PostdoC: JGI fungal and Algal multi-omics

Postdoctoral Scholar Positions at the Joint Genome Institute in Berkeley, CA
Apply at https://lbl.referrals.selectminds.com/jobs/postdoctoral-scholar-2226

Berkeley Lab’s Joint Genome Institute (JGI) Division has an opening for a Postdoctoral Scholar. You will work as part of the Fungal and Algal Program in the Joint Genome Institute division investigating genomes and multi-omics of fungi and algae, both represent promising targets for sustainable bioenergy. The key to algae’s potential as a renewable energy source involves the increase of algal biomass production. Fungi are critical for both the growth of plants and plant biomass decomposition and encode collections of enzymes and pathways to use for bioenergy applications. You will collect and analyze genomics, metabolomics, and other ‘omics’ data to model biological processes in these organisms. You will develop and use new approaches and tools for machine learning, metabolic reconstruction, and gene network analysis. 

What You Will Do:

  • Assemble, annotate and analyze genomes of fungi and algae using JGI annotation pipelines and comparative genomics tools.
  • Use advanced cheminformatic and bioinformatic approaches to analyze and integrate the metabolomics results with other omics datasets.
  • Develop and apply innovative computational and mass spectrometry-based metabolite profiling approaches to characterize algal or fungal metabolism including novel secondary metabolites and their pathways.
  • Publish scientific papers in peer-reviewed journals, release data onto public data repositories, and present findings at seminars and conferences.
  • Collaborate with other members of the program project research team both onsite/offsite team at Berkeley Lab.
  • Develop Unix-based scripts for data analysis; analyze data using both high-performance computing and web-based genome portals.

What Is Required:

  • Ph.D. within the last three years in Life Sciences, Computer Sciences, Bioinformatics, or related field.
  • Experience with genomics, transcriptomics, metabolomics or related analytical approaches
  • Strong cheminformatic or bioinformatics training.
  • Robust understanding of organismal biology, metabolic processes, and gene networks.
  • Programing experience (python/perl) and familiarity with database systems (MySQL).
  • Demonstrated ability to interact effectively with technical and scientific staff.
  • Proven ability to perform independent research and organize data for publications and presentations.
  • Effective oral and written communication skills to present findings at group meetings and conferences, and to publish results.

Additional Desired Qualifications:

  • Experience in algal or fungal characterization.
  • Strong background in LC/MS/MS.
  • Strong publication record.

Berkeley Lab (LBNL) addresses the world’s most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab’s scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the U.S. Department of Energy’s Office of Science.

Equal Employment Opportunity: Berkeley Lab is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, or protected veteran status. Berkeley Lab is in compliance with the Pay Transparency Nondiscrimination Provision under 41 CFR 60-1.4.  Click here to view the poster and supplement: “Equal Employment Opportunity is the Law.”

Click here to apply: https://lbl.referrals.selectminds.com/jobs/postdoctoral-scholar-2226

Contact: Igor Grigoriev, PhD
Head, Fungal and Algal Genomics Program, DOE Joint Genome Institute, Walnut Creek, CA 
Senior Scientist, Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA
Adjunct Professor, Department of Plant and Microbial Biology, University of California, Berkeley, CA

Job: Assistant Professor in Fungal Biology – Cornell University

Assistant Professor; Fungal Biology; tenure track, academic year appointment (9-month) https://academicjobsonline.org/ajo/jobs/15107

The search is looking for someone with research interests and expertise in the biology of plant-associated fungi and are particularly interested in learning of talented postdoctoral scholars or junior faculty who are or identify with underrepresented groups in science, representing diversity in its broadest sense.

The School of Integrative Plant Science at Cornell University (https://sips.cals.cornell.edu) invites applications for a tenure track position at the Assistant Professor level in the area of biology of plant associated fungi. With an immense diversity of virulence mechanisms and lifestyles, plant pathogenic fungi cause disease throughout the plant kingdom and are a major threat to global food security. Conversely, fungal mutualists improve plant stress tolerance and health. The new faculty member is expected to develop a strong, internationally recognized program that addresses the biology of fungi and/or oomycetes that associate with plants. Candidates whose research integrates empirical, genetics, genomics and/or metabolomics approaches to fungi and/or fungal populations with computational approaches are particularly sought. Examples of research topics include, but are not limited to: i) the exploration of basic cellular processes related to fungal pathogenic or mutualistic lifestyles, ii) virulence determinants (e.g. secondary metabolites and protein effectors), iii) translational research that builds solutions to agricultural problems based on mechanistic understanding of fungal genetics and cell biology, iv) dynamics and variation in fungal populations, and ecology and evolutionary biology of genome adaptation with regard to pathogenicity.

The ideal candidate will thrive in the highly collaborative environment of Cornell University, which includes diverse faculty and vibrant graduate programs affiliated with the School of Integrative Plant Science (SIPS) in the College of Agriculture and Life Sciences (CALS), the university-wide Cornell Institute of Host-Microbe Interactions and Disease, the Boyce Thompson Institute for Plant Research, and the USDA Agricultural Research Service. The expected affiliation for the position will be the SIPS Section of Plant Pathology and Plant-Microbe Biology (PPPMB) on the Ithaca campus. The position will have a 60% research and 40% teaching responsibility, and the successful candidate will teach in the broad area of the biology of fungi in courses that match the PPPMB core curriculum and the candidate’s expertise (such as Ecology and Evolution of Plant-Pathogen Interactions or Filamentous Fungal Genomics and Development).

SIPS and CALS at Cornell embrace diversity and seek candidates who will create a climate that attracts students of all races, nationalities, and genders. Diversity and Inclusion are a part of Cornell University’s heritage. We are a recognized employer and educator valuing AA/EEO, Protected Veterans and Individuals with Disabilities. Cornell understands the needs of dual career couples, which it attempts to meet through a Dual Career program and membership in the Upstate New York Higher Education Recruitment Consortium, which assists dual career searches.

Visit http://www.hercjobs.org/ to see positions available in higher education in the upstate New York area. Cornell and Ithaca are family-friendly communities: Cornell offers a rich array of services, programs and benefits to help employees advance in their career and enhance the quality of personal life, including employee wellness, workshops, childcare and adoption assistance, parental leave and flexible work options. For more details,
see: https://hr.cornell.edu/sites/default/files/documents/family_resources_faculty.pdf.

Qualifications: Ph.D. in a relevant field. The candidate should welcome the opportunity to work in a multidisciplinary and multicultural setting and create a collegial professional environment. Well- qualified applicants are expected to have a demonstrated record of publication excellence. Preferred qualifications include postdoctoral experience, ability to work as part of a team, and ability to communicate effectively with students, colleagues, and broader audiences.

Salary and Benefits: Salary is competitive and commensurate with background and experience. An attractive fringe benefits package is provided.

Application procedure: Submit as a single PDF file to Academic Jobs Online (https://academicjobsonline.org/ajo/jobs/15107) a cover letter, a statement of research accomplishments, interests and future plans (4 pages maximum), a statement of teaching experiences, philosophy and interests (2 page maximum), a statement of contribution to diversity, equity and inclusion (https://cals.cornell.edu/about/leadership/ofa/hr/statement-contribution- diversity-equity-and-inclusion/), a detailed curriculum vitae, and the names and contact information of three or four references. (Letters will be requested after the applications are reviewed.) Inquiries may be sent to Prof. Maria Harrison, Search Chair (mjh78@cornell.edu) or Prof. Gillian Turgeon, PPPMB Section Chair (bgt1@cornell.edu). Initial screening of applications will begin on November 20, 2019 and continue until the position is filled.

Opportunity: The School of Integrative Plant Science Section of Plant Pathology and Plant-Microbe Biology includes internationally renowned faculty with abundant interactions and active teaching, research and extension programs in the College of Agriculture and Life Sciences (CALS). CALS is a pioneer of purpose-driven science and Cornell University’s second largest population of students, faculty and staff. CALS members work across disciplines to tackle the challenges of our time through world-renowned research, education and outreach. The questions we probe and the answers we seek focus on three overlapping concerns: natural and human systems; food, energy and environmental resources; and social, physical and economic well-being

Cornell University is an innovative Ivy League university and a great place to work. Our inclusive community of scholars, students and staff impart an uncommon sense of larger purpose and contribute creative ideas to further the university’s mission of teaching, discovery and engagement. With our main campus located in Ithaca, NY, Cornell’s global presence includes the medical college’s campuses on the Upper East Side of Manhattan and Doha, Qatar, as well as the new Cornell Tech campus on Roosevelt Island in the heart of New York City.

Employment Assistance: If you require an accommodation for a disability in order to complete an employment application or to participate in the recruiting process, you are encouraged to contact Cornell University’s Office of Workforce Policy and Labor Relations at voice (607) 255-6866, fax (607) 255-0298, or email at equalopportunity@cornell.edu.

Applicants who do not have internet access are encouraged to visit your local library, or local Department of Labor. You may also visit Cornell’s Office of Workforce Recruitment and Retention Monday – Friday between the hours of 8:30 a.m. – 4:30 p.m. to use a dedicated workstation to complete an online application.

Notice to Applicants: Please read the required Notice to Applicants statement at https://hr.cornell.edu/important-notice-applicants . This notice contains important information about applying for a

Postdoc positions UMich

Bridging Positions in Ecology & Evolutionary Biology

The University of Michigan Department of Ecology & Evolutionary Biology (https://lsa.umich.edu/eeb) invites applicants for two bridging postdoctoral programs: the Literature, Science, and the Arts Collegiate Fellows Program (LCFP) and the U­M Presidential Post­doctoral Fellowship Program (PPFP). Faculty members in EEB have successful records of providing a nurturing and productive postdoctoral experience through these programs. We are especially interested in future colleagues who engage in research in the fields of 1.) plant biodiversity or 2.) population and evolutionary genetics (with an emphasis on theoretical approaches).

The University of Michigan Department of Ecology & Evolutionary Biology views these postdoctoral fellowships as providing an exceptional opportunity to recruit potential new faculty to the University by offering the possibility of either a postdoc alone or a combined postdoc and tenure track faculty appointment.

N.B. Applications for the LCFP and PPFP open September 1. In addition to the materials required by both programs, applicants should submit their materials directly to EEB by October 1.

Eligibility

• Ph.D. in a relevant field

• Demonstrated potential for high scholarly impact

• Evidence of successful classroom teaching experience (as a student or professional)

• A strong commitment to diversity, equity, and inclusion

• Candidates with tenure track appointments are not favored in the selection process unless there

is a clear explanation of how an award to the candidate would further the goals of the LCFP or PPFP

How to Apply:

  1. Send materials to the LCFP (https://lsa.umich.edu/ncid/fellowships­awards/lsa­collegiate­ postdoctoral­fellowship.html) and/or PPFP http://presidentspostdoc.umich.edu/#) via their respective online applications, and
  2. Send materials electronically to EEB by emailing Molly Hunter at mollyiz@umich.edu.

https://lsa.umich.edu/content/dam/eeb-assets/eeb-documents/bridging_position_combined_ad.pdf

Postdoctoral Positions in the Tri-Institutional Molecular Mycology and Pathogenesis Training Program (Tri-I MMPTP) at Duke University, UNC-Chapel Hill, and North Carolina State University

Postdoctoral Positions in the Tri-Institutional Molecular Mycology and Pathogenesis Training Program (Tri-I MMPTP) at Duke University, UNC-Chapel Hill, and North Carolina State University

The Tri-Institutional Molecular Mycology and Pathogenesis Training Program is seeking Postdoctoral Fellowship applicants.  This program was founded in 2004 and has been continuously funded by an NIH/NIAID T32 training grant over the past 15 years, and was renewed recently for a fourth five year funding period.  Two fellowship positions are available as of August 1, 2019 or thereafter.  The program funds both basic and clinical fellows working on all aspects of mycology encompassing model fungi, plant pathogenic fungi, and human pathogenic fungi.  Areas of interest span DNA repair and recombination in model yeasts, virulence of human and plant fungal pathogens, antifungal drug targets and mechanisms of action and therapeutic development, evolution of fungi, and clinical infectious diseases, among others. The program is tri-institutional and features training mentors in all thematic areas throughout the Triangle Area of North Carolina, and supports fellows at all three institutions.  The program is co-directed by Joe Heitman, Andy Alspaugh, and Bill Steinbach, and supports career development through a series of ongoing activities including a monthly lunch meeting series, annual symposia, travel awards to meeting and courses, and regular meetings with scientific advisory committee members and visiting speakers including advisory board members.  The program has an illustrious group of alumni (some are listed below), many of whom are leaders in medical mycology or with leadership positions in pharma, industry, and government/NIH. Women and individuals representing diversity in science are encouraged to apply.  Interested applicants are encouraged to contact the program co-directors and send a letter of interest, cv, reprints, and references. Further information at the program website: https://mmptp.mgm.duke.edu/

Many program alumni are excelling in independent positions: Robert Cramer (Dartmouth),  Brian Smith (Duke), Michael Price (Liberty University), Kirsten Nielsen (University of Minnesota), Crystal Icenhour (CEO Aperiomics), Xiaorong Lin (University of Georgia), Alex Idnurm (University of Melbourne), Marianela Rodriguez-Carres (BASF-RTP), Jarrod Fortwendel (University of Tennessee), Josh Burgess (Epicentre), Min Ni (Regeneron), Wenjun Li (NCBI), Richard Festa (Irvine Scientific), Soo Chan Lee (University of Texas, San Antonio), Xuying Wang (GlaxoSmithKline), Jelena Catania (University of Central Florida College), Ryoko Oono (UC Santa Barbara), and Chelsea Boyd (NIH/NIAID).

Please send application materials to Joseph Heitman at heitm001@duke.edu, Andy Alspaugh at Andrew.alspaugh@duke.edu, and Bill Steinbach at bill.steinbach@duke.edu

Postdoc: suppressive soil microbiomes, Univ Minnesota

Post-doctoral researcher position:  Two, three-year post-doctoral positions are available in the Kinkel laboratory at the University of Minnesota.  We are seeking post-doctoral scientists to work on two new project studying the factors the mediate the composition and functional capacities of soil microbiomes to support plant productivity.  One project utilizes a unique, long-term, 5-species crop monoculture experiment to test predictions of a mechanistic model for the development of disease-suppressive microbiomes.  The second project explores variation in the coevolutionary dynamics of soil microbiomes in response to diverse treatments.  Both projects will integrate data on microbial community composition (amplicon sequencing), microbial functional characteristics (using culture-based approaches), and analyses of soil chemical characteristics, including carbon profiles, to evaluate ecological and evolutionary factors that mediate the pathogen-suppressive and other functional capacities of soil microbiomes.  This research will contribute to the development of novel strategies for managing soil microbiomes for enhanced crop productivity. 

Preferred Qualifications:Familiarity with fundamental concepts in ecology, evolutionary biology, plant pathology, and microbiology; experience with microbiome analyses using sequence-based approaches, and microbial culturing; experience with programming using R and/or Python; willingness to interact broadly with diverse scientists in a fast-paced laboratory setting; ability to work independently, to accomplish goals, and to meet deadlines. 

Salary: Starting salary, $48,426 annually, commensurate with experience.

Application instructions:   Individuals should apply through the University of Minnesota website: (https://humanresources.umn.edu/content/find-job) Job ID# 327351 & Job ID# 328479.  Any questions, please contact Linda Kinkel (kinkel@umn.edu).  

GradStudent: Two open PhD Positions in Evolutionary Genetics of Fungal Host-shifts

We are seeking candidates to fill two fully funded PhD positions for a period of 3 years in the Applied Evolutionary Ecology research group lead by Henrik H. De Fine Licht at the University of Copenhagen, Denmark (https://plen.ku.dk/english/research/organismal_biology/aee/).

We are looking for committed and enthusiastic graduate students to work with insect-pathogenic fungal genetics, evolution and ecology. We specifically aim to explore how phenotypic plasticity and epigenetic modifications influence the evolution of fungal pathogen host shifts using insect-pathogenic fungi as a model. The project will explore gene transcription profiles and epigenetic modification of artificial fungal host-shift events created in the lab, coupled with phenotypic changes in growth and virulence of fungal pathogens. Further scientific background information can be found in the recent paper by De Fine Licht (PLoS Pathogens 14(5): e1006961). The successful PhD students will thus obtain competences within insect-fungus interactions, fungal genomics and transcriptomics, and applied bioinformatics. We are looking for candidates with experience in any or all of the following areas: Fungal pathogen biology, mycological techniques, molecular genetic laboratory techniques, and computational analysis of genomic sequence data. Most importantly, the successful candidates are enthusiastic, have a good grasp of evolutionary biology and are interested in host-pathogen evolution.

The project is funded by a Danish Research Council Sapere Aude Starting Grant and involves researchers at University of Copenhagen and University of Maryland (USA). The PhD students will be supervised by Associate Professor Henrik H. De Fine Licht and co-supervised by Associate Professor Nicolai V. Meyling.

To apply, please first contact Henrik H. De Fine Licht (Email: hhdefinelicht@plen.ku.dk, include subject-line in email: “PhD student fungal host-shift genetics”). This way, Henrik H. De Fine Licht and the potential applicant can discuss the formal application and requirements (e.g. applicants with English as second language need to provide a copy of a specific English test score sheet and the documentation of academic degrees obtained (diplomas) must be in English/officially approved translation to English) before submission. The deadline for formal application is 1 April 2019, so contact Henrik H. De Fine Licht as soon as possible if you are interested.

Time to register for Fungal Genetics

It is time to get excited for that biennial gathering of fungal geneticists, mycologists, and generally scientists who study fungal biology at many scales from communities to molecules. Registration is open for 30th Fungal Genetics Conference held at Asilomar Conference Center in Pacific Grove, California.  The abstract submission deadline is December 5 and that is also the early registration deadline (save money!). 

I look forward to this meeting as it is a chance to hear about the latest work on fungi from genetics, genomics, molecular biology, evolution, medical mycology, and molecular ecology. Personally it was the meeting I first attended as a graduate student where I built so many collaborations, was introduced to mentors, and established friendships that have carried me in my career. It also is an important meeting to get the pulse of what are the trends in technology and molecular techniques that are can improve the way research questions are framed and tested. 
The program schedule and list of invited talks and session topics is posted here and there will be more talks chosen from submitted abstracts as well as multiple poster sessions to hear about and share your work.

 So go register!

Postdoc: Bioinformatics for Fungal Genomics and Transcriptomics, UC Davis, California

BACKGROUND

The Stergiopoulos lab at the Department of Plant Pathology at the University of California Davis is seeking for a highly skilled and motivated post-doc in the field of fungal genomics and transcriptomics. The lab studies the molecular mechanisms of fungal pathogenesis on plants with an emphasis on characterizing computationally and by functional analyses critical molecular and cellular functions required for virulence. As part of our studies we use a systems-level approach that integrates comparative genomics, genome-wide transcriptome profiling, targeted proteomics, and functional analysis of selective gene candidates to study the mechanisms that control gene expression and transcriptome diversity of fungal virulence associated genes.

JOB DESCRIPTION
The successful candidate will work on sequencing using cutting-edge next- generation sequencing technologies and assembling at the chromosome level the genomes of important fungal pathogens of agronomic importance as well as mining these genomes for candidate pathogenicity genes. The candidate is also expected to analyze and mine dual RNAseq data of compatible plant- pathogen interactions that are already available in the lab. The position will become available in January 2019 and is initially for one year, renewable for a second year upon satisfactory performance. Salary is based on experience and qualifications according to UC Davis pay-scales. UC Davis provides a highly vibrant intellectual atmosphere, a pleasant college environment and career development activities specifically designed for post-doctoral scholars.

EXPERIENCE
Highly motivated candidates with an interest in applying cutting-edge next- generation sequencing-based technologies to host-microbe interactions research are encouraged to apply. Ideal candidates should have received recently a Ph.D. in bioinformatics, computational biology or related fields. A strong record of scientific accomplishment by peer-reviewed publications as well as experience in analyzing high-throughput genomics and transcriptomics data is a plus for this position. Candidates should also be proficient in at least one of the common programming languages used in bioinformatics (C, C++, Java etc.) and have excellent verbal and written communication skills

APPLICATION
Interested candidates should send to Prof. Ioannis Stergiopoulos (istergiopoulos@ucdavis.edu) a single pdf file that includes a cover letter, their full CV, a statement of research interests, and contact information of three references.

http://sterg001.wixsite.com/stergiopoulos-lab

PDF of the job announcement UC Davis_Postdoc in Fungal Genomics and Transcriptomics

Job: Assistant/Associate Professor of Microbiology, Cal State Chico

Chico-state-logoThe Department of Biological Sciences is searching for a tenure-track Assistant or Associate Professor to start August 21, 2019. California State University, Chico seeks faculty who are competent in their field, collaborative with colleagues and staff, and committed to student success.

The minimum education requirement for appointment to this position is a PhD in microbiology or a related field, with a specialization in prokaryotic or eukaryotic (protist or fungal) pathogens. Candidates nearing completion of the terminal degree may be considered; however all requirements for conferral of the degree must be met no later than August 21, 2019. A demonstrated ability or potential to establish externally-funded research, a record of publication, and a strong interest in teaching excellence and enthusiasm for mentoring undergraduate and graduate students in research are also required. The successful candidate should provide evidence of their commitment to or experience promoting and fostering a learning environment that is supportive of individuals from diverse backgrounds.

https://jobs.csuchico.edu/postings/5093