ISCB Affiliated Group Logo

Job Offers

(Bio-) Informatiker*in am Max-Planck-Institut für Verhaltensbiologie in Radolfzell/Konstanz

Sie werden in einem Projekt eingesetzt, das Teil des neuen, landesweiten Netzwerks bioDATEN (http://www.biodaten.info/) ist. Dort erarbeiten wir in einem interdisziplinären Team aus Biologen, Informatikern und Informationswissenschaftlern Schnittstellen dieser Disziplinen in der Analyse großer *omics Datensätze. Das Teilprojekt in Konstanz befasst sich mit der Ökologie und Evolution der Immungene von Vögeln. Dabei nehmen wir an den globalen Projekten B10K (https://b10k.genomics.cn/) und VGP https://vertebrategenomesproject.org/ teil.

 

Links: https://ab.iwww.mpg.de/177862/job_full_offer_13636535

Data Scientists in Bioinformatics (m/f/d) (100%) [Dr. rer. nat. Catherine Drescher Cluster of Excellence ImmunoSensation2]

Data Scientists in Bioinformatics (m/f/d) (100%)

The two positions are initially limited to three years with the possibility of extension.

ImmunoSensation2 is a Cluster of Excellence funded by Germany’s Excellence Strategy at

theUniversity of Bonn. Its scientists are dedicated to investigating innate immunity beyond the

boundaries of classical immunology. In a joint effort, immunologists, neurobiologists, systems

biologists and mathematicians from the University of Bonn and the German Center for

Neurodegenerative Diseases (DZNE) of the Helmholtz Association aim to investigate the status of the

immune system, the metabolism and the nervous system connect in health and disease.

ImmunoSensation2 is embedded in the outstanding research environment of the University of Bonn,

the University Hospital and the DZNE. Furthermore, ImmunoSensation2 is internationally connected

and maintains research partnerships with Australia (Melbourne University), Japan (Osaka University,

Waseda University, Kyoto University) and the Netherlands (Radboud University, Nijmegen).

The announced position will be integrated into the Core Unit for Bioinformatics Data Analysis (CUBA)

of the Medical Faculty at the University of Bonn, which provides quantitative and computational

analyses, training and consultation for all members of the faculty. CUBA benefits from a shared

computing infrastructure and exchange of expertise due to its embedding and liaison with the Institut

für Medizinische Biometrie, Informatik und Epidemiologie (IMBIE) and the Institute for Genomic

Statistics and Bioinformatics (IGSB). It operates in close collaboration with other core units like the

NGS, flow cytometry and mass spectrometry core. The unit aims to establish a platform for

computational biology, to facilitate quantitative approaches and to share and offer validated methods,

expertise and resources. These methods will continuously evolve according to the needs of

collaborators and progress in science to provide state-of-the-art bioinformatics and data analyses.

 

Your tasks:

 

Analysis and processing of high-volume data sets such as next generation sequencing

Design, implementation and application of tailored analysis workflows

Statistical analysis and visualization

Interaction and collaboration with researchers

o Consultation regarding the planning and design of experiments

o Presentation and reporting of results

o Recommendation of publicly available resources and tools

Working in a team with bioinformatic and computational colleagues

Selection and adaption of (bioinformatical) methods and tool

Training courses and education

 

Your profile:

 

Master or PhD in bioinformatics, computational biology, computer science,

statistics, mathematics or any other related field

Strong expertise in the analysis of next generation sequencing data (NGS), such as single

cell genomics, RNA-Seq, ChIP-Seq and ATAC-Seq

Profound knowledge of statistics, data analysis and visualisation techniques

Proficiency in programming, e.g. with R/Bioconductor or Python

Experience with Linux and high-performance computing (HPC)

Background in molecular biology concepts and an interest in immunology

Knowledge of high-throughput image analysis (FACS ImageStream) is considered a plus

Good communication and presentation skills and fluency in written and spoken English

Team player capable of adapting to a rapidly evolving and interdisciplinary

research environment

 

We offer:

Outstanding research opportunities

Collaborative work environment

Salary according to the German salary scale TV-L (EG 13)

Supplementary benefits (e.g. pension plan according to VBL)

A “Jobticket” (subsidized public transport)

 

The University of Bonn is committed to diversity and equal opportunity. It is certified as a family-

friendly university. It aims to increase the proportion of women in areas where women are under-

represented and to promote their careers in particular. It therefore urges women with relevant

qualifications to apply. Applications will be handled in accordance with the

Landesgleichstellungsgesetz (State Equality Act). Applications from suitable individuals with a certified

serious disability and those of equal status are particularly welcome.

Applicants should send their application in a single pdf file (max. 5 MB), including a motivation letter,

CV, scanned academic degrees, a list of publications and the contact details of two references. More

information on the scientific projects and project leaders can be found

at www.immunosensation.deand information on CUBA can be found at https://cores.ukb.uni-

bonn.de/bioinformatics/

 

Further details will also be provided during the recruitment process. Applications will be accepted on

rolling basis and successful candidates can begin on August 1, 2019 or later.

Please send your application by email using the reference number 350_2019_FABI to:

Dr. rer. nat. Catherine Drescher

Cluster of Excellence ImmunoSensation2

University Hospital Bonn

Venusberg-Campus 1,

53127 Bonn

Email: applications_immunosensation(at)ukbonn.de

www.immunosensation.de

 

Lead Bioinformatician (m/f/d) for high-throughput genome assembly and annotation [Job offer ref. # 12-19005]

Job offer ref. # 12-19005

The Senckenberg Gesellschaft für Naturforschung (SGN) is a member of the Leibniz Association and is based in Frankfurt am Main, Germany. LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG) is a joint venture of the Senckenberg Gesellschaft für Naturforschung (SGN), Goethe-University Frankfurt, Justus-Liebig-University Giessen and Fraunhofer Institute for Molecular Biology and Applied Ecology IME aiming to intensify biodiversity genomics in basic and applied research. We will establish a new and taxonomically broad genome collection to study genomic and functional diversity across the tree of life and make genomic resources accessible for societal-demand driven applied research.

The Senckenberg Gesellschaft für Naturforschung and the LOEWE-TBG invite applications for a

 

Lead Bioinformatician (m/f/d)

for high-throughput genome assembly and annotation

(100%)

 

Your tasks:

·         Lead a team of bioinformaticians to develop, maintain and run high-throughput pipelines for the assembly and annotation of de novo genomes from diverse eukaryotes

·         Implementing and documenting the work-flow from receiving data, issue assembled genomes to users and archiving data in public databases

·         Communication with user groups, service providers and external database managers

 

Your profile:

·         PhD in Bioinformatics or related subjects

·         Experience with de novo genome assembly of non-model organisms and developing large scale, high-throughput procedures for de novo genome assembly and annotation

·         Proven understanding of comparative genomics or evolutionary biology research preferably in non-model organisms

·         Familiarity in leading a service orientated unit and excellent communication skills

 

What is awaiting for you?

·         A central role in an innovative large-scale genomics project with the opportunity to create an own research profile

·         A motivated and dynamic team of international researchers at an internationally recognized biodiversity research institution

·         An opportunity to build a central research and service unit within LOEWE-TBG and Senckenberg

·         Excellent opportunities to expand your scientific network across disciplines

·         Flexible working hours – annual special payment – company pension scheme – 30 days holidays

 

Salary and benefits are according to a full time public service position in Germany                   (TV-H E14/15 according to qualification and experience). The contract should start as soon as possible and will initially be limited to December 31th, 2021. The Senckenberg Gesellschaft für Naturforschung support equal opportunity of men and women and therefore strongly invites women to apply. Equally qualified handicapped applicants will be given preference. The place of employment is in Frankfurt am Main, Germany. The employer is the Senckenberg Gesellschaft für Naturforschung.

Please send your application, mentioning the reference of this job offer (ref. #12-19005) before July 28th, 2019 by e-mail (attachment in a single pdf document) and including a cover letter detailing research interests and experience, a detailed CV and a copy of your certification to:

 

Senckenberg Gesellschaft für Naturforschung

Senckenberganlage 25

60325 Frankfurt am Main

E-Mail: This email address is being protected from spambots. You need JavaScript enabled to view it.

 
 

 

 

Wissenschaftlicher Mitarbeiter (w/m/d) im Bereich Bioinformatik [Tierärztliche Hochschule Hannover]

Am Institut für Tierzucht und Vererbungsforschung der Tierärztlichen Hochschule Hannover ist ab dem 01. Oktober 2019 eine Stelle als

wissenschaftlicher Mitarbeiter (w/m/d) im Bereich Bioinformatik

mit 65% der vollen Arbeitszeit zu besetzen. Die Stelle ist auf drei Jahre befristet. Ein Promotionsvorhaben auf der Stelle wird unterstützt und ausdrücklich erwünscht.

Aufgaben sind die die Mitarbeit in aktuellen Forschungsaktivitäten der Arbeitsgruppe „Genomics and Bioinformatics of Infectious Diseases“. Dazu zählen vor allem die Weiterentwicklung und Anwendung von statistisch-bioinformatischen Methoden für die Analyse von High-Throughput-Sequenzdaten und High-Throughput-Genexpressionsdaten (NGS-, Microarrays-Daten).

Voraussetzung für eine Bewerbung ist ein abgeschlossenes wissenschaftliches Hochschulstudium mit Masterabschluss in Bioinformatik, Biostatistik oder einem vergleichbaren Fach. Darüber hinaus werden Kenntnisse in der Shell-Programmierung unter Linux sowie in der Programmierumgebung R

erwartet.

Die Vergütung erfolgt nach E 13 TV-L.

Schwerbehinderte Bewerberinnen und Bewerber werden bei gleicher Eignung vorrangig berücksichtigt. Bitte senden Sie Ihre aussagekräftige Bewerbung per E-Mail bis spätestens 31.07.2019 an Herrn Prof. Dr. Klaus Jung (This email address is being protected from spambots. You need JavaScript enabled to view it.), Institut für Tierzucht und Vererbungsforschungs, Tierärztliche Hochschule Hannover. Weitere Auskünfte zu der Stelle werden gerne über diese E-Mail- Adresse erteilt.

 

Ihre personenbezogenen Daten werden vertraulich behandelt (www.tiho-hannover.de/ds-bew).]

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.