Skip to main content

This job has expired

Postdoctoral Researcher (Computational Biology)

Employer
The Knight Cancer Institute
Location
Portland, Oregon (US)
Salary
DOE commensurate with experience, education, and equity
Closing date
Jun 9, 2023

View more

Discipline
Life Sciences, Computational Biology, Genomics, Cancer Research
Position Type
Full Time
Job Type
Postdoc
Organization Type
Academia

Cancer Early Detection Advanced Research (CEDAR) center is a collaborative institution within the OHSU Knight Cancer Institute. The Knight Cancer Institute, known as one of the pioneers in personalized cancer medicine, is an international leader in research and cancer treatment. At CEDAR our mission is to detect and stop lethal cancers at the earliest stage because early detection saves lives. This is an ambitious goal, one that requires novelty, creativity, and innovation. We are composed of biologists, chemists, biomedical engineers, computationalists, and clinicians conducting groundbreaking translational cancer research to help people maintain a high quality of life and reduce cancer mortality, to create a global early detection community, and to have a positive impact on the Oregon economy.

We are currently hiring for 1-2 highly motivated fellows with expertise in Computational Biology to work in the following areas. Candidate would work with CEDAR and OHSU scientists including Gurkan Yardimci, Hisham Mohammed, Andrew Adey, Srivathsan Ranganathan, and Xiaolin Nan initially and with increasing collaborations over time:

  • Machine Learning/Statistics – Developing machine learning methods and/or statistical models to study the organization of the epigenome and three dimensional structure of the genome using cutting edge genomics and super resolution microscopy datasets.  Developed algorithms will be used to deeply characterize cell populations and identify features that are indicative of cell state. Techniques such as (but not limited to) dimensionality reduction, clustering, and predictive modeling will be utilized.
  • Genomics/single cell genomics Modeling and analyzing next-generation sequencing datasets that measure the transcriptome and the epigenome, with an emphasis on the single-cell variants, such as single cell RNA-seq and single cell ATAC-seq. The successful candidate will use both existing tools and develop their own computational methods to analyze such datasets for characterization of healthy and cancerous cell populations.
  • Multiomics– Developing computational methods for the analysis of single-cell multiomics technologies that are able to characterize multiple “omes” of a single cell concurrently, such as the epigenome and the transcriptome (see references below). These methods will be utilized for deep characterization of healthy and cancerous cells and investigate the links between the transcriptome, the epigenome and 3D conformation of chromatin.
  • Imaging – Performing analysis of existing genomics data of cancerous cells to aid the design of super high resolution microscopy experiments for imaging the chromatin organization of cancerous cells. The successful candidate will have the opportunity to analyze cutting edge super high resolution microscopy experiments and develop computational methods for joint analysis of genomics and imaging data. 
  • Molecular Modeling - Performing 3D structural modeling of proteins, nucleic acids and small molecules towards predicting biomolecular structure and interactions using MD simulations, molecular docking, and free-energy calculations. Implement AI/machine learning approaches to predict atomic level structures and interactions of proteins using Alphafold, RosettaFold etc.

Select references:

  • https://www.nature.com/articles/s41586-019-1825-8
    https://www.nature.com/articles/nbt.4112
  • https://science.sciencemag.org/content/361/6409/1380
  • https://www.nature.com/articles/s41467-020-18181-6
  • https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008173

Duties Include:

  • Prepare manuscripts, and present research findings as abstracts or oral presentations (travel may be required)
  • Attend weekly group meetings and 1:1 meetings to: 1) present data and interpretation of results; 2) troubleshoot research results and 3) suggest next steps
  • Attend research related meetings including but not limited to Thursday PM SPORE seminars, Cancer Biology meetings, 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 problem solve. Stay on top of the literature and build skills to maximize the projects’ potential.
  • Duties as assigned

CEDAR is committed to increasing the diversity of the campus community. We at CEDAR are dedicated to promoting inclusion and multiculturalism to build a successful organization by having outstanding researchers of diverse backgrounds work together on multiple projects. We encourage high-risk, high-reward research projects because defeating cancer requires unproven, out-of-the-box thinking. Our research is milestone driven to ensure that each project is fulfilling its stated goals.

CEDAR funds its own research projects, expediting the process of discovery. Our research is milestone-driven to ensure that each project is fulfilling its stated goals. CEDAR offers a unique opportunity for outstanding, driven, and creative postdoctoral fellows to perform cutting edge and high-risk research, ranging from understanding basic cancer biology to developing novel technologies to aid detection. Our focus on early detection requires novel approaches to reliably identify small/rare signals in diverse data types, with an emphasis on minimally invasive sampling techniques.

Get job alerts

Create a job alert and receive personalized job recommendations straight to your inbox.

Create alert