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Postdoctoral Fellow Position in Machine Learning for Drug Discovery at the Western Norway University of Applied Sciences

A postdoc position is available at the Western Norway University of Applied Sciences in the research group of Alexander Selvikvåg Lundervold (This email address is being protected from spambots. You need JavaScript enabled to view it.).
 
The position is associated with the RESPOND3 project “Towards better computational approaches and responsible innovation strategies in early drug discovery: application to antibiotics and COPD”. RESPOND3 is part of the Centre for Digital Live Norway (https://digitallifenorway.org ) and 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 Computer Science, Electrical Engineering and Mathematical Sciences 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.
 
The RESPOND3 research team will eventually consist of four postdocs, three PhD students and five principle investigators, covering medicinal chemistry, computational chemistry and biology, structural biology, computer science, mathematics, and law. In addition to working with the RESPOND3 team, the postdoctoral fellow will be part of the vibrant research community at the recently established Mohn Medical Imaging and Visualization Center (MMIV, https://mmiv.no ), Haukeland University Hospital, with access to world-class computing infrastructure and to top expertise in life sciences, machine learning and computation. The researcher will also be associated with the ICT-oriented strategic research programme in computer science at HVL (http://ict.hvl.no) which spans the areas of software engineering, sensor networks, machine learning, and engineering computing.
 
The announced postdoc position will focus on applications of machine learning in drug discovery and development. The exact direction of research will depend on the background and interests of the successful candidate. Potential research areas and directions include
  • 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 potential for machine learning methods in de novo structure generation (e.g. using variants of generative adversarial networks)
 
In addition, the successful candidate will
  • Assist in the supervision of MSc students and PhD candidates.
  • Contribute to the development of joint project applications for external funding in collaboration with permanent research staff members at HVL, MMIV and UiB
 

 

More details about this position and information on how to apply can be found here: https://www.jobbnorge.no/en/available-jobs/job/177135/postdoctoral-fellow-position-in-machine-learning-for-drug-discovery. Deadline November 24th 2019.

2x PhD student pos., Comp. biochem./chem. or struct. bioinf., U of Duesseldorf, Gohlke group

Applications are invited for two PhD student positions in the Computational  Pharmaceutical Chemistry & Molecular Bioinformatics group of Prof. Dr. Holger Gohlke at the Heinrich-Heine-University, Duesseldorf, Germany.

PhD student position 1
:

o    Topic: Development of novel modulators for the nicotinic acetylcholine receptor for the treatment of nerve agent poisoning

o    Availability: The position is available as of now.

PhD student position 2:

o    Topic: Enzymatic halogenation: enzyme identification, characterization, application

o    Availability: The position is available as of 01.12.2019.

Please find more detailed information regarding the respective topic under: https://cpclab.uni-duesseldorf.de/index.php/Openings

Requirements
Ideal candidates will have a record of excellence and a strong background in computational biochemistry, molecular informatics, and computational structural biology as well as a high interest in working in an interdisciplinary research field, and profound knowledge in state-of-the-art molecular dynamics simulations (Amber) software and molecular modelling.

 

Application process
Applicants should submit applications (a one-page letter of motivation why they are interested in the respective project and how they can contribute to the project’s success, a current CV, and contact data of three references) by email to
This email address is being protected from spambots. You need JavaScript enabled to view it. . Please provide all documents as one PDF file and specify for which position you are applying.

Wissenschaftlicher Mitarbeiter im Bereich Bioinformatik/ Evolutionäre Entwicklungsgenetik

In der Abteilung Evolutionäre Entwicklungsgenetik der Georg-August-Universität Göttingen ist zum nächst möglichen Zeitpunkt die Stelle einer/eines

 

wissenschaftliche_n Mitarbeiter_in (w/m/d)

 

mit 65 % der regelmäßigen wöchentlichen Arbeitszeit (zzt. 25,9 Stunden/Woche) befristet für die Dauer von 3 Jahren zu besetzen. Eine Verlängerung wird angestrebt. Die Entgeltzahlung erfolgt nach Entgeltgruppe 13 TV-L.

 

In dem DFG-geförderten Projekt soll die projektspezifische Datenbank iBeetle-Base mit phäntoypischen Daten zu einer Informationsressource für die entwicklungsbiologische Community ausgebaut werden. Zudem soll mit den bereits vorhandenen Daten an einer spezies-übergreifenden Analyse gearbeitet werden (data mining). Das bisherige Backend soll in einzelne Mikroservices überführt werden, die eine anwendungsneutrale Daten-API bieten. So soll die Nutzung der Daten durch beliebige und eigene bioinformatische Tools ermöglicht werden. Mit einem ontologie-basierten Datenformat soll die Integration von möglichst vielen weiteren Daten aus der Community ermöglicht werden. Eine build- und deploy-Pipeline wird zur Orchestrierung der Services in einem Kubernetes-Cluster benötigt. In dem Projekt ist neben dem Zoologischen Institut die Bioinformatik, die Staats- und Universitätsbibliothek Göttingen und die GWDG beteiligt, wodurch ein Einblick in verschiedene Institutionen und Arbeitsweisen gewährt wird.

 

 

Ihre Aufgaben

-  Sie implementieren Mikroservices für alle Daten und Funktionen, die das Projekt anbietet

-  Zusammen mit den Projektpartnern entwickeln Sie ein Konzept für den langfristigen Betrieb

-  Sie entwickeln Datenmodelle für phäntoypische Daten und recherchieren nach internationalen Standards

-  Sie entwickeln neue Methoden zur weiteren Analyse vorhandener Daten, wie z. B. einer spezies-übergreifenden Suche nach

    Phänotypen

 

Ihr Profil

   -  Abgeschlossenes wissenschaftliches  Hochschulstudium in Bioinformatik, angewandter Informatik oder vergleichbarem

      Studienfach

-  Gutes Verständnis von biologischen Grundlagen und bioinformatischen Methoden

-  Interesse an der Arbeit in einem interdisziplinären Team

-  Motivation sich selbständig in ein Themengebiet einzuarbeiten und Lösungen zu entwickeln

-  Sehr gute Kenntnisse der Programmierung und Softwareentwicklung

-  Kenntnisse von aktuellen Methoden der Softwareentwicklung, wie z.B. Domain Driven Design, DevOps oder Docker-

    Container

-  Fließendes Englisch in Wort und Schrift

-  Hohe Motivation, Teamfähigkeit und Eigeninitiative

 

Die Stelle soll der Qualifizierung des wissenschaftlichen Nachwuchses dienen und bietet die Möglichkeit zur Promotion.

 

Die Universität Göttingen strebt in den Bereichen, in denen Frauen unterrepräsentiert sind, eine Erhöhung des Frauenanteils an und fordert daher qualifizierte Frauen nachdrücklich zur Bewerbung auf. Sie versteht sich als familienfreundliche Hochschule und fördert die Vereinbarkeit von Wissenschaft/Beruf und Familie. Die Universität hat sich zum Ziel gesetzt, mehr schwerbehinderte Menschen zu beschäftigen. Bewerbungen Schwerbehinderter erhalten bei gleicher Qualifikation den Vorzug.

 

Bewerbungen mit den üblichen Unterlagen werden innerhalb von drei Wochen nach Erscheinen,

gern auch in elektronischer Form, erbeten an

Georg-August-Universität Göttingen, Abt. Evolutionäre Entwicklungsgenetik,

Justus-von-Liebig-Weg 11, 37077 Göttingen, E-Mail: This email address is being protected from spambots. You need JavaScript enabled to view it.

 

Für Rückfragen steht Ihnen Herr Jürgen Dönitz

Telefon:0551-39-14927, E-Mail: This email address is being protected from spambots. You need JavaScript enabled to view it.

zur Verfügung. Für weiter Informationen siehe auch

http://www.bioinf.med.uni-goettingen.de/research/knowledge-management/iBeetle-Base

 

Hinweis:

Wir weisen darauf hin, dass die Einreichung der Bewerbung eine datenschutzrechtliche Einwilligung in die Verarbeitung Ihrer Bewerberdaten durch uns darstellt. Näheres zur Rechtsgrundlage und Datenverwendung finden Sie im: Hinweisblatt zur Datenschutzgrundverordnung (DSGVO) https://www.uni-goettingen.de/hinweisdsgvo  

Links: http://www.bioinf.med.uni-goettingen.de/research/knowledge-management/ibeetle-base/

IT and Computational Biology Expert [Korbel group in the Genome Biology Unit, EMBL]

EMBL is seeking an expert in Computational Biology and IT to join Dr. Jan Korbel's group in the Genome Biology Unit. The position holder will actively participate in the design, development, and adjustment of interoperable workflows and pipelines to enable the analysis of data from the latest next-generation DNA sequencing platforms, including from single cell technologies. The post holder may get involved in analysing large numbers of human genomes, including from cancer patients and normal individuals of varying age to unravel the relationship of somatic mutations and ageing.

Your role

·         Develop new computational workflows and analytical methods for human genome data analysis

·         Design and implement cloud-based workflows for single-cell sequencing protocols, particularly Strand-Seq

·         Integrate tools in pipelines and workflows and optimize their interoperability, efficiency, usability and portability

·         Participate in cutting-edge research projects of the Korbel group by helping with data analysis and data management tasks

·         Interact with other scientists at EMBL and partner networks (Elixir, de.NBI) in an international, interdisciplinary, and highly collaborative work environment

You have

·         A M.Sc. or PhD in Computational Biology, Bioinformatics, Physics or Computer Science with a background in large-scale genomics data handling

·         Advanced programming skills in at least one high level programming language (Java, C, or C++), R Statistics and one scripting language (Python, Julia)

·         A solid knowledge in database technologies (SQL), cloud computing frameworks (OpenStack, GNOS), containerization technologies (Singularity, Docker), code version control (git) and continuous integration services (CI)

·         A strong interest in computational data analysis and data management

·         Strong communication skills as well as the ability to interact with other scientists and to work in an international and interdisciplinary team

·         A basic understanding of molecular genetics and cancer research

What else you need to know

The Korbel group at the European Molecular Biology Laboratory (EMBL) combines experimental and computational approaches – including single-cell sequencing technology, genome sequencing, big data analytics, and machine learning – to unravel determinants and consequences of germline and somatic genetic variation. Our group is using bulk as well as single cell-based omics approaches for investigating mechanisms behind complex phenotypes in humans, ranging from common diseases including cancer to ageing. An over-arching theme centers on the formation and selection of germline and somatic genetic variation in health and disease states, in particular genomic structural variation (SV).

 

Postdoc-Stelle am Zentrum für Bioinformatik Hamburg

Am Zentrum für Bioinformatik Hamburg ist ab dem 1. Dezember 2019 in dem Projekt "DASHH - Data Science in Hamburg - Helmholtz Graduate School for the Structure of Matter" eine Postdoc-Stelle zu besetzen.

Näherere Informationen entnehmen Sie bitte dem vollständigen Ausschreibungstext: https://www.uni-hamburg.de/uhh/stellenangebote/wissenschaftliches-personal/fakultaet-mathematik-informatik-und-naturwissenschaften/28-10-19-514-verl.pdf

RESEARCH ASSOCIATE (DATA SCIENTIST/MODELLER) IN CONJUNCTION WITH A PH.D.

What we expect from you

You hold a scientific, mathematical/(bio-)informatics, engineering or content-related higher educational degree (e.g. with a focus on data analysis, statistics,
artificial intelligence (AI) or modelling) and are familiar with common script and high-level programming languages such as R, Phython, Shell and C/C ++ in
the Linux environment.

You enjoy analyzing data and developing mathematical models for the underlying processes. In addition to a high affinity to mathematical and programming
issues, you have a strong interest in research in the life sciences, have a high degree of initiative and show strong team and communication skills. Good
English spoken and written skills are a matter of course for you.

What you can expect from us

We offer you an exciting and innovative research topic at the interface between biotechnology, medicine and mathematics/computer science. 
You find out which culture conditions are optimal for our cell and tissue cultures and which drugs work best in which patients. 
You use up-to-date information technologies, expand your knowledge of data analysis and develop your own data mining or modelling
approaches.

Our area of activity offers you the following possibilities:

- Analysis of biomolecular, functional and clinical data (multiomics, high throughput/high content, treatment response, survival)
- Data integration and identification of biomarkers for individually customized optimal therapies
- Methodic implementation using statistics, machine learning, chemoinformatics, modelling, effective result analysis
- Development of processing pipelines and installation of a screening database
- Cooperation with internal and external partners, publication of your results

You can use the Fraunhofer Life Science infrastructure and become part of a dynamic team in an innovative scientific environment (pharmaceutical companies, biotech,
diagnostics, clinics, academic partners). You significantly shape our application-oriented technological solutions and further expand the screening and data analysis
capacities at the Fraunhofer ITEM. Our location at the UNESCO World Heritage Regensburg offers you many leisure time options and an attractive environment.

The remuneration is 65% of an EG 13 TVöD.
The position is initially limited to 3 years and linked to the preparation of a doctoral Thesis.
A longer-term employment is aimed at.
The weekly working time is 39 hours.
People with disabilities are given preference if equally qualified.
Please note that the chosen occupational title also includes the third gender. The Fraunhofer Society attaches importance to gender-independent professional equality.

We are looking forward for your online application under the following link: https://recruiting.fraunhofer.de/Vacancies/47526/Description/2

Questions about this position will readily be answered by:
Dr. rer. nat. Martin Hoffmann
Tel: +49 941 298480-28
http://www.item.fraunhofer.de Job Reference: ITEM-2019-50 Closing Date: 15.10.2019


We are looking forward for your online application under the following link: 
https://recruiting.fraunhofer.de/Vacancies/47526/Description/2

PhD theses in the fields of Bioinformatics, Medical Informatics and Personalized Oncology

At the Institutes for Medical Bioinformatics, Medical Informatics and the Clinic for Oncology of the University Medical Center Göttingen, several positions for doctoral theses in the fields of Bioinformatics, Medical Informatics and Personalized Oncology are to be filled as soon as possible for an interdisciplinary project in the area between Medicine and Informatics.

 Links: https://www.umg.eu/karriere/stellenangebote/stellenanzeigen-detail/?jobId=2907

2x wiss. Mitarbeiter am Lehrstuhl für Bioinformatik (FSU Jena)

Am Matthias-Schleiden-Institut für Genetik, Bioinformatik und Molekulare Botanik der Fakultät für Mathematik und Informatik der Friedrich-Schiller-Universität Jena ist zum 01.11.2019 eine Stelle als

Wissenschaftliche Mitarbeiterin / Wissenschaftlicher Mitarbeiter (m/w/d)

zu besetzen.

Die Forschung am Lehrstuhl Bioinformatik zielt auf ein Verständnis der komplexen Prozesse in lebenden Zellen und deren Interaktionen mittels mathematischer Modellierung und Computersimulation.

Ihre Aufgaben:

    • Bioinformatische und systembiologische Forschung 

    • Kooperation mit experimentell arbeitenden Gruppen 

    • Durchführung von Lehrveranstaltungen in Bioinformatik (Übungen, Proseminare etc.)

    • Klausurkontrolle, Prüfungsprotokolle

    • Betreuung von Abschlussarbeiten im B.Sc. Bioinformatik

    • Es wird von dem/der Bewerber/in erwartet, dass er/sie an einem wissenschaftlichen Weiterqualifizierungsprojekt arbeitet, i.d.R. Promotion zum Dr. rer. nat. 

 

Unsere Anforderungen:

    • Master- oder Diplom-Abschluss in Bioinformatik, Informatik, Biologie, oder einem anderen naturwissenschaftlichen Fach 

    • Interesse an mathematischer Modellierung biologischer Prozesse

    • Kenntnisse in der Computerprogrammierung

 

Wir bieten:

    • attraktive Nebenleistungen z.B. Vermögenswirksame Leistungen, Job-Ticket (Vergünstigungen für öffentliche Verkehrsmittel), betriebliche Altersvorsorge (VBL)

    • ein spannendes Tätigkeitsfeld mit Gestaltungsspielraum

    • eine universitäre Gesundheitsförderung und ein familienfreundliches Arbeitsumfeld mit flexiblen Arbeitszeiten

    • Vergütung nach den Bestimmungen des Tarifvertrages für den öffentlichen Dienst der Länder (TV-L) entsprechend den persönlichen Voraussetzungen bis zur Entgeltgruppe 13

 

Die Stelle ist zunächst auf 3 Jahre befristet. Es handelt sich um eine halbe Stelle.

Schwerbehinderte Menschen werden bei gleicher Eignung, Befähigung und fachlicher Qualifikation bevorzugt berücksichtigt.

 

Bewerbungen mit vollständigen Bewerbungsunterlagen (tabellarischer Lebenslauf, Zeugnisse) sind unter Angabe der Registrier-Nummer 295/2019 bis zum 15.10.2019 zu richten an:

 

Prof. Dr. Stefan Schuster (Email: This email address is being protected from spambots. You need JavaScript enabled to view it. )

Friedrich-Schiller-Universität Jena

Fakultät für Biowissenschaften

Matthias-Schleiden-Institut 

Professur für Bioinformatik

Ernst-Abbe-Platz 2

07743 Jena

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