Postdoctoral Position in Bioinformatics – University of Ottawa

The Corradi Lab is currently seeking a postdoctoral fellow in Bioinformatics to work on projects related to Comparative and Population Genomics. The research will be led by Dr. Nicolas Corradi and carried out in a CIFAR (Canadian Institute for Advanced Research) – affiliated laboratory located in the Department of Biology of the University of Ottawa, Canada.

Website: http://corradilab.weebly.com/

The position is initially funded for one year, with the possibility of renewal for up to three years, depending on performance. The candidate is expected to work on two ongoing lab projects:

  1. Populations genomics of global samples of the bee-pathogen Nosema ceranae

    The recent decline in global populations of honey-bees has been attributed to a many factors, including infections from the microsporidian pathogen Nosema ceranae. Despite the potential threat that this parasite may have on global bee populations, the basic biology of this species is not well understood.
    The present project aims to increase our knowledge of the N. ceranae’s biology by exploring the extent, nature and function of genome diversity that exist both within and between dozens of parasite samples isolated globally (i.e. Spain, France, Turkey, Thailand, USA..etc…).
  2. Population genomics of global isolates of the model plant symbiont, Rhizophagus irregularis

    The Arbuscular Mycorrhizal Fungi (AMF) are ubiquitous plant symbionts that improve the ability of roots to uptake nutrients from soil and provide protection against plant pathogens. These organisms are intriguing as they harbor many nuclei within one cytoplasm throughout their entire life cycle. The genetic organization of these nuclei has been debated for years, but recent genome analyses in our lab are providing essential insights to this debate.

    The proposed projects aims to increase our knowledge of biology and evolution of these curious fungi and critical symbionts by investigating the genome diversity within and across different strains of the model AMF R. irregularis sampled globally.

For specific enquiries please contactDr. Nicolas Corradi (ncorradi@uottawa.ca).

Applicants are expected to have a strong background in either comparative genomics or populations genomics. Experience in either population genetics, environmental genomics, metagenomics, or ab-initio gene annotation and programming will be seen as an asset for the final selection of the candidate. Some basic training in bioinformatics (Perl, Python, or R) is desired.

A complete application package includes a CV, a one-page description of past research accomplishments and future goals, and the names and e-mail addresses of at least 2 references. The position opens immediately, and evaluation of applications will continue until a suitable candidate is found.

The University of Ottawa is a large, research-intensive university, hosting over 40,000 students and located in the downtown core area of Canada’s capital city. Ottawa is a vibrant, multicultural city with a very high quality of life.

Applications can be sent to Dr. Nicolas Corradi (ncorradi@uottawa.ca).

Representative publications:

  • Pelin A., Selman M., Laurent Farinelli, Aris-Brosou S. and N. Corradi. 2015. Genome analyses suggest the presence of polyploidy and recent human-driven expansions in eight global populations of the honeybee pathogen Nosema ceranae. Environmental Microbiology
  • Ropars J. and N. Corradi. 2015. Heterokaryotic vs Homokaryotic Mycelium in the Arbuscular Mycorrhizal Fungi: Different Techniques, Different Results? New Phytologist
  • Corradi, N. 2015. Microsporidians: Intracellular Parasites Shaped by Gene Loss and Horizontal Gene Transfer. Annual Review of Microbiology
  • Riley R., Charron P., Idnurm A., Farinelli F., Yolande D. , Martin F. and N. Corradi. 2014. Extreme diversification of the mating type–high?mobility group (MATA?HMG) gene family in a plant?associated arbuscular mycorrhizal fungus. New Phytologist
  • Tisserant E., Malbreil M. et al. 2013. Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis. PNAS

Postdoc: Oslo Fungal molecular ecology

Three year position as Postdoctoral Research Fellow in fungal molecular ecology available at the University of Oslo, Norway:

Soil fungi play important functional roles in forest ecosystems; while saprotrophic taxa are essential for organic matter decomposition; mycorrhizal root-associated fungi mediate the link between living plants and the below-ground community. Recent studies indicate that plant-fungi interactions through mycorrhiza affect the efficiency of decomposition by fungi, and works as a main driver for soil carbon sequestration in forest ecosystems. The goal of this project (MycoSoil), which is funded by the Norwegian Research Council, is to make fundamental progress in the understanding of the community ecology and functions of fungi in boreal forest soils, how they are organized spatiotemporally and how they influence on carbon sequestration processes. We will take advantage of linking the project to two long-term surveys of boreal forests. State-of-the art DNA metabarcoding and metatranscriptomics approaches will be used to analyze spatiotemporal variation in the soil fungal communities.

For more information see http://uio.easycruit.com/vacancy/1352849/96323?iso=no or contact Håvard Kauserud at haavarka@ibv.uio.no

Postdoc: Comparative genomics and bioinformatics

Postdoc position in comparative genomics and bioinformatics

Applications are invited for a bioinformatics postdoctoral position in ?the research group of Laszlo G Nagy (Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary). We are now looking to hire new people with a background in bioinformatics, phylogenetics or fungal evolution. The Lab offers excellent training opportunities in fungal comparative genomics, cutting edge projects, abundant funding, an inspiring atmosphere and extensive collaborator network.

The primary focus of the lab is understanding the general principles of convergent evolution and fungal multicellularity through comparative genomics, transcriptomics and single-cell transcriptomics of multicellular fruiting bodies in Basidiomycetes. Fruiting bodies represent some of the most complex morphological structures found in fungi, yet, their developmental and evolutionary origins are hardly known. Complex fruiting bodies have evolved independently several times in the Basidiomycetes, offering an excellent model system to study the genetic mechanisms of convergent evolution.

The successful Candidate has:

  • PhD in bioinformatics, evolutionary biology, mycology or other relevant field
  • Experience in genomics, Perl and/or Python scripting
  • Good team player traits
  • Experience in working with fungi is a plus

Contact and application – The starting date of the project is September 2015. The position will last for one year with the possibility of extension up to 4 years. If interested, send a motivation letter along with your CV to Laszlo Nagy (lnagy@brc.hu).


Dr. Laszlo Nagy
Fungal Evolution & Genomics Lab
Synthetic and Systems Biology Unit, Institute of Biochemistry
Biological Research Center, HAS
Hungary

http://group.szbk.u-szeged.hu/sysbiol/nagy-laszlo-lab-index.html

Apply for EuPathDB workshop

Dear Colleague,

We are pleased to announce the 10th annual EuPathDB workshop to be held in Athens, Georgia, USA from May 31 – June 3rd, 2015.

Learn how to effectively use EuPathDB resources and mine available data to help guide your research.

For more information and to apply, please visit: http://workshop.eupathdb.org/current/

*********************

Databases covered: EuPathDBAmoebaDB, CryptoDB, FungiDB, GiardiaDB, HostDB, MicrosporidiaDB, OrthoMCL, PiroplasmaDB, PlasmoDB, ToxoDB, TrichDB, TriTrypDB

Costs and Fees: The course is free. Housing, all training materials and lunches are covered. Attendees are expected to provide their own transportation to the course and pay for a few of their meals. Letters of acceptance will be mailed early to facilitate the solicitation of outside travel funds.

When: 6:30pm on Sunday, May 31 to 5:00pm on Wednesday, June 3, 2015

Where: University of Georgia, Athens, GA, USA
Davison Life Sciences Building, room C128.

Application deadline: February 1, 2015. Click here to apply. NOTE: Deadline extended apply before Feb 20!

If you have any questions or concerns please email help@eupathdb.org

Postdoc: Agaricus bisporus genomics and transcriptomics

Applications are invited for a bioinformatics postdoctoral position in
the research group of David Fitzpatrick (Department of Biology, Maynooth University, Ireland). My group is interested in genomics,
transcripomics, proteomics and molecular evolution of fungal species.
The project start date is the 1st of February 2015 and sets out to
investigate the genome of Agaricus bisporus.

Agaricus bisporus strain A15 is the most widely cultivated white
mushroom strain in Europe. Currently there are significant financial and time costs associated with ensuring A15 inoculum is genetically
identical to parent culture. This project sets out to undertake an
extensive genetic analysis of A. bisporus A15, via genomic and
transcriptomic sequence analysis. Ideally this genetic characterisation will act as the starting point for development of a molecular diagnostic test to determine if new inoculum is genetically identically to parent culture. We also aim to produce a high quality map for the genome of A. bisporus A15. This will be invaluable for future breeding of new A. bisporus strains.

The position will last for 18 months, with the possibility of extension.
I am looking for somebody who has experience in genome/transcriptomic assembly and experience in handling large datasets. The successful candidate will have published in peer reviewed literature and have their PhD awarded by the start of the project.

Send a CV and covering letter to david.fitzpatrick@nuim.ie with the
subject line “post-doc position on Agaricus bisporus ”


Dr. David Fitzpatrick
Genome Evolution Laboratory
Department of Biology
Maynooth University
Maynooth
Co. Kildare
Ireland.

E: david.fitzpatrick@nuim.ie
T: +353-1-7086844
F: +353-1-7083845
M: +353-860681715
W: https://www.maynoothuniversity.ie/people/david-fitzpatrick
W: http://bioinf.nuim.ie/

Job: Faculty Positions at Institute Pasteur

FACULTY POSITIONS IN MYCOLOGY

The Institut Pasteur in Paris announces an international call for outstanding candidates at all levels to establish independent research groups in the Mycology Department. Preference will be given to studies on human pathogenic filamentous fungi and yeasts, fungal cell biology or population genetics and genomics. Research on model species will be also considered when connecting to fungal pathogenesis. Attractive start-up and ongoing support includes salary, equipment, and operating costs. In addition, Institut Pasteur provides access to state-of-the-art technology platforms, and to laboratories and research infrastructure in disease-endemic regions through the Pasteur International Network. Further information on the Institute and on-campus facilities can be found at http://www.pasteur.fr. Further information on the Mycology Department can be found at http://www.pasteur.fr/mycology.

The application should comprise the following (in order) in a single pdf file: i) A brief introductory letter, ii) A Curriculum Vitae, a list of 10 selected publications and a full publication list, iii) A description of past and present research activities (up to 3 pages), iv) The proposed research project (up to 6 pages, including a summary).

Junior candidates [1] should also provide:
v) The names of 3 scientists from whom letters of recommendation can be sought, together with the names of scientists with a potential conflict of interest from whom evaluations should not be requested.

Applications and requests for information should be addressed to myco_call2015@pasteur.fr by February 27, 2015. Short-listed candidates will be invited for interviews in spring 2015 and decisions will be announced by summer 2015.

[1] Institut Pasteur is an equal opportunity employer. Junior group leaders should be less than 8 years after PhD at the time of submission. Women are eligible up to 11 years after their PhD if they have one child and up to 14 years after their PhD if they have two or more children.

Flier from the posting DeptMyco_call2015

Job: 5 faculty position at Oregon State University

5 faculty positions (Assistant Professor) are advertised at Oregon State University

  • COMPLEX SYSTEMS IN THE LIFE AND ENVIRONMENTAL SCIENCES (2 position) – in any domain where the life or
    environmental sciences intersect with the quantitative or physical sciences. Posting #0013430; Closes February 6, 2015. Contact: Brett Tyler
  • QUANTITATIVE SYSTEMS BIOLOGIST- Department of Integrative Biology (70%) and the Departments of Mathematics or Statistics Posting #0013398. Closes January 25, 2015. Contact: Tara Bevandich
  • MARINE EVOLUTIONARY SYSTEMS BIOLOGIST – Department of Integrative Biology Posting #0013400. Closes
    January 25, 2015. Contact: Tara Bevandich
  • GENOMICS AND BIOINFORMATICS OF CROP PLANTS –  Department of Horticulture Posting #0013285; Closes January 25, 2015. Contact: Bill Braunworth

See the advertisement posting Systems Biology, Genomics and Bioinformatics

Postdoc: Yeast evolutionary genomics, UW Madison

Chris Hittinger at UW Madison is seeking a highly motivated postdoctoral researcher with an exceptional background in bioinformatics, functional genomics, or evolutionary genomics. Experience analyzing Illumina sequence data, computer programming proficiency, and training in ecological or evolutionary genetics are highly desirable.

The lab has recently received generous funding for yeast
evolutionary genomics research from the National Science
Foundation¢s Dimensions of Biodiversity Program
(http://www.nsf.gov/news/news_summ.jsp?cntn_id=132506)
and the Pew Charitable Trusts
(http://www.pewtrusts.org/en/about/news-room/press-releases/2014/06/24/pew-grants-22-young-scientists-support-for-biomedical-research).

With Antonis Rokas (Vanderbilt) and Cletus P. Kurtzman (USDA), the Y1000+ Project (http://www.nsf.gov/awardsearch/showAward?AWD_ID=1442148&HistoricalAwards=false) seeks to sequence and analyze the to complete genomes of all ~1,000 known species of Saccharomycotina yeasts and determine the genetic basis of their metabolic, ecological, and functional diversification. Yeasts are genetically more diverse than vertebrates and have remarkable metabolic dexterity, but most remain minimally characterized. They compete vigorously for nutrients in every continent and biome and can produce everything from beer to oil. The history of yeasts is recorded in their genome sequences. Now is the time to read it and tell their story!

The Hittinger Lab has diverse funding for other basic and applied research from NSF, DOE, and USDA, but we are specifically expanding our basic research in ecological and evolutionary genomics.

The complete advertisement and application instructions can be found here: http://hittinger.genetics.wisc.edu/Research/Funding/PostDocAd2014.html.

The precise start date is flexible, but candidates should apply by November 30th to receive full consideration.

Sincerely,

Chris Todd Hittinger, Assistant Professor of Genetics
Genome Center of Wisconsin
J. F. Crow Institute for the Study of Evolution
University of Wisconsin-Madison
425-G Henry Mall, 2434 Genetics/Biotechnology Center
Madison, WI 53706-1580
cthittinger@wisc.edu, (608) 890-2586
http://hittinger.genetics.wisc.edu

Job: Senior Lab Tech in Microbial Ecology at UNM

The Taylor Lab in the Department of Biology at the University of New Mexico is seeking a Senior Lab Tech in Microbial Ecology. The lab investigates fungal biodiversity and the evolutionary ecology of plant-microbe interactions, particularly mycorrhizae and biological nitrogen fixation, using field and molecular methods. This position will involve molecular analyses related to two recent NSF grants, one investigating climate-change related disruption of grass-endophyte interactions along elevational gradients in the Rocky Mountains, the second investigating the potential for associations with mycorrhizal fungi to underlie niche-partitioning in hyperdiverse epiphytic orchid communities of Costa Rican rainforest (see award IDs 1354972 and 1355155). For more information about the lab, please see taylorlabunm.weebly.com anborealfungi.uaf.edu.

The senior technician will be involved in various aspects of laboratory management, including student mentoring. The main duties will be to push forward cutting-edge plant microbiome molecular analyses. A core duty will be the preparation of amplicon libraries for NGS sequencing. There may also be opportunities to participate in fieldwork in Costa Rica and Alaska. Leadership and success in bringing projects to fruition will be rewarded with numerous opportunities for authorship on scientific publications.

A bachelors degree in biology, biochemistry, microbiology or related field is required, an MS is preferred. Experience beyond the classroom with standard microbiological and molecular methods including DNA extraction, PCR and sequencing is essential. Skills in more advanced methods, especially NGS methods such as RADseq, RNAseq, or anchored-hybrid-enrichment-sequencing are desirable. Strong organizational skills and basic data management experience are also essential, while scripting/programming skills (e.g. linux system administration, Perl, PHP, python) would be a major plus.

For additional information and to apply for the position, please follow this link:
unmjobs.unm.edu/applicants/Central?quickFind=80401
Applications should include a cover letter, resume, unofficial transcripts and contact information for at least three references. Start date is flexible and position is open until filled; for best consideration, applications should be received before December 15th.

The University of New Mexico is the flagship university in the state with 36,000 students and 40 PhD programs. Interactions with Los Alamos and Sandia National Labs contribute to a vigorous research climate. The main UNM campus is located in Albuquerque, a city of ~800,000 situated on the Rio Grande River at 5000 feet in elevation. Days are sunny and warm while nights are cool. At the transition between the Sonoran Desert and the Great Plains Grasslands and surrounded by mountains, Albuquerque is ideally situated for both cultural and outdoor explorations. The 10,000 foot Sandia Crest is only a 40 minute drive, while the epicurean, cultural and artistic delights of Santa Fe are only an hour away. Numerous other attractions may be found in all directions, such as Chaco Canyon, Bandolier National Park, White Sands National Monument, and many mountain ranges and ski resorts.

If you have questions about the position, please email Lee Taylor at fflt@unm.edu.