Steinbeck group joins de.NBI as associate member
It is our pleasure to join the German Network for Bioinformatics (de.NBI) as an associate member.
SteinBlog
New group member Dr. Maria Sorokina
We would like to extend a warm welcome to our new group member Dr. Maria Sorokina who joins us from the University of Cologne. Maria will work with us on aspects of enzyme bioinformatics for the elucidation of metabolomes.
NMReData – a concise way to report NMR data and assigned structures
We had the privilege to contribute to a novel data format – NMReData – to report 1D and 2D NMR data and their assignments to chemical structures. To quote from NMReData.org: “ We use the existing âStructure Data Formatâ (suffix: .sdf) files containing a chemical structure (in the .mol format) and SDF tags. The SDF tags allows to associate to the structure diverse kinds of data (such as melting point Reverse Phone Lookup , mass, etc.). The NMRedata initiative decided to define the format of a set of tags to include signals assignment https://puttydownload.biz , chemical shifts, couplings, lists of 2D correlations and links to the spectra. The format of these tags is an important part of the work of the initiative.”
The new format is supported by NMR instrument manufacturers such as Bruker, software vendors such as ACD Labs as well as journals, such as Magnetic Resonance in Chemistry.
The work has just been published in [tpsingle key=”Pupier:2018jo” link=true]
Postdoc Position in Computational Metabolomics
A postdoc position is available in my research group at Friedrich-Schiller-University Jena, Germany.
Open Positions:
Postdoc: We are looking for a talented cheminformatician, bioinformatician or someone with comparable skills to work on the development cloud-based methods for computational metabolomics. The successful candidate will work closely with the H2020 e-infrastructure project PhenoMeNal, a European consortium of 14 partners. This position requires excellent skills in at least one modern, object-oriented programming language. A strong interest in metabolomics and cloud computing as well as the ability to work in a distributed team will be advantageous. The postdoc will also have the opportunity to participate in the day-to-day management of the group as well as in the organisation of seminars and practical courses for our students
The position requires a strong interest in metabolomics, molecular informatics and current IT technologies, programming skills a modern object oriented programming language and the ability to work in geographically distributed teams.
Please send applications in PDF format by email to christoph.steinbeck@uni-jena.de. We will accept applications until the position is filled.
Background information:
The Friedrich Schiller University Jena (FSU Jena), founded in 1558, is one of the oldest universities in Europe and a member in the COIMBRA group, a network of prestigious, traditional European universities. The University of Jena has a distinguished record of innovations and resulting educational strengths in major fields such as optics, photonics and optical technologies, innovative materials and related technologies, dynamics of complex biological systems and humans in changing social environments. It has more than 18,000 students. The university’s friendly and stimulating atmosphere and state-of-the-art facilities boost academic careers and enable excellence in learning, teaching and research. Assistance with proposing and inaugurating new research projects and with establishing public-private partnerships is considered a crucial point.
Postdoc and PhD positions in Cheminformatics at Jena University, Germany
One postdoc position and three phd positions are available in my newly founded research group at Jena University, Germany.
I am currently moving from my previous position as Head of Cheminformatics and Metabolism at the European Bioinformatics Institute (EBI) to the Institute for Analytical Chemistry as Professor for Analytical Chemistry, Cheminformatics and Chemometrics at Jena University. The successful candidates will help forming the nucleus of the new research group and work in an exciting network of local and international collaborations, such as the PhenoMeNal project funded by the European Commission in their Horizon2020 framework program.
Open Positions:
- Postdoc: We are looking for a talented cheminformatician, bioinformatician or someone with comparable skills to work on the development cloud-based methods for computational metabolomics. The successful candidate will work closely with the H2020 e-infrastructure project PhenoMeNal, a European consortium of 14 partners. This position requires excellent skills in at least one modern, object-oriented programming language. A strong interest in metabolomics and cloud computing as well as the ability to work in a distributed team will be advantageous. The postdoc will also have the opportunity to participate in the day-to-day management of the group as well as in the organisation of seminars and practical courses for our students.
- PhD student, biomedical information mining: In this phd project the candidate will combine methods of text mining, image mining and cheminformatics to extract information about metabolites and natural products from the published primary literature. This includes opportunities to work with the OpenMinTed consortium, where we have been leading the biomedical use case in the last 1.5 years, as well as with the ContentMine team.
- PhD student, cheminformatic prediction of natural product structures: Depending on skills and interests of the successful candidate, this project can target the problem of structure prediction of natural products and metabolite from either the side of spectroscopic information which one might have about an unknown natural product or starting from the genome of a natural product producing organism. Two positions are available in this area.
All PhD positions require a strong interest in molecular informatics and current IT technologies, programming skills a modern object oriented programming language and the ability to work in geographically distributed teams.
Please send applications in PDF format by email to christoph.steinbeck@uni-jena.de. We will accept applications until the position is filled.
Background information:
The Friedrich Schiller University Jena (FSU Jena), founded in 1558, is one of the oldest universities in Europe and a member in the COIMBRA group, a network of prestigious, traditional European universities. The University of Jena has a distinguished record of innovations and resulting educational strengths in major fields such as optics, photonics and optical technologies, innovative materials and related technologies, dynamics of complex biological systems and humans in changing social environments. It has more than 18,000 students. The university’s friendly and stimulating atmosphere and state-of-the-art facilities boost academic careers and enable excellence in learning, teaching and research. Assistance with proposing and inaugurating new research projects and with establishing public-private partnerships is considered a crucial point.
Postdoc in Bioinformatics for Anti-Obesity Strategy
Courtesy of Frank Genten
The Steinbeck Group at European Bioinformatics Institute (EMBL-EBI, Cambridge, UK), together with the Lab of Tony Vidal-Puig (U. Cambridge/ WT Sanger), are excited to announce a joint opening for a Post-doc position to work on a multi-omics project to identify new players in the human brown and beige adipocyte recruitment as an anti-obesity strategy. The project involves data analysis of multi-omics data sets (metabolomics putty download , transcriptomics, proteomics, among others) and integration of that data into different mathematical modelling frameworks (discrete logical models, kinetic ODE-based, FBA). With these models and data, the fellow will identify novel pharmaceutical strategies to induce BAT generation/WAT browning. The models will be used to evaluate in silico the potential effect of drugs on adipocytes. Finally, the best candidate molecules will be applied to the human pluripotent stem cell models to confirm their capacity to induce brown/beige adipogenesis in-vitro. Experiments will be performed with the support of experts at WTSI.
Experience in applying mathematical modelling techniques is desirable, as well as previous exposure to large data sets, but it is not expected of course that the candidate has expertise in all of the listed above, as training will be given on parts were the applicant has less experience.
The EMBL-EBI is part of the European Molecular Biology Laboratory (EMBL) and it is a world-leading bioinformatics centre providing biological data to the scientific community with expertise in data storage https://phonefindservice.info , analysis and representation. EMBL-EBI provides freely available data from life science experiments, performs basic research in computational biology and offers an extensive user training programme, supporting researchers in the academic and industrial sectors.
EMBL-EBI and Wellcome Trust Sanger Institute share the Wellcome Genome Campus. This proximity fosters close collaborations and contributes to an international and vibrant campus environment. Researchers are supported by easy access to scientific expertise, well-equipped facilities and an active seminar programme.
The EMBL-EBI–Sanger Postdoctoral (ESPOD) Programme builds on the strong collaborative relationship between the two institutes, offering projects which combine experimental (wet lab) and computational approaches.
Please apply here: http://www.embl.de/jobs/searchjobs/index.php?ref=EBI_00732&newlang=1
Internship in Bioinformatics/Cheminformatics
We are looking for a candidate for an internship/trainee position in bioinformatics/cheminformatics at the European Bioinformatics Institute (EMBL-EBI) to work on a high-performance generator for chemical structures. This position requires strong programming skills in Java, a reasonable working knowledge in chemical structures and graph theory as well as an interest in learning about Apache Hadoop and related technologies.
The initial contract will be for 6 month with a monthly internship salary of £800.
Please send your application to steinbeck@ebi.ac.uk
PhD position in computational metabolomics or cheminformatics
We have an open PhD position in computational Metabolomics or Cheminformatics at my group at the European Bioinformatics Institute in Cambridge. Application deadline is soon and you need to register your interest even sooner 🙂
http://www.embl.de/training/eipp/application/index.html PuTTY SSH with key authentication
Open Position for Bioinformatician/Ontologist
We are seeking to recruit an experienced Bioinformatician/Ontologist to work on the eNanoMapper EU project. This project is building a computational infrastructure for toxicological data management of engineered nanomaterials (ENMs) based on open standards, ontologies and an interoperable design to enable a more effective, integrated approach to European research in nanotechnology. You will join the Cheminformatics & Metabolism team at the European Bioinformatics Institute (EMBL-EBI) located at the Wellcome Genome Campus near Cambridge in the UK.
Our group is leading work package 2 of this project, which is developing an ontology for the full domain of nanosafety research, based on existing ontologies and using the standard Semantic Web ontology language OWL. You will work with the eNanoMapper partners on ontology software development and editing, addressing the requirements outlined by the consortium.
The EBI is part of the European Molecular Biology Laboratory (EMBL) and it is a world-leading bioinformatics centre providing biological data to the scientific community with expertise in data storage, analysis and representation. EMBL-EBI provides freely available data from life science experiments, performs basic research in computational biology and offers an extensive user training programme, supporting researchers in academic and industry.
Qualifications and Experience
You will be a capable software engineer, able to work comfortably in Java, and be familiar with the OWL language and associated APIs such as the OWL API. You furthermore need to be familiar with version control (GitHub) and continuous integration systems (Jenkins). You will also need to be able to use the Protégé ontology editing tool to create ontology content according to user requirements.
In addition to your technical expertise some familiarity with the biomedical domain is required; domain expertise in an area closely related to nanosafety would be a bonus.
You will have also experience with:
• Maven
• Batch/Script/Shell programming
You will have a strong interest in ontologies, solid technical skills, and an outgoing, collaborative personality. You must be able to work as part of a team but at the same time be self-driven, trustworthy and able to make progress towards objectives independently. You must also be meticulous and careful, with good communication skills, and willing to travel to European project meetings.
Benefits
EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation. The remuneration package comprises a competitive salary, a comprehensive pension scheme and health insurance, educational and other family related benefits where applicable, as well as financial support for relocation and installation.
We provide a dynamic, international working environment and have close ties with both the University of Cambridge and the Wellcome Trust Sanger Institute.
EMBL-EBI staff also enjoy excellent sports facilities, a free shuttle bus to Cambridge and other nearby centres, an active sports and social club and an attractive working environment set in 55 acres of parkland.
The initial contract is for a period of 1 year and 4 months with the possibility of a fixed-term extension.
Application Instructions
We welcome applications irrespective of gender and appointment will be based on merit alone. Applications are welcome from all nationalities – visa information will be discussed in more depth with applicants selected for interview.
Please apply online through www.embl.org/jobs
Open Positions in PhenoMeNal project (Metabolomics e-Infrastructure)
European Bioinformatics Institute – South Building
We are seeking to recruit a number of experienced people for our PhenoMeNal H2020 grant, to create an international e-infrastructure for large-scale computing and analysis of medical metabolomics data. You will join the Cheminformatics and Metabolism team at the European Bioinformatics Institute (EMBL-EBI) located at the Wellcome Genome Campus near Cambridge in the UK.
We are looking for a full-time project manager, a senior bioinformatician and a software engineer.
This is a project with a budget of €8M, distributed over 13 partners with about 830 person-months / 65 deliverables scheduled over a 3-year period. The PhenoMeNal project will develop and deploy an integrated, secure, permanent, on-demand service-driven, privacy-compliant and sustainable e-infrastructure for the processing, analysis and information-mining of the massive amount of medical molecular phenotyping and genotyping data that will be generated by metabolomics applications now entering research and clinic.
The EBI is part of the European Molecular Biology Laboratory (EMBL) and it is a world-leading bioinformatics centre providing biological data to the scientific community with expertise in data storage, analysis and representation. EMBL-EBI provides freely available data from life science experiments, performs basic research in computational biology and offers an extensive user training programme, supporting researchers in academic and industry.
Please apply via the EMBL online recruiting system following the individual links for the full-time project manager, the senior bioinformatician and the software engineer.