ISCB Affiliated Group Logo

Job Offers

2 PhD and 1 postdoc position in computational chemistry / machine learning [Norway.]

Two PhD positions and one postdoc position are available at the University of Bergen and , Western Norway University of Applied Sciences . All positions are associated with the RESPOND3 project “Towards better computational approaches and responsible innovation strategies in early drug discovery: application to antibiotics and COPD”. The project is a cross disciplinary collaboration between research groups at the Centre for Advanced studies in Biomedical Innovation Law at the University of Copenhagen, the Department of Computing, Mathematics and Physics at the Western Norway University of Applied Sciences as well as the Department of Biomedicine and the Department of Chemistry at University of Bergen. The main focus of RESPOND3 will be hit and lead optimization for targets for antibiotics (SAM riboswitch) and chronic obstructive pulmonary disease (proteinase 3) guided by the use of computational methods as well as the development of new scoring functions using machine learning. The entire project is embedded in a responsible research and innovation strategy.

One of the available PhD positions is in the group of Prof. Nathalie Reuter at the Department of Chemistry, University of Bergen. The main tasks of this position are:

- Modelling of target-compound interactions for compounds targeting serine proteases, and compounds targeting riboswitches;

- Quantification, through the use of molecular dynamics simulations and free energy calculations, of the relative affinity of datasets of compounds for the two above-mentioned targets;

- Contributions to development and validation of multi-site lambda dynamics, using experimental affinity data generated by the project.

- Application of multi-site lambda dynamics to ligand discovery and design for the targets noted above.

More details about this position and information on how to apply can be found here: https://www.jobbnorge.no/en/available-jobs/job/172204/phd-position-in-computational-chemistry

 

The other PhD position is in the group of Prof. Ruth Brenk at the Department of Biomedicine, University of Bergen.

The main objectives of this position are:

- to derive data sets for the development of new scoring functions for protein-ligand interactions with machine learning methods

- to retro- and prospectively evaluate the derived scoring functions

- to design ligands with improved affinities for the targets in the RESPOND3 project

- to supervise master students

More details about this position and information on how to apply can be found here: https://www.jobbnorge.no/en/available-jobs/job/172060/phd-structure-based-design-machine-learning

 

The postdoc position is in the group of Prof. Alexander Selvikvåg Lundervold, Faculty of Engineering and Science, Western Norway University of Applied Sciences.

The main objectives of this position are:

- Development of new scoring functions for protein-ligand interactions using both in-house data and publicly available data sets.

- Attempts at combatting the tendency for scoring functions to exploit uninteresting features in the training data (data leakage) using e.g. various debiasing techniques. The improved scoring functions will be evaluated prospectively.

- Investigation of the the potential for machine learning methods in de novo structure generation (e.g. using variants of generative adversarial networks).

- Assist in the supervision of MSc students and PhD candidates.

More details about this position and information on how to apply can be found here: https://www.jobbnorge.no/en/available-jobs/job/172249/postdoctoral-fellow-in-drug-discovery-and-machine-learning

 

Scientific Programmer / Bioinformatician [EMBL, Heidelberg]

We are seeking a highly motivated scientific programmer and data manager to join the new Zimmermann research group in the Structural and Computational Biology unit. The Zimmermann group combines high-throughput mass spectrometry, bacterial genetics, multi-omics analyses and computational models to investigate the interactions within microbial communities and between microbes and their environment. Your role would be to develop analysis pipelines, infrastructure and data management systems within the group and externally. It includes the development and maintenance of bioinformatics software for different research projects, adaptation of existing code and pipelines, and providing programming and statistics support to the group. The position involves large scale data handling from mass-spectrometry and sequencing experiments (metabolomics, NGS). The duties range from generic bioinformatics and IT support to development of own independent research projects.

Requirements:

—a Ph.D. degree in bioinformatics, computational biology, statistics, or related subjects

—substantial experience in software development and/or scientific computing

—experience with large-scale data analysis and management

—experience with the Linux/Unix shell

—advanced skills in a high level programming language (>2 years of experience)

—ability to work independently and in a team, and at the interface between life sciences and informatics

—willingness to learn new skills and programming languages as projects require

—good communication, interpersonal and English language skills

 

Links: https://www.embl.de/jobs/apply_page/?jobId=QHPFK026203F3VBQB688N79SB-1098&langCode=en_GB. 

MitoIntegrOMICS - An integrated multiOmics approach to increase the diagnostic power for mitochondrial diseases

Mitochondrial diseases (MD) are rare disorders caused by deficiency of the mitochondrial respiratory chain, which provides energy in each cell. MD are caused by alterations (variants) on genes involved in mitochondrial functions. The diagnosis of MD is based on the identification of the disease responsible gene(s), that will allow to be able to offer genetic counseling, prenatal diagnosis, to consider therapeutic approaches and to improve the care of patients. Nowadays, technologies currently used for detecting causal variants is far from complete, ranging from 25 to 50%.

To address these needs our research teams propose to gather three different domains: medical, bioinformatic and machine learning, in order to set up an integrated multi-omics approach to identify novel causal variants. We foresee that this project will contribute to set up new diagnostic tools to reduce the number of patients with a diagnostic stalemate. This study will settle the milestones to transfer the conjoint use of multi-omics technologies from research fields to diagnostic environment.

Postdoc - Systems Biology of Infection [Uni Greifswald]

We have an opening for a Postdoc in Systems Biology of infection within the KoInfekt project: Elucidation of Pathomechanisms of Bacterial-Viral Co-infections with new Biomedical Models .

Applicants should have a strong research record in theoretical Systems Biology or related fields, ideally with experience in machine learning in systems biology, in multi-OMICs data integration, or modeling of biological processes using differential equations, and with a strong algorithmical and mathematical background. We expect the applicant to be willing to collaborate closely with both theory and experimental collaboration partners within the KoInfect consortium.

The position is paid according to the German TV-L salary scale (E-13), and is available immediately until December 2020, with possible extension. 

Links: http://www.kaderali.org/jobs.html

Scientific Programmer / Bioinformatician [ Zimmermann research group, EMBL]

We are seeking a highly motivated scientific programmer and data manager to join the new Zimmermann research group in the Structural and Computational Biology unit. The Zimmermann group combines high-throughput mass spectrometry, bacterial genetics, multi-omics analyses and computational models to investigate the interactions within microbial communities and between microbes and their environment. Your role would be to develop analysis pipelines, infrastructure and data management systems within the group and externally. It includes the development and maintenance of bioinformatics software for different research projects, adaptation of existing code and pipelines, and providing programming and statistics support to the group. The position involves large scale data handling from mass-spectrometry and sequencing experiments (metabolomics, NGS). The duties range from generic bioinformatics and IT support to development of own independent research projects.

Requirements:

—a Ph.D. degree in bioinformatics, computational biology, statistics, or related subjects

—substantial experience in software development and/or scientific computing

—experience with large-scale data analysis and management

—experience with the Linux/Unix shell

—advanced skills in a high level programming language (>2 years of experience)

—ability to work independently and in a team, and at the interface between life sciences and informatics

—willingness to learn new skills and programming languages as projects require

—good communication, interpersonal and English language skills 

Links: https://www.embl.de/jobs/apply_page/?jobId=QHPFK026203F3VBQB688N79SB-1098&langCode=en_GB

2 Phd positions in Computational Biology [Center for Molecular Medicine, Frankfurt]

The group of Prof. Marcel Schulz  is looking to fill the position of two Phd students (E13 TV-G-U, 65%) to start as early as possible at the Computational Epigenomics & Systems Cardiology group at the Institute for Cardiovascular Regeneration, Center for Molecular Medicine, Frankfurt (https://schulzlab.github.io).

Exact payment is based on previous research experience according to the work laws of Goethe University (TV-G-U).

Tasks:

We offer a Phd position for method development for integrative analysis methods targeted for analysis of single cell assays that are conducted with multiple assays simultaneously, for example RNA-seq and DNA methylation or ATAC-seq. Another position is about method development of novel approaches for the prediction of gene expression. Different approaches from Machine Learning should be tested and novel approaches for the interpretability of complex non-linear methods or Deep Learning based approaches should be developed to unravel gene-specific regulatory codes from a large catalogoue of epigenomics data.

Requirements:

·       Masters degree in Bioinformatics, Machine Learning, Computer Science or a related discipline

·       good programming skills

·       experience in the application of machine learning methods is advantageous

·       experience in the analysis of sequencing data is advantageous

·       we are working in an interdisciplinary team and are looking for people with good organizational and communication skills, as well as high creativity to address novel research problems

·       good knowledge of the English language

Please send your application with CV and two names of references latest until 15.06.2019 (preferably by email) to:

Prof. Marcel Schulz, Institut für Kardiovaskuläre Regeneration, Zentrum für Molekulare Medizin, Goethe-Universität Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, E-Mail: marcel.schulz AT em.uni-frankfurt.de

Please do not send original documents by mail, because there will be no return of such documents. All electronic documents should be combined into one pdf document. Travel and application costs are not being reimbursed.

Goethe University is comitted to increase the amount of female researchers and we encourage their application. Applicants with a disability and equal qualifications will be favoured.

 

Postdoc Computational Biology [Center for Molecular Medicine, Frankfurt]

The group of Prof. Marcel Schulz is looking to fill the position of a

Postdoc (E13 TV-G-U, 100%)

to start as early as possible at the Computational Epigenomics & Systems Cardiology group at the Institute for Cardiovascular Regeneration, Center for Molecular Medicine, Frankfurt (https://schulzlab.github.io).

Exact payment is based on previous research experience according to the work laws of Goethe University (TV-G-U).

Tasks:

·       The Postdoc position is part of a large project about the analysis of high-dimensional data to understand gene regulation in heart diseases. It involves the development of new methods for the analysis of single cell data and application of machine learning methods to address problems of data heterogeneity and integration of datasets from different cellular levels (RNA, DNA methylation, chromatin).

 

Requirements:

·       Masters degree in Bioinformatics, Machine Learning, Computer Science or a related discipline

·       Phd degree in Bioinformatics, Machine Learning, Computer Science or a related discipline

·       good programming skills

·       experience in the application of machine learning methods

·       experience in the analysis of sequencing data

·       we are working in an interdisciplinary team and are looking for people with good organizational and communication skills, as well as high creativity to address novel research problems

·       good knowledge of the English language

Please send your application with CV and two names of references latest until 15.06.2019 (preferably by email) to:

Prof. Marcel Schulz, Institut für Kardiovaskuläre Regeneration, Zentrum für Molekulare Medizin, Goethe-Universität Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, E-Mail: marcel.schulz AT em.uni-frankfurt.de

Please do not send original documents by mail, because there will be no return of such documents. All electronic documents should be combined into one pdf document. Travel and application costs are not being reimbursed.

Goethe University is committed to increase the amount of female researchers and we encourage their application. Applicants with a disability and equal qualifications will be favoured. 

13 positions for PhD students available including a computational molecular design topic

Within the Research Training Group "Chemical Biology of Ion Channels (Chembion)" funded by the Deutsche Forschungsgemeinschaft (DFG) and established at the Westfälische Wilhelms-Universität in Münster 13 positions for PhD students, 13 TV-L (65 %) are available.

13 scientists of the Westfälische Wilhelms-Universität Münster have teamed up with their complementary expertise to focus on the chemical biology of ion channels. The interdisciplinary research activities are centered on five topics: ligand recognition, subtype specific modulation, molecular imaging, molecular and cellular physiology, integrative (patho)physiology. Our vision of this interdisciplinary project is to solve physiological questions in the field of ion channels with innovative chemical methods, to bring together the molecular world of chemistry/pharmacy with the function-centered world of medicine and to develop the internationalization of our doctoral students.

One topic is of special interest for the bioinformatics/cheminformatics community: "In-silico studies of ion channels and their modulators using computational molecular design".

Further details can be obtained from the Chembion homepage: www.uni-muenster.de/chembion

 

Wissenschaftlicher MitarbeiterIn (m/w/d) (DoktorandIn oder Postdoc, TV-L E13/100%) in Bioinformatik

In der Arbeitsgruppe von Prof. Dr. Caroline Friedel an der Ludwigs-Maximilians-Universität München ist frühestens zum 1.7.2019 die Stelle einer/s

Wissenschaftlichen Mitarbeiter/in (TV-L 13, 100%)

als Promotions- oder Postdoc-Stelle zu besetzen. Der Beginn der Stelle ist flexibel bis zum 31.3.2020, daher ist eine Bewerbung auch bereits jetzt möglich, wenn Master oder Promotion erst in einigen Monaten abgeschlossen werden.

Diese Stelle ist Teil des durch die DFG geförderten Projektes „Large-scale investigation of short read archives for disruption of transcription termination and circular splicing“.  

Ziel dieses Projektes ist dabei die Entwicklung und Anwendung von neuen Methoden zum Durchsuchen großer Read-Datenbanken wie die NCBI SRA nach Evidenz für Störungen in der Transkriptionsterminierung und speziellen Splicing-Ereignissen.

Kandidatinnen und Kandidaten sollten ein Hochschulstudium (Master/Diplom) bzw. eine Promotion für die Postdoc-Stelle in Bioinformatik oder einem nahe verwandten Fachgebiet absolviert haben oder kurz vor dem Abschluss stehen. Vorausgesetzt werden gute Programmierkenntnisse (Java, Python und/oder Perl) und Interesse an quantitativer Datenanalyse und bioinformatischer Methodenentwicklung. Erfahrungen mit der Analyse von Hochdurchsatz-Daten, insbesondere Next-Generation Sequencing-Daten, wären von Vorteil.

Bewerbungen mit den üblichen Unterlagen (Lebenslauf, Zeugniskopien, Master/Diplom-Arbeit bzw. Doktorarbeit als PDF per Email) bzw. Fragen zur Stellenausschreibung sind zu richten an:

Prof. Dr. Caroline Friedel
Lehr- und Forschungseinheit für Bioinformatik
Institut für Informatik
Ludwig-Maximilians-Universität München
This email address is being protected from spambots. You need JavaScript enabled to view it.
 
 

 

 

Bioinformatician (full time) [Heidelberg University Hospital ]

We have an opportunity for a a talented and motivated bioinformatician to join the Portugal laboratory in the Parasitology Department of Heidelberg University Hospital.

We are seeking a Bioinformatics Scientist (BSc, MSc or PhD [title and rank will be determined based on experience and degree]) with background in biology, statistics and programming. Expertise in R and familiarity with analytic tools and public genomic and clinical databases.

Project Description: We have recently shown that dry season Plasmodium falciparum infections are maintained asymptomatically during the 6-month dry season in Mali, while P. falciparum-specific humoral responses decrease (Portugal, S. et al. 2017). We are currently investigating parasite transcription and transcriptional regulation, during the dry season through NGS, comparing leucocyte-depleted blood of Malian children with persistent subclinical P. falciparum infections at the end of the dry season, and that of age- and gendermatched Malian children presenting with their first clinical malaria case in the ensuing transmission season.

We aim to investigate parasite transcription, including the expression of genes coding for parasite variant surface proteins on the surface of the host erythrocyte, and RNA-protein-DNA interactome, chromatin accessibility, and epigenetics. The person we seek will be working at the interface of wet lab and field researchers as well as P. falciparum bioinformaticians with whom we collaborate to further develop analytic tools. The ideal candidate should have or quickly develop excellent communication skills and the ability to work with interdisciplinary teams, be fluent in English and be willing to present results internally and externally.

Collaboration Partners: Peter Crompton (NAID, NIH), Boubacar Traore (FMPOS, ICER Mali), Thomas Lavstsen (Copenhagen University), Thomas Otto (University of Glasgow)

Profile of candidate’s qualification:

-           Graduate, Master’s or PhD Degree in Informatics, Biology or related areas;

-           Expertise in bioinformatics and molecular/cellular biology and experience with “Omics” data analysis.

-           Background in Statistics

-           Excellent knowledge of spoken and written English and excellent communication skills and team spirit; organizational skills and ability to keep detailed records of experiments;

-           Critical mind, enthusiasm; and ability to work in multidisciplinary and multicultural teams.

Contact for questions: This email address is being protected from spambots. You need JavaScript enabled to view it.

Please send your application (including motivation letter, curriculum vitae, transcripts & certificates, and contact details of two academic references) via email by July 15th indicating Bioinformatician call on the email subject.

We use cookies on our website. Some of them are essential for the operation of the site, while others help us to improve this site and the user experience (tracking cookies). You can decide for yourself whether you want to allow cookies or not. Please note that if you reject them, you may not be able to use all the functionalities of the site.