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Biomedical Data Curator
RANK: Assistant Specialist, Step 1–Associate Specialist, Step 1
posted 4/30/08
Center for Biomolecular Science & Engineering
Baskin School of Engineering
The Center for Biomolecular Science & Engineering seeks a biological scientist to analyze new large-scale biomedical data sets, help ensure that they are of the highest possible quality, and assist in integrating them into the UCSC genomics database and web works. The curator will write descriptive text aimed at other scientists and answer questions from the user community. The data sets include DNA, RNA, and protein sequence data on human genetic variation and associated phenotypes, gene expression data, and in situ imagery. The work requires a scientist with a broad understanding of molecular and cellular biology, a facility with computer systems, strong writing skills, and the ability to read and understand scientific literature in the fast-evolving field of biomedical genomics. A postgraduate degree is required for this position; a PhD is preferred. The work will involve testing software tools developed in-house to display and analyze the data in a web browsing context and offering feedback to the software developers.
CBSE operates an important scientific website for use by researchers worldwide, genome.ucsc.edu. More than 7000 scientists use the site every day to access the fruits of the human genome project. The site combines cutting-edge research in genomics with solid software engineering and maintains a simple but flexible user interface. The UCSC Center for Genomic Sciences, part of the CBSE, is a talented cross-disciplinary team that builds databases and develops software for the UCSC Genome Browser, a tool that facilitates genome analysis and comparison within and across multiple species. The browser provides views of assembled genome sequences that are integrated with details of evolutionary conservation, synteny, genetic map markers, known and predicted genes, SNPs, transcript structure, alternative splicing, and a host of other critical data.
MINIMUM QUALIFICATIONS: A Master’s degree in biology or a related discipline and knowledge and experience equivalent to at least one year of college-level computer science are required. Experience working with scripting languages in a UNIX or Linux environment is essential, as is familiarity with relational database concepts and SQL. Broad knowledge, background, or experience in molecular and cellular biology and the analytical ability to study and assimilate technical structure, data, and requirements of genome analysis software are also required. The successful candidate will be customer-oriented, articulate, organized, detail-oriented, independent, self-motivated, and have a strong commitment to quality.
TERM OF APPOINTMENT: Initial appointment is for 2 years, with continuation of appointment dependent on availability of funding and positive performance review.
START DATE: As soon as possible after closing
TO APPLY: Applicants should send a letter of application, curriculum vitae, copies or URLs of not more than three research papers, and the names and contact information for three recommenders* to Search Committee—Data Curator, cbsehr@soe.ucsc.edu. Electronic submission is preferred. Please refer to position #T08-58 in your reply.
CLOSING DATE: Position is open until filled. To ensure full consideration, applications must be received by May 29, 2008. Applications received after May 29, 2008 may not be considered.
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Research Specialist in Bioinformatics/HIV-1 Vaccine Research
RANK: Associate Specialist, Step 1–Specialist, Step 5
posted 3/31/08
Department of Biomolecular Engineering
Baskin School of Engineering
An experienced bioinformatics specialist is sought to join a research program focused on HIV vaccine research and antigenic variation. This is an ideal position for someone with a bioinformatics background that is interested in expanding their skill set to include training in “wet lab” molecular biology and immunology. The position requires training and experience in relational database design and development, the alignment and analysis of large DNA and protein data sets containing multiple insertions and deletions, phylogenetic analysis, and the ability to import and analyze data from public databases. The candidate will be expected to interface with bioinformatics specialists at several institutions on a collaborative project to characterize intra-patient and inter-patient HIV sequence variation and to relate virus variation to neutralization sensitive and resistant phenotypes. The position also requires coordination, assembly, and analysis of new sequence data generated by the “next generation” DNA sequencers. The successful candidate needs to have an excellent understanding of the basic principles of protein structure, be able to work with large public databases, including the UCSC Human Genome Browser, Genbank, and the Los Alamos HIV Sequence Database. The successful candidate will also be expected to be the local repository of information on the use of common laboratory software for statistics and computational tools for molecular biology such as alignment software, restriction mapping, primer design, motif recognition, and recombination analysis. Familiarity with C and SQL programming languages and the ability to write new code in a Unix environment is essential.
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Bioinformaticist
RANK: Assistant Project Scientist or Associate Project Scientist
posted 2/8/08
Department of Molecular, Cell, and Developmental Biology
The Strome lab in Molecular, Cell and Developmental Biology invites applications from outstanding scientists for the position of Bioinformaticist. We seek an experienced, creative, and enthusiastic problem-solver to drive the bioinformatic analysis of data related to chromatin regulators, using existing software programs and algorithms and working with collaborators to develop new algorithms and tools. Our lab investigates chromatin regulators in the nematode C. elegans. Building upon a strong foundation based on genetics, biochemistry, and imaging approaches, new avenues of investigation include microarray analysis of transcript accumulation profiles and analysis of protein distributions across the genome by chromatin immunoprecipitation followed by tiling microarray analysis (ChIP-chip). The microarray-based approaches require intensive bioinformatic analysis.
The successful candidate must be analytical, articulate, interactive, able to learn and integrate technical information quickly, and have a strong commitment to quality and best bioinformatic practices. The position requires independence and self-motivation in a team environment. The individual should be able to work effectively with other experts on campus and elsewhere, as well as train students and postdocs in the lab in data analysis. Good communication skills are important, as the hired individual will be expected to help write papers and grants and to give oral presentations locally and at conferences.
The Bioinformaticist will manage, analyze, display, and compare large gene expression and ChIP data sets, and identify or develop appropriate computational algorithms and approaches for answering our biological questions. Some of the needs for microarray and ChIP-chip analysis are methods of normalization, statistical analysis, calling ChIP peaks, determining gene ontology of targets, comparing data sets for different tissues and target proteins, and searching for shared sequence motifs.
The recruited bioinformaticist will work extensively with and be supervised by Susan Strome. The Strome lab currently consists of a team of 7 postdocs, graduate students, and research associates. We interact extensively with a multi-national modENCODE team of 8 ChIP and bioinformatics labs, the numerous chromatin labs in MCD Biology, and members of the UCSC Genome Browser team and bioinformatics community at UCSC.
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Software Developer and Functional Genomics Database Curator
RANK: Junior Specialist, Step 1-2
posted 1/14/08
Department of Biomolecular Engineering
Baskin School of Engineering
The Department of Biomolecular Engineering at the University of California-Santa Cruz has been awarded a grant from the National Science Foundation to fully develop a model organism database and genome browser for all Archaea and extremophile bacteria, similar in purpose to SGD, FlyBase, and other important organism-specific databases. A major objective of the database is seamless integration of functional genomic data from DNA microarrays, proteomics studies, and high-throughput cDNA sequencing. A functional genomics data repository also will be established specifically for the archaeal research community based on an existing system. Under the direction of Asst. Professor Todd Lowe, the Center for Archaeal and Extremophile Genome Research is now seeking to fill several new positions immediately, including the full-time position of Software Developer and Functional Genomics Database Curator.
The Archaeal and Extremophile Genome Database (http://archaea.ucsc.edu) currently hosts 70+ archaeal and bacterial genomes, and will continue to expand in the number of genomes and sources of gene function information. As part of the Archaeal genome database team, duties will include improving and maintaining a microarray / proteomic data repository and CGI interface for submitting new data, helping design and implement new interfaces for functional genomic data queries and comparisons within the genome browser, automating gene keyword searches on scientific literature and helping automate content curation tasks, integrating new “tracks” of bioinformatic analyses into the genome browser, developing improved collaborative Wiki tools tied into the genome browser for community-based gene re-annotation efforts, and thoroughly testing new browser features and tracks, identifying and fixing bugs or systematic errors in the database.
This is an ideal opportunity for a computer scientist/programmer with strong programming skills to gain highly valued skills in an interdisciplinary biological research setting, including advanced comparative genomics and computational biology analysis. Co-authorship on scientific publications also is possible, dependent on contributions to research projects in the lab.
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Archaeal Genome Database Content Curator
RANK: Assistant Specialist, Step 1-3
posted 1/14/08
Department of Biomolecular Engineering
Baskin School of Engineering
The Department of Biomolecular Engineering at the University of California-Santa Cruz has been awarded a grant from the National Science Foundation to fully develop a model organism database and genome browser for all Archaea and extremophile bacteria, similar in purpose to SGD, FlyBase, and others. Under the direction of Asst. Professor Todd Lowe, the Center for Archaeal and Extremophile Genome Research is now seeking to fill several new positions immediately, including the position of Database Content Curator.
The Archaeal and Extremophile Genome Database (http://archaea.ucsc.edu) currently hosts 70 genomes, and will continue to expand in the number of genomes and sources of gene function information. As part of the Archaeal Genome Database team, development duties will include regular updates of gene function based on automated and manual curation using primary literature, integration of functional genomics data, and refinement of collaborative Wiki resources for community-based input and feedback.
Working within an interdisciplinary research lab, the content curator also will be trained to use tools for comparative genomics, protein and non-coding RNA gene searches, microarray analysis, multiple sequence alignment, regulatory region sequence analysis, phylogenomics, and simple Perl programming (if desired). This is an ideal opportunity for a microbiologist with a strong molecular genetics background to gain highly-valued skills in advanced genome analysis, and interact regularly with the top researchers in archaeal and extremophile research. Co-authorship on several publications also is likely dependent on contributions to on-going research projects in the lab.
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Biological Database Testing & User Support Technician
Programmer/Analyst 1
Posted 11/20/07
Full time career position
The Center for Biomolecular Science & Engineering (CBSE, http://www.cbse.ucsc.edu/) at UC Santa Cruz seeks a customer-oriented individual with strong analytical skills and a commitment to quality to test biological software and data and to research and answer user questions. The successful candidate must be articulate, organized, detail-oriented, and adaptable. The position requires independence and self-motivation in a team environment.
OVERVIEW OF THE ORGANIZATION
CBSE operates an important scientific web site for use by researchers worldwide, genome.ucsc.edu. More than 7000 scientists use the site every day to access the fruits of the human genome project. The site combines cutting-edge research in genomics with solid software engineering and maintains a simple but flexible user interface. Keeping the site up to date is no small job, and two of the most important aspects of this job are biological database testing and user support.
ESSENTIAL FUNCTIONS
Under close supervision of the Quality Assurance Manager, the incumbent systematically tests software, data, and databases before public release. Researches answers to user questions regarding underlying biological assumptions and computational methods in the genome software and databases. Works as part of a team of people performing similar work alongside a group of software developers. Interacts extensively with manager, software developers, other team members, and genome researchers from throughout the world. Fast-paced work that is varied and requires both great attention to detail and a broad understanding of the entire genome browser.
MINIMUM QUALIFICATIONS
BA or BS in a biological science, or BA or BS in a computer science plus coursework or experience in biology, or an equivalent combination of education and experience; broad knowledge in biology and deep knowledge of gene sequence organization, genome maintenance, and gene expression and regulation in eukaryotes; familiarity with UNIX; solid web surfing skills
For more information and to apply, visit the UCSC Staff Employment web site and search for job number 0701391.
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