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Stellenangebote

Ph.D./Posdoc position in computational detection of RNA-DNA triple helices

The Institute for Computational Genomics, RWTH Aachen University
performs cutting edge research on computational and genomic methods
for understanding regulatory and epigenetic processes driving cell
differentiation and diseases (Gusmao, Nature Methods, 2016, Li, Genome
Biology, 2019). This project aims studying RNA-DNA interactions as
mechanisms of transcriptional control. We have recently shown how
long-noncoding RNAs (HOTAIR, GATA6-AS, NEAT1) interacts with DNA via
triple helices to control the expression of genes during cell
differentiation (Kalwa et al., NAR, 2016; Kuo, NAR, 2019; Frank, Cell
Stem cell, 2019).

We are looking for a phd/postdoc candidate to work on sequence
analysis algorithms and statistical models for detection of RNA-DNA
triple helices. This includes the analysis of novel in vitro
transcription experiments and target sequencing protocols, which
capture triple helix forming RNA and DNA molecules. This project will
be performed in collaboration with cell biologists of RWTH Aachen,
University of Cologne and University of Oslo.

Applicants should hold a M.Sc. or Ph.D. in Bioinformatics or Computer
Science. Experience in the analysis of biological sequences and
regulatory genomics is required. The candidate should have solid
programming skills (C, Python and/or R) and acquaintance with
Unix/Linux. Experience with high performance computing is a plus. The
working language of the group is English. The position is a will be
initially for 3 years with possibility of extension. The salary
corresponds to level 13 TV-L.

Interested candidates should send a brief statement of research
interests, CV and the names of three references to Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!.

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

Applications are invited for two PhD student positions in the Computational Pharmaceutical Chemistry & Molecular Bioinformatics group (Prof. Dr. Holger Gohlke, http://cpclab.uni-duesseldorf.de/) at the Heinrich-Heine-University, Düsseldorf, Germany.

PhD student position 1: Overcoming lantibiotics resistance in bacterial pathogens: Nisin as a model system
Topic: Lantibiotics are antimicrobial peptides that are produced by Gram-positive bacteria and bactericidal against other bacteria in the low nanomolar range. Because of their high selectivity and stability, lantibiotics are considered valuable future anti-infective agents. The best-studied lantibiotic is Nisin. Various human pathogenic strains of bacteria have been found to have natural immunity to nisin, attributed to, e.g., the nisin resistance protein (NSR) or ABC transporter NsrFP. By structure-based design, hit molecules have been identified that inhibit NSR, and a structural model of NsrFP has been generated. In this project within the DFG-funded GRK 2158 (http://www.grk2158.hhu.de/en.html), the inhibitory, physicochemical, and pharmacokinetic properties of the hits will be improved by structure-based and computer-aided drug design, analog searches, synthesis, and in vitro and in vivo testing. Furthermore, the mechanism of NsrFP will be scrutinized by molecular simulations with the aim to identify novel compounds that inhibit the transporter. Our group has a strong background in computational pharmaceutical chemistry and molecular informatics and will collaborate with the Smits, Pfeffer, Kalschauer, Stork, Pietruszka and Müller groups of the GRK 2158.
Availability: The position is available as of 01.10.2019.

 

PhD student position 2: Functional analyses in silico and in vitro of consequences of cholestasis-associated mutations
Topic: Mutations in several genes (ATP8B1, ABCB11, ABCB4, TJP2, NR1H4, MYO5B) contribute to the development of severe forms of intrahepatic cholestasis. Since most mutations are only found in one or two families, their clinical consequences are often unknown. In particular, biological consequences of missense mutations (38-66% of mutations in ATP8B1, ABCB11, and ABCB4 in patients with severe cholestasis) are less clear. In this project performed within the BMBF-funded Hereditary Intrahepatic Cholestasis Translational Network (HIChol), novel missense mutations will be structure-based analyzed for their potential impact on interactions with surrounding residues, substrate and cofactor binding, protein stability, structural dynamics. While molecular models have been established for ABCB11 and ABCB4, and experimental structural information is (in part) available for TJP2, FXR, and MYO5B, a structural model of FIC1 will be generated. In collaboration with the Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital, Heinrich Heine University Düsseldorf, results from molecular modelling and simulations will be tested for selected mutations by transfection of mutated cDNA into polarized hepatoma cell lines and HEK293 cells. Trafficking, subcellular localization, and function will then be studied. The cell culture approach will be used to optimize the predictions from molecular modelling and simulations. Results from this project will allow for classification of detected missense mutations into subgroups according to their cell biological consequences (e.g., maturation, trafficking, targeting, or function), and selected mutations will be further analyzed within HIChol.
Availability: The position is available immediately.

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 modeling.

How to apply: 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*uni-duesseldorf.de. Please provide all documents as one PDF file and specify for
which position you are applying.

Detailed information about living and studying in Düsseldorf is provided here:

 

http://www.uni-duesseldorf.de/home/leben-in-duesseldorf.html

Bioinformatics PhD [FibroOmics]

This PhD position will provide sophisticated bioinformatics analysis for a new project initiative, FibroOmics, which aims to accelerate improvements in the understanding and treatment of lung fibrosis. This project involves cutting edge molecular and analytical techniques, including single cell RNA sequencing (scRNA-seq), signal deconvolution, therapeutic target discovery, and interactive software development. FibroOmics has strong translational relevance and unique access to patient samples for Omics studies.

The successful candidate will apply and develop sophisticated bioinformatics algorithms, drawing on methodologies of the domains of statistics, computer science and machine learning. Previously published methodologies will be utilized as a starting point, but it should be emphasized that there will be a need for novel algorithm development.

The position will be located at Hannover Medical School (MHH) in the context of its membership in the German Center for Lung Research (DZL, Deutsche Zentrum für Lungenforschung), an association of the leading university and non-university institutions dedicated to translational lung research in Germany. At the DZL site in Hannover (BREATH) biomedical researchers utilize the full spectrum of high throughput molecular techniques (“Omics”) metagenomics, whole genome and exome sequencing, RNA-seq, among others to lung diseases such as cystic fibrosis, chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, lung transplantation as well as rare genetic disorders.  This combination of proximity to the clinic with cutting edge Omics applications makes the BREATH site a unique workplace for bioinformaticians to help impacting patient outcomes.

Basic Requirements

·        Master’s degree in Bioinformatics, Molecular Biology, Computer Sciences, Statistics or Mathematics or other related field.

·        Analytical ability founded either in statistics, mathematics, or computer science principles

·        Proficiency in at least one programming / scripting language such as python, c/c++, Java, R, perl etc.

Desired Qualifications

·        Previous experience in Bioinformatics (desired, but optional)

·        Experience working with Next Generation Sequencing technologies (desired, but optional)

·        Expertise in at least one of the relevant interdisciplinary pillars: genetics, molecular biology, machine learning, statistics, computer science, mathematics (at least one is required)

Important Characteristics

·        Strong drive and interest in interdisciplinary approaches

·        A thirst for knowledge

·        Enjoyment of working in a team

·        A desire to hold one’s self to the highest standards of professional and academic excellence

This position offers:

·        A doctoral degree in the natural sciences – Dr. rer. nat. upon successful completion and ample opportunities for writing publications.

·        Salary is in accordance with the Tarifvertrag für den Öffentlichen Dienst der Länder (TV-L)

·        An interdisciplinary and collaborative work environment

·        Comprehensive health-promotion programs

·        Reliable family services, including emergency child care

The position start date is planned for October 1st, 2019.

The MHH is committed to supporting the professional careers of women and applications form women are particularly desired. People with disabilities will be preferred when their qualifications match or exceed those of other applicants.

Please direct inquiries to Dr. David DeLuca, Tel. +49 511-532 7873 and send your applications by email to Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!

 

 

Postdoctoral Researcher (f/m/d) on omics data analyses of cellular senescence, for 3 years, with the possibility of a 2-year extension

The Institute for Biostatistics and Informatics in Medicine and Ageing Research at the Rostock University Medical Center seeks, starting 1. Sept 2019 or as soon as possible thereafter, a Full-time Postdoctoral Researcher (f/m/d) on omics data analyses of cellular senescence, for 3 years, with the possibility of a 2-year extension, subject to budgetary approval.

** Interviews/inquiries possible at ISMB'19, e.g. at the Career Fair Thu 12:40-2pm,
and at the "Bioinformaticians in Aging & Senescence Research" Birds-of-a-feather,
Wed 12:45-1:45pm, see https://www.iscb.org/ismbeccb2019-program/ismbeccb2019-bof **

+ Your tasks:
* Analysis of the data of an in-depth biomarker study investigating the senescence-related molecular processes behind cancer and stroke, in human and mouse, to establish a biomarker kit
* Sequence data analysis, machine learning and data integration
* Analysis of transcriptomics, proteomics, clinical chemistry, and questionaire data
* Writing of scientific papers and applications, and contributions to joint papers and applications
* Qualification towards Habilitation (post-doctoral degree certifying research and teaching expertise)

+ Advantages for you:
* A stimulating environment where your contribution has a real impact
* An exciting project, aiming at biomarkers for senotherapy
* Collaboration with experimental and clinical groups, marked by aiming at first/last authorships that count for your Habilitation

+ What you need to bring to the table:
* Doctorate related to bioinformatics, or a research field in the medical/life/natural/mathematical sciences
* Programming/scripting skills, preferably including expertise in R
* Strong communication skills (oral presentations and in writing)
* (Nice to have): Biostatistics expertise (Cox hazard modeling; descriptive statistics)

+ If this describes you and your intentions then please send your application in a single PDF document, consisting of:
* CV
* Brief statement of research interests and qualifications
* Contact information for 2-4 scientists who may write a letter of recommendation

For further information:
Prof. Dr. Fuellen, Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!, +49 381-494-7360,
Director of the Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock.

The University of Rostock is an equal opportunity employer. To increase the number of women in research and teaching, female applicants are recommended to apply. Applicants with disabilities will be favoured if they are equally qualified. 

Image processing specialist (f/m/d) [Leibniz Institute for Experimental Virology (HPI)]

The Heinrich Pette Institute, Leibniz Institute for Experimental Virology (HPI), in the context of the Leibniz ScienceCampus “Integrative analysis of pathogen-induced compartments” (InterACt) seeks to recruit an 

Image processing specialist (f/m/d).

HPI is committed to research on the biology of different human viruses as well as the pathogenesis of viral diseases and offers the opportunity to perform cutting-edge research in a world-class research environment with excellent facilities. The Leibniz ScienceCampus InterACt is newly established and will link and strengthen the unique competence in infection research of the Leibniz Center Infection (LCI) with complementary expertise in structural biology, biophysics, chemistry and informatics at the Universität Hamburg, including excellent imaging infrastructures at HPI and the Centre for Structural Systems Biology (CSSB).

The Microscopy and Image Analysis technology platform at HPI offers both, a variety of electron microscopic techniques, such as transmission and serial block phase scanning electron microscopy, as well as innovative light and fluorescence microscopy plus dedicated expertise and workflows for their correlative application to analyze virus-infected cells and tissues. 

We are looking for a bioinformatician, computer scientist, experimental virologist, cell biologist or scientist with similar background having expertise and interest in analyzing and quantifying complex multiscale imaging data from virus-infected cells. The candidate should develop analysis tools to integratively analyze the dynamics of pathogen-induced compartments from data across scales. Additionally, the image processing specialist should train users and will serve as first line user support to explore the full information and full potential of their imaging data sets. The successful candidate should actively participate and be an integral part of the newly established Leibniz ScienceCampus InterACt and will benefit from its framework of collaborations.

Applicants should hold a doctoral degree (or equivalent) in the field of bioinformatics, computer sciences, molecular biology, molecular life sciences, biophysics, cell biology or similar, ideally with a research expertise in live-cell imaging data analysis, correlative microscopy or integrated imaging. A benefit would be knowledge about optimized single particle tracking algorithms and modern computational methods like machine learning. 

The position is available from August 2019 and is to be filled as soon as possible. The funding is through the Leibniz ScienceCampus InterACt for 4 years with the possibility of a 4-year extension. Payment and social benefits will be in accordance with the regulations of the German TV-AVH (salary agreement for public service employees).

If you have further questions regarding InterACt or the position, please do not hesitate to contact Kay Grünewald (Email: Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!) or Frederike Ahr (Email: Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!)

We aim to increase the percentage of women in research, and therefore encourage female scientists to apply. Equally qualified candidates with disabilities will be considered preferentially. 

Please submit your application until August 1, 2019. Late applications may be considered until the position is filled. 

Heinrich Pette Institute, Leibniz Institute for Experimental Virology

Personnel Department

Martinistraße 52, 20251 Hamburg

e-mail: Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein! 

Wissenschaftler Datenvisualisierung (m/w/div) am Museum für Naturkunde Berlin (MfN)

Bezeichnung: Wissenschaftler Datenvisualisierung (m/w/div)

Arbeitszeit: Vollzeit

Befristung: Drittmittelbefristung, zum nächstmöglichen Zeitpunkt, befristet zum 31.03.2021

Entgeltgruppe: E13 TV-L

 

Das Museum für Naturkunde Berlin (MfN) ist mit seinen über 30 Millionen Sammlungsobjekten eines der größten Naturkundemuseen weltweit. Zusammengetragen als Beleg für die Diversität der Natur, sind seine Sammlungen zugleich Zeugnisse der Wissenschafts- und der Kulturgeschichte. Das Museum für Naturkunde Berlin ist als Forschungseinrichtung und Stiftung des Öffentlichen Rechts seit 1. Januar 2009 Mitglied der Leibniz-Gemeinschaft.

In dem vom Umweltbundesamt (UBA) geförderten und vom Deutschen Meeresmuseum Stralsund koordinierten Kooperationsprojekt „Hörfähigkeiten von Pinguinen“ werden experimentelle Untersuchungen zum Hören der Tiere (Erstellung von Audiogrammen) sowohl unter Wasser als auch an Land durchgeführt. Hintergrund des Projektes ist die zunehmende Lärmbelastung in den Gewässern der Antarktis und deren potentieller Einfluss auf Tiere der Antarktis. In den am Museum für Naturkunde angesiedelten Arbeitspaketen geht es um den Aufbau einer umfassenden Forschungsdatenbank für bioakustische Untersuchungen in der Antarktis (Audiogramme, Daten zur Hörphysiologie, Geräusche unter und über Wasser, Lautäußerungen, Lärmquellen) sowie um Umweltbildung und mediale Begleitung des Projektes.

 

Aufgabengebiet:

  •     Konzeption und Entwicklung von Werkzeugen (Algorithmen) für die Kommunikation und Darstellung komplexer wissenschaftlicher Zusammenhänge im Bereich Bioakustik mit Schwerpunkt auf dem Thema Lärm
  •     Aufbau einer digitalen Plattform für Wissenskommunikation im Bereich Bioakustik (Themenfokus: Unterwasserlärm)
  •     Konzeption, Entwicklung und Implementierung einer Datenbank für Hörphysiologie mit entsprechenden Analyse-, Recherche- und Publikationsfunktionen

 

Anforderungen:

  •     abgeschlossenes wissenschaftliches Hochschulstudium eines ingenieur- bzw. naturwissenschaftlichen Studienganges, Biologie, Ökologie, (Bio-)Informatik, oder eines Studiengangs welcher Aspekte dieser Disziplinen beinhaltet, oder mindestens 3-jährige Berufserfahrung in zuvor genannten Bereichen und Mitwirkung in entsprechenden Referenzprojekten
  •     Sehr gute Kenntnisse und praktische Erfahrungen in der Konzeption und Gestaltung von webbasierten Applikationen und Informationssystemen
  •     Sehr gute Kenntnisse in der Visualisierung von Daten und Erstellung von Visualisierungskonzepten
  •     Kenntnisse in mindestens einer höheren Programmiersprache (z.B. C#, C++, Java)
  •     Gute Kenntnisse in mind. einem Statistik-Programm (R, SPSS, Mathlab) bzw. zugehöriger Programmiersprache für statistische Berechnungen
  •     Gute Kenntnisse und praktische Erfahrungen in der strategischen Konzeption von Datenflüssen, -standards und Fachdatenbanken
  •     Kenntnisse und praktische Erfahrungen im Bereich der Analyse und Qualitätssicherung bioakustischer Daten
  •     Nachweis aktiver wissenschaftlicher Publikationstätigkeit
  •     selbstständiges und strukturiertes Arbeiten
  •     sehr gute Kommunikationsfähigkeiten und Präsentationsfähigkeiten
  •     sehr gute Deutsch- und Englischkenntnisse in Wort und Schrift

 

Hinweise:

 

Zur Sicherung der Gleichstellung sind Bewerbungen qualifizierter Frauen besonders willkommen. Schwerbehinderte Bewerber/innen werden bei gleicher Eignung bevorzugt.

 

Ihre Bewerbungen mit den üblichen Unterlagen (Anschreiben, Lebenslauf, Zeugnisse) sind bis zum 19.07.2019 unter eindeutiger Angabe der Kennziffer 48/2019 an das Museum für Naturkunde, SE Personal, Invalidenstraße 43, 10115 Berlin oder bevorzugt per E-Mail an Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein! zu richten.

 

Bitte beachten Sie, dass eine Rücksendung von Unterlagen und Bewerbungsmappen nur mit beigefügtem Rückumschlag erfolgt. Zu unserer Entlastung bitten wir Sie von der Zusendung von Bewerbungsmappen abzusehen.

 

Links: https://jobs.museumfuernaturkunde.berlin/jobposting/1a25445928f1a2663b4a13897ed1490f12be5a68 

Professorship (W3) for Computational Systems Biology

We are happy to announce a new Bioinformatics Professorship (W3) at the Universität Hamburg with a focus on Systems Biology. Possible research topics include modeling of cellular networks and systems in the context of infection processes; modeling of resistance formation; and simulation of cell systems. The consolidation and integration of large sets of heterogeneous biological data should form an essential part of the research.

The position is located in the Informatics Department and Center for Bioinformatics in Hamburg offering established study programs in Computing in Science and Bioinformatics. It is also part of the upcoming Leibniz-WissenschaftsCampus InterAct strengthening connection to Leibniz-Institutes in the field of infection and structural biology and the Center for Structural Systems Biology (CSSB) on the DESY Campus.

A complete announcement can be fould here:

https://www.uni-hamburg.de/en/uhh/stellenangebote/professuren/22-08-19-w3-2309en.pdf

Researcher (f/m/d) at Freiburg University

Biological Anthropology at Albert Ludwig University Freiburg is looking for a highly motivated

Researcher (f/m/d)

within a DFG-funded project developing scientific software for research in biological anthropology.

Our research project ″Establishing Semantic Research Data Modelling in Biological Anthropology″ aims to improve research data management and curation in biological anthropology by providing appropriate infrastructure. This involves creating a web-based information system for acquisition and tracking of osteological data and subsequent research using the curated data base.

The main task will be adaptation of an existing software framework for a domain-specific RDF ontology. This work will mainly concern the front end but might entail framework adjustments. The primary sub-tasks will be

    • Designing the software concept with us

    • Autonomous implementation of said software concept

    • Testing and optimising the software

    • Tight collaboration with international project partners

 

We offer

    • advanced training to improve individual skills in semantic information systems

    • opportunities for active participation in international conferences

 

Qualifications and requirements

We expect a very high level of self-organisation as well as a creative and solution-oriented mindset. Applicants will be responsible to keep to the production schedule and should be capable of excellent time management, of working in a team and of actively communicating both in-house and with partners abroad. Compliance with predefined workflows is mandatory.

The project is experimental in nature and specific to modelling osteological research data in biological anthropology. As a consequence, we are looking for a creative and open-minded collaborator instead of targeting applicants with specific qualifications.

 

Required skills

    • Master or equivalent degree

    • Experience with semantic web technologies (RDF, SPARQL) OR experience in software development

    • Excellent oral and written knowledge of English

 

Desired qualifications

    • Background in biological or related sciences

    • Adequate knowledge of the code versioning system git

    • Knowledge of the programming language TypeScript

 

The position is limited to two years. Payment and benefits will be according to the German TV-L pay scale (E 13). A first evaluation of applications is scheduled for 31 August 2019. The search will be continued until the position is filled.

Freiburg University seeks to increase the number of women in areas in which they are under-represented and therefore explicitly encourages women to apply. The University Freiburg is also committed to increasing the number of individuals with disabilities in its workforce and therefore encourages applications from such qualified individuals.

We look forward to receiving your application. Please upload your documents as a compressed archive file – including a letter of motivation, CV, research statement (max. 1 page), a list of publications and contact information of two references – to our portal:

https://ckan.anthropologie.uni-freiburg.de/owncloud/index.php/s/U5Dbib2uDBjYBeL

For further inquiries, please contact Dr. Stefan Schlager (phone +49 / 761 / 203 – 5522; Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!)

 

Links:

http://ckan.anthropologie.uni-freiburg.de/dataset/a0524158-9711-438a-8953-ab1e674a12b6/resource/12038ede-43a7-4d8f-bee9-1a7f2aff55f3/download/employmentnotice-researcherbiologicalanthropology.pdf

 

4 PhD positions in Bioinformatics at Bielefeld University

The graduate school "Digital Infrastructure in the Life Sciences" (DILS) of the newly established "Bielefeld Institute for Bioinformatics Infrastructure" (BIBI) at Bielefeld University, Germany, offers four PhD positions (3 years, 100% TV-L E13) starting October 2019.

The institute's research program focuses on scientific and service aspects in the area of bioinformatics infrastructure in close cooperation with the "German Network for Bioinformatic Infrastructure" (de.NBI) as well as the "Information Centre for Life Sciences" (ZB MED).

The qualification program of the DILS graduate school includes a joint research program, dedicated courses, workshops, retreats, etc.

Candidates must demonstrate broad background in the interdisciplinary field of bioinformatics in general and deep knowledge in the area they apply for (see project descriptions for detailed requirements). Good communication skills and knowledge of the English language is required, whereas German is not necessary.

The application deadline is 31 July 2019. Application instructions, project descriptions, contact information, and other details can be found on the institute's website.

Links: http://bibi.uni-bielefeld.de

 

 

 

(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