NATALIE R. DAVIDSON, Ph.D.
Department of Biomedical Informatics University of Colorado Anschutz Medical Campus 1890 N Revere Ct, Aurora, CO | www.natalie-r-davidson.com natalie.davidson@cuanschutz.edu |
Research Interests
Ovarian cancer is a heterogeneous disease with several histologically and molecularly defined subtypes. In addition to the subtype heterogeneity, there is variability within the tumor microenvironment and across different populations. I will build an interdisciplinary lab that utilizes cutting-edge machine learning techniques to disentangle the molecular and clinical features of ovarian cancer and to identify drivers of tumor progression and treatment response. |
Education
Ph.D. | Weill Cornell Medical College Tri-Institutional Program in Computational Biology and Medicine Advisor: Dr. Gunnar Ratsch | 2013-2019 |
M.S. | University of California, Los Angeles Department of Computer Science, focus: Computational Biology Advisor: Dr. Jason Ernst | 2011-2013 |
B.S. | University of California, Santa Barbara Department of Computer Science | 2006-2011 |
Research Experience
Post Doctoral | University of Colorado, Anschutz Medical Campus Topics: Ovarian cancer subtype prediction Inferring missing biological or perturbation states by integrating multiple sequencing technologies | 2019-2020 |
Post Doctoral | Swiss Federal Institute of Technology Topic: Interpretable machine learning methods to understand disease-specific pathway changes | 2019 |
Ph.D. | Weill Cornell Medical School Research locations: Swiss Federal Institute of Technology Memorial Sloan Kettering Cancer Center Topic: Quantifying and interpreting RNA alterations in cancer | 2013-2019 |
M.S. | University of California, Los Angeles Topic: Prediction of transcription factor binding patterns | 2011-2013 |
Funding
National Institutes of Health: Pathway to Independence K99/R00 (1K99HG012945) PI: Natalie Davidson Ph.D. Title: Domain adaptation approaches to unify established and emerging sequencing technologies | 2023-2025 |
Publications
Preprints (* equal contribution, ^ co-corresponding)
- Davidson NR*, Barnard ME*, … (2023) Molecular subtypes of high grade serous ovarian cancer across racial groups and gene expression platforms. bioRxiv doi:10.1101/2023.11.01.565179
- Davidson NR, and Greene CS (2023) BuDDI: Bulk Deconvolution with Domain Invariance to predict cell-type-specific perturbations from bulk. bioRxiv doi:10.1101/2023.07.20.549951
- Hippen AA, Davidson NR, Barnard ME, Weber LM, Gertz J, Doherty JA, Hicks SC and Greene CS, (2023) Deconvolution reveals compositional differences in high-grade serous ovarian cancer subtypes. bioRxiv doi:10.1101/2023.06.14.544991
Peer-Reviewed
- Davidson NR, and Greene CS (2023) Analysis of science journalism reveals gender and regional disparities in coverage. Highlighted in a Nature Magazine editorial.
eLife doi:10.7554/eLife.84855.1 - Hippen AA*, Davidson NR* and Greene CS (2022) Computational audits combat disparities in recognition.
Nature Human Behaviour doi:10.1038/s41562-021-01279-2 - Salloum D, Singh K, Davidson NR, Cao L, Kuo D, Sanghvi VR, Jiang M, Lafoz MT, Viale A, Ratsch G and Wendel HG (2022) A rapid translational immune response program in CD8 memory T lymphocytes.
The Journal of Immunology doi:10.4049/jimmunol.2100537 - Simmler P, Cortijo C, Koch LM, Galliker P, Angori S, Bolck HA, Mueller C, Vukolic A, Mirtschink P, Christinat Y, Davidson NR, Lehmann KV, Pellegrini G, Pauli C, Lenggenhager D, Guccini I, Ringel T, Hirt C, Marquart KF, Schaefer M, Rätsch G, Peter M, Moch H, Stoffel M, Schwank G (2022) SF3B1 facilitates HIF1-signaling and promotes malignancy in pancreatic cancer.
Cell Reports doi:10.1016/j.celrep.2022.111266 - Markolin P*, Davidson NR*, Hirt CK, Chabbert CD, Zamboni N, Schwank G, Krek W and Rätsch G (2021) Identification of HIF-dependent alternative splicing in gastrointestinal cancers and characterization of a long, coding isoform of SLC35A3.
Genomics doi:10.1016/j.ygeno.2020.12.039 - Stark SG, Gut G, Rätsch G^ and Davidson NR^ (2021) pmVAE: Learning Interpretable Single-Cell Representations with Pathway Modules.
ICML Computational Biology Workshop - PCAWG Transcriptome Core Group*, Calabrese C*, Davidson NR*, Demircioğlu D*, Fonseca NA*, He Y*, Kahles A*, Lehmann KV*, Liu F*, Shiraishi Y* and Soulette CM*, et al. (2020) Genomic basis for RNA alterations in cancer. Included as part of a Nature special collection
Nature doi:10.1038/s41586-020-1970-0 - Krishnamoorthy GP, Davidson NR, Leach SD, Zhao Z, Lowe SW, Lee G, Landa I, Nagarajah J, Saqcena M, Singh K and Wendel HG (2019) EIF1AX and RAS mutations cooperate to drive thyroid tumorigenesis through ATF4 and c-MYC.
Cancer discovery doi:10.1158/2159-8290.CD-18-0606 - Davidson NR, Godfrey KR, Alquaddoomi F, Nola D and DiStefano III JJ (2017) Disting: A web application for fast algorithmic computation of alternative indistinguishable linear compartmental models.
Computer Methods and Programs in Biomedicine doi:10.1016/j.cmpb.2017.02.025 - Waldman YY, Biddanda A, Davidson NR, Billing-Ross P, Dubrovsky M, Campbell CL, Oddoux C, Friedman E, Atzmon G, Halperin E and Ostrer H (2016) The genetics of Bene Israel from India reveals both substantial Jewish and Indian ancestry.
PLoS One doi:10.1371/journal.pone.0152056
Consortium Contributions
- Tumor Profiler Consortium (2021) The tumor profiler study: integrated, multi-omic, functional tumor profiling for clinical decision support.
Cancer cell doi:10.1016/j.ccell.2021.01.004 - International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA) Pan-Cancer Analysis of Whole Genomes Consortium (2020) "Pan-cancer analysis of whole genomes"
Nature doi:10.1038/s41586-020-1969-6 - Coronavirus Census Collective (2020) Building an international consortium for tracking coronavirus health status.
Nature medicine doi:10.1038/s41591-020-0929-x
Honors
University of Colorado, Anschutz Postdoctoral Association, Postdoc of the Month | 2023 |
International Society for Computational Biology, Rocky Mountain Bioinformatics Conference, Best Poster | 2021 |
Swiss Institute of Bioinformatics, Recognition of Remarkable Output | 2020 |
Intelligent Systems For Molecular Biology Student Council, Best Student Talk | 2017 |
Intelligent Systems For Molecular Biology Student Council, 3rd Best Student Talk | 2016 |
Selected to Participate in the Leena Peltonen School of Human Genetics | 2016 |
Professional Presentations
Invited Panelist
Reporting With Education Research, “News source diversity” | 2023 |
Open Innovation in Life Sciences, “Crowd-sourcing your research” | 2020 |
Oral Presentations
Quantitative Cell and Molecular Biology Summer School Symposium, BuDDI: Bulk Decomposition with Domain Invariance Colorado State University | 2023 |
Department of Biomedical Informatics Retreat, Trainee Presentations BuDDI: Bulk Decomposition with Domain Invariance University of Colorado, Anschutz Medical Campus | 2023 |
Intelligent Systems for Molecular Biology, Equity-Focused Research Analysis of science journalism reveals gender and regional disparities in coverage Madison, Wisconsin | 2022 |
CU Denver Data Science Symposium Analysis of science journalism reveals gender and regional disparities in coverage Virtual | 2021 |
International Conference on Machine Learning, Machine Learning for Global Health Anonymous Survey System and Methodology to Enable COVID-19 Surveillance Virtual | 2020 |
RECOMB Computational Cancer Biology Integrating Diverse Transcriptomic Alterations to Identify Cancer-Relevant Genes Paris, France | 2018 |
Intelligent Systems for Molecular Biology, Student Council Identification and Characterization of Hypoxia-Inducible Factor (HIF) -Dependent Alternative Splicing Events in Pancreatic Cancer Chicago, IL | 2018 |
Intelligent Systems for Molecular Biology, Student Council and HiT-Seq Integrating Diverse Transcriptomic Alterations to Identify Cancer-Relevant Genes Prague, Czech Republic | 2017 |
Intelligent Systems for Molecular Biology, Student Council Differential Expression Method for Related Samples Orlando, FL | 2016 |
Poster Presentations
ISMB, Machine Learning in Computational and Systems Biology BuDDI: Bulk Decomposition with Domain Invariance Lyon, France | 2023 |
ISMB, Machine Learning in Computational and Systems Biology BuDDI: Bulk Decomposition with Domain Invariance Madison, WI | 2022 |
ISCB Rocky Mountain Bioinformatics Conference BuDDI: Bulk Decomposition with Domain Invariance Snowmass, CO | 2021 |
Intelligent Systems for Molecular Biology, Translational Medicine ssPATHS: Single Sample PATHway Score Basel, Switzerland | 2019 |
Intelligent Systems for Molecular Biology, RegSys Identification and Characterization of hypoxia-inducible Factor (HIF) -Dependent Alternative Splicing Events in Pancreatic Cance Chicago, IL | 2018 |
Intelligent Systems for Molecular Biology, Integrative RNA Biology Differential Expression Method for Related Samples Orlando, FL | 2016 |
The Cancer Genome Atlas' 4th Scientific Symposium Integrative Analysis of Transcriptome Variation in Uterine Carcinosarcoma and Comparison to Sarcoma and Endometrial Carcinoma Bethesda, MD | 2015 |
Teaching
Computational Biomedicine (Lecturer) Taught methods and techniques to MS students for utilizing bulk and single-cell data. | 2019-2020 |
Digital Medicine (Lecturer) Taught methods and techniques to medical students for utilizing health-related data. | 2020 |
Learning and Intelligent Systems (Teaching Assistant) Taught introduction to probabilistic modeling. | 2017-2019 |
Intro to Machine Learning (Teaching Assistant) Taught introduction to probabilistic modeling and kernels. | 2017-2019 |
Mentorship
CU Anschutz WiSTEM Mentor Mentor to two CU Anschutz students. I will meet monthly with the students to provide research and career advice | 2023 |
Co-advisor for 2 CPBS Summer Students, one continued as a semester intern / 6 months Student 1 Thesis Title: Predicting Cell Types from scATAC-seq using Machine Learning Work was selected for a poster presentation at Rocky Mountain Bioinformatics Conference and was submitted as an entry to the Kaggle competition “Multimodal Single-Cell Integration” Student 2 Thesis Title: Data Pipeline for Signal Processing of scATAC-Seq Data Work was presented as a poster at the conclusion of the CPBS summer program | 2022 |
Co-Advisor Master Student / 9 months Thesis Title: Auto-Encoding Regulatory Processes in Cancer. Work led to a first authorship highlight paper in the ICML CompBio Workshop. | 2020 |
Co-Advisor Master Student / 6 months Thesis Title: Detection of epithelial to mesenchymal transition using expression data. Student won the best presentation at the ISCB Student Council | 2019 |
Co-Advisor Semester Student / 2 months Project Title: Joint estimation of pathway disruption. | 2019 |
Co-Advisor Semester Student / 3 months Project Title: Identifying hypoxic, RAS, and P53 pathway activation in TCGA data and predicting drug resistance in external cohorts. | 2018 |
Co-Advisor Master Student / 6 months Thesis Title: Identifying subpopulations of cancer cells and their interactions using proteomic single-cell data. | 2017 |
Reviewer
Nature Methods | Nature Communications | Bioinformatics | NAR Genomics and Bioinformatics |
GigaScience | PLOS Genetics | PLOS One | PLOS Computational Biology |
Service
Department of Biomedical Informatics, Seminar Committee | 2023 - |
Science Ambassador Scholarship, Advisory Board Member & Judge | 2020 - |
Postdoctoral Search Committee Head, Greene Lab, Dept. of Biomedical Informatics | 2023 |
Postdoctoral Search Committee, Pividori Lab, Dept. of Biomedical Informatics | 2023 |
Aurora Science and Tech, Seminar Speaker | 2022 |
Postdoctoral Search Committee Head, Way Lab, Dept. of Biomedical Informatics | 2021 |
Social Chair, Tri-I Computational Biology and Medicine Ph.D. Program | 2014-2015 |
GRASSHOPR Mentor, Cornell University | 2013-2014 |