency in large pharmacogenomic studies. iBRIGHT Symposium, MD Anderson Cancer Center, 2015 November 1, Houston, Texas, USA. Presenter: Benjamin Haibe-Kains. Slides




Investigating key players in breast cancer microenvironment interactions. Canadian Cancer Research Conference, 2015 November, Montreal, Canada. Presenter Venkata Manem. Poster




Integration of pharmacogenomic datasets enables identification of tumor­-specific isoforms as expression­-based biomarkers predictive of drug response. Canadian Cancer Research Conference 2015, November 2015, Montreal, Canada. Presenter: Zhaleh Safikhani. Poster



BIG data for health: Boom or Bust? Techna Symposium: The BIG Machine, Techna Institute, 2015 October 29, Toronto, Ontario, Canada. Presenter: Benjamin Haibe-Kains. Slides




Impact of reproducibility in cell-based drug screening for biomarker development. Basel Life Science Week, 2015 September 23, Basel, Switzerland. Presenter: Benjamin Haibe-Kains. Slides




From CMAP to L1000. LINCS Microenvironment meeting, Videoconference, Oregon Health & Science University, 2015 September 17, Portland, Oregon, USA. Presenter: Benjamin Haibe-Kains. Slides




Pharmacogenomics. Summer Student Seminar Series, Department of Medical Biophysics, University of Toronto, 2015 August 10, Toronto, Ontario, Canada. Presenter: Benjamin Haibe-Kains. Slides




Inference of causal gene regulatory networks from transcriptomic data. BIRS Statistical and Computational Genomics Program, 2015 August 4, Banff, Alberta, Canada. Presenter: Benjamin Haibe-Kains. Slides




Evaluating the genomic integrity within cancer cell lines. James Lepock Memorial Symposium, 2015 July 8, Toronto, Canada. Presenter: Rene Quevedo. Poster




Integration of GTEx with Pharmacogenomic Datasets Enables Identification of Novel Biomarkers Predictive of Drug Response. GTEx Community Meeting, University of Chicago, 2015 June 24, Chicago, Illinois, USA. Presenter: Zhaleh Safikhani / Benjamin Haibe-Kains. Slides



Integrative biomarkers of drug response: Challenges in Pharmacogenomics. Center for Mathematical Medicine Seminar Series, The Fields Institutes, 2015 June 18, Toronto, Ontario, Canada. Presenter: Benjamin Haibe-Kains. Slides




Integrative biomarkers and new therapeutic strategies in breast cancer. Breast Rounds, Princess Margaret Cancer Centre, 2015 June 2, Toronto, Ontario, Canada. Presenter: Benjamin Haibe-Kains. Slides




Applying BIG data to unlock the mysteries of cancer therapeutics. Behind the Scenes, Princess Margaret Cancer Foundation, 2015 April 20, Toronto, Ontario, Canada. Presenter: Benjamin Haibe-Kains. Slides




Biomarker Discovery Using In Vitro Drug Sensitivity: The Good, the Bad and the Ugly. Toronto Bioinformatics Users Group, 2015 February 25, Toronto, Ontario, Canada. Presenter: Benjamin Haibe-Kains. Slides




A Genome-Wide Search for Alternatively Spliced Isoforms as Predictive Biomarkers of Drug Response. Personalizing Cancer Medicine Conference, February 2015, Toronto, Canada. Presenter: Zhaleh Safikhani. Poster




Does clonal heterogeneity affect drug response in cancer cell lines? Precursors to breast cancer and tumor evolution, 14th Annual BCI-McGill Workshop, 2015 January 29, Holetown, Barbados. Presenter: Benjamin Haibe-Kains. Slides

2014

Transcriptional responses to chemicals in hepatocytes in vivo and in vitro. The 16th MicroArray and Sequencing Quality Control Project, Standardizing Genomics and Bioinformatics for Personalized Medicine, 2014 November 8, Shanghai, China. Presenter: Benjamin Haibe-Kains. Slides



Inconsistency in large pharmacogenomic studies: how do we move forward? The 16th MicroArray and Sequencing Quality Control Project, Standardizing Genomics and Bioinformatics for Personalized Medicine, 2014 November 8, Shanghai, China. Presenter: Benjamin Haibe-Kains. Slides



Lack of reproducibility of drug sensitivity data in large pharmacogenomic studies. School of Pharmacy, Fudan University, 2014 November 4, Shanghai, China. Presenter: Benjamin Haibe-Kains. Slides




A Cautionary Tale about Genomic Biomarkers in Cancer, Beyond the Genetic Prescription Pad: Personalized Cancer Medicine in 2014, 2014 February 11, Toronto, Ontario, Canada. Presenter: Benjamin Haibe-Kains. Slides