Stellenangebote

Bioinformatics Engineer (6 months) in Clinical Bioinformatics

Details: Veröffentlicht: Freitag, 22. Januar 2021 12:51

Mission:

In prevision of a maternity leave, a fixed-term contract of 6 months is available from April 2021 within the Clinical Bioinformatics Group included inside the Diagnostic and Theranostic Medecine Division of Curie Institute.

Main activities:

Implementation of analysis pipelines
Developpement of custom tools for clinical diagnostic

Calibration and validation of analysis pipelines
Help to functionally interpret results using various databases
Contribute to the evolution and maintenance of diagnostic pipelines: updates, bug reporting, validations
Contribute to research projects associated with clinical trials
Regular progress meetings with biologists

Technological watch

Required skills:

Proficient with Unix/Linux environment
Proficient in at least of the following programming languages (ideally with experience with several of them): python, java, R or any other object-oriented programming language
Good knowledge of standard bioinformatics tools for analyzing and interpreting Next Generation Sequencing data (DNA and RNAseq)

Have an interest for interactions with biologists
Rigorous, dynamic, autonomous
Excellent team work

Desired skills:

Good knowledge in algorithmics

Code versioning using git
Proficient in English (oral and written)
Some skills in one or several of the following is highly advantageous: usage of calculation cluster (SGE / SLURM / LSF / MOAB, etc.), experience with distributed programming, usage of GPU, experience in machine learning / deep learning
Some knowledge in oncology is advantageous

Diploma:

A PhD or MSc in Bioinformatics
A first experience Next Generation data analysis is preferred

In order to apply, please send an email to bioinfo-clinique[AT]curie.fr

Bioinformatician [Collaborative Research Centre TRR 305]

Details: Veröffentlicht: Freitag, 22. Januar 2021 12:50

In the framework of the newly funded Collaborative Research Centre TRR 305 „Striking a moving target: From mechanisms of metastatic organ colonisation to novel systemic therapies“, we are looking for a

Bioinformatician (m/f/d)

to support project partners in the bioinformatics analysis of omics data.

Your tasks will include:

setting up and maintaining pipelines for sequencing data analyses (bulk and single-cell RNA-Seq, ATAC-Seq, ChIP-Seq);
closely interacting with CRC project partners to support post-processing analyses of omics data (e.g. functional enrichment, visualisation and interpretation of results, data integration with publicly available datasets, preparation of publication-ready figures);

Your qualifications:

academic degree (MSc/PhD) in bioinformatics, computational or life sciences. A PhD is preferred but not essential.
prior experience in the analysis of next-generation sequencing data is advantageous;
familiarity with working in a Linux/Unix environment;
strong programming skills (e.g. Python, Perl, R);
excellent communication skills and fluency in English.

The position will initially be available for 4 years, with the possibility of further extension.

Applications should be sent to Dr. Fulvia Ferrazzi, Institute of Pathology, FAU Erlangen-Nürnberg (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!) and Wencke Wallusch (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!), and include a CV (containing a list of publications, if applicable), a brief description of research experience, as well as contact information of two references.

The EU funded International Training Network (ITN) "ALPACA" announces 14 PhD positions, to be filled in 2021

Details: Veröffentlicht: Freitag, 22. Januar 2021 12:50

Please see https://alpaca-itn.eu/vacancies for a list of participating institutions / companies, and brief descriptions of the individual projects. Project start will generally be no later than September 2021, but depends on particular arrangements with the individual institution.

Applicants are asked to apply for up to a maximum of 5 positions. Applying for several positions is favorable, because applications may be discussed on a network wide level. However, applying for more than 5 positions may render the application ineligible.

Please apply directly at the institutions of your choice, following the links to the institutions listed at https://alpaca-itn.eu/vacancies.

Deadlines for submission of applications can vary by institution. As a general guideline, it is favorable to submit applications before 15th of February to receive full consideration.

Looking forward to receiving your application.

Wissenschaftlicher Mitarbeiter/-in (Postdoc) (m/w/d)

Details: Veröffentlicht: Freitag, 22. Januar 2021 12:47

Aufgabengebiet:
- Forschung im Arbeitsgebiet "Statistische oder algorithmische Bioinformatik" (AG Vingron);
- Mitarbeit in der Lehre in Bioinformatik am Fachbereich

Link:
https://www.fu-berlin.de/universitaet/beruf-karriere/jobs/wiss/19_fb-mathematik-und-informatik/MI-BioInf_WiMi2021.html

Ph.D. position in plant RNA bioinformatics

Details: Veröffentlicht: Freitag, 22. Januar 2021 12:47

We are seeking a Ph.D. student for a project to discover and understand structured RNAs in plants. The position is in the research group of bioinformatician Dr. Zasha Weinberg (https://zashaweinberglab.org) at Leipzig University, and is a collaboration with Prof. Andreas Wachter (https://mps-imp.biologie.uni-mainz.de), whose lab studies plant biology at the University of Mainz.

The last 20 years have seen a revolution in our understanding of the impact and versatility of non-coding and cis-regulatory RNAs in biology, i.e., RNAs that do not function as a simple messenger. Our goal is to develop novel bioinformatics approaches to find new types of plant RNAs, and to study these RNAs to better understand plant biology, especially alternative splicing. Your role will be to design and program new computational methods, analyze the resulting predictions from a bioinformatic and biological perspective and interact with the Wachter lab.

More information and how to apply: https://zashaweinberglab.org/plants/

Doktorand/in/Postdoc: Integrative Zellbiologie und Bioinformatik

Details: Veröffentlicht: Dienstag, 19. Januar 2021 09:13

Der Zustand jeder Zelle wird durch das komplexe Zusammenspiel vieler verschiedener epigenetischerMechanismen gesteuert, welche somit für die Entwicklung eines Organismus sowie Krankheitsbildung verantwortlich sind. Die zugrundeliegenden regulatorischen Faktoren können mithilfe moderner Sequenzierungsverfahren genomweit charakterisiert werden.Die kürzlich gegründete Forschungsgruppe Integrative Zellbiologie und Bioinformatik(https://icb.uni-saarland.de/)beschäftigt sich mit der Entwicklung und Anwendung computergestützter Verfahren um diejenigen molekularen Mechanismen, die für den Zellzustand im Kontext von Entwicklung und Krankheit verantwortlich sind, zu entschlüsseln. Dies umfasst insbesondere die Analyse und Integration großer multi-omics Datensätze. Hierzu forschen wir an der Schnittstelle zwischen Epigenomik, Biostatistik, Algorithmen und maschinellem Lernen in interdisziplinären Kollaborationen zwischen Molekularbiologie und Informatik.Wir suchen motivierte und kreative Mitarbeiter/innen für unser Team. Die Möglichkeit zur Promotion wird beiErüllung der Vorraussetzungengegeben.

Links: [bitte verwenden Sie html Links im Text oder geben Sie hier gewünschte Links durch Angabe des Stichworts und der Link-Adresse an]
https://icb.uni-saarland.de/?p=215

Bioinformatics Scientist and Software Engineer

Details: Veröffentlicht: Donnerstag, 14. Januar 2021 14:08

The _Institute for Virology _ <http://virologie.uk-koeln.de/>(Director: Univ.-Prof. Dr. Florian Klein) specializes in diagnostics and research pertaining to human pathogenic viruses. We apply a wide spectrum of molecular biological and bioinformatics techniques. Research topics include the identification and assessment of the development of viral resistance as well as research on new vaccination and therapeutic strategies. This research is performed in the _Laboratory for Resistance Analysis_ <http://virologie.uk-koeln.de/forschung/ag-kaiser>directed by Dr. Rolf Kaiser. In collaboration with the Max Planck Institute for Informatics in Saarbrücken we have developed algorithms and implemented software (_geno2pheno_ <http://www.geno2pheno.org/>) that is used internationally and facilitates bioinformatics analyses of viral resistance for HIV as well as the hepatitis C and hepatitis B viruses. Directed by _Prof. Dr. Thomas Lengauer_ <https://bioinf.mpi-inf.mpg.de/homepage/index.php?&account=lengauer>, who directed the development of the server and who is currently affiliated with our Institute we are continuing our research on the respective methods and applications. Furthermore we are extending our research to bacterial infections and cancer.
You will work in a highly interdisciplinary environment that is internationally excellently interconnected and provides opportunities for innovative research on patient-related and medically highly relevant topics. Collaboration with research groups in medicine, computational biology and computer science at Cologne University are existing or available. Your research will uniquely combine basic research on computational methods with medical applications. Perspectives for scientific advancement towards PhD or beyond are included in the profile of the position.
Application materials include letter of motivation, CV, documents and transcripts, publication list, research statement (detailed description of previous experiences in research and programming as well as sketch of research perspectives) and names of two references – or employer’s reference letters, also from recent times, for applicants from an industrial background. We ask for supplying complete applications with all requested documents. Please apply at the portal accessed via the link at the bootm of the announcement at https://jobs-uk-koeln.de/index.php?ac=jobad&id=1979 <https://jobs-uk-koeln.de/index.php?ac=jobad&id=1979>

Your tasks

* Research on bioinformatics methods for processing and analyzing
    comprehensive genomic and clinical datasets (viral and bacterial infections)
    Support of porting the geno2pheno server from Saarbrücken to the University
    of Cologne and advancing the respective methods and software
* Administration and continuing development of the software that is provided
    by the Laboratory for Resistance Analysis
* Development, implementation and application of corresponding software

Your Profile

* Master or PhD in bioinformatics/computational biology, biostatistics,
    computer science or a closely related field
* Extensive knowledge and experience with programming languages and
    environments (e.g. R, Python, Perl, PHP, C++, Java, Javascript, Oracle,
    Webserver), to be documented via central contributions to larger programming
    projects (programming experience within curricular courses or practicals is
    not sufficient)
* Proactive team player with excellent communication and writing skills
* Extensive knowledge and experience with methods of statistics and
    statistical learning including their mathematical foundation

Our Offer

* A research environment that offers exciting and diverse opportunities
    Perspectives for further scientific qualification
* Flexible working hours
* Opportunity for further scientific qualification towards PhD or
    habilitation, respectively
* Three-year term, possibility of subsequent permanent employment after
    successful evaluation
* your salary will be based on TV-L until EG 14, depending on requirements

Links:
https://jobs-uk-koeln.de/index.php?ac=jobad&id=1977 <https://jobs-uk-koeln.de/index.php?ac=jobad&id=1977>
https://jobs-uk-koeln.de/index.php?ac=jobad&id=1979 <https://jobs-uk-koeln.de/index.php?ac=jobad&id=1979>

Wissenschaftler und Software Ingenieur in Bioinformatik

Details: Veröffentlicht: Donnerstag, 14. Januar 2021 14:07

Das_Institut für Virologie_ <http://virologie.uk-koeln.de/>(Direktor: Univ.-Prof. Dr. Florian Klein) ist spezialisiert auf die Diagnostik und Erforschung humanpathogener Viren und nutzt dazu ein breites Spektrum an molekularbiologischen und bioinformatischen Analysen. Zu den Forschungsschwerpunkten des Instituts gehören unter anderem die Erkennung und Beurteilung von viralen Resistenzentwicklungen und die Entwicklung neuer Impf- und Therapiekonzepte. Die Forschungen werden in der _AG Resistenzforschung_ <http://virologie.uk-koeln.de/forschung/ag-kaiser>, die von Dr. Rolf Kaiser geleitet wird, vorgenommen. Unsere in Kooperation mit dem Max-Planck-Institut für Informatik entwickelten Algorithmen und implementierte Software (_www.geno2pheno.org_ <http://www.geno2pheno.org/>) werden international verwendet und erlauben bioinformatische Analysen zur Resistenzbestimmung sowohl bei HIV als auch bei Hepatitis B und C Viren. Unter Leitung von _Prof. Dr. Thomas Lengauer,_ <https://bioinf.mpi-inf.mpg.de/homepage/index.php?&account=lengauer>unter dessen Leitung der geno2pheno Server entstand, und der derzeit mit unserem Institut affiliiert ist, führen wir die betreffenden methodischen Arbeiten fort. Des Weiteren wenden wir die hier gewonnenen Erkenntnisse auch bei bakteriellen Infektionen und Krebserkrankungen an.
Sie arbeiten in einer hoch interdisziplinären und international exzellent vernetzten Umgebung, die hervorragende Ansätze zu innovativer Forschung an patientennahen medizinisch hoch relevanten Themen bietet. Kollaborationen mit Medizin, Biowissenschaften und Informatik an der Universität zu Köln sind vorhanden oder möglich. Ihre Arbeit vereint in einzigartiger Weise methodische Grundlagenforschung mit medizinischer Anwendung. Weiterbildung in Richtung auf Promotion bzw. Habilitation ist im Arbeitsplatzprofil mit einbegriffen.
Die Bewerbungsunterlagen umfassen Motivations-Anschreiben, Lebenslauf, Zeugnisse, Publikationsliste, Forschungsstatement (ausführliche Beschreibung bisheriger Forschungs- und Programmiererfahrungen sowie Skizzierung von Forschungsabsichten) und Nennung von zwei Referenzen bzw. bei BewerberInnen aus dem industriellen Umfeld Vorlage von Arbeitszeugnissen, auch aus jüngerer Zeit. Wir bitten um vollständige Einsendung aller geforderten Bewerbungsunterlagen. Bitte bewerben Sie sich über das Portal, das durch den Link am unteren Ende der Ausschreibung auf https://jobs-uk-koeln.de/index.php?ac=jobad&id=1977 <https://jobs-uk-koeln.de/index.php?ac=jobad&id=1977>angesteuert werden kann.

Ihre Aufgaben

* Forschung zu bioinformatischen Methoden für die Prozessierung und
    statistische Analyse umfangreicher genomischer und klinischer Datensätze
    (virale und bakterielle Infektionen)
* Entwicklung, Implementierung und Anwendung von Software zur selben Thematik
* Administration der von der AG Resistenzanalyse angebotenen Software und
    deren Weiterentwicklung
*» Ihr Profil*

* Diplom, Master oder Promotion in Bioinformatik, Biostatistik, Informatik
    oder einem eng verwandten Bereich
* Umfangreiche Erfahrungen mit Methoden der Statistik und des statistischen
    Lernens inklusive der unterliegenden mathematischen Grundlagen
* Umfangreiche Kenntnisse und Erfahrung in Programmiersprachen und Umgebungen
    (z.B. R, Python, Perl, PHP, C++, Java, Javascript, Oracle, Webserver)
    belegbar durch zentrale Beiträge zu größeren Programmierprojekten
    (Programmiererfahrungen aus Lehrveranstaltungen reichen nicht aus)
* Proaktiver Teamplayer mit hervorragender Kommunikations- und Schreibkompetenz

Unser Angebot

* Ein vielfältiges und chancengerechtes Arbeitsumfeld
* Flexible Arbeitszeitenmodelle
* Möglichkeit zur wissenschaftlichen Weiterqualifizierung in Richtung
Promotion bzw. Habilitation
* Befristung auf drei Jahre, Möglichkeit der anschließenden Entfristung nach
erfolgreicher Evaluierung
* Die Vergütung erfolgt nach TV-L bis EG 14, je nach Voraussetzung

Links:
https://jobs-uk-koeln.de/index.php?ac=jobad&id=1977 <https://jobs-uk-koeln.de/index.php?ac=jobad&id=1977>
https://jobs-uk-koeln.de/index.php?ac=jobad&id=1979 <https://jobs-uk-koeln.de/index.php?ac=jobad&id=1979>

Bioinformatician (f/m/d) [Cardio-CARE research group, Medizincampus Davos, Switzerland]

Details: Veröffentlicht: Freitag, 08. Januar 2021 11:51

The Cardio-CARE research group, Medizincampus Davos, Switzerland, funded by the Kühne Foundation, is searching for one highly motivated

Bioinformatician (f/m/d)

for ambitious collaborative projects in cardiovascular disease. In the largest ongoing project, 9000 subjects from the Hamburg City Health Study are undergoing whole genome sequencing at the University Hospital Zurich until summer 2021. All data analysis will be done at Cardio-CARE in Davos in close collaboration with the Department of Cardiology from the University Medical Center in Hamburg, Germany.

What Is Special About Davos?

Davos is the largest resort in the Alps for mountain holidays and sport. It is at 1560 m the highest town in the Alps and has one of Switzerland’s biggest ski resorts. In winter you can enjoy more than 300 km of slopes, and in summer explore 700 km of hiking trails. Davos is also the traditional host of the World Economic Forum.

What Would Be Your Main Responsibilities?

• You perform the complete bioinformatics analysis, starting from FASTQ files to annotated joint called VCF files • You perform data analysis, integration and visualization
• You participate in maintaining and administering the High Performance Computing (HPC) cluster
• You provide training and support in programming and bioinformatics to team members

• You participate in the publication of research findings

Why We Want You To Join Our Team?

• You have a background in Bioinformatics, Computational Biology, Computer Science or similar
• You are experienced in next-generation sequencing data analysis and have good working knowledge of standard bioinformatics tools, such as GATK or samtools
• You are familiar with GNU/Linux environments and HPCs
• You are proficient in R, including RMarkdown, Knitr and Shiny
• You are familiar with one or more programming languages, such as C/C++, Python or Java
• You have hands-on experience of reproducible workflows and version control
• You might have additional skills, such as a good understanding of molecular or cell biology, machine learning or Bayesian statistics
• You love to communicate, to collaborate, to connect different scientific disciplines and to contribute to multidisciplinary teams

Why You Want To Join Our Team?

• You want to be an important researcher who plays a critical role in expanding a research infrastructure • You want to pursue meaningful international research projects at the highest level
• You value our many possibilities for personal and professional growth
• You value quality of life and the opportunity to work in a magnificent scenery

• We are happy to provide help in terms of relocation procedures

Interested?

We look forward to receiving your application with a brief explanation why you are the ideal candidate for this position, your detailed curriculum vitae and contact details of 2-3 referees. Your application should be sent as a single pdf file containing all of your application documents to Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!. Questions regarding the positions should be directed to Prof. Dr. Andreas Ziegler, phone: +49 175 8081883. Initial application deadline is January 31, 2021 but the call will remain open until the positions are filled. Candidates will be contacted by us on a rolling basis.

Due to Swiss immigration regulations, priority will be given to applicants holding a Swiss passport, a valid Swiss working permit or EU/EFTA passport.

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

Details: Veröffentlicht: Freitag, 08. Januar 2021 11:50

We invite applications for one PhD student position in the Computational Pharmaceutical Chemistry & Molecular Bioinformatics group (Prof. Dr. Holger Gohlke) at the Heinrich-Heine-University, Duesseldorf, Germany.

Topic

Functional state modulation of membrane proteins by dynamic association and dissociation.

Background

Find more detailed information regarding this position here or under:

https://cpclab.uni-duesseldorf.de/index.php/Openings

Availability

The position is available immediately.

Requirements
Ideal candidates will have a record of excellence and a strong background in computational biochemistry/chemistry or structural bioinformatics, a high interest in working in an interdisciplinary collaboration, and profound knowledge in state-of-the-art molecular dynamics simulations (Amber) software, molecular modelling (in particular, protein-protein docking), and QM/MM calculations.

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 gohlke[at]uni-duesseldorf.de . Please provide all documents as one PDF file and specify for which position you are applying.

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