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.

Job: Assistant Prof Bioinformatics at UC Riverside

University of California, Riverside
POSITION ANNOUNCEMENT:
ASSISTANT PROFESSOR OF BIOINFORMATICS

POSITION: The University of California, Riverside is searching for a new faculty member at the ASSISTANT PROFESSOR level in the area of Bioinformatics. Areas of preferred interest include developing and deploying methods for genomic data analysis such as variant identification, transcriptomics, genome assembly, comparative genomics. An emphasis on development and application of statistical methods and software to next generation sequencing data and large dataset analysis is desired. However, candidates developing approaches for analysis of metabolomic, proteomic, image analysis for biological systems are also in the scope of the position. Candidates employing experimental data collection as well as computational methods are welcomed. Study systems that address research in plant, animal, and microbial organisms are all encouraged to apply. Appointees in this series are expected to conduct mission oriented, translational research that has an ultimate goal of solving societal problems relevant to the mission of the Agricultural Experiment Station http://cnas.ucr.edu/about/anr/.

TITLE/RANK: Assistant Professor. Salary will be competitive and commensurate with accomplishments.

LOCATION: University of California, Riverside. The successful candidate will become a member of a major academic department within the College of Natural and Agricultural Sciences in his/her area of expertise with opportunities for a secondary appointment in a variety of departments and colleges.

BACKGROUND: The college is actively expanding its bioinformatics program which impacts many of its departments and interdepartmental graduate programs. Interdisciplinary bioinformatics research at UCR involves multiple departments, centers, and institutes including the Institute for Integrative Genome Biology. The Institute for Integrative Genome Biology (IIGB) connects theoretical and experimental researchers from different departments in Life, Physical and Mathematical Sciences, Medicine, Engineering and various campus based Centers. The IIGB is organized around a 10,000 sq.ft. suite of instrumentation facilities that serve as a centralized, shared-use resource for faculty, staff and students, offering advanced tools in bioinformatics, microscopy and imaging, proteomics and genomics. The IIGB Center for Bioinformatics is equipped with a modern high-performance compute (HPC) and high performance data storage infrastructure.

QUALIFICATIONS: Applicants must have a Ph.D. and postdoctoral experience.

RESPONSIBILITIES: Qualified candidates are expected to have excellent publication and research records in bioinformatics or related areas, such as computational biology, genome biology and genomics, statistics, or computer science. The successful candidate will be expected to establish and maintain a vigorous, innovative and well-funded, state-of-the-art research program, teach effectively at the undergraduate and graduate levels, and participate in departmental and interdepartmental graduate programs. Teaching responsibilities will include participating in the current bioinformatics curriculum and contributing to development of new offerings at graduate and undergraduate level.

TO APPLY: Review of applications will begin December 3, 2014 for full consideration and will continue until the position is filled. Interested individuals should apply at https://aprecruit.ucr.edu/apply/JPF00269 with required documents: (1) a curriculum vitae, (2) a statement of research interests, and (3) three letters of reference. For additional information, visit http://genomics.ucr.edu/jobs.html or http://cnas.ucr.edu

The University of California is an Equal Opportunity/Affirmative Action/Disability/Veterans Employer.

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.

Job: Faculty position in Molecular Genetics & Microbiology, Duke University School of Medicine

Applications for tenure-track and tenured faculty position, Department of Molecular Genetics and Microbiology

This is an open position seeking individuals that employ genetic and/or genomic approaches to investigate important and fundamental biological questions. The following areas are of special interest to this search

  1. genetic basis for behavior or disease in model systems and/or humans
  2. host and/or pathogen genetic variation that influences infectious disease outcome and progression
  3. genomic and epigenetic mechanisms of disease

See the full advertisement flier 2014 Duke MGM Faculty Search and apply at http://academicjobsonline.org/ajo/jobs/4304

Deadline for applications is November 15, 2014.
Further inquiries should be directed to Kasey Carroll kasey.carroll@duke.edu

Grad Student: Synthetic Ecology and the Evolution of Symbiosis

Graduate Assistantships in Synthetic Ecology and the Evolution of Symbiosis

Graduate assistantships are available to support Masters or PhD students in Erik Hom’s laboratory at the University of Mississippi (Ole Miss).  The Hom lab is generally interested in understanding how biotic and abiotic factors facilitate the formation, persistence, and evolution of species interactions, notably those that are symbiotic.  We are particularly fond of studying the interactions between fungi and algae and use a predominantly synthetic approach to address our questions (see Science 345:94-98).  Our lab is seeking bright, highly motivated students with an appetite for learning to join us in pursuing research projects of mutual interest in areas that include (but are not limited to): experimental evolution, synthetic ecology, EcoEvoDevo, eukaryotic metagenomics, bioinformatics, and the ecology of microbial consortia.  Stipend support will be a combination of research and teaching assistantships, and includes tuition waivers and health benefits.

The University of Mississippi is in an exciting phase of institutional growth and is located in Oxford, a vibrant and idyllic college town in northern Mississippi, about 75 mi south of Memphis, TN.  If you are into football, William Faulkner, local music, and/or fine food, Oxford is a fun town!  Requirements for graduate admissions can be found here: http://goo.gl/t1CfcR.  The desired start date for these positions is August 2015 (although January 2015 may be possible).  Women and underrepresented minorities are strongly encouraged to apply.  Those with a strong interest in STEM education and outreach within an underserved region are also encouraged to apply.

For consideration and/or more information, please contact Dr. Hom (erik@olemiss.edu, +1-662-915-1731, http://darwinsdaemon.com).  To apply, please send a single PDF file that includes:

1) a cover letter explaining your specific research interest(s) and qualifications/research experience,
2) your curriculum vitae,
3) a scientific writing sample,
4) school transcript(s),
5) GRE scores (note: quantitative and verbal scores should each be >150), and
6) contact information for at least 3 references.

Job: Asst Prof of Computational Systems Biology at UC Riverside

Assistant Professor of Computational Systems Biology

The Department of Botany and Plant Sciences at the University of California, Riverside seeks outstanding candidates for an open Computational Systems Biologist position at the rank of Assistant Professor. We are interested in candidates involved in research in systems biology, using computational approaches or a combination of both experimental and computational approaches. A Ph.D. in a relevant discipline is required including several years of postdoctoral research. The successful candidate will hold an academic appointment in the Department of Botany and Plant Sciences with the option of a secondary cooperating faculty appointment in a quantitative department such as statistics, computer science, engineering or related. The candidate will also join the innovative and multidisciplinary Institute for Integrative Genome Biology (IIGB) which connects theoretical and experimental researchers from different departments in Life, Physical and Mathematical Sciences, Medicine, Engineering and various campus based Centers. The IIGB is organized around a 10,000 sq.ft. suite of Instrumentation Facilities that serve as a centralized, shared-use resource for faculty, staff and students, offering advanced tools in bioinformatics, microscopy, proteomics and genomics. Its bioinformatic component is equipped with a modern high-performance compute (HPC) infrastructure. This position will include an appointment in the Agricultural Experiment Station, which includes the responsibility to conduct research and outreach relevant to the mission of the California Agricultural Experiment Station (http://cnas.ucr.edu/about/anr/).

Qualified candidates are expected to have excellent publication and research records in computational systems biology or related areas, such as bioinformatics or computational genome biology. The research program should be heavily focused on involving modern high-throughput data, especially from next generation sequencing technologies. An additional requirement is a strong commitment to teaching in computational systems biology.

Review of applications will begin November 7, 2014 and continue until the position is filled. Interested individuals should: (1) submit a curriculum vitae, (2) provide a statement of research, and (3) three letters of reference. A teaching statement is strongly recommended. Please submit your applications through the AP Recruit job link: https://aprecruit.ucr.edu/apply/JPF00230

The University of California is an Equal Opportunity/Affirmative Action/Disability/Veterans Employer.

LEARN MORE

More information about this recruitment: http://plantbiology.ucr.edu/