Advertised Summary Job Description: The Department of Systems Biology at Columbia University Medical Center has an opening for a Bioinformatics Software Developer for Dr. Andrea Califano's laboratory. We are looking for a full-stack software engineer to lead the design and implementation of innovative new tools for visualization, data sharing and pipeline development for large-scale, omics-based models of human disease.
The Califano lab researches the molecular determinants of human pathophysiology, with a specific focus on cancer and stem cell biology. We pursue a novel strategy to target cancer, focusing on protein activity and its relationship to the genomic drivers of disease, rather than focusing on the genomics alone. This approach, implemented by a suite of network-based algorithms, identifies the master regulators of human disease and of other pathophysiologic phenotypes from molecular profiles of individual tissues and single cells. We can then prioritize small molecule compounds that are optimally suited to target these mechanisms, and design clinical trials to evaluate the effectiveness of prioritized compounds for individual patients.
We seek a software developer/bioinformatician with experience developing web-based front-ends driving bioinformatics pipelines running on a large-scale distributed computing architecture. The preferred candidate will use his or her understanding of software and API design to lead the development of intuitive tools that will allow our lab to share knowledge involving large-scale gene interaction networks, including proteins, genes and other biomolecules, as well as their role in determining biologically and clinically relevant phenotypes. Experience or a strong interest in biology is a plus as is the ability to team up with computational biologists to design the most effective applications for interpreting complex datasets of cancer and other disease. And not necessary but highly desired, the ideal candidate will also have experience in network/systems biology, including analysis of regulatory networks, integrative analysis to combine evidence from multiple data modalities, and expertise with Bioconductor packages.
Characteristic Duties and Responsibilities:
-Architect and build a high availability web applications to allow members of the scientific community to query results from state-of-the-art computational methods and support integrative data analysis in a variety of human disease and normal physiology settings.
-Become familiar, debug, and maintain robust, fully automated computational pipelines implemented by lab members to elucidate molecular mechanisms and associated small molecule compound dependencies in human disease and human physiology based on the integrative, network-based analysis of multiple 'omics data types.
-Collect and curate publicly available 'omics data sets to support integrative analysis in systems biology based studies.
-Design novel integrative and automation frameworks to create novel pipelines for the analysis of 'omics data.
Additional Specific Minimum Qualifications:
Preferred Qualifications: -The ideal candidate will have a MS or other advanced degree in Computational Biology, Bioinformatics or Genetics, or equivalent. -Prior experience in software engineering and in the design of software for the bioinformatics/systems-biology analysis of biological systems is highly desirable. -The ideal candidate will have significant experience in R and in the use of R packages for bioinformatics analyses, including the Bioconductor framework. - Experience with graph database design and languages (e.g. Neo4j) is desired.
As a member of the National Collegiate Athletic Association (NCAA) and the Council of Ivy Group Presidents (Ivy League), it is imperative that members of the Columbia University community, in all matters related to the intercollegiate athletics program, exhibit the highest professional standards and ethical behavior with regard to adherence to NCAA, Conference, University, and Department of Intercollegiate Athletics and Physical Education rules and regulations.
Columbia University is an Equal Opportunity/Affirmative Action employer.
Internal Number: 126_168993
About Columbia University
Columbia University is one of the world's most important centers of research and at the same time a distinctive and distinguished learning environment for undergraduates and graduate students in many scholarly and professional fields. The University recognizes the importance of its location in New York City and seeks to link its research and teaching to the vast resources of a great metropolis. It seeks to attract a diverse and international faculty and student body, to support research and teaching on global issues, and to create academic relationships with many countries and regions. It expects all areas of the university to advance knowledge and learning at the highest level and to convey the products of its efforts to the world.
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