An open letter to the fungal research community regarding genome database resources

An open letter to the fungal research community regarding genome database resources (from the Broad Institute & FungiDB/EuPathDB):

As many of you are already aware, fungal genome websites at the Broad Institute are undergoing a major transition. These resources were originally developed in support of sequencing projects, many of which have long-since been completed. While we have tried to keep such sites operational for as long as possible without funding, infrastructure changes now underway will make these websites nonfunctional over the coming weeks. We are therefore replacing formerly interactive websites with a static page providing information on fungal projects, along with links to the Broad FTP site where datasets can still be downloaded, and links to NCBI – the primary repository for all genomic data, where all genomes and annotation have been deposited and can be accessed, queried, and downloaded. We are also working to incorporate genomic data into other sites that support comparative analysis of fungal genomes, including FungiDB and MycoCosm.

The EuPathDB family of databases (funded by NIAID/NIH and the Wellcome Trust) supports a wide range of microbial eukaryotes; FungiDB includes many fungal (and oomycete) species, including non-pathogens. This resource has been designed to provide sustainable, cost-effective automated analysis of multiple genomes, integrating curated information (when available), with comments and supporting evidence from the user community (PubMed IDs, phenotypic information, images, datasets, etc). In addition to gene records, browser views, and data downloads, FungiDB offers sophisticated tools for integrating and mining diverse Omics datasets that fungal biologists will find quite useful. See the sidebar on the FungiDB web site for access to tutorials, videos, and exercises.

MycoCosm (supported by JGI/DOE) offers the largest available collection of fungal genomes, for comparative genomics across phylo- and eco-groups, along with interactive web-based tools for genome downloading, searching and browsing, and a form for nominating new species for sequencing to fill gaps in the Fungal Tree of Life.

For many years the Broad has been pleased to work closely with various fungal research communities, and we will continue to work with EuPathDB and MycoCosm to transition data valued by the community. Please direct any inquires or requests for help to help@FungiDB.org

Meeting: Exploring the genomic complexity and diversity of eukaryotes

Registration for the 2015 EMBO meetingExploring the genomic complexity and diversity of eukaryotes is open. The meeting is held from 17 – 22  of October 2015 in Sant Feliu de Guixols, Spain. This is a beautiful venue and a It should be an excellent opportunity to discuss and hear about work on genome evolution, pathogenesis, and complexity in fungi and protists.

Unicellular eukaryotes comprise the overwhelming majority of eukaryotic diversity, pervading all branches of the eukaryotic tree of life. Recent sequencing efforts have significantly increased the number and diversity of unicellular eukaryotes for which genomic/cellular/proteomic data is available. Metagenomics, transcriptomics, single- cell genomics, and other ‘omics’ approaches are being applied to unravel the ecology, physiology, diversity and evolution of microbial eukaryotes and are shedding light on fundamental questions such as the origin of the eukaryotic cell, endosymbiosis, the origin of multicellularity and the evolution of major cellular processes in eukaryotes.

Job: Montana State University Assist/Assoc/Full Environmental Microbiology

The Department of Microbiology & Immunology at Montana State University- Bozeman (http://www.montana.edu/mbi) invites candidates with a PhD in Microbiology or related area to apply for a full-time, nine-month tenure-track position in Environmental Microbiology (Assistant/Associate/Full Professor) beginning January 2016. The successful candidate will have postdoctoral and/or Assistant Professor experience and will be responsible for developing/growing an extramurally funded, nationally recognized research program within the broad field of environmental microbiology. Scientists that use interdisciplinary approaches that include biochemical, cellular, physiological, ecological, genomic, and/or molecular tools to investigate areas including microbe-environment interactions, microbe biology/ecology, and/or microbial engineering are encouraged to apply. We are seeking an individual with a research program to complement and expand expertise in the Department. The Department, which is nationally recognized for its strengths in both environmental and human-related microbiology, includes state-of-the-art core facilities both in the department and campus research centers. The Department strives to maintain a diverse faculty group, and women and underrepresented minorities are encouraged to apply. The position includes a competitive institutional salary (9-months) and generous start- up package. While a funded research program is preferred, it is not required. Full details about the position and application procedure are available at https://jobs.montana.edu/postings/2601.

Potential candidates are encouraged to contact the Search Committee Chairperson, Dr. Matthew Fields, (matthew.fields@biofilm.montana.edu) for more details. Screening will begin September 9th, 2015 and will continue until a suitable applicant is hired. ADA/EO/AA/Veterans Preference.

PDF of the advertisement: Faculty Position in Microbiology at MSU

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