Senior Bioinformatician, Echinobase

Echinobase is hiring. Applications will be accepted until we fill the position so apply immediately.

Application Instructions

Applications, including a cover letter, curriculum vitae indicating your interest should be submitted electronically via Interfolio (https://apply.interfolio.com/140269).

Veronica Hinman is a PI on a newly renewed NIH grant that funds an international team to develop Echinobase (Echinobase.org), a community resource for echinoderm genomic research. The Department of Biological Sciences at Carnegie Mellon University is seeking candidates for a full-time Senior Bioinformatician to improve the contiguity and accuracy of echinoderm genome assemblies, enhance the annotation of gene models through orthology mapping, improve Gene Ontology and integration with external sources and process bulk RNA-seq data for subsequent use in viewing phenotypes and relative expression across multiple species. Opportunities for independent projects are available depending on interest and experience. Opportunities to teach and mentor students are also available depending on the candidate’s interests and experience.

Responsibilities will include:

● Continued integration (full or partial) of community-provided assemblies.

● Improving the assembly and annotations for existing genomes (e.g. Patiria miniata).

● Enhance the functional annotation of genomic elements and datasets.

● Automated merging of multiple genome annotations.

● Addressing many:X homology relationships by considering orthogroups.

● Whole-proteome ontology analyses of supported species (e.g. PFAM, InterPro).

● Coordination of external resource integration (e.g. UniProt, AGR, PhylomeDB).

● Deployment of SRA / GEO pipeline for gene expression visualization.

● Compute “Expression Phenotypes” to be provided to Curate for the ECAO.

● Process and prepare single-cell data for visualization across multiple species.

● Implement UCSC cell browser to browse single-cell datasets.

Flexibility, excellence, and passion are vital qualities within MCS. Inclusion, collaboration, and cultural sensitivity are valued competencies at CMU. Therefore, we are in search of a team member who is able to effectively and professionally interact with a varied population of internal and external partners. We are looking for someone who shares our values and who will support the mission of the university through their work.

Qualifications

● PhD degree in a computational biology, bioinformatics, evolutionary or developmental biology or related fields is required.

● An interest in echinoderm genomics.

● Ability to summarize and communicate technical information in a clear, concise manner to multiple audiences.

● Ability to publish computational and biological results in peer-reviewed journals.

● Ability to work with an international team on the development of tools.

● Compensation will be commensurate with experience.

The Mellon College of Science (MCS) is home to four departments and many programs and research centers that cross disciplines. We approach scientific problems from fresh angles using creative interdisciplinary approaches while drawing on our departmental strengths in the core sciences. MCS faculty members are nationally and internationally recognized for their research in various fields, including molecular and cellular biology and genomics.