Postdoc: Algorithmic Developments to Automatically

2 maanden geleden

Leiden, Nederland Universiteit Leiden Voltijd

Vacancy number

15203

Job type

Academic staff

Hours (in fte)

1,0

External/ internal

External

Location

Leiden

Placed on

15 October 2024

Closing date

30 November 2024 46 more days to apply

The Faculty of Science / the Institute for Biology is looking for a:
**Postdoc: Algorithmic developments to automatically detect RiPP structural features from untargeted LC-MS/MS based metabolomics data**

**Vacancy number:15203**

Ribosomally synthesized and post-translationally modified peptides (RiPPs) represent a class of microbial metabolites with high potential as antibiotics. In addition, they may well serve as plant biocontrol agents, because many of them have narrow-spectrum biological activities and exhibit low levels of toxicity. While recently several tools have been developed to facilitate the detection of RiPP pathways in microbial genomes, the automated detection of RiPP signatures in untargeted LC-MS/MS based metabolomics data is still a challenge.

The current project aims at developing algorithms for the automated detection of characteristic RiPP structural features in the microbial metabolome, identified through the characteristic MS/MS fragmentation pattern associated with them. This will facilitate the quick assessment of whether or not RiPPs are being produced by the bacteria, and the identification of the RiPP class being produced together with typical RiPP post translational modifications (PTMs). The resulting algorithms will be implemented into existing software solutions that work with metabolomics data and will facilitate integrative omics mining for RiPPs by recognizing structural features from mass spectrometry data that can also be predicted from the genome.

For this project we seek an enthusiastic postdoctoral researcher who will be appointed for a period of two years, working under the supervision of Dr. Justin van der Hooft from Wageningen University & Research, and Dr. Somayah Elsayed from Leiden University. The postdoc will be imbedded within a larger multidisciplinary NWO project, KIC Microbiome Mission, involving several public/private organizations in the Netherlands and abroad, that aims at the identification and implementations of RiPPs as potential plant biocontrol agents.

**Key responsibilities**
- Cataloging the different classes of RiPPs identified with LC-MS/MS so far, their structural features, and their characteristic MS/MS fragmentation patterns.
- Developing algorithms that detect the MS/MS fragmentation patterns that recognize RiPPS, and are specific to the different RiPP classes and PTMs.
- Testing the generated algorithms on both in house and publicly available MS/MS data.
- Implementing the new algorithms into existing software tools such as FERMO.

**Selection Criteria**
- PhD in computational metabolomics or related field.
- Strong knowledge in organic chemistry and mass spectrometry.
- Knowledge in MS-based metabolomics data analysis, and machine learning algorithms.
- Experience in peptide sequencing using MS/MS is a pré.
- Experience with programming, in particular in Python
- Proficiency in spoken and written English.
- Feels at home in a diverse, multinational environment.
- Excellent communication skills and a collaborative attitude.

**Research at our faculty**
The Faculty of Science is a world-class faculty where staff and students work together in a dynamic international environment. It is a faculty where personal and academic development are top priorities. Our people are committed to expand fundamental knowledge by curiosity and to look beyond the borders of their own discipline; their aim is to benefit science, and to make a contribution to addressing the major societal challenges of the future.

**The Institute for Biology**
The research within the Institute of Biology Leiden (IBL) aims to work on the science base of biodiversity and health, which is reflected in our leading principle Harnessing Biodiversity for Health. We perform innovative curiosity-driven research to answer fundamental questions, and solutions-driven research to help solving major societal challenges. The latter include protecting nature’s biodiversity, creating sustainable biotechnology and agriculture and increasing good health. Our research focuses on four Research Themes: Bioactive Molecules, Host-Microbe Interactions, Development & Disease and Evolution & Biodiversity. Located in a thriving scientific environment with our Faculty of Sciences, Naturalis Biodiversity Centre, the Leiden University Medical Centre and the Leiden Bioscience Park, IBL offers an exciting, internationally oriented and inclusive place to work and study.

**Terms and conditions**
We offer a full-time, 2 year term position. Salary range from € 3.345;
- to € 5.278;
- gross per month (pay scale 10 in accordance with the Collective Labour Agreement for Dutch Universities).

Netherlands may be eligible for a substantial tax break.

**Information**

**Applications**
Applications for this vacanc

  • Postdoc: Algorithmic Developments to Automatically

    2 maanden geleden

    Leiden, Nederland Universiteit Leiden Voltijd

    Vacaturenr. 15203 Functie-categorie Omvang (fte) 1,0 Extern/intern Extern Locatie Leiden Geplaatst op 15 oktober 2024 Sluitingsdatum 30 november 2024 The Faculty of Science / the Institute for Biology is looking for a: **Postdoc: Algorithmic developments to automatically detect RiPP structural features from untargeted LC-MS/MS based metabolomics...

  • Post-doc : Algorithmic Bias in Ageing Societies

    1 maand geleden

    Leiden, Nederland Universiteit Leiden Voltijd

    Vacancy number 15261 Job type Hours (in fte) 0,8 External/ internal External Location Leiden Placed on 12 November 2024 Closing date 4 December 2024 22 more days to apply **Post-doc : Algorithmic Bias in Ageing Societies** Are you interested in exploring how AI-induced bias and discrimination affects our societies, especially with respect to...

  • Postdoc on Causal Machine Learning for Spatio-temporal Datasets

    4 maanden geleden

    Leiden, Nederland Universiteit Leiden Voltijd

    The Faculty of Science and the Leiden Institute of Advanced Computer Science (LIACS) are looking for a: Postdoc on Causal Machine Learning for Spatio-temporal Datasets The is looking for an excellent Postdoc researcher (1.0 FTE) with a background in Computer Science (or a closely related field) to join a project focused on developing an advanced...

  • Postdoc in DNA double-strand break repair

    3 maanden geleden

    Leiden, Nederland Leiden Bio Science Park Voltijd

    Offer As a postdoc, your salary ranges from € 3,493 to € 5,504 gross per month (scale 10, CAO UMC). These figures are based on a full-time position. Your contract will be for a one-year term with the possibility of extension. Your career at the LUMC Driven by health; that's our mission. This applies not only to our patients...

  • Data Science Postdoc, Medical Imaging Computer

    4 weken geleden

    Leiden, Nederland Johnson & Johnson Voltijd

    Janssen Research & Development LLC, a Johnson & Johnson company, is recruiting for a postdoc located in Netherlands, Beerse, Belgium; Zug, Switzerland. Remote positions will also be considered. The Data Science Analytics & Insights team within Janssen R&D develops innovative solutions using a variety of data sources across multiple different disease areas....

  • Postdoctoral Fellow to Study Trajectories of Coral

    6 maanden geleden

    Leiden, Nederland Naturalis Biodiversity Center Voltijd

    the Plankton & Diversity group is looking for a Postdoc for the Marine Time Machine project - Postgraduate degree- Fulltime (36 hours per week)- Fixed-term during project- € 3.468 - € 4.506**About** **Naturalis**: Our research group Plankton Diversity & Evolution is looking for a Postdoc for the Time Machine project. **About** **Naturalis**: -...

  • Postdoc - Translational Pharmacology in antibiotic regimen development

    6 maanden geleden

    Leiden, Nederland Leiden Bio Science Park Voltijd

    Offer Our organization Working at the Faculty of Science means being part of an exciting, dynamic scientific environment which sets high standards for its students and staff. The research carried out at the Faculty of Science is diverse, ranging from computer science, mathematics, astronomy, physics, chemistry and...

  • Business Development Coordinator

    4 weken geleden

    Leiden, Zuid-Holland, Nederland Leiden Bio Science Park Voltijd

    Leiden Bio Science Park Career OpportunityWe are seeking a motivated Business Development Intern to join our team at Leiden Bio Science Park.About the RoleThis is an exciting opportunity for a Business Development Intern to contribute to the development of next-generation medicines that protect against airborne viruses.This challenging position will allow...

  • Scientist

    7 maanden geleden

    Leiden, Nederland Johnson & Johnson Voltijd

    The Research & Development department of J&J Innovative medicine discovers and develops innovative medical solutions to address important unmet medical needs in oncology, immunology, neuroscience, infectious diseases, and vaccines, cardiovascular and metabolism, and pulmonary hypertension. The Drug Substance Development (DSD) department in Leiden will focus...

  • Internship: Business Development

    7 maanden geleden

    Leiden, Nederland Leiden Bio Science Park Voltijd

    Offer An energizing, full-time internship in a growing biotech company. A chance to apply your theoretical knowledge in a practical setting. An opportunity to contribute to environmentally friendly solutions and make a tangible impact on the product’s development. Hands-on experience in business development within the biotech...

  • Scientist Drug Product Development

    7 maanden geleden

    Leiden, Nederland Pharming Group Voltijd

    **About Pharming** Pharming Group N.V. (Nasdaq: PHAR/Euronext Amsterdam: PHARM) is a global biopharmaceutical company dedicated to transforming the lives of patients with rare, debilitating, and life-threatening diseases. Pharming is commercializing and developing an innovative portfolio of protein replacement therapies and precision medicines, including...

  • Lab Technician to Study Plastic Particles in Food

    3 maanden geleden

    Leiden, Nederland Universiteit Leiden Voltijd

    Vacancy number 15151 Job type Non-academic staff Hours (in fte) 1,0 External/ internal Internal, External Location Leiden Placed on 24 September 2024 Closing date 3 October 2024 9 more days to apply The Faculty of Science and Institute of Environmental Sciences are looking for: **Lab technician to study plastic particles in food chains (1.0...

  • Senior Development Manager

    1 maand geleden

    Leiden, Zuid-Holland, Nederland Leiden Bio Science Park Voltijd

    Job OverviewWe are seeking an experienced Senior Development Manager to join our dynamic team at Leiden Bio Science Park.This challenging full-time position involves managing and guiding our high-tech development team, ensuring seamless execution of projects and fostering a collaborative environment.The ideal candidate will have a strong background in...

  • Software Development Specialist

    2 maanden geleden

    Leiden, Zuid-Holland, Nederland Medis Medical Imaging Systems Voltijd

    Job Description:We are currently seeking a skilled Software Development Specialist to join our team at Medis Medical Imaging Systems. As a key member of our development team, you will be responsible for designing, developing, and maintaining our cutting-edge medical software applications.Key Responsibilities:- Develop and maintain front-end applications...

  • Echocardiographic Image Annotator

    7 maanden geleden

    Leiden, Nederland Medis Medical Imaging Systems Voltijd

    Applied Research - 40 hours / week - Leiden / Hybrid Modern image segmentation approaches use Deep Learning (DL) to analyze many data sets as automatically as possible. However, to build DL solutions, large volumes of image data sets need to be segmented/annotated manually by experts before the DL activity / training can begin. **Role description**: -...

  • Business Development Representative

    2 maanden geleden

    Leiden, Nederland Samotics B.V. Voltijd

    **Hi, we are Samotics!** Our AI-driven solutions help industrial companies cut energy waste, prevent pollution, and eliminate unplanned downtime. With a mission to reduce global energy consumption by 15%, we're leading in technological innovation. We're seeking an experienced Business Development Representative to support Samotics’ growth and contribute...

  • Quantitative Analyst Internship

    3 maanden geleden

    Leiden, Nederland Northpool Voltijd

    **Grasp the opportunity**: Commodity markets are all around the news. The energy transition towards a green society is picking up steam and creating new energy market trends. Digitalization of energy and automated trading will be at the forefront of this transformation. As a Quantitative Analyst intern, you will be building predictive models, developing...

  • Data Scientist for AI Bias Research Position in Leiden University

    2 weken geleden

    Leiden, Zuid-Holland, Nederland Universiteit Leiden Voltijd

    Job Description:We are seeking a talented Data Scientist to join our team at the Universiteit Leiden, specializing in AI bias research. This two-year position offers an exciting opportunity to contribute to groundbreaking research and projects.About the Job:The successful candidate will work within an international multi-disciplinary project focused on...

  • Biotech Business Development Professional

    4 weken geleden

    Leiden, Zuid-Holland, Nederland Leiden Bio Science Park Voltijd

    Leiden Bio Science Park Job OfferWe are seeking a talented individual to fill the role of Biotech Business Development Professional.Job DescriptionAn opportunity to apply theoretical knowledge in a practical business setting within the biotech sector.Key Responsibilities:Contribute to the development of environmentally friendly solutions.Gain hands-on...

  • Atmospheric Scientist

    3 weken geleden

    Leiden, Nederland SRON Voltijd

    **Are you our new colleague?**: Are you an ambitious, highly motivated, and result driven (postdoctoral) scientist with experience in interpreting atmospheric observations using transport modelling? Then you are the person we are looking for. **You and SRON Netherlands Institute for Space Research**: Reducing methane emissions has become an absolute...