Herbold Computational Biology Job Openings

Overview

Cures Start Here. At Fred Hutchinson Cancer Research Center, home to three Nobel laureates, interdisciplinary teams of world-renowned scientists seek new and innovative ways to prevent, diagnose and treat cancer, HIV/AIDS and other life-threatening diseases. Fred Hutch’s pioneering work in bone marrow transplantation led to the development of immunotherapy, which harnesses the power of the immune system to treat cancer. An independent, nonprofit research institute based in Seattle, Fred Hutch houses the nation’s first cancer prevention research program, as well as the clinical coordinating center of the Women’s Health Initiative and the international headquarters of the HIV Vaccine Trials Network. Careers Start Here.

At Fred Hutch, we believe that the innovation, collaboration, and rigor that result from diversity and inclusion are critical to our mission of eliminating cancer and related diseases. We seek employees who bring different and innovative ways of seeing the world and solving problems. Fred Hutch is in pursuit of becoming an antiracist organization. We are committed to ensuring that all candidates hired share our commitment to diversity, antiracism, and inclusion.

A Computational Biologist/Bioinformatics Analyst position in the laboratory of Dr. Erick Matsen and the Computational Biology Program is available immediately. The position is to develop novel variational Bayes approaches to phylogenetics.

Responsibilities

We will work together to develop and implement new algorithms in our C++ library, as well as maintain/refactor our codebase as it evolves in response to what we learn in our research. We will collaborate with research groups across the world, including:

• Marc Suchard, a leading biostatistician especially known for his work in “phylodynamics”: the intersection of phylogenetics, immunology, and epidemiology
• Mathieu Fourment, who has led the development of fixed-tree variational inference for time-tree models
• Cheng Zhang (张成), who has led the development of flexible-tree variational inference

Qualifications

This position has no formal education or academic publication requirements. We welcome people to apply whatever their background. This position is budgeted for a junior-level programmer, but more experienced developers are encouraged to get in touch and we will see what we can do.

Minimum qualifications

• Bachelor’s degree in the quantitative or physical sciences, or equivalent experience
• 2-4 years of experience with scientific computing, ideally in the domain of biomedical/scientific research and genomics/proteomics
• 2+ years of experience programming in R and/or Python, ideally both
• 2+ years of experience with high-performance computing (i.e., the development of multi-core or multi-threaded computational jobs)
• Strong analytical abilities and problem-solving skills
• Experience in data management and developing data-processing pipelines
• Knowledge of databases, including relational databases and no-SQL databases, e.g., MongoDB
• A solid understanding of high-level programming concepts, data structures and algorithms
• Familiarity with inferential statistics and machine learning
• Familiarity with software development best practices (e.g., unit testing, version control)
• Excellent written and oral communication skills

Essential skills

• demonstrated coding ability
• desire to produce clean (clear, factored, and tested) code
• motivation to learn new topics and dive into a complex programming language (C++17)
• ability to work in a team and communicate
• ability to find solutions independently

 
Additional helpful skills

• experience with C++, and with modern C++ idioms
• background in probability and Bayesian inference
• experience with Python
• experience with a modern git-based workflow
• experience with PyTorch or TensorFlow
• experience with Docker and continuous integration
• experience developing in a Linux environment

Application instructions

• If you are interested in this position, please submit the following materials:
• A code sample showing work that you are proud of. This has to be nontrivial, but doesn’t have to be long. Ideally it would be publicly accessible, e.g. on GitHub, but if that’s not possible an emailed attachment is fine too.
• A CV summarizing your work experience so far
• The names and email addresses of three references

A statement describing your commitment and contributions toward greater diversity, equity, inclusion, and anti-racism in your career or that will be made through work at Fred Hutch is requested of all finalists.

Overview

Cures Start Here. At Fred Hutchinson Cancer Research Center, home to three Nobel laureates, interdisciplinary teams of world-renowned scientists seek new and innovative ways to prevent, diagnose and treat cancer, HIV/AIDS and other life-threatening diseases. Fred Hutch’s pioneering work in bone marrow transplantation led to the development of immunotherapy, which harnesses the power of the immune system to treat cancer. An independent, nonprofit research institute based in Seattle, Fred Hutch houses the nation’s first cancer prevention research program, as well as the clinical coordinating center of the Women’s Health Initiative and the international headquarters of the HIV Vaccine Trials Network. Careers Start Here.

At Fred Hutch, we believe that the innovation, collaboration, and rigor that result from diversity and inclusion are critical to our mission of eliminating cancer and related diseases. We seek employees who bring different and innovative ways of seeing the world and solving problems. Fred Hutch is in pursuit of becoming an antiracist organization.  We are committed to ensuring that all candidates hired share our commitment to diversity, antiracism, and inclusion.   

Post-Doctoral Research Fellow/Research Associate - Postdoctoral position to develop Bayesian methods for B cell receptor sequence lineages

The goal of our project is to develop, implement, and apply Bayesian evolutionary algorithms for the analysis of B cell receptor sequence lineages. These lineages are important for understanding the events leading to the development of high-affinity antibodies.

We are motivated to:

• use a Bayesian approach to appropriately account for uncertainty in phylogenetic inferences (which is considerable in this case)
• fit and use complex models of somatic hypermutation and selection that violate the commonly-applied IID assumption in phylogenetics
• develop efficient, elegant, and robust implementations of the newly developed methodology and make them available in open-source software for the community.

Responsibilities

We will work together to develop novel models, implement these models in open-source software, write tests to verify correctness, apply the methods to a variety of data sets, and write papers describing the results.

We’ll have the opportunity to work with a broad range of leading researchers, including:

• biologists Jesse Bloom, Leslie Goo, Julie Overbaugh, Gabriel Victora, and their labs
• statisticians Vladimir Minin, Noah Simon, Marc Suchard, and their groups.
   

You can find out more about our group by visiting: 

http://matsen.fredhutch.org/
http://github.com/matsengrp

Qualifications

The ideal candidate for this project would have experience with the statistical underpinnings of Bayesian phylogenetic analysis, as well as experience implementing models in code. However, we welcome applications from candidates with less statistical expertise but a deep desire to expand their skills in this area. We hope applicants will want to improve their coding abilities through clean coding practices, code review, and a modern development workflow. The ideal candidate would also be motivated to improve biological understanding through computation, and so would be enthusiastic about working closely with our leading biologist collaborators.

MINIMUM QUALIFICATIONS:

• Ph.D. in biology, computer science, math, or another relevant area
• Solid foundation in Bayesian phylogenetics or other challenging Bayesian estimation problem
• Computer programming experience
• Clear ability to perform independent research
   

If you are interested in this position, please submit the following materials:

• Two representative publications
• A code sample
• CV

A statement describing your commitment and contributions toward greater diversity, equity, inclusion, and antiracism in your career or that will be made through work at Fred Hutch is requested of all finalists.

Overview

Cures Start Here. At Fred Hutchinson Cancer Research Center, home to three Nobel laureates, interdisciplinary teams of world-renowned scientists seek new and innovative ways to prevent, diagnose and treat cancer, HIV/AIDS and other life-threatening diseases. Fred Hutch’s pioneering work in bone marrow transplantation led to the development of immunotherapy, which harnesses the power of the immune system to treat cancer. An independent, nonprofit research institute based in Seattle, Fred Hutch houses the nation’s first cancer prevention research program, as well as the clinical coordinating center of the Women’s Health Initiative and the international headquarters of the HIV Vaccine Trials Network. Careers Start Here.

At Fred Hutch, we believe that the innovation, collaboration, and rigor that result from diversity and inclusion are critical to our mission of eliminating cancer and related diseases. We seek employees who bring different and innovative ways of seeing the world and solving problems. Fred Hutch is in pursuit of becoming an antiracist organization. We are committed to ensuring that all candidates hired share our commitment to diversity, antiracism, and inclusion.

The laboratory of Dr. Gavin Ha in the Computational Biology Program of the Public Health Sciences and Human Biology Divisions has an open position for a Research Laboratory Manager. We are seeking a highly motivated individual who has the experience and leadership to support the group’s development of innovative computational and experimental approaches to study the genetics and epigenetics of cancer. Candidates who are excited to be part of a team working on large/complex ‘omics’ data analysis of cancer genomes and “liquid biopsy” approaches to study cancer are encouraged to apply. The position has a competitive salary with great benefits. 

The Ha Laboratory is located in the Lake Union Steam Plant Building, which is the newest Fred Hutch facility. Steam is home to 23 laboratories consisting of 275 experts in computational biology, data science, and immunotherapy who use cutting-edge technologies and tools to revolutionize cancer treatment. The Ha Laboratory is seeking a motivated individual to plan and implement start-up of wet-lab operations in a newly renovated laboratory space, and to manage experimental and computational projects. 

We work in an interdisciplinary team environment with many local and external experts. All of our projects involve partnering with investigators and laboratories who have diverse expertise in computational, molecular, experimental, and cancer biology, and in clinical research.  

Responsibilities

The study areas for this position center on cancer genomics, tumor microenvironment, chromatin and epigenetic profiling, cell-free DNA from liquid biopsies, and translation of cancer biomarkers to improve treatment strategies.  

The successful applicant will engage in the following: 

• Plan, implement, and manage startup of wet-lab operations in the experimental laboratory at Steam
• Develop management plan for reproducible science including documentation plan for analysis, code, and laboratory SOPs. Provide tutorials, workshops, individual training on experimental design, data analysis, and instrumentation use. 
• Perform complex lab experiments and manage laboratory/program projects and resources
• Supervise laboratory-based studies and provide day-to-day supervision, guidance, training, and support for lab members. Supervise direction and performance management. Allocate and monitor effort and progress, manage workloads and priorities, redistribute or negotiate addition of resources as required.  
• Manage financial forecasting and reporting activities for laboratory/program
• Manage experimental and computational projects. Work with internal and external partners to define project goals, resources, priorities.
• Coordinate meeting agendas, track project progress, write progress reports. Ensure deliverables are completed within projected timelines. 
• Facilitate and track communications and serve as laboratory/program representative to PI in meetings with collaborators, vendors, administration, and regulatory agencies/depts, as necessary to ensure success of the research program
• Ensure regulatory and policy compliance with human genomic data security, privacy and confidentiality
• Participate in and assist in grant preparation process, including application and renewal process, progress reports, reviewing proposals for accuracy
• May participate in and assist with manuscript preparation for publication in scientific journals and presentation preparation for conferences and symposiums

Other responsibilities may include: 

• Interview new hires and facilitate onboarding
• Support new Ha lab members to integrate into and navigate the lab and Hutch culture, resources, compute environments, and connect with people or groups throughout the Hutch
• Foster creativity and enthusiasm in the lab, encouraging a positive environment where everyone’s unique skills are nurtured and strengthened

Qualifications

Applicants must have at least a bachelor’s degree with training in one or more of these disciplines: 

• Biology, biochemistry, genetics, molecular biology, cell biology, immunology or related field is required

Applicants require more than 5 years of research laboratory experience and two years laboratory management experience and must have the following skills: 

• Works well in team environments, has strong communication/organization skills and is detail oriented
• Highly motivated individual who thinks independently and also enjoys working in dynamic, collaborative, multidisciplinary teams
• Excellent verbal and written communication skills are essential

Preferred applicants will have some or all of the following skills and experience: 

• Expertise/skills in molecular biology techniques is desired: RT-PCR, immunohistochemistry, ELISA, cell culture
• Experience with cell-free DNA, ATAC-seq, ChIP-seq, epigenomics, single-cell assays is a strong asset
• Experience with programming (R, Python, C/C++, Perl, Java, Matlab or other languages for research) is a plus
• Experience with analyzing sequencing data and cancer genome data is considered a plus
• Experience with high performance computing environments and cloud computing environments is a plus
• Demonstrated scientific publication track record
• Leadership and management training a plus

To apply, please submit your application with the following: 

• A statement of research interests 
• CV 
• names and email addresses of three references 

A statement describing your commitment and contributions toward greater diversity, equity, inclusion, and anti-racism in your career or that will be made through work at Fred Hutch is requested of all finalists.