Tag Archives: metagenomics

Research Microbiologist at USDA-ARS (UC Davis)

 

Research Microbiologist, USDA-ARS

A new Research Microbiologist position is available with the USDA-ARS located on the campus of the University of California, Davis.  The successful candidate will conduct independent research to discover and develop novel fumigation independent approaches to control soil-borne pathogens.  This work will focus on developing an understanding of the ecological, structural and functional aspects of the soil-borne microbial communities shown to suppress target pathogens.  Applicants with a strong computational biology/metagenomics background are encouraged to apply.  We would greatly appreciate it if you would forward this announcement to prospective candidate(s) for their consideration.  The position announcement can be found at https://www.usajobs.gov/GetJob/ViewDetails/405228600

This is a competitive, permanent appointment and U.S. citizenship is required.  For further details about this position and how to apply, go to the vacancy on-line at:  www.USAJobs.gov  vacancy announcement number ARS-D15W-0129 (all US citizens) or ARS-M15W-0128 (Current federal employees).  For questions contact: Dr. Daniel Kluepfel, Research Leader at daniel.kluepfel@ars.usda.gov

Job: Faculty Computational Microbial Genomics UNC-Charlotte

Tenure Track Faculty Position, Computational Microbial Genomics @ UNC Charlotte, NC (US) 

SUMMARY:
The Department of Bioinformatics and Genomics seeks a data scientist in computational microbial genomics to fill a tenure-track position at the Assistant or Associate Professor level. This position is part of a larger university-wide research initiative in Data Science and Analytics.

RESPONSIBILITIES:
The successful candidate will teach courses in bioinformatics and data mining at the graduate and undergraduate level, and will develop and maintain an externally funded research program. Examples of research programs of interest include, but are not limited to: (i) algorithm development for the analysis of large data sets generated from mixed microbial (metagenomic) communities from the external environment or associated with plants or animals; (ii) tracking development of antibiotic resistance or changes in microbial phenotype to the content of genes and genomes using next-generation sequencing; (iii) source tracking of pathogens across space and time in the external environment or within industrial, agricultural or hospital settings; (iv) utilizing microbial genomics for molecular epidemiological studies and precision medicine; (v) studies of microbial evolution and genomic structure; (vi) developing tools for visualization of microbial datasets; (vii) using computational tools to enhance agriculture and nutrition by manipulation of plant-associated microbes.

COMPENSATION:
We offer a collegial environment with excellent wet laboratory and computational facilities and a competitive nine-month salary commensurate with experience.

HOW TO APPLY:
Applications must be made electronically at https://jobs.uncc.edu (position #1913) and must include a CV, contact information for 4 references, and statements on research and teaching. Initial, confidential, inquiries can be made to the Search Committee via its Chair, Dr. Daniel Janies, at djanies[at]uncc.edu.

POLICY:
The University of North Carolina at Charlotte is an EOE/AA employer and an NSF ADVANCE Institution.

For additional information, please visit website at http://bioinformatics.uncc.edu.

Via bioinformatics.org job forum posting.

Postdoc: Institute for Environmental Genomics, University of Oklahoma

Postdoctoral Positions Available at the University of Oklahoma

Multiple postdoctoral positions are available at the Institute for Environmental Genomics (IEG) and Department of Microbiology and Plant Biology, the University of Oklahoma (OU) located in Norman, Oklahoma. The city of Norman is a university town with approximately 100,000 people and easy access to Oklahoma City, OK and Dallas, TX, and the University is working closely with the City on community and economic development. Norman was ranked #6 among the best places to live in 2008 by the CNN/Money Magazine on America’s best small cities.

The Institute for Environmental Genomics, led by Dr. Jizhong Zhou, has state-of-the-art facilities for the study of microbial functional genomics, microbial ecology, metagenomics, and biotechnology development to address fundamental scientific questions.

Three research themes are pursued at IEG:

  1. functional and comparative genomics for understanding gene function, regulation, networks and evolution,
  2. microbial ecology and community genomics for understanding the diversity, composition, structure, function and dynamics of microbial communities related to global change, bioremediation, land use, bioenergy, and agricultural practices as well as their linkages with ecosystem functioning using metagenomics approaches, such as functional gene arrays, high-throughput sequencing, and single cell genomics, and
  3. development of metagenomic and bioinformatic tools for high throughput data analysis and predictive modeling of molecular ecological networks.

IEG researchers have pioneered the development and application of functional gene arrays (e.g., GeoChips), and metagenomic sequencing (e.g., MiSeq sequencing of phylogenetic and functional gene amplicons) approaches for microbial community analysis. IEG is also establishing Raman-based single cell genomics facility.

The selected candidates will apply these technologies to understand the diversity, composition, structure, function, dynamics and interaction of microbial communities, and address fundamental questions related to global change, bioremediation, land use, and agricultural operations.

Candidates with strong background, interests, and experience in microbiology, microbial ecology, soil science, theoretical ecology, and/or metagenomics are encouraged to apply. Additional experience is desirable but not required in bioinformatics, mathematics, computer science, and/or statistics. All individuals will work cooperatively with scientists at different institutions, such as Lawrence Berkeley National Laboratory, Oak Ridge National Laboratory, Stanford University, University of California at Berkeley, Michigan State University, University of Florida, University of New Mexico, University of Arizona, and Georgia Institute of Technology as well as foreign countries like China, Korea and Singapore. Interested individuals should send their curriculum vita, a description of research interests and accomplishments (e.g., publications), and the names and telephone numbers of at least three references to Dr. Jizhong Zhou (jzhou@ou.edu). Salary will be competitive, depending on experience, expertise and skills. Further information can be found on the IEG web site. The University of Oklahoma is an Affirmative Action/Equal Opportunity employer and encourages diversity in the workplace.

A printable flier is available PostdocPositions-OU-13Jun2014.

Microbial Ecology in Science

Science has a section dedicated to Microbial Ecology including a review describing microbial biogeography studying communities on the basis of trait rather than taxonomic diversity. Certainly this interlinks with metagenomic approaches well, something I’ve been thinking about more after visiting some of the folks at Montana State Thermal Biology Institute and all the increasingly massive datasets like what CAMERA provides.

(re)Annotating GenBank

NCBI LogoTom Bruns, Martin Bidartondo and 250 others sent a letter to Science describing the current problems with fixing annotation in GenBank. There is an entertaining accompanying news article that interviews several people about the problem of updating annotation and species assigned to sequences in the database. In particular the problem for mycologists that many fungi found from metagenomic approaches are only identified through molecular sequences and having the wrong species associated with a sequence can be difficult when studying community ecology composition.  This problem is not limited to fungi by any means, but recent reports find as many as 20% of fungal Intergenic Spacer (ITS) sequences are mis-attributed to the wrong species. 

There’s a nice quote in the news article from Steven Salzberg talking about the difficulties in getting sequences, especially from big centers, updated. I’m sure he is thinking of many examples, like reclassifying some Drosophila sequence traces.

Continue reading (re)Annotating GenBank

Tracking honeybee decline

HoneybeeAn early access to article in Science A Metagenomic Survey of Microbes in Honey Bee Colony Collapse Disorder (direct link since DOI is not updated yet) using the current favorite buzzword, metagenomics, of course, describes some early work to try and discover what is killing the honeybees. It is early access and non-free and ScienceExpress is not part of our subscription here so I’ve not actually had a chance to read it yet, but the gist of the reporting about it suggest that a virus is to blame. This is in line with what Joe DeRisi and collaborators found using their Virus chip based on some news reports earlier this year, but no scientific article yet to follow this up.

Some links to today’s SFChronicle article and an article “Stung” from the New Yorker in August that alluded to this Science article.