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Bioinformatics student project [Schulte lab, Charité, Berlin]

The Schulte lab at the Charité Virchow campus in Berlin is looking for a dedicated bioinformatics student to join us in spring/summer 2017 for the research project

Identifying circRNAs in Neuroblastoma

Scientific background
Circular RNAs (circRNAs) have been found to make up a relevant proportion of spliced transcripts from coding and non-coding genes [1], yet the function of the vast majority of circRNAs is still unclear.Neuroblastoma is the most common extra-cranial solid tumour in childhood. As neuroblastoma is marked by extremely few coding mutations, other defects in the regulatory program of cell proliferation and differentiation can be suspected, potentially involving epigenetics and non-coding RNAs.

Schulte lab
In the Schulte lab at Charité, we use genomics and wet-lab experiments to gain new insights into neuroblastoma. The group consists of physicians, molecular biologists and bioinformaticians working together towards an increased understanding of tumour development.

Project description
The student will develop algorithms for identifying circRNAs from RNA-Seq data and contribute to computational tools for functional annotation of circRNAs. The student will be based at the Charité Virchow campus as part of the interdisciplinary project team and mainly supervised by Dr. Joern Toedling. The project lends itself to becoming a master’s or diploma thesis, in which case it will be reviewed by Professor Schulte (Charité) and a second reviewer from the student’s home university, to be suggested by the student. In case the methods developed by the master student or any of her/his findings are going to be used in a publication, the student will be credited with a co-authorship on that publication. The project is a collaboration between our group at the Charité and Professor Rajewsky (MDC Berlin).

Requirements
A strong interest in non-coding RNAs and some knowledge of next-generation sequencing data processing are required. The student should arrange for staying at least 3 to 6 months full-time in our lab in Berlin.

How to apply?
Please send applications, as well as informal requests, to This email address is being protected from spambots. You need JavaScript enabled to view it..

References
[1]Szabo L, Salzmann J. Detecting circular RNAs: bioinformatic and experimental challenges. Nature Reviews Genetics, November 2016.
[2]Schulte lab: https://paedonko.charite.de/en/research/schulte_lab

 

Postdoc- oder Doktorandenstelle in der Genominformatik an der Universität Duisburg-Essen, Universitätsklinikum Essen (E13, 3 Jahre)

Am Lehrstuhl für Genominformatik des Instituts für Humangenetik ist ab 01.05.2017 die Stelle einer/eines wissenschaftlichen Mitarbeiterin / Mitarbeiters (Entgeltgruppe 13 TV-L, befristet) in Vollzeit zu besetzen. Die Eingruppierung richtet sich nach den persönlichen und tarifrechtlichen Voraussetzungen. Die Beschäftigung ist zunächst befristet vorgesehen. Aufgrund des Wissenschaftszeitvertragsgesetzes bzw. des Teilzeit- und Befristungsgesetzes wird die Vertragsdauer abhängig von den persönlichen Voraussetzungen festgelegt. Es besteht Gelegenheit zur persönlichen Weiterqualifikation z.B. zu einer Promotion, Habilitation oder im Bereich der Forschung zu Algorithmen
für die bioinformatische Datenanalyse auf DNA-Sequenzdaten.

Ihre Aufgaben:
- Forschung zu probabilistischen Algorithmen für die Analyse sehr grosser DNA-Datenmengen
- Auswertung von multi-omics Daten (insbes. Transkriptom-, Exom- und Methylomdaten)
- Wissenschaftliches Publizieren

Ihr Profil:
- Sehr guter Hochschulabschluss (Diplom oder Master) oder Dr. rer. nat. in Bioinformatik oder (theoretischer) Informatik
- Sehr gute Programmierkenntnisse in Python, belegbar durch abgeschlossene Projekte
- Erfahrungen mit dem Python Scientific Stack (z.B. numpy, scipy) oder in C sind hilfreich.
- Sicheres Arbeiten mit der Linux Shell (bash)
- Gute Englisch-Kenntnisse in Bezug auf wissenschaftliche Vorträge und Texte

Die Mitarbeit bei Nebentätigkeit richtet sich nach der Hochschulnebentätigkeitsverordnung des Landes Nordrhein-Westfalen.
Schwerbehinderte Bewerberinnen / Bewerber und Gleichgestellte i.S. des § 2 Abs. 3 SGB IX werden bei gleicher Eignung bevorzugt berücksichtigt.
Die Universität Duisburg-Essen strebt eine Erhöhung des Anteils von Frauen beim wissenschaftlichen Personal an. Bewerbungen von Frauen sind ausdrücklich erwünscht. Frauen werden bei gleicher Eignung, Befähigung und fachlicher Leistung bevorzugt berücksichtigt, sofern nicht in der Person des Mitbewerbers liegende Gründe überwiegen. Die ausgeschriebene Stelle ist grundsätzlich auch für Teilzeitbeschäftigte geeignet.

Bitte senden Sie Ihre aussagekräftigen Bewerbungsunterlagen unter Hinweis auf die Ausschreibungsnummer 387 innerhalb von 2 Wochen nach Erscheinen dieser Anzeige per E-mail an This email address is being protected from spambots. You need JavaScript enabled to view it. (auch bei Rückfragen).

Links: http://genomeinformatics.uni-due.de

Postdoctoral position - Bioinformatics for Next Generation Sequence Analysis [Braunschweig]

The Helmholtz Centre for Infection Research (HZI) has an opening for a
Postdoctoral position - Bioinformatics for Next Generation Sequence Analysis
The Computational Biology for Infection Research (BIFO) Department of the HZI is offering a bioinformatics position at the advanced postdoctoral level.
The successful candidate will have the opportunity to collaborate with Next Generation Sequence (NGS) experts and infection biologists.

Area of research
The BIFO lab is based at the Braunschweig Centre for Systems Biology (BRICS) on the campus of Technical University of Braunschweig.
Key aspect of the applicant’s work will be the evaluation and analysis of next-generation sequencing data in various research projects conducted with partners from HZI,
the Medical School Hannover (MHH) and within the German Centre for Infection Research (DZIF), ranging from RNA sequencing, epigenomics and metagenomics to
de novo sequencing and comparative resequencing of bacterial, viral and human genomes. A server based computational infrastructure is established.
Applicants are expected to continuously improve and newly establish pipelines for processing primary sequence reads,
generated for example by the lllumina Genome Analyzer or the Pacific Biosciences technology, to obtain user-friendly data output for the researchers.

We offer a challenging work environment in a multidisciplinary team, composed of bioinformaticians, molecular biologists, computer scientists, biochemists, biologists and medical scientists.

Prerequisites

· PhD in bioinformatics, with proven publication record
· Familiarity with NGS analysis; experience with a scripting language like Perl/Python or Java/C
· Proficiency in major programming languages and in handling large datasets
· Ability to work independently and as part of a team, lead bioinformatics projects and supervise
  junior scientists
· High self-motivation and enthusiasm
· Excellent English communication skills (written and spoken)

Equal opportunities are part of our personnel policy – qualified women are especially invited to apply. Qualified applicants with a disability will be given preference.

Location                                Braunschweig (Germany)

Starting date                         As soon as possible.
Initial contract for 2 years.

Probation period                  6 months

Salary                                    TVöD E14

Published on                         13.02.2017

Closing date                          26.03.2017


Please send your application with a cover letter outlining briefly your research experience, motivation for applying for the position,
your scientific interests and a complete curriculum vitae, including a list of publications and academic references, referring to code 16/2017 to

Helmholtz Centre for Infection Research
Department of Human Resources
Inhoffenstrasse 7
38124 Braunschweig

or by email: This email address is being protected from spambots. You need JavaScript enabled to view it.

All documents and information should be provided in English.

For questions regarding the bioinformatics projects, please contact Prof. Alice McHardy  (This email address is being protected from spambots. You need JavaScript enabled to view it.).
Entitle your email with the subject line ‘DZIF postdoc application’.

The Helmholtz Centre for Infection Research (HZI) is a member of the Helmholtz Association of German Research Centres,
the largest scientific organization in Germany. The HZI offers a unique research environment in the field of infection biology,
excellent state-of-the-art equipment, a stimulating scientific community and intensive training of scientific and personal skills.


Links:

https://www.helmholtz-hzi.de/de/forschung/forschungsschwerpunkte/bakterielle_und_virale_krankheitserreger/bioinformatik_fuer_infektionsforschung/unsere_forschung/

 

Postdoctoral position - Bioinformatics for Next Generation Sequence Analysis

The Helmholtz Centre for Infection Research (HZI) has an opening for a
Postdoctoral position - Bioinformatics for Next Generation Sequence Analysis
The Computational Biology for Infection Research (BIFO) Department of the HZI is offering a bioinformatics position at the advanced postdoctoral level.
The successful candidate will have the opportunity to collaborate with Next Generation Sequence (NGS) experts and infection biologists.

Area of research
The BIFO lab is based at the Braunschweig Centre for Systems Biology (BRICS) on the campus of Technical University of Braunschweig.
Key aspect of the applicant’s work will be the evaluation and analysis of next-generation sequencing data in various research projects conducted with partners from HZI,
the Medical School Hannover (MHH) and within the German Centre for Infection Research (DZIF), ranging from RNA sequencing, epigenomics and metagenomics to
de novo sequencing and comparative resequencing of bacterial, viral and human genomes. A server based computational infrastructure is established.
Applicants are expected to continuously improve and newly establish pipelines for processing primary sequence reads,
generated for example by the lllumina Genome Analyzer or the Pacific Biosciences technology, to obtain user-friendly data output for the researchers.

We offer a challenging work environment in a multidisciplinary team, composed of bioinformaticians, molecular biologists, computer scientists, biochemists, biologists and medical scientists.

Prerequisites
· PhD in bioinformatics, with proven publication record
· Familiarity with NGS analysis; experience with a scripting language like Perl/Python or Java/C
· Proficiency in major programming languages and in handling large datasets
· Ability to work independently and as part of a team, lead bioinformatics projects and supervise
  junior scientists
· High self-motivation and enthusiasm
· Excellent English communication skills (written and spoken)

Equal opportunities are part of our personnel policy – qualified women are especially invited to apply. Qualified applicants with a disability will be given preference.

Location                                Braunschweig (Germany)

Starting date                         As soon as possible.
Initial contract for 2 years.

Probation period                  6 months

Salary                                    TVöD E14

Published on                         13.02.2017

Closing date                          26.03.2017


Please send your application with a cover letter outlining briefly your research experience, motivation for applying for the position,
your scientific interests and a complete curriculum vitae, including a list of publications and academic references, referring to code 16/2017 to

Helmholtz Centre for Infection Research
Department of Human Resources
Inhoffenstrasse 7
38124 Braunschweig

or by email: This email address is being protected from spambots. You need JavaScript enabled to view it.

All documents and information should be provided in English.

For questions regarding the bioinformatics projects, please contact Prof. Alice McHardy  (This email address is being protected from spambots. You need JavaScript enabled to view it.).
Entitle your email with the subject line ‘DZIF postdoc application’.

The Helmholtz Centre for Infection Research (HZI) is a member of the Helmholtz Association of German Research Centres,
the largest scientific organization in Germany. The HZI offers a unique research environment in the field of infection biology,
excellent state-of-the-art equipment, a stimulating scientific community and intensive training of scientific and personal skills.

SOFTWAREENTWICKLER (M/W) FÜR KÜNSTLICHE INTELLIGENZ

Wir, FUSE-AI, sind der Spezialist für Künstliche Intelligenz und intelligente Bilderkennung im Gesundheitswesen. Unser Ziel ist es, die Kapazitäten, Aufgaben und Kompetenzen eines Arztes mittels Artificial Intelligence zu ergänzen - beispielsweise in den Bereichen der Fenstertechnik nuklearmedizinischer Untersuchungsmethoden (Hounsfield-Skala), Medical Apps und Virtual Reality.
Wir bieten Ihnen spannende Zukunftsprojekte im Umfeld Medizin, Medizintechnik und IT. Ihr Thema ist Künstliche Intelligenz und Sie sind ein Teil firmenübergreifender, interdisziplinärer Projektteams bestehend aus verschiedenen Medizintechnik-Herstellern (u.a. Olympus Medical), Kliniken (u.a. Asklepios) und Biobanken.

Unser Wunsch:
- Erfolgreich abgeschlossenes Studium z.B. Medizininformatik, Informatik, Machine Learning, Cognitive Science oder vergleichbare Qualifikation.
- Erste Erfahrung mit Methoden und Tools aus dem Bereich Künstliche Intelligenz und Maschinelles Lernen.
- Sie sehen ihre Zukunft in der Softwareentwicklung und möchten das Thema Artificial Intelligence in Healthcare vorantreiben.
- Sie interessieren sich für Technologietrends und arbeiten gerne im interdisziplinären Team.

Bei uns finden Sie flache Hierarchien, verantwortungsvolle Aufgaben und eine gute Arbeitsatmosphäre in einem Büro direkt am Hamburger Rathaus.
Gerne unterstützen wir Sie bei der Wohnungssuche.
Frau Margit Frahm freut sich auf Ihre Fragen und Ihre Bewerbung.
This email address is being protected from spambots. You need JavaScript enabled to view it.
040 450 318-13

Link: http://fuse-ai.de/en/home/

 

Ph.D. Students (m/f) in the field of computational biophysics/molecular physiology

The Leibniz Institute for Molecular Pharmacology (FMP) is a research institute of the Forschungsverbund Berlin e.V. (FVB). The FVB represents eight institutes of natural sciences, life sciences and environmental sciences in Berlin with joint funding by the federal and state governments. The institutes are members of the Leibniz Association. FMP pursues a broad scientific scope with the sections Molecular Physiology, Structural Biology and Chemical Biology. It is located on the research campus Berlin-Buch.

The research groups of Dr. Andrew Plested and Dr. Han Sun invite applications for two positions for Ph.D. Students (m/f) in the field of computational biophysics/molecular physiology with part-time employment (65%). The period of employment is initially two years. The position will be available from April 2017.

Job Description:

We are two young and interdisciplinary research teams. Dr. Plested’s lab is focused on studying ion channel receptors by using a variety of different biophysical methods. Dr. Sun’s lab is interested in understanding protein dynamics and their relationship to protein function by employing computational simulations. The objective of our joint research project is to identify molecular mechanisms of ion permeation and activation in AMPA receptors, which are relevant for the integrity and flexibility of fast synaptic transmission in the brain. This project is part of the Deutsche Forschungsgemeinschaft (DFG, German Research Council) Research Group 2518. The students will have opportunities to study a variety of different biophysical techniques and work with leading scientists in the field.

Requirements:

The candidates should have a good master/diploma degree in Biophysics, Chemistry, Bioinformatics, Biochemistry or a related field and ideally have a basic knowledge in computational simulations. Experiences in coding and raw data analysis are preferred. A strong interest in interdisciplinary projects and cooperation with scientists from different backgrounds is required.

Further Information:

For more information about the position please contact Dr. Andrew Plested; Email: This email address is being protected from spambots. You need JavaScript enabled to view it.; Web: http://www.leibnizfmp.de/research/molecular-physiology-and-cell-biology/research-groups/plested

Dr. Han Sun; Email: This email address is being protected from spambots. You need JavaScript enabled to view it.; Web: http://www.leibnizfmp.de/research/structuralbiology/researchgroups/han-sun  

Salary will be paid according to TVöD regulations in accordance to the applicant's qualifications and experience. FMP hires on the basis of merit and is committed to employment equity. At equal aptitude, women and handicapped individuals will be given priority. Please apply by sending a letter of motivation, your CV and contact details of at least 2 referees to Mrs. M. Spors (This email address is being protected from spambots. You need JavaScript enabled to view it.).

 

 

PostDoc in Bioinformatics/Biostatistics [Göttingen]

The Department of Medical Statistics is offering a position for a PostDoc in Bioinformatics/Biostatistics with focus on data management, integration and analysis
(initially for two years, with possibility of extension, fulltime position | salary according to TV-L)

The University Medical Center Göttingen is a tertiary care center and offers great development potential. Its 7000 employees work in over 60 departments and facilities to provide top-quality patient care, excellent research and modern teaching. Göttingen, “City of Science”, lies near the center of Germany and its University is embedded in the city’s attractive network of scientific research facilities. Within the Center of Statistics, Informatics and Epidemiology several institutes are working together in the research and application of statistical and informatics methodology to analyze and interpret biomedical data.

Job Description:

The position primarily involves the management and integration of complex biomedical data for research purposes within various projects and consortia. This will include the setup and maintenance of knowledge and data management servers (e.g. openBIS, Wikis, tranSmart) as well as the implementation of ETL data pipelines. Further tasks will include statistical analyses and the integration of high-troughput data and clinical records as well as external data sources.

Requirements:

An appropriate university degree in computer science or bioinformatics Experience in Unix server administration Knowledge in data management
Ideally, experience with openBIS and in setting up Wiki-systems as exchange and communication platforms
Experience with a general-purpose programming and scripting language (such asR, Python, Shell, Java, optional C/C++/C#)
Ideally, experience with data workflow systems (e.g. KNIME) and knowledge in statistical analyses of biomedical data

Please send your application until 09/01/2017 to

Universitätsmedizin Göttingen
Prof. Dr. Tim Beißbarth
Department of Medical Statistics
37099 Göttingen
Tel.: 0551/39-4990
Fax: 0551/39-4995
E-Mail: This email address is being protected from spambots. You need JavaScript enabled to view it.

Contact person:
Ms Dorit Meyer (secretariat)


Women are especially encouraged to apply. Applicants with disabilities and equal qualifications will be given preferential treatment. Please send your application only via e-mail as a PDFfile.

Links: http://www.ams.med.uni-goettingen.de/stellen-de.shtml

Master’s Thesis: A human genome-wide CRISPR/Cas9 target database

The Gene Editing Group led by Manuel Kaulich is located at the Institute of Biochemistry 2 of the Goethe-University Frankfurt. We work on the cutting edge of gene editing technologies and employ a variety of  CRISPR/Cas9-associated applications to efficiently perturbate genes in mammalian cells. To intensify our efforts, we seek an ambitious Master’s student in informatics/bioinformatics. We plan to implement a public database that integrates the currently available knowledge on CRISPR/Cas9 target sites in the human genome. The first step will be to evaluate the applicability of available database models, e.g., relational vs. big data systems. Once a suitable model is found, the implementation of the database and the integration of data are the next steps. Depending on the progress of the work the optional last step will be the implementation user-friendly web-based graphical interface. The applicant will join a highly motivated team and benefit from our interdisciplinary environment. Additionally, the successful candidate will have the opportunity to present his/her results in peer-reviewed publications.

Applications including a cover letter, a short CV, and the names and contact details should be adressed as a single PDF file directly to Dr. Manuel Kaulich: kaulich(at)em.uni-frankfurt.de

Links:

https://www.jobvector.de/jobs-stellenangebote/biologie-life-sciences/datenbanken-datenverarbeitung/masters-thesis-a-human-genome-wide-crispr-cas9-target-database-82198.html

https://www.biochem2.com/index.php/19-ibcii/geg/104-frontpage-geg

Postdoc in der Genominformatik gesucht

Für die Technische Fakultät, Arbeitsgruppe Genominformatik, suchen wir zum 01. Januar 2017 in Vollzeit eine/n Wissenschaftliche Mitarbeiterin/ Wissenschaftlichen Mitarbeiter (E 13 TV-L) (befristet)

Ihre Aufgaben:

Die Arbeitsgruppe Genominformatik entwickelt und untersucht effiziente Algorithmen mit Anwendungen in Bioinformatik und Genomforschung. Aktuelle Arbeitsbereiche sind die Analyse von Hochdurchsatzsequenzierdaten und die komparative Genomik.
* Forschungstätigkeiten im Bereich der komparativen Genomik, insbesondere Weiterentwicklung und Durchführung des existierenden Forschungsprogramms für die genfamilienfreie Analyse im Hinblick auf die Detektion und Organisation von syntenischen Bereichen in mehreren großen eukaryotischen Genomen. (75 %)
* Mitarbeit im Rahmen der Lehre und Betreuung von Bachelor- und Masterstudenten (25 %)

Ihr Profil:

Das erwarten wir:
* abgeschlossenes wissenschaftliches Hochschulstudium der Informatik, Bioinformatik oder einer angrenzenden Disziplin
* Promotion in Bioinformatik oder einer verwandten Fachrichtung
Das wünschen wir uns:
* Publikationstätigkeit und Auslandserfahrung
* Erfahrungen bei der Entwicklung von mathematischen Modellen und Algorithmen zur komparativen Genomik, insbesondere zum genfamilienfreien Genomvergleich, zu genomischen Distanz- und Ähnlichkeitsmaßen und zur Detektion syntenischer Bereiche
* Erfahrung bei der Betreuung von studentischen Projekt- oder Abschlussarbeiten

Unser Angebot:

Die Vergütung erfolgt nach der Entgeltgruppe 13 für den öffentlichen Dienst der Länder (TV-L). Die Stelle ist gem. § 2 Abs. 1 Satz 2 WissZeit VG für die Dauer von drei Jahren befristet (entsprechend den Vorgaben des WissZeitVG und des Vertrages über gute Beschäftigungsbedingungen kann sich im Einzelfall eine abweichende Vertragslaufzeit ergeben). Die Beschäftigung ist der wissenschaftlichen Qualifizierung förderlich. Auf Wunsch ist grundsätzlich auch eine Stellenbesetzung in Teilzeit möglich, soweit nicht im Einzelfall zwingende dienstliche Gründe entgegenstehen.

Die Universität Bielefeld legt Wert auf die Entwicklung ihrer Mitarbeiterinnen und Mitarbeiter. Sie bietet attraktive interne und externe Fortbildungen und Weiterbildungsmaßnahmen. Zudem können Sie eine Vielzahl von Gesundheits-, Beratungs- und Präventionsangeboten nutzen. Die Vereinbarkeit von Beruf und Familie hat einen hohen Stellenwert.

Interessiert? Wir freuen uns über Ihre Bewerbung per Post oder E-Mail in einem einzigen pdf-Dokument an This email address is being protected from spambots. You need JavaScript enabled to view it. bis zum 02. Dezember 2016. Bitte geben Sie in jedem Fall die Kennziffer: wiss16011 an. Bitte verzichten Sie auf Bewerbungsmappen und reichen Sie ausschließlich Fotokopien ein, da die Bewerbungsunterlagen nach Abschluss des Auswahlverfahrens vernichtet werden. Weitere Informationen zur Universität Bielefeld finden Sie auf unsere Homepage unter www.uni-bielefeld.de

Bewerbungsanschrift: Universität Bielefeld, Technische Fakultät, Prof. Dr. Jens Stoye, Postfach 10 01 31, 33501 Bielefeld

Ansprechpartner: Prof. Dr. Jens Stoye, 0521 106-3852, This email address is being protected from spambots. You need JavaScript enabled to view it.

Die Universität Bielefeld ist für ihre Erfolge in der Gleichstellung mehrfach ausgezeichnet und als familiengerechte Hochschule zertifiziert. Sie freut sich über Bewerbungen von Frauen. Dies gilt in besonderem Maße im wissenschaftlichen Bereich sowie in Technik, IT und Handwerk. Bewerbungen geeigneter schwerbehinderter und ihnen gleichgestellten behinderten Menschen sind ausdrücklich erwünscht.

Links:
https://gi.cebitec.uni-bielefeld.de
http://www.uni-bielefeld.de/Universitaet/Aktuelles/Stellenausschreibungen/Anzeigen/Wiss/wiss16011.pdf

 

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