Employment Opportunities at NESCent

Employment Opportunities at NESCent

Graduate Student Assistant - Assessment Analyst for Evolutionary
Biology Programs (Paid)

The National Evolutionary Synthesis Center (NESCent), which is a multi-university center funded by the National Science Foundation (NSF), is looking for a graduate student assistant to support our 'Science of Science' project as an Assessment Analyst. The Science of Science project has been collecting assessment data on visiting scientists, including data on who they collaborate with and what outcomes they have achieved.

Job description: The Assessment Analyst will assist in analyzing data and creating statistical reports based on the assessment data, thus prior experience with SAS, SPSS, R, or other statistical software is required. The Assessment Analyst would work as part of an interdisciplinary team, and gain experience applying statistical knowledge to the domain of scientific collaboration. Please see Science of Science for more information about this project and NESCent.

How to apply: Interested applicants should contact Phillip Grosshans Assistant Director for Administration, at phillipg@nescent.org.

Postdoctoral Fellow: Vertebrate Morphology and Bioinformatics

We are seeking a scientist with training in comparative vertebrate anatomy to participate in the Phenoscape informatics initiative to render morphological data computable and interoperable with genetic data. The successful candidate will: 1) lead data curation and ontology development for early living and extinct vertebrates (fishes) and amphibians as part of a team comprised of scientists and software developers, and 2) conduct large-scale, data driven evo-devo research on the store of phenotypic and genetic data in the knowledgebase.

Job description: This position presents a unique opportunity to pursue bioinformatic research relating to broad questions concerning the evolution of morphology in relation to linked developmental and genetic data. The postdoc will use state of the art tools for evolutionary biology to curate morphological from the literature on early vertebrates (fishes) and living and extinct amphibians, annotating anatomical features using ontologies, to populate a database that will be integrated with the existing databases of phenotypic and genetic data from model vertebrates (ZFIN, zebrafish; Xenbase, Xenopus; MGI, mouse).

Responsibilities center on contributing to a large and growing vertebrate phenotype knowledgebase, including annotation of comparative fin/limb skeletal phenotypes and homologies from the scientific literature. The incumbent will work closely to coordinate efforts with the curators of fin-limb mutant phenotypes from the vertebrate model organism databases; participate in regular virtual meetings with a distributed project team; develop and document curation standards for comparative data and best practices for ensuring consistency across taxa; and collaborate with software developers in the design of curation workflow tools and interfaces, including tools for semi-automated extraction of comparative phenotype data from the literature. In addition, the incumbent will have ample opportunities to leverage the data in the knowledgebase, and associated tools for large-scale analysis of phenotype similarities, towards addressing his/her own research questions. The postdoc will supervise undergraduate workers in gathering/digitizing the literature and basic data entry; publish and give conference presentations on research results; and attend project meetings as required, including annual project team meetings.

Starting date: This two year postdoctoral position is available to be filled as early as January 2012.

Required qualifications:

  • Ph.D. degree in biological sciences with expertise in comparative vertebrate anatomy and evolution
  • Ability to communicate well and work as part of a distributed research team
  • Excellent English language skills
  • Interest or experience in informatics methods

How to apply: The postdoctoral fellow will work with Paula Mabee (University of South Dakota) and David Blackburn (California Academy of Sciences). The position will be based in South Dakota, with opportunities to travel to other sites for this project including the National Evolutionary Synthesis Center (NESCent), the University of Chicago, and the California Academy of Sciences.

Please contact Dr. Mabee (pmabee@usd.edu) with any questions about this position. Applications should be directed to Dr. Mabee and include a cover letter, CV, a brief statement detailing your research interests and career goals, and three letters of reference.

Project team:

This work is funded by a collaborative NSF grant to PIs Paula Mabee (University of South Dakota) and Todd Vision (University of North Carolina Chapel Hill) with co-PIs David Blackburn (California Academy of Sciences), Judith Blake (Mouse Genome Informatics, Jackson Laboratories), Hilmar Lapp (NESCent), Paul Sereno (University of Chicago), Monte Westerfield (University of Oregon, ZFIN), and Aaron Zorn (Cincinnati's Children's Hospital and Medical Center, Xenbase).

For more information about Phenoscape:
Please see the Phenoscape and Knowledgebase web-sites for more information.

The University of South Dakota is an Affirmative Action/Equal Opportunity Employer committed to increasing the diversity of its faculty, staff and students.

Postdoctoral Opportunity: Semantic Reasoning for Biological Phenotypes

Phenoscape is an initiative to bridge the domains of evolutionary biology and model organism developmental genetics through machine reasoning over ontologically structured phenotype data. The project recently received funding from the National Science Foundation to develop tools that can be used to integrate phenotype data throughout the vertebrates.

Job Description: We are currently recruiting for a postdoctoral scholar in computational biology. The postdoctoral scholar will contribute to two important research strands within the project: 1) Development of computational and statistical methodology for measuring semantic similarity between sets of phenotypes, in order to support searches within extremely large phenotype datasets; and 2) Development and testing of methods for automatically generating ontologically based phenotype expressions from structured excerpts of natural language.

The position is based in the informatics group at the National Evolutionary Synthesis Center (NESCent), and is administered through the University of North Carolina at Chapel Hill (UNC-CH) under the supervision of Hilmar Lapp at NESCent and Dr. Todd Vision at UNC-CH. The research will be in collaboration with Dr. Chris Mungall at Lawrence Berkeley National Lab and Dr. Hong Cui at the University of Arizona. The project also includes biologists and bioinformaticists from the University of South Dakota, the University of Chicago, the University of Kansas, in addition to the model organism databases for mouse (MGD), zebrafish (ZFIN), and Xenopus (Xenbase). The position is for two years, pending satisfactory performance and availability of funds.

Required Qualifications:

  • Applicants should have a PhD in Computer Science or related field
  • Prior experience with machine reasoning using ontologies is strongly preferred

How to Apply: Please provide a cover letter, CV, and contact information for three references. Inquries and applications may be sent to Hilmar Lapp at hlapp@nescent.org. The post is open immediately and will remain open until filled. For more information, please see http://phenoscape.org.

GMOD User Support Specialist

Are you fascinated by genomics and bioinformatics? Are you passionate about collaborative open-source software? Do you enjoy teaching and working with scientists? The Generic Model Organism Database project (GMOD) is a collection of open source software tools for creating and managing biological, and particularly genomic, databases. GMOD has a large, highly distributed, and dynamic community of software users and developers. The University of North Carolina at Chapel Hill has an opening for a GMOD user support specialist, to be based at the US National Evolutionary Synthesis Center (NESCent, www.nescent.org) in Durham, North Carolina, while serving the international community of GMOD users.

Job Description: The GMOD user support specialist will maintain online documentation; respond to mailing list help requests; present tutorials; organize short courses, conference sessions and other community building activities; survey user needs, and recruit members of the community to assist with these functions. The incumbent will collaborate closely with the GMOD Coordinator (Scott Cain, The Ontario Institute for Cancer Research) and other distributed personnel. See GMOD Help Desk for more background on the activities of the user support specialist. The salary range is $68,906 to $82,687, depending on qualifications, and the incumbent will receive a comprehensive benefits package as an SPA employee within the UNC system.

Qualifications: Required qualifications include: excellent written and verbal communication skills; team orientation with strong interpersonal skills. Preferred qualifications include: an MS or PhD in biology, computer science or related field; three or more years of experience with web programming and relational database management systems; three or more years of experience with genome database administration or curation, preferably in a GMOD environment; at least one year of experience with web content management, ideally using MediaWiki; freedom to travel 5-15 weeks/yr.

How to apply: Please provide a cover letter and CV, including contact information for three references, to Hilmar Lapp, Assistant Director of Informatics, NESCent, at hlapp@nescent.org, and submit materials through http://bit.ly/h9l74r. For phone inquiries, please call 919.668.5288.

Student Assistant, TreeBASE Data Curation and User-Interface Design

The National Evolutionary Synthesis Center (NESCent) has an opening for a student to assist with data curation and usability assessment for the community resource TreeBASE.  TreeBASE is the primary digital repository for evolutionary trees and their underlying data published in peer-reviewed scientific articles, often in the form of supplementary online material data.

Job Description: The incumbent will:

  • identify published studies for which evolutionary trees have not been archived, or have not been deposited in TreeBASE;
  • work with article authors, NESCent Informatics staff, and collaborating community resources to obtain relevant data;
  • input this data into TreeBASE;
  • document bottlenecks and usability issues in the data deposition process, and suggest possibilities for improvement.

Qualifications: We are interested in students with interests in evolutionary biology, information / library science, bioinformatics and / or user interface design. Details and relative time allocations of tasks may be tailored to suit the specific interests of the successful applicant.  

NESCent is an NSF-funded center dedicated to cross-disciplinary research in evolutionary science, located in the Erwin Mill building at the corner of 9th and Main St in Durham. All NESCent software products are open-source, and the Center has a number of initiatives to actively promote collaborative development of community software resources.

How to apply: Please send a CV to Dr. Karen Cranston, Bioinformatics Project Manager, at karen.cranston@nescent.org. Informal inquiries to Dr. Cranston by email or phone (919.613.2275) are welcome.