Tag-arkiv: Umeå University

Postdoctoral position (2 years) in bioinformatics – Impact of climate change on flowering and diversity of boreal forest trees

Institutionen för ekologi, miljö och geovetenskap

Apply

before 2019-11-15

  • Temporary position longer than 6 months
  • 100%
  • Umeå

The Department of Ecology and Environmental Science (Umeå University, Sweden) invites applicants for a postdoctoral position focused on analyzing time series of shotgun metagenomics data aiming at understanding climate impact on boreal forest trees. Application deadline is November 15th, 2019.

Project description and working tasks
Many of the keystone boreal forest trees, like Norway spruce and Scots pine, rely solely on sexual reproduction for regeneration. As climate change is expected to affect directly phenology and distribution of boreal forest species, we need to understand how flowering phenology and gene flow respond to the changes.

The project has access to a unique archive of air filters that represents an unbroken 40-year line of samples collected weekly in northern Sweden and genome-wide diversity data for both pine and spruce over their entire range. Together with publicly available genetic data as well as weather and land-use data, this project will address questions such as:

  • Has the reproductive phenology of boreal tree species responded to changing climate conditions?
  • To what extent do climate change influence the regularity of flowering and the relative proportion of trees involved in reproduction?
  • Is long distance pollen dispersal common among tree species and has the pattern changed over time?
  • Has the genetic diversity of the major tree species participating in reproduction changed over the time period as measured by sequence diversity of captured pollen?

The research will mainly include modelling and NGS data analyses. NGS analysis will mainly consist of identifying genetic variants in the air filter data (~400 samples shotgun sequenced to a depth of 200-800 million 150 bp PE reads). The postdoc will also have the freedom to contribute to other ongoing projects and to develop own projects that are aligned with the group’s interests.

The appointment is for 2 years (full-time employment). The employment is planned for a start late 2019 or early 2020.

Qualifications
A PhD degree in bioinformatics, genetics, ecology, or a related field is a demand. We seek highly motivated candidates with a broad experience in genomics and NGS data analysis as well as experience in programming and working in Linux environments. To be eligible for this fellowship, you should have completed your doctoral degree a maximum three (3) years before the end of the application period unless special circumstances exists. Good ability to co-operate is required as well as good skills in written and spoken English.

Experience with large-scale sequence analysis is a merit as well as familiarity with phylogenomic analyses, statistics, population genetics and various modelling approaches.

Application
The full application should include:

  • A cover letter describing why you are interested in the project and your suitability (max. 2 pages).
  • A CV, including a list of your publications
  • Copies of your doctoral thesis and relevant publications (maximum 5)
  • Copy of doctoral degree certificate and other relevant degree certificates.
  • Names and contact details (email and phone) of three reference persons.
  • Any other documents you wish to refer to.

The application, written in English (preferably) or Swedish, is made through our electronic recruitment system. Documents sent electronically must be in Word or PDF format.The closing date is November 15th, 2019.

Contact
For more information, contact Dr. Per Stenberg (per.stenberg@umu.se), Dr. Johanna Leppälä (johanna.leppala@umu.se) or Prof. Xiao-Ru Wang (xiao-ru.wang@umu.se).

For more information about our research, please visit: https://www.umu.se/en/research/groups/evolutionary-biology/

The Department of Ecology and Environmental Science (www.emg.umu.se) carries out research and postgraduate education in ecology, environmental science and physical geography. The department has about 150 employees, about 15 of whom are post-docs.

Admission

According to agreement

Contact

Dr. Per Stenberg

090-7869646

Dr. Johanna Leppälä

090-7867121

Prof. Xiao-Ru Wang

090-7869955

Registration number

AN 2.2.1-1282-19

Salary

Monthly salary

Union representative

SACO

090-786 53 65

SEKO

090-786 52 96

ST

090-786 54 31

Read the job description at the university homepage

Apply

before

2019-11-15 Umeå University wants to offer an equal environment where open dialogue between people with different backgrounds and perspectives lay the foundation for learning, creativity and development. We welcome people with different backgrounds and experiences to apply for the current employment. We kindly decline offers of recruitment and advertising help.

Post expires on Friday November 15th, 2019

PhD-position in Chemistry with focus on Biochemistry – Autophagy mechanisms

Kemiska institutionen

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before 2019-11-11

  • Temporary position longer than 6 months
  • 100%
  • Umeå

At the Department of Chemistry we are looking for a doctoral candidate within the project autophagy mechanisms. Last day to apply is 11 November, 2019.

The lab is located within the cross-disciplinary Chemical Biological Centre (video) (https://www.umu.se/en/chemical-biological-centre/) at Umeå University and provides excellent facilities and state-of-art equipment and platforms in a creative, inspiring, international and highly interactive environment. Facilities include Protein Expertise Platform, X-ray, Proteomics, NMR (850-400 MHz), Cryo-EM and Biochemical Imaging Centre (confocal, FLIM, spinning disk, TIRF, STORM). The recent breakthrough researches from Umeå University include deciphering the molecular mechanisms of the bacterial CRISPR-Cas9 system and repurposing it into a tool for genome editing.

Project description
Autophagy is an evolutionarily conserved self-eating process mainly to eliminate or recycle dysfunctional cellular organelles or unused proteins. Autophagy plays an important role in physiology including development and ageing and has been associated with diverse human diseases, including cancer, neurodegeneration, cardiac hypertrophy, and pathogen infection. Autophagy modulation is implicated in the treatment of diseases such as neurodegeneration and cancer. Despite extensive work, the models of autophagosome formation and autophagy regulation are not yet well established. Our laboratory has elucidated fundamental mechanisms underlying autophagosome formation and new mechanisms of autophagy regulation (eLife 2017, Angew Chem 2017, Nat Chem Biol 2019). We will combine cell biological, biochemical, and novel chemical and chemo-optogenetic approaches to understand the mechanism of autophagic membrane morphogenesis and bacterial interaction with host autophagy. The PhD student will focus on cell imaging, western blotting, knock-out/down, analysis of cellular phenotypes, protein expression and purification, biochemical and structural characterization. The project is funded by European Research Council (ERC) and Wallenberg Foundation. The project is interdisciplinary with strong collaborations across scientific disciplines.

Qualifications
To be admitted for studies at third-cycle level you are required to have completed a second-cycle level degree, or completed course requirements of at least 240 ECTS credits, of which at least 60 ECTS credits are at second-cycle level or have an equivalent education from abroad, or equivalent qualifications.

To fulfil the specific entry requirements to be admitted for studies at third-cycle level in chemistry, you are required to have completed first-cycle courses of at least 90 ECTS credits within the field of chemistry or another subject considered to be directly relevant to the specialization in question. Of those 90 ECTS credits, at least 15 ECTS credits shall have been acquired at second-cycle level within the specialization or an equivalent subject.

Very good language skills in English, both spoken and written, is required. Experiences in cell imaging, western blotting, molecular cloning, siRNA, CRISPR-Cas, and/or protein expression and protein purification are strong merits.

Terms of employment
The appointment aims at a PhD degree and the main task of the PhD student is to pursue their doctoral studies, which includes participation in research projects as well as postgraduate courses. In the assignments, teaching and other departmental work (up to a maximum of 20%) can be included. The employment is limited to four years full-time or up to five years when part-time teaching. The salary placement takes place according to the established salary level for doctoral employment.

Application
A complete application should contain the following documents: 

  • A cover letter including a description of your qualifications, research interests and motivation for applying (max 2 pages)
  • A Curriculum Vitae
  • Copies of degree certificates or equivalent, including documentation of completed academic courses and obtained grades
  • Name and contact information of at least two reference persons.

Applications must be submitted via our e-recruitment system. The last day to apply is 11 November, 2019. For further information you are welcome to contact Professor Yaowen Wu, E-mail: yaowen.wu@umu.se. Website: https://www.biostruct.umu.se/principal-investigators/yaowen-wu/.

About us
The Department of Chemistry is one of the largest departments within the Faculty of Science and Technology with approximately 200 employees, of which approximately 40 PhD students, and a strong and expanding research. The Department has three major research areas: Biological Chemistry, Environmental and Biogeochemistry, and Technical Chemistry. https://www.umu.se/en/department-of-chemistry/. Information about doctoral studies in chemistry, see: https://www.umu.se/en/faculty-of-science-and-technology/education/doctoral-studies/chemistry/. For more information about working at Umeå University, see: https://www.umu.se/en/work-with-us/.

Admission

By agreement

Registration number

AN 2.2.1-1301-19

Salary

Monthly salary

Union representative

SACO

090-786 53 65

SEKO

090-786 52 96

ST

090-786 54 31

Read the job description at the university homepage

Apply

before 2019-11-11
Umeå University wants to offer an equal environment where open dialogue between people with different backgrounds and perspectives lay the foundation for learning, creativity and development. We welcome people with different backgrounds and experiences to apply for the current employment. We kindly decline offers of recruitment and advertising help

Post expires on Monday November 11th, 2019

Postdoctoral position (2 years) in multivariate analysis and deep learning

Kemiska institutionen

Apply

before 2019-10-02

  • Temporary position longer than 6 months
  • 100%
  • Umeå

Department of Chemistry is looking for a postdoctor to a project where we will develop new e-science methods that fundamentally integrates Deep Learning and Multivariate analysis. The main task for the postdoctor will be to conduct R&D in multivariate analysis and deep learning. The employment is full-time for a period of two years with starting date as soon as possible or as agreed betweenthe two parties.

Project description and working tasks
In recent years, new tools, concepts and technologies, have brought new hope for fundamental understanding of chemistry, biology and medicine to drive the future development of systems medicine and systems biology. The main drivers have been new pioneering technologies (e.g. robotics, analytics, AI) in instruments that will fundamentally transform how research is conducted and the results thereof. Deep learning and multivariate analysis have both proven to be key data driven modelling technologies for delivering on this promise. The goal of this project is the integration of these new advanced data analytics solutions that builds on the complementary values of deep learning and multivariate analysis to model complex systems.

In this project we will develop new e-science methods that fundamentally integrates deep learning and multivariate analysis. We will apply and validate these methods in several ongoing projects, among others “Wine as a system” project – in collaboration with Stellenbosch, South Africa and Umeå Plant Science Centre (UPSC), from where we will take benefit of large-scale systems biology data, in a truly ambitious, yet realistic attempt to study wine from a systems biology perspective.

More specifically, this project will be focused on hybrid modeling, meaning integration of different modeling techniques, for example how multivariate analysis technology can be used to train and fine-tune deep learning models and vice-versa, how deep learning can be used as pretreatment tool for multivariate analysis.

In the working tasks are included:

  • Conducting R&D in multivariate analyses and deep learning
  • Developing methods for deep learning based analysis of unstructured data
  • Developing state-of-the-art algorithms in deep learning including methods for improving interpretation and robustness of deep learning models
  • Developing new workflows for efficient training of deep learning models when labels are scarce.

Qualifications
The required qualification is a doctoral degree or a foreign degree that is deemed equivalent in computer science, computer engineering, mathematics, physics or equivalent. To be eligible the degree must have been completed a maximum of three years before the end of the application period unless certain circumstances exist.

A solid understanding of linear algebra, algorithms, machine learning, optimization, numerical methods is required as well as experience with data science tools including scripting, preferably in Python. Good skills in English both spoken and written are required. A structured and solution-oriented approach and good communication skills and ability to work in a team are also requirements. Experience in Design-of-Experiments and data analytics is desirable.

Application
The application must contain the following documents:

  • A cover letter that describes qualifications, research interests, and motivation for application (maximum 2 pages)
  • A curriculum vitae, including a publication list
  • A copy of PhD thesis and relevant publications
  • A copy of doctoral degree certificate or equivalent and other relevant degree certificates and grades,
  • Name and contact information of at least two reference persons
  • Other relevant documents

Application should be written in English or Swedish. Applications must be submitted via our e-recruitment system Varbi no later than October 2, 2019.

For more information please contact Professor Johan Trygg, email: johan.trygg@umu.se

Information about the department
Department of Chemistry is the largest department in the Faculty of Science and Technology, with approximately 200 employees, including about 40 doctoral students, and with a strong and expanding research. Three major areas of research; Biological Chemistry, Environmental and Biogeochemistry and Technical Chemistry, represents the research and chemistry education of our department. We are also a strong partner in KBC, The Chemical-Biological Centre. For more information about working at Umeå University: www.umu.se/en/work-with-us/

Admission

As soon as possible or by agreement

Registration number

AN 2.2.1-1066-19

Salary

Monthly salary

Union representative

SACO

090-786 53 65

SEKO

090-786 52 96

ST

090-786 54 31

Read the job description at the university homepage

Apply

before 2019-10-02 Umeå University wants to offer an equal environment where open dialogue between people with different backgrounds and perspectives lay the foundation for learning, creativity and development. We welcome people with different backgrounds and experiences to apply for the current employment. We kindly decline offers of recruitment and advertising help.

Post expires on Wednesday October 2nd, 2019