Experience
| 2023-present | Deputy Chair, Department of Epidemiology and Biostatistics |
| 2023-present | Professor, City University of New York Graduate School of Public Health and Health Policy and Institute for Implementation Science in Public Health |
| 2018-2023 | Associate Professor, City University of New York Graduate School of Public Health and Health Policy and Institute for Implementation Science in Public Health |
| 2016–2018 | Assistant Professor, City University of New York Graduate School of Public Health and Health Policy and Institute for Implementation Science in Public Health |
| 2013–2016 | Assistant Professor, City University of New York School of Public Health at Hunter College. |
| 2010-2013 | Post-doctoral Fellow, Harvard University School of Public Health. |
| 2008-2010 | Post-doctoral Fellow, Ontario Cancer Institute |
| 2007-2008 | Post-doctoral Fellow, University of Toronto |
| 2005-2007 | Post-doctoral Fellow, Royal Roads University |
Education
| 1998-2005 | PhD, University of Toronto, Faculty of Arts & Science (Wood Physics) |
| 1996-1998 | MS, University of Waterloo, Faculty of Science (Physics) |
| 1991-1995 | BS, University of British Columbia, Faculty of Science (Physics) |
Publications
| See publications page. |
Software
| See software page. |
Current Funding
| 2023 - 2025 | Michael J. Fox Foundation for Parkinson’s Research, The centralized microbiome analytic core (MAC) - Bioinformatics Support |
| This project supports microbiome data analysis and harmonization across the MJFF microbiome research teams. |
| 2021 - 2026 | NIH 5U24HG004059 (co-I), Bioconductor: An Open-Source, Open-Development Computing Resource for Genomics |
| This project supports the core development team and the software/data infrastructure of Bioconductor. |
| 2019-2024 | NIH 1U01 CA230551 (PI), Exploiting public metagenomic data to uncover cancer-microbiome relationships. |
| This project improves the ability to identify new roles of the human microbiome in cancer by 1) enabling comprehensive comparisons of microbiome studies to previously published results and known microbial physiology, 2) developing higher- resolution approaches to identifying viruses and bacterial strains from metagenomic shotgun data, and 3) making all methods and resources easily usable by a broad research community. |
| 2019 - 2024 | NIH 2U24 CA180996 (co-PI), Cancer genomics: integrative and salable solutions in R/Bioconductor. |
| Researchers collect diverse types of complex genetic information about factors that contribute to cancer. This proposal provides software and data resources to help researchers manage and analyze this information using advanced computational and statistical approaches. |
| 2018 - 2028 | NIH 5U24 HG010263 (co-PI), Implementing the genomic data science analysis, visualization, and informatics lab-space (AnVIL). |
| The goal of this project is to create a cloud-based computational analysis and visualization workspace for genomic research. The research enabled by this workspace will accelerate our understanding of the genetic components of human health and disease and progress towards precision genomic medicine. |
Completed Funding
| 2016-2019 | NIH 1R21 AI 121784-01 (Co-I), The representative microbiome: social determinants and tools for population research. |
| The purpose of this study is to describe sociodemographic variation in the oral microbiome in a national population-based sample. Links between the human microbiome and health are just beginning to emerge and could provide novel prevention and intervention strategies for health disparities. |
| 2016-2016 | US Department of State Fulbright Scholar Program, Applied statistics for high-throughput biology; Enhanced estimation of the cancer proteome from the transcriptome Assays. |
| Visiting professor to the Center for Integrative Biology, Trento, Italy. |
| 2015-2018 | NIH 1R03 CA 191447 – 01A1 (PI), Validation and clinical relevance of ovarian cancer subtypes. |
| This project employs meta-analysis to resolve uncertainty around the robustness and relationship to patient outcome of proposed molecular subtypes of ovarian cancer. It establishes whether genetic heterogeneity within tumors is likely to be an obstacle to subtype-specific therapies. It provides open-source implementations of all proposed subtypes to facilitate their usage by other translational researchers. These objectives will facilitate adoption of the most clinically relevant molecular subtypes to inform precision treatment of ovarian cancer. |
| 2015-2016 | Weill Cornell School of Medicine CTSC Pilot Award (Co-PI), Non-invasive quantitative ultrasound imaging in assessment of patients undergoing native kidney biopsy. |
| 2014-2019 | NIH U24CA180996 (Co-I), Cancer genomics: integrative and scalable solutions in R/Bioconductor. |
| Researchers collect diverse types of complex genetic information about factors that contribute to cancer. This proposal helps researchers manage and analyze this information using advanced computational and statistical approaches. |
| 2013-2018 | NIH 5R01MH101028-03 (Co-I), HIV care coordination: comparative effectiveness, outcome determinants, and costs. |
| This study aims to assess the effectiveness of the NYC Ryan White comprehensive HIV Care Coordination Program (CCP) relative to that of usual care outside the CCP for persons living with HIV and residing in NYC, to determine what individual and program-level factors are associated with optimal care outcomes for CCP participants and to determine the cost-effectiveness of the CCP relative to usual care outside the CCP. |
Teaching
| See teaching page. |
Service
| 2023-Present | Deputy Chair, Department of Epidemiology and Biostatistics, CUNY SPH |
| 2022-Present | President, Microbiome Virtual International Forum Association |
| 2022-2023 | Vice President, Bioconductor Executive Committee |
| 2019-2022 | Secretary, Bioconductor Technical Advisory Board |
| 2019 | Organizing Committee member, European R Users Meeting 2020 |
| 2019-2022 | Chair, Bioconductor Code of Conduct committee |
| 2018-Present | Chair, Bioconductor annual conference committee |
| 2017-2019 | Organizer, New York City R/Bioconductor for Genomics |
| 2017-Present | Member, CUNY High Performance Computing Center Advisory Committee |
| 2013-Present | Member, Bioconductor Technical Advisory Board |