Postdoctoral Scholar Job at Oregon Health & Science University
Department Overview:
As an organization devoted to the health and well-being of people in Oregon and beyond, OHSU requires its employees to be fully vaccinated against COVID-19.
OHSU Knight Cancer Institute, known as one of the pioneers in personalized cancer medicine, is an international leader in research and cancer treatment. Driven by its mission to end cancer as we know it, the institute is building upon its expertise in targeted treatments to advance the early detection of cancer when the disease is most treatable.
An exciting opportunity has been created for an experienced researcher to join Dr. Theodore Braun’s and Gurkan Yardimci’s research groups as a Post-Doctoral Fellow at Oregon Health & Science University in Portland, OR.
Dr. Braun and Yardimici have several collaborative projects investigating how 3D genome organization contributes to normal and malignant blood cell development. Dr. Braun is a physician scientist whose lab studies the process of clonal evolution in myeloid malignancies using high sensitivity and single cell epigenetic analysis of murine models and primary patient samples. Dr. Yardimci is a computational biologist whose lab develops new approaches for the analysis and interpretable modeling of single cell multi-omics assays to characterize cell states in heterogenous cell populations. This position will be a computational position with the fellow jointly mentored by Dr. Braun and Dr. Yardimci.
Key publications relevant to this position include:
- Yashar WM, Kong G, VanCampen J, Smith BM, Coleman DJ, Carbone L, Yardimci GG, Maxson JE, Braun TP, (2022) GoPeaks: Histone Modification Peak Calling for CUT&Tag. Genome Biology 23(144).
- Braun TP, Okhovat M, Coblentz C, Carratt SA, Foley A, Schonrock Z, Smith BM, Nevonen K, Davis B, Garcia B, LaTocha D, Weeder BR, Grzadkowski MR, Estabrook JC, Manning HG, Watanabe-Smith K, Jeng S, Smith JL, Leonti AR, Ries RE, McWeeney S, Di Genua C, Drissen R, Nerlov C, Meshinchi S, Carbone L, Druker BJ, Maxson JE, (2019). Myeloid lineage enhancers drive oncogene synergy in CEBPA/CSF3R mutant acute myeloid leukemia. Nature Communications, Nov 29;10(1):5455. PMID: 31784538.
- Braun TP, Coblentz C, Smith BM, Schonrock Z, Carratt SA, Maniaci B, Druker BJ, Maxson JE, (2020). Combined inhibition of JAK/STAT pathway and lysine-specific demethylase 1 as a therapeutic strategy in CSF3R/CEBPA mutant acute myeloid leukemia, PNAS. June 16; 117(24):13670-13679. PMID: 32471953.
- Yashar WM, Smith BM, Coleman DJ, VanCampen J, Kong G, Macaraeg J, Estabrook J, Demir E, Long N, Bottomly D, McWeeney SK, Tyner JW, Druker BJ, Maxson JE, Braun TP (2022). Dual Targeting of FLT3 and LSD1 Disrupts the MYC Super-Enhancer Complex in Acute Myeloid Leukemia, bioRxiv. doi: https://doi.org/10.1101/2022.01.17.476469
- Hyeon-Jin Kim*, Galip Gürkan Yard¿mc¿*, Giancarlo Bonora, Vijay Ramani, Jie Liu, Ruolan Qiu, Choli Lee, Jennifer Hesson, Carol B. Ware, Jay Shendure, Zhijun Duan, William Stafford Noble. Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data, PLOS Comp Bio, 2020
- Ryan M. Mulqueen, Dmitry Pokholok, Brendan L. O’Connell, Casey A. Thornton, Fan Zhang, Brian J. O’Roak, Jason Link, Galip Gürkan Yard¿mc¿, Rosalie C. Sears, Frank J. Steemers & Andrew C. Adey. High-content single-cell combinatorial indexing, Nature Biotechonology, 2021
- Yashar WM, Kong G, VanCampen J, Smith BM, Coleman DJ, Carbone L, Yardimci GG, Maxson JE, Braun TP GoPeaks: histone modification peak calling for CUT&Tag, Genome Biology, 2022
This position will involve analysis and interpretation of single cell multi-omic data sets generated in the Braun lab using single cell combinatorial indexing workflows applied to blood cells from human and mouse models. The fellow will work closely with the wet lab researchers to interpret data as well as design novel analysis approaches and algorithms to establish the relationship between chromatin accessibility, DNA methylation and 3D genome organization in cancerous blood cells. We are particularly interested in candidates who are experienced in genomics, epigenetics, chromatin organization and single cell biology. Strong candidates will have experience with genomic analysis tools as well as R and Python programing languages. Applicants will need to possess strong organizational and communication skills as well as the ability to work independently. Some weekend work is required.
Duties will include:
- Every Knight Cancer employee is expected to embody our guiding principles:
- We act BOLDLY—Breakthroughs require pushing the boundaries of science, exploring new frontiers, and thinking differently
- We SUPPORT each other—Respect leads to trust, which leads to excellence
- We work as a CONNECTED team — We must leverage our collective brain power to conquer cancer because no one individual can do it alone
- Prepare manuscripts, and present research findings as abstracts or oral presentations. Travel may be required.
- Attend weekly group meetings and 1:1 meeting to: 1) Present data and interpretation of results; 2) Troubleshoot research results; 3) Suggest next steps.
- Attend research-related meetings. These could include but are not limited to: team meeting, seminars, and journal clubs.
- Perform experiments utilizing appropriate lab or computational techniques with proficiency, evaluate results, and determine the next steps to complete project and present data. Think independently and solve problems. Stay on top of scientific literature and build skills to maximize project potential.
- Duties as assigned.
Education & Experience:
- PhD with major coursework in the one of the following areas: genomics, genetics, computational biology, statistics, computer science or machine learning
Job Related Knowledge, Skills and Abilities (Competencies):
- Ability to utilize computational genomics software. These include (not exhaustively) utilization of omics data processing pipelines, clustering/trajectory analysis of single-cell omics data, enrichment analysistools/methods. Differential expression analysis methods.
- Experience in scripting/coding in one or more of the following languages: R, python, bash scripting
Education & Experience:
- Minimum of 3 years as a graduate student
Job Related Knowledge, Skills and Abilities (Competencies):
- Experience in application and/or development of computational approaches for modeling genomics data, using methodologies such as deep learning, dimensionality reduction, Bayesian statistics, graphical models
- Experience in working with existing software for the analysis of next generation sequencing genomics data such as RNA-seq, ATAC-seq and Hi-C, including their single-cell and multiomic versions.
Please submit a resume and cover letter for your application to be considered.
Please note: As of Oct. 18, 2021, all OHSU employees are required to be fully vaccinated against COVID-19. Fully vaccinated means you have received both doses of a two-dose, or one dose of a single-dose, FDA- or WHO-authorized COVID-19 vaccine and at least 14 days have passed since your final dose of COVID-19 vaccine. If you apply for and are offered a position, you must be fully vaccinated prior to starting work.
If the position you are offered does not require direct, in-person patient care contact, you may request an exception to the vaccine policy for medical or religious reasons. OHSU uses very narrow criteria under the law to allow an exception and very few requests are being approved.
All are welcome: Oregon Health & Science University values a diverse and culturally competent workforce. We are proud of our commitment to being an equal opportunity, affirmative action organization that does not discriminate against applicants on the basis of any protected class status, including disability status and protected veteran status. Individuals with diverse backgrounds and those who promote diversity and a culture of inclusion are encouraged to apply. To request reasonable accommodation contact the Affirmative Action and Equal Opportunity Department at 503-494-5148 or aaeo@ohsu.edu.
As an organization devoted to the health and well-being of people in Oregon and beyond, OHSU requires its employees to be fully vaccinated against COVID-19.
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