BIPED2 Application Portal

Currently open positions

Scientific Associate Research IT (60-100%)

Starting immediately or as per agreement

The Biozentrum of the University of Basel is one of the leading life sciences institutes in the world. It consists of 32 groups and 500 employees that research how molecules and cells create life, spanning the scale from atom to organism. Founded in 1971, the Biozentrum has been the birthplace of many fundamental discoveries in biology and medicine, spawning several Nobel Laureates.

The Research IT technology platform is the primary contact point for scientific IT projects at the Biozentrum. Our group supports the Biozentrum’s scientists and staff with expertise, services and custom software development. We facilitate the management and analysis of research data and provide ICT tools that enable digital collaboration and communication in our research institute.

Your position

You will support the specific needs of the research groups and administrative units at the Biozentrum in collaboration with the other members of our team. This position is very interactive with a variety of research groups tackling research questions at the forefront of life science research, and your own experience in life science research will be helpful in designing pragmatic, robust solutions for these challenges. Within the portfolio of the group, there is some flexibility to adapt your role to your specific skillset and expertise.

Your responsibilities

  • Provide consulting and support to research and administrative units at the Biozentrum on IT solutions for specific research or administrative requirements.
  • Domain-specific consulting, support and training for research data management, including topics such as working with large data sets, Data Management Plans, FAIR data.
  • Planning, design and operation of service infrastructure, such as software, web applications, databases for these specific requirements, possibly extending into software development, predominantly in Python and PHP.
  • Provide analytical expertise to research projects where applicable, for instance in the field of bioinformatics analysis, big data, ML/AI.
  • Active participation in ongoing Research IT projects, such as capturing requirements with users, developing scenarios and solutions, as well as occasional training.

Your profile

We are looking for an enthusiastic and goal-oriented person with a degree in Bioinformatics, molecular biology or computer science and relevant experience in a similar role in a research institution. You like to work in an agile academic work environment and embrace a service-oriented approach. You enjoy working with wet lab scientists to provide solutions for their research projects and data. At the same time, you also help to ensure that our production services run smoothly. You combine expertise in life sciences, bioinformatics and/or ICT with outstanding analytical and collaborative skills that you enjoy bringing to the table in cross-functional projects. Good communication skills in English are required, knowledge of German is an asset.

We offer

The Biozentrum offers a cutting-edge research infrastructure, a highly international environment that provides numerous opportunities to learn more, and excellent working conditions. The University of Basel stands for excellence and is committed to diversity, equal opportunities and family friendliness. Female applicants are explicitly encouraged to apply. The position is initially for 2 years, with the possibility of permanent employment. Salary and benefits according to University of Basel standards.

Application / Contact

Please apply online with a CV, letter of motivation, a summary of past projects you worked on and the name/address of three references. Please note that only online applications will be accepted.

Reviewing of applications will start on 12 April 2021 and continue until the position is filled.

Further information about Research IT: https://www.biozentrum.unibas.ch/researchit
For specific questions, feel free to contact Michael Podvinec, PhD, Head of Research IT (michael.podvinec@unibas.ch).
Apply now

Postdoctoral Researcher – Establishing 3D microtissue models for studying urogenital bacterial infections (100%)

The Biozentrum of the University of Basel is one of the leading Life Sciences Institutes in the world. It accommodates 30 research groups and 500 employees investigating how molecules and cells create life, spanning the scale from atom to organism. Founded in 1971, the Biozentrum has been the birthplace of many fundamental discoveries in biology and medicine, spawning several Nobel Laureates.

A postdoctoral position is available in the group of Prof. Christoph Dehio (www.biozentrum.unibas.ch/dehio).

This position is supported by the NCCR AntiResist: New Approaches to Combat Antibiotic-Resistant bacteria. NCCR AntiResist (https://nccr-antiresist.ch/) is a Swiss-wide interdisciplinary center for antibiotic research with strong collaborations between biologists, clinicians, engineers, computational scientists and chemists. The goals of NCCR AntiResist are to elucidate pathogen physiology in infected patients, followed by the development of in-vitro models that faithfully mimic conditions in the patient, and to use these laboratory models to discover innovative strategies to combat antibiotic-resistant bacteria. In this position, the candidate will focus on establishing 3D microtissue models for studying urogenital bacterial infections. This research project is embedded within the work package Escherichia coli of NCCR AntiResist (www.nccr-antiresist.ch/en/research/work-packages-overview/escherichia-coli)

Your responsibilities are

  • to develop microtissue models of the human urogenital tract (e.g., bladder and kidney)
  • to utilize these microtissue models for studying infection with uropathogenic bacteria, and to visualize and quantify changes in bacterial physiology at single-cell level upon treatment with antibiotics
  • to analyze data using appropriate statistical methods
  • to present data in a professional format suitable for publication
  • to act as an experienced resource, and demonstrate clear and professional verbal and written communication skills

Your profile

You obtained a PhD in one of the following disciplines: microbiology, cellular/molecular biology, biophysics, or image analysis. You have a profound expertise in 3D microtissue or other microphysiological models of diseases, host-pathogen interaction or the development and use of single-cell analysis methods based on microfluidics, live-cell imaging and image analysis. Experience with advanced imaging techniques, single-cell reporters, machine learning-based image analysis or microfluidics would be of great advantage. Good teamworking skills are indispensable.

We offer

A highly motivated team as part of a multidisciplinary group at the Biozentrum including microbiologists and cell biologists with an expertise in virulence and persistence of Escherichia coli and other human pathogens. Moreover, the Biozentrum offers excellent internal support from various core facilities with expert staff as well as a very strong multidisciplinary collaborative environment within the frame of the NCCR AntiResist.

The position is available immediately and the prospective funding period is for at least three years.

Basel is an international city with people from 150 nations. Located on the border between Switzerland, Germany and France, it is Europe’s most important Life Science hub. Basel provides a high standard of living and a rich and varied cultural atmosphere. NCCR AntiResist embraces diversity and equal opportunity. We are committed to building a team that represents a variety of backgrounds, perspectives, and skills. The more inclusive we are, the better our work will be.

Application / Contact

Please apply online and upload the following three separate PDF documents: 1) Your CV with contacts for three references 2) Motivation letter explaining why you are a good candidate for this job offer 3) List of all your publications (including pre-prints). For up to three publications most relevant to this job offer describe shortly (up to 200 words) your role as well as why the publication is relevant (for example: what techniques you learned, what experience you gained, etc.).

Incomplete applications will be disregarded. Reviewing of applications will begin on April 1, 2021 and continue until the position is filled. For general inquiries, please send an e-mail to dehiostelle@unibas.ch.

Apply now

Aquatic Animal Care Technician (80-100%)

Starting immediately or upon mutual agreement

The Biozentrum of the University of Basel is one of the leading life sciences institutes in the world. It consists of 30 groups and 500 employees that research how molecules and cells create life, spanning the scale from atom to organism. Founded in 1971, the Biozentrum has been the birthplace of many fundamental discoveries in biology and medicine, spawning several Nobel Laureates.

The Schier Lab is searching for a highly motivated 80-100% Aquatic Animal Technician to support Laboratory Animal Services in maintaining and monitoring animal husbandry, health, production, and the technical surroundings in various aquatics care environments.


Your responsibilities

The successful applicant will join a dynamic research group studying vertebrate development and behavior using zebrafish, cichlids and other fish species as a model.

Your responsibility will be to maintain colonies of different fish species. Your work will include fish feeding, food preparation, tank cleaning, monitoring animal health and well-being, water quality and environmental parameters. Your activities will also involve breeding fish, performing tail fin biopsies and DNA genotyping, embryo collection, disinfection and other interventions. Furthermore, you will be involved in monitoring and maintaining the technical equipment and in the organization of facility logistics while complying with standard operating procedures.

Your profile

Applicants minimum requirements should include a high school diploma or equivalent. Previous aquatics experience is not required, but preference will be given to those with a biology background and prior animal caretaking experience, and/or LTK accreditation.

The role requires flexibility, excellent organizational and communication skills, and the ability to multi-task. Enthusiasm and motivation for biological research are critical. The shift will be Monday through Friday and may require occasional weekend and holiday work. The primary language of the laboratory and the Biozentrum is English.

We offer

This position offers an exciting opportunity for a highly motivated individual to work as a member of a vibrant international research team. Working with different fish species, technical maintenance and managing facility logistics offers diverse activities and responsibilities. You will directly interact with scientists and help them with their animal experiments.

The initial contract will be for one year with the possibility of longer-term extension. Salary and benefits are according to University of Basel standards.

Application / Contact

The application should include a brief personal statement, explaining how your qualifications and experience relate to the role, together with a full, up-to-date CV and contact information of two references.

We will review applications starting April 1, 2021 until the position is filled. In all cases, you will be notified of the outcome of your application. Please note that only online applications will be accepted.

For any informal enquiries, please contact: alba.apariciofernandez@unibas.ch
Apply now

Scientist/Engineer - BioEM lab at Biozentrum, University of Basel (100%)

Starting immediately or upon mutual agreement

The Biozentrum of the University of Basel is one of the leading life sciences institutes in the world. It consists of 30 groups and 500 employees that research how molecules and cells create life, spanning the scale from atom to organism. Founded in 1971, the Biozentrum has been the birthplace of many fundamental discoveries in biology and medicine, spawning several Nobel Laureates.

We are looking to recruit a highly motivated and enthusiastic specialist in biological cryoEM data collection and analysis to join the BioEM lab.


Your responsibilities

  • to operate cryo electron microscopes and support user operation
  • to develop and support tools and software for cryo-EM
  • to analyze and process data for customers and collaborators
  • to support and contribute technological and scientific projects
  • to manage data in collaboration with IT and scientific computing units

Your profile

We are looking for an enthusiastic and goal-oriented person with a completed scientific or engineering degree (Msc/PhD), and expertise in cryoEM-based structural biology. You have good knowledge of electron microscopy hardware, and hands-on, in-depth experience in operating cryo-electron microscopes using automation software such as SerialEM and EPU. You have successfully analyzed single-particle data to determine structures of biomolecules and are an experienced user of cryoEM analysis software, including relion, with practical skills in scripting and programming. You like to work in an agile academic work environment and embrace a service-oriented approach. Good communication skills in English are required.


We offer

We offer an exciting and stimulating work environment with state-of-the art equipment and ample opportunities for interactions with academic and industrial partners at the department, in the region and internationally. Salary and benefits are attractive.

Basel is an international city with people from 150 nations. Located on the border where three countries meet - Switzerland-Germany-France -, it is Europe’s most important life sciences hub. Basel provides a high standard of living and a rich and varied cultural atmosphere.

Application / Contact

The application should include a brief personal statement, explaining how your qualifications and experience make you a good fit for this position, together with a full, up-to-date CV and addresses of 2 references.

For more information about Biozentrum and the BioEM lab, see www.biozentrum.unibas.ch/bioem/

We will review applications starting 26 Apri 2021 until the position is filled. In all cases, you will be notified of the outcome of your application. Please note that only online applications will be accepted.

For any informal enquiries, please contact: mohamed.chami@unibas.ch
Apply now

PhD position (no. 3) in biological microED and single molecule electron diffraction

Starting on 1 September or as per agreement

The Biozentrum of the University of Basel is one of the leading life sciences institutes in the world. It consists of 30 groups and 500 employees that research how molecules and cells create life, spanning the scale from atom to organism. Founded in 1971, the Biozentrum has been the birthplace of many fundamental discoveries in biology and medicine, spawning several Nobel Laureates.

A PhD position funded by the Swiss National Science Foundation is available from September 2021 onwards in the group of Prof Jan Pieter Abrahams at the Biozentrum of the University of Basel.

Cryo-electron microscopy can reveal the atomic structures of biological molecules by focusing the electrons that are scattered by the sample into an image. These electron images have low contrast and are very noisy, because electron beam damages the sample.

The Abrahams group has generated strong evidence that the signal-to-noise ratio of the electron image can be boosted significantly by measuring the scattered electrons directly. This resulted in the development of protein nano-crystallography (micro-ED) and we are extending the method to include non-crystalline samples and single molecule electron diffraction (simED). Novel, dedicated hardware will allow us to develop methods for automatically generating vast amounts of electron diffraction data short periods of time. We aim to develop novel tools based on Artificial Intelligence and Big Data technologies for interpreting these data. An important biological focus of our group is on molecular machines for protein degradation. (I. Mohammed, K. A. Schmitz, N. Schenck, T. Maier, J. P. Abrahams, Catalytic cycling of human mitochondrial Lon protease. Sci. Adv. 7, eabf0156 (2021). Part of the work will be performed at, and will be supported by the Paul Scherrer Institute (https://www.psi.ch/en).


Your project

Optimal data acquisition for protein simED. A dedicated single molecule diffraction instrument, based on a JEOL F200 with post-column energy filter and hybrid pixel detectors will be commissioned at the PSI (summer 2021), with a data collection capacity of 20 Gbyte/s. Optimizing beam – and scanning parameters, in close collaboration with a PhD student working on optimal data acquisition for microED, is part of your project. Data will be generated by scanning a narrow, parallel electron beam across a sample at liquid N2 temperature of biological macromolecular complexes suspended in a vitrified aqueous buffer. The thickness of the vitreous layer will be in the order of 100 nm and preferably less. The biomolecular complexes can range between 10 nm and 100 nm in diameter. We will pilot data collection with thin hydrated, vitrified protein samples containing nanocrystals (e.g. catalase) or TMV, a 300 nm long, 20 nm diameter cylindrical plant virus with helical symmetry.


Your profile

We are looking for a talented PhD student with the following research profiles:
  • -Background in either structural biology, crystallography, and/or electron microscopy
  • -A keen interest in developing break-through technologies

The project is highly synergistic, and you will work collaboratively as an enthusiastic team towards achieving the common goals. You will have prime responsibility for one particular project, while providing strong support for the other projects.


We offer

We offer an exciting and stimulating work environment with scientific collaborations within the institute and worldwide.

Basel is an international city with people from 150 nations. Located on the border where three countries meet - Switzerland-Germany- France -, it is Europe’s most important life sciences hub. Basel provides a high standard of living and a rich and varied cultural atmosphere.

Application / Contact

Please apply online with a cover letter, CV, reference letters, diplomas and contact information of two referees: Please note that only online applications will be accepted:

For any informal enquiries, please contact: jp.abrahams@unibas.ch
Apply now

PhD position (No. 4) in biological microED and single molecule electron diffraction

Starting on 1 September or as per agreement

The Biozentrum of the University of Basel is one of the leading life sciences institutes in the world. It consists of 30 groups and 500 employees that research how molecules and cells create life, spanning the scale from atom to organism. Founded in 1971, the Biozentrum has been the birthplace of many fundamental discoveries in biology and medicine, spawning several Nobel Laureates.

A PhD position funded by the Swiss National Science Foundation is available from September 2021 onwards in the group of Prof Jan Pieter Abrahams at the Biozentrum of the University of Basel.

Cryo-electron microscopy can reveal the atomic structures of biological molecules by focusing the electrons that are scattered by the sample into an image. These electron images have low contrast and are very noisy, because electron beam damages the sample.

The Abrahams group has generated strong evidence that the signal-to-noise ratio of the electron image can be boosted significantly by measuring the scattered electrons directly. This resulted in the development of protein nano-crystallography (micro-ED) and we are extending the method to include non-crystalline samples and single molecule electron diffraction (simED). Novel, dedicated hardware will allow us to develop methods for automatically generating vast amounts of electron diffraction data short periods of time. We aim to develop novel tools based on Artificial Intelligence and Big Data technologies for interpreting these data. An important biological focus of our group is on molecular machines for protein degradation. (I. Mohammed, K. A. Schmitz, N. Schenck, T. Maier, J. P. Abrahams, Catalytic cycling of human mitochondrial Lon protease. Sci. Adv. 7, eabf0156 (2021). Part of the work will be performed at, and will be supported by the Paul Scherrer Institute (https://www.psi.ch/en).


Your project

Phasing protein simED data. Your project is part of an overall project of our group to establish novel technologies and methods for biomolecular structure determination. This project has several sub-goals: (i) identifying diffraction patterns that likely correspond with single molecules, (ii) low-resolution phasing, for instance by molecular replacement methods or (in collaboration with another project) imaging and/or ptychography, (iii) phase extension through model building and refinement. This project is anticipated to lean heavily on novel concepts for pattern recognition, using Artifical Intelligence / neural network analysis of big data sets.


Your profile

We are looking for a talented PhD student with the following research profiles:
  • Background in either structural biology, crystallography, software development / big data analysis.
  • -A keen interest in developing break-through technologies

The project is highly synergistic, and you will work collaboratively as an enthusiastic team towards achieving the common goals. You will have prime responsibility for one particular project, while providing strong support for the other projects.


We offer

We offer an exciting and stimulating work environment with scientific collaborations within the institute and worldwide.

Basel is an international city with people from 150 nations. Located on the border where three countries meet - Switzerland-Germany- France -, it is Europe’s most important life sciences hub. Basel provides a high standard of living and a rich and varied cultural atmosphere.

Application / Contact

Please apply online with a cover letter, CV, reference letters, diplomas and contact information of two referees: Please note that only online applications will be accepted:

For any informal enquiries, please contact: jp.abrahams@unibas.ch
Apply now

Postdoc position in biological microED and single molecule electron diffraction

Starting on 1 September or as per agreement

The Biozentrum of the University of Basel is one of the leading life sciences institutes in the world. It consists of 30 groups and 500 employees that research how molecules and cells create life, spanning the scale from atom to organism. Founded in 1971, the Biozentrum has been the birthplace of many fundamental discoveries in biology and medicine, spawning several Nobel Laureates.

A postdoc position funded by the Swiss National Science Foundation is available from September 2021 onwards in the group of Prof Jan Pieter Abrahams at the Biozentrum of the University of Basel.

Cryo-electron microscopy can reveal the atomic structures of biological molecules by focusing the electrons that are scattered by the sample into an image. These electron images have low contrast and are very noisy, because electron beam damages the sample.

The Abrahams group has generated strong evidence that the signal-to-noise ratio of the electron image can be boosted significantly by measuring the scattered electrons directly. This resulted in the development of protein nano-crystallography (micro-ED) and we are extending the method to include non-crystalline samples and single molecule electron diffraction (simED). Novel, dedicated hardware will allow us to develop methods for automatically generating vast amounts of electron diffraction data short periods of time. We aim to develop novel tools based on Artificial Intelligence and Big Data technologies for interpreting these data. An important biological focus of our group is on molecular machines for protein degradation. (I. Mohammed, K. A. Schmitz, N. Schenck, T. Maier, J. P. Abrahams, Catalytic cycling of human mitochondrial Lon protease. Sci. Adv. 7, eabf0156 (2021). Part of the work will be performed at, and will be supported by the Paul Scherrer Institute (https://www.psi.ch/en).


Your project

Validating simED and comparing to cryo-electron ptychography. Your project is part of an overall project of our group to establish novel technologies and methods for biomolecular structure determination. For validation, we will initially use well characterized samples of which high resolution structures are available. These may include 3D crystals, helical structures (e.g. TMV, bacterial flagella of samples we analyzed by imaging), single macromolecular complexes (ribosomes, LonP1 samples). For these samples, we already know the whole structure or at least substantial parts of the structure in near-atomic resolution. Especially for the LonP1 samples, we will investigate if we can distinguish additional conformations to enhance the resolution. It will be augmented with density modification to get a clearer view of the parts for which no atomic model is available. The postdoc is also expected to help coordinating the overall project goals and instruct and assist the PhD students in cryo-EM data collection.


Your profile

We are looking for an expert in biological EM, preferably with in-depth knowledge of single cryo-EM data collection methods and data analysis. The project is highly synergistic, and you will work collaboratively as an enthusiastic team towards achieving the common goals. You will have prime responsibility for one particular project, while providing strong support for the other projects.


We offer

We offer an exciting and stimulating work environment with scientific collaborations within the institute and worldwide. This position is funded by the Swiss National Science Foundation (SNF). The salary complies with the guidelines of the SNF. The initial contract is limited to one year, with the possibility to extend it up to 4 years.

Basel is an international city with people from 150 nations. Located on the border where three countries meet - Switzerland-Germany- France -, it is Europe’s most important life sciences hub. Basel provides a high standard of living and a rich and varied cultural atmosphere.

Application / Contact

Please apply online with a cover letter, CV, reference letters, diplomas and contact information of two referees: Please note that only online applications will be accepted:

For any informal enquiries, please contact: jp.abrahams@unibas.ch
Apply now

Proteomics LC-MS Specialist (Technician, 100%)

Starting immediately or upon agreement

The Biozentrum of the University of Basel is one of the leading life sciences institutes in the world. It consists of 30 groups and 500 employees that research how molecules and cells create life, spanning the scale from atom to organism. Founded in 1971, the Biozentrum has been the birth place of many fundamental discoveries in biology and medicine, spawning several Nobel Laureates.

We are seeking a highly motivated LC-MS Specialist to join the Proteomics Core Facility (PCF).

The PCF provides state-of-the-art proteomic techniques to support life science research at the Biozentrum. It is tightly integrated in an internationally leading scientific surrounding. The main focus of the group is the development of new data-independent mass spectrometric workflows for sensitive, quantitative protein and post-translational modification profiling and their integration in interdisciplinary biological projects.

Your responsibilities

The primary responsibilities for this position will include the operation and maintenance of liquid handing platforms for automated sample preparation (Tecan Evolution for SP3 and TMT workflows) and latest LC-MS systems (Dionex Ultimate/Exploris 480) as well as the assistance of researchers performing proteomics analyses at the Biozentrum and general lab management. Duties will include preparation of clinical (bacteria) samples using liquid handling platforms, analyzing samples by LC-MS/MS and data analysis via a suite of software tools with a focus on developing methods for targeted protein profiling using PRM/SWATH.

Your profile

The ideal candidate should have proof of proficiency in LC-MS based proteomics techniques, including sample preparation, operation of LC-MS platforms, data analysis software tools and practical experience in organizing a laboratory. Prior experience in data-independent MS workflows and with liquid handling platforms would be advantageous. The successful candidate should be highly organized, detail-oriented and computer literate. The candidate should have good written and verbal communication skills, be able to work both independently and within a team and have an apprenticeship as laboratory technician (or other degree such as DUT) with work experience or higher education (e.g. Bachelor or Master) in a biology or chemistry related subject with 2+ years of experience. High proficiency in spoken and written English is required.

We offer

The position offers a challenging opportunity to join a growing and rapidly evolving bioanalytical field and to work in a team of highly motivated scientists. The position is part of the NCCR “AntiResist” program, initially for 2 years, with the possibility of further extension after positive evaluation. Salary and benefits according to University of Basel standards.

Application / Contact

The application should include a brief personal statement, explaining how your qualifications and experience make you a good candidate for this job, together with a full, up-to-date CV and addresses of 2 references.

We start reviewing applications from 5 April 2021 until the position is filled. In all cases, you will be notified of the outcome of your application. Please note that only online applications will be accepted.

For further information, please contact Dr. Alexander Schmidt, Head of Proteomics Core Facility, +41 61 207 20 59, alex.schmidt@unibas.ch
Apply now

International PhD Program "Biozentrum PhD Fellowships" Summer Call 2021

Excellent students from all over the world are encouraged to apply for the prestigious "Biozentrum PhD Fellowships" program.

The aim of the fellowships which are sponsored by the Werner Siemens-Foundation and the University of Basel is to select and promote highly talented graduate students in the area of Life Sciences. The fellowships offer direct access to the PhD program of the Biozentrum, University of Basel, additional financial support, a rotation-based selection of the research group, and support for the attendance of scientific meetings and courses during the PhD.
Apply now