Tag Archives: genomics

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

Postdoc: Fungal Endophyte Genomics, U’Ren lab, U Arizona

Postdoc Position Fungal Endophyte Genomics • U’Ren lab

A postdoctoral position is available in the lab of Jana U’Ren at the University of Arizona to study the ecology and evolution of plant-endophyte symbioses. The project centers on enriching genomic, transcriptomic, and metabolomic knowledge of phylogenetically diverse endophytic fungi in collaboration with the DOE Joint Genome Institute. The start date is flexible, but anticipated to be in Fall/Winter 2018 or when the suitable candidate is identified. The position has an initial appointment for one year with a strong likelihood of extension to a second year pending performance review.

The ideal candidate will be skilled in bioinformatics, molecular biology, and microbiology with a background in plant-microbe interactions, ecology, and evolution. Minimum requirements: a PhD in ecology, evolutionary biology, microbiology, mycology, plant pathology, or a related discipline. Preference will be given to candidates with proficiency in both bioinformatics and molecular biology. Preferred candidates will have excellent communication skills, high motivation, and a strong willingness to work independently and as part of an integrative team. Potential duties include (but are not limited to) comparative genomic and transcriptomic analyses, functional trait assays, and plant inoculation experiments, with potential for the development of independent research projects related to plant-fungal interactions.

As part of the UA Ecosystem Genomics Initiative and the BIO5 Institute, the successful candidate will have extensive opportunities to collaborate across departments at UA, as well as with collaborators at other universities. This collaborative environment is conducive to development of a pathway to independence in academic research. The position also includes opportunities to mentor graduate and undergraduate researchers from diverse backgrounds.

Home to the world-class University of Arizona, Tucson is a vibrant southwestern city with a rich and distinctive heritage, fabulous access to outdoor activities, and diverse opportunities for cultural engagement. Outstanding UA benefits include health, dental, vision, and life insurance; paid vacation, sick leave, and holidays; UA/ASU/NAU tuition reduction for the employee and qualified family members; access to UA recreation and cultural activities; and more!

Applicants should submit a cover letter, CV, contact information for three references, and copies of three recent publications. All application materials should be submitted in a single email to Dr. Jana U’Ren (juren@email.arizona.edu).

PDF: Postdoc-URen-Lab-Arizona-2

Postdoc: Computational Transcriptomics. Massey University (NZ)

Postdoctoral Fellow in Computational Transcriptomics with Professor Barry Scott, Massey University, New Zealand

We are looking for a computational biologist with the necessary academic training and competency to analyse a large transcriptome data set generated from endophyte infected grass tissue. The project is collaborative with Professor Christopher Schardl at the University of Kentucky and Professor Murray Cox at Massey University. We are interested in identifying genes that are differentially expressed during the onset of stromata (sexual stage) development on the grass host. We have isolated RNA from different tissues of three different fungal-grass associations. We have gene models for the fungal components of all three associations but gene models for just one host. The post doc will be expected to develop their own hypotheses in analyzing this very large data set and work with a wider group working on the genomics, transcriptomics and functional analysis of fungal-grass associations. The analytical position requires solid quantitative and computational skills, with the ability to develop and apply new bioinformatics applications to the analyses.  At a minimum, some confidence in bioinformatics and a programming language is required. Training in fungal biology or genomics can be provided as needed, and candidates from non-standard research backgrounds with a clear fit to the position are encouraged to apply.

Funding is available for just one year from a research sub-contract with the Bioprotection Research Centre to Massey University. Salaries are competitive starting at $69,841 for step 1 of the post-doctoral scale.

The position will be based with Professor Barry Scott at Massey University in the city of Palmerston North.
Please email if you have any further questions: d.b.scott@massey.ac.nz

PDF of job ad: Post doc in computational biology

To submit an application, please provide:

  1.  A brief statement of research interests and experience, focusing on short to medium term
    career goals and your fit for this position
  2. Curriculum vitae, including qualifications and scientific publications
  3. The names and contact details of three referees willing to provide a confidential letter of recommendation upon request

Closing Date: to be readvertised

JOB DESCRIPTION
Purpose Statement: To carry out individual and team-based research on changes in gene expression associated with the onset of endophyte sexual development on grass hosts.

Responsible To: The Head of the Institute of Fundamental Sciences through Professor Barry Scott

Key Accountability Areas:
The Fellow is required to:

  • Undertake computational research on fungal transcriptomics
  • Undertake other relevant duties as specified and approved by the Principal Investigator
  • Maintain accurate and orderly records of experiments, procedures and code, and store these records and data in the laboratory group archive.
  • Report weekly to the Principal Investigator summarizing research progress and planned future research, with a focus on work towards research publications
  • Publish at least one peer-reviewed publication in an international scientific journal
  • Be familiar with Institute guidelines and rules for safety and approved practices in experimental work
  •  Maintain an organised and safe working environment
  • Be familiar with Institute guidelines and safety rules.
  • Participate fully in the academic activities of the Institute and the University
  • Provide two monthly written reports to the project leader that summarise research progress and planned future experiments with a focus on publications
  • Devote themselves full-time to University duties
  • Diligently and faithfully serve the University and use their best endeavours to promote and protect the interests of the University
  • Maintain confidentiality both during and after the appointment as Postdoctoral Fellow

 

Qualifications:  A PhD in bioinformatics, computational biology, or otherwise applicable field (interpreted broadly)

Experience:
Miniumum Qualifications

  • Able to conduct independent cutting-edge research
  • Proven research experience, including evidence of a publication record
  • Quantitative skills, including some background in statistics and programming

Preferred Qualifications

  • Candidates will be conversant in at least one programming language (broadly defined)
  • Additional bioinformatics, computational and/or statistical experience would be an advantage
  • Candidates with a background in biology together with applied mathematics, physics or computer science are encouraged to apply
  • Some knowledge of biological systems

Attributes and Skills:

  • good quantitative skills
  • experimental and intellectual creativity
  •  initiative and enthusiasm
  • proven ability to write, and potential to take the lead on scientific publications
  • commitment to quality improvement, up-skilling and personal development
  • ability to organize and maintain quality records
  • integrity and confidentiality
  •  good time-management skills
  • ability to work as a member of a team

Postdoc: Fungal Evolution and Population, USDA-ARS

Postdoctoral Position in Fungal Evolution and Population Biology

USDA-ARS, Peoria, Illinois

We are searching for a highly-motivated postdoctoral associate with strong molecular and computational biology research experience with fungi or other microorganisms to conduct research aimed at understanding the diversity, global population structure, and evolutionary dynamics of Fusarium head blight (FHB) pathogens.  Scientists in the Mycotoxin Prevention and Applied Microbiology (MPM) Research Unit at the USDA-ARS in Peoria have an outstanding record of discovery and publication regarding Fusarium biology, chemistry, and evolution.  Thus, opportunities exist for the postdoc to engage in these and other areas of interest. This full-time position is funded for 1 year ($61,218 + benefits) with the possibility for annual renewal up to 4 years.  The successful candidate must hold a PhD in Biology or related field by appointment start date, be proficient in both written and oral English, and have experience in population genomic analyses.  To apply, please email a single PDF to Todd Ward (todd.ward@ars.usda.gov) that includes: (1) a cover letter with a short description of why you are interested in and qualified for the position, (2) a current CV that includes a list of peer-reviewed publications, and (3) names and contact information for three references.  Evaluation of applications will begin immediately.  U.S. Citizenship is required.

USDA/ARS is an equal opportunity employer and provider

Postdoc: UMichigan Fungal Genomics

The lab of Tim James in the Department of Ecology and Evolutionary Biology at the University of Michigan is looking to hire a postdoctoral fellow in the area of single cell and comparative genomics. The research is centered on understanding the phylogeny and molecular evolution of uncultured and poorly known fungi, including the Cryptomycetes, Zygomycetes, and Chytridiomycetes through genomic analyses. The ultimate goals of the project are to produce a well-resolved phylogeny of the basal branches of the fungal kingdom, to identify key evolutionary events associated with diversification and reproduction, and to use genomics to predict ecological roles of uncultured lineages. A major component of the work will be to develop or improve methods for sequencing fungal genomes and transcriptomes using single or few cells or genome assembly using metagenomic approaches. This work will involve collaborations with the ZyGOLife research network (zygolife.org) and the Joint Genome Institute (JGI). The projects are supported by NSF and two JGI Community Sequencing Projects.

The ideal candidate will be skilled in bioinformatics, molecular biology, and microbiology with an interest in fungi. Preference will be given to candidates with proficiency in both bioinformatics and molecular biology. Possible duties include environmental sampling, cell sorting (FACS, micromanipulation), microscopy, genome assembly and annotation, and comparative analyses of genome evolution. Opportunities for mentoring undergraduates or research associates will be provided. The initial appointment is for one year with a possibility of extension to a second year pending performance review.

Our lab (www.umich.edu/~mycology) pursues diverse projects in mycology, and the environment is conducive to development of a pathway to independence in academic research. The lab is in the Department of Ecology and Evolutionary Biology (http://www.eeb.lsa.umich.edu/eeb/index.html), which has strengths in phylogenetics, evolutionary genomics, and disease ecology.

Interested applicants should email Tim James (tyjames@umich.edu) with a CV, cover letter, and the names and contact information of three references.

Anticipated Start Date: Between Oct. 1, 2016 and Jan. 1, 2017.

The University of Michigan is a non-discriminatory/affirmative action employer. The Department of Ecology & Evolutionary Biology at the University of Michigan harbors multiple labs with a focus on evolutionary genetics (http://www.lsa.umich.edu/eeb).

Timothy Y. James
Associate Professor
Associate Curator of Fungi
Department of Ecology and Evolution
University of Michigan
Ann Arbor, MI 48109
734-615-7753
tyjames@umich.edu
http://www.umich.edu/~mycology/

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

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/

UC Merced Prof of Biostatistics

The University of California, Merced is a dynamic new university campus in Merced, California, which opened in September 2005 as the tenth campus of the University of California and the first American research university in the 21st century. In keeping with the mission of the University to provide teaching, research and public service of the highest quality, UC Merced offers research-centered and student-oriented educational opportunities at the undergraduate, master’s and doctoral levels through three academic schools: Engineering, Natural Sciences and Social Sciences/Humanities/Arts.

http://jobs.ucmerced.edu/n/academic/position.jsf?positionId=3D4252
The Molecular Cell Biology group in the School of Natural Sciences at the University of California, Merced invites applications from exceptional scholars and teachers at the Assistant Professor (tenure track) level in Biostatistics.

Biostatistics is the development and use of statistical methods for medical and biological datasets including, but not limited to applications in experimental design, quantitative biology, epidemiology, medical informatics, nutrition, evolutionary biology, sequence bioinformatics, genomics, metabolomics, and systems biology. Current strengths of the Molecular Cell Biology group at UC Merced include cancer metabolism, diabetes, inflammation, infectious disease, and mechanisms of cell fate decisions. Ideally, applicants should demonstrate successful grantsmanship and nationally recognized research. We encourage applications from women and members of ethnic minorities.

The University of California at Merced is an affirmative action/equal opportunity employer with a strong institutional commitment to the achievement of diversity among its faculty, staff, and students. The University is supportive of dual career couples.

Qualifications:  Strong applicants should have a Ph.D. and show a track-record in development and/or application of methods in biostatistics, biomedical informatics, epidemiology, multiple hypothesis testing, Bayesian estimation and model selection, Markov chain Monte Carlo, machine learning and/or other areas. The successful candidate will be expected to cultivate collaborative research relationships with faculty in biology, health sciences, and may also collaborate with applied mathematics.

Other qualifications include:
(1) Quality, importance, and impact of past and current research in an area of biostatistics as judged by publications, awards, and letters of recommendation.

(2) External funding history or potential for obtaining external funding.

(3) Likely importance and impact of future research as judged by research plan and
letters of recommendation.

(4) Research interests that complement and strengthen those of current faculty
in the biological sciences.

(5) Potential ability to mentor graduate and/or post-graduate students and to contribute to graduate education and training, particularly of minorities underrepresented in health and
STEM fields.

(6) Potential effectiveness as an educator at both undergraduate and graduate levels based on teaching statement, experience, teaching evaluations, and letters from former students (as available).

Closing Date:         12/10/2012

Univ of Oregon Faculty position in Genomics, Bioinformatics, Statistical Genetics

UNIVERSITY OF OREGON

Faculty Positions in Genomics, Bioinformatics, Statistical Genetics

The Departments of Biology (http://biology.uoregon.edu) and Mathematics (http://math.uoregon.edu ) at the University of Oregon announce a cluster hire of up to three tenure-related faculty positions in Fall 2013. One of these positions may be at the level of Associate or Full Professor with indefinite tenure. These hires are part of an integrated effort to strengthen research and scholarship at the nexus of statistics/mathematics and biology at the University of Oregon, and will serve as a catalyst for future growth in this area. We are broadly interested in recruiting candidates working in areas developing statistical methodology related to the life sciences. Examples of these areas include, but are not limited to, statistical analysis of large data sets, algorithms for analyzing sequence data, and stochastic models for neuroscience, population genomics and molecular evolution. Successful candidates will bolster our emerging strengths in biomathematics, maintain an outstandi
ng research program that focuses on solving core problems in this area, and have a commitment to excellence in teaching. Ph.D. required. Position responsibilities include undergraduate teaching.

Interested persons should apply online to the MATHBIO SEARCH, University of Oregon at https://www.mathjobs.org/jobs/jobs/4035. Applicants should submit a cover letter, a curriculum vitae including a publication list, a statement of research accomplishments and future research plans, a description of teaching experience and philosophy, and three letters of recommendation. Ideally the research description and at least one of the letters of recommendation would include descriptions of the statistical/mathematical tools or models used in the applicant’s research. To ensure consideration, application materials should be uploaded by November 15th, 2012, but the search will remain open until the positions are filled.

Women and minorities are encouraged to apply. The University of Oregon is an Equal Opportunity/Affirmative Action Institution committed to cultural
diversity and compliance with the Americans with Disabilities Act, and supportive of the needs of dual career couples. We invite applications
from qualified candidates who share our commitment to diversity.

A HyphalTip: Get a bunch of SRA data

[Trying to post some simple tips from time-to-time, they’ll be in this same category]

For those wanting to get a large dataset from NCBI SRA trace archive, you may be annoyed to click on each link and wait for the download. For example if you read a recent paper on Population Genomics in Neurospora crassa and saw the 48 RNA-Seq datasets which is accession number SRP004848, you might be interested to download all these data for your own re-analysis, as a great dataset for teaching, or even to see how the splicing and expression looks for your favorite gene.

I put together some scripts in this folder to make it easy to see how to download, rename, and extract fastq from these data.  In a future HyphalTip, I’ll detail how you can map these to the genome to get expression values and improve gene annotation.

For cmdline users, after installing the aspera plugin, you can do this to download the sra light data.  Aspera will give you 10-100x speedup – I was downloading at 300 MB/s vs 5Mb/s with wget or ncftp (FTP download). See Morgan’s info about downloading as well. You can run this command or see it in this script.

hyphaltip $ ~/.aspera/connect/bin/ascp -k 1 -l 300M -QTr -i ~/.aspera/connect/etc/asperaweb_id_dsa.putty \
anonftp@ftp-private.ncbi.nlm.nih.gov:/sra/sra-instant/reads/ByStudy/litesra/SRP/SRP004/SRP004848 ./

Now the IDs you will have for all these files will be for the SRA accessions not the original strain numbers which may be more informative/meaningful. This can be confusing because the accession for a particular experiment is SRR080688 is the strain D110/FGSC 8870. You can get the list of the trace accession and the strain IDs in this link. Sadly there isn’t 1 place to get the SRR accession to strain name, but if you download the brief listing and then the FTP listing (as text) you can map from each ID to the other and make this file with a little bit of Perl-Fu. You can then run this renaming script which will help you rename the files using the remapping file.

Finally to convert these to fastq you can run this dump_fastq.sh script which will dump out fastq files suitable for use in the future steps. These files are all single-end RNA-Seq but if it had been paired end, a _1.fastq and _2.fastq file would have been made for every SRA file (plus a .fastq one for reads that failed in someway).

cd SRP004848
rmdir SRR*
for file in *.lite.sra
do 
  base=`basename $file .lite.sra` 
  fastq-dump -alt 1 -A $base $file
done

Together this is a pretty automated way to get the data you want, once you’ve figured out which accessions you need and how you want to rename them.