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Stellenangebote

Bioinformatician (full time) [Heidelberg University Hospital ]

We have an opportunity for a a talented and motivated bioinformatician to join the Portugal laboratory in the Parasitology Department of Heidelberg University Hospital.

We are seeking a Bioinformatics Scientist (BSc, MSc or PhD [title and rank will be determined based on experience and degree]) with background in biology, statistics and programming. Expertise in R and familiarity with analytic tools and public genomic and clinical databases.

Project Description: We have recently shown that dry season Plasmodium falciparum infections are maintained asymptomatically during the 6-month dry season in Mali, while P. falciparum-specific humoral responses decrease (Portugal, S. et al. 2017). We are currently investigating parasite transcription and transcriptional regulation, during the dry season through NGS, comparing leucocyte-depleted blood of Malian children with persistent subclinical P. falciparum infections at the end of the dry season, and that of age- and gendermatched Malian children presenting with their first clinical malaria case in the ensuing transmission season.

We aim to investigate parasite transcription, including the expression of genes coding for parasite variant surface proteins on the surface of the host erythrocyte, and RNA-protein-DNA interactome, chromatin accessibility, and epigenetics. The person we seek will be working at the interface of wet lab and field researchers as well as P. falciparum bioinformaticians with whom we collaborate to further develop analytic tools. The ideal candidate should have or quickly develop excellent communication skills and the ability to work with interdisciplinary teams, be fluent in English and be willing to present results internally and externally.

Collaboration Partners: Peter Crompton (NAID, NIH), Boubacar Traore (FMPOS, ICER Mali), Thomas Lavstsen (Copenhagen University), Thomas Otto (University of Glasgow)

Profile of candidate’s qualification:

-           Graduate, Master’s or PhD Degree in Informatics, Biology or related areas;

-           Expertise in bioinformatics and molecular/cellular biology and experience with “Omics” data analysis.

-           Background in Statistics

-           Excellent knowledge of spoken and written English and excellent communication skills and team spirit; organizational skills and ability to keep detailed records of experiments;

-           Critical mind, enthusiasm; and ability to work in multidisciplinary and multicultural teams.

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Please send your application (including motivation letter, curriculum vitae, transcripts & certificates, and contact details of two academic references) via email by July 15th indicating Bioinformatician call on the email subject.

Postdoc in Computational Biology [HZI]

The Department of Computational Biology for Infection Research at the HZI, led by Prof Dr Alice C. McHardy, is looking for excellent postdocs in computational biology or bioinformatics. 

The goal of our projects is the development of algorithms and computer-aided methods to analyze (meta)-omics data of the human microbiome, viral and bacterial pathogens, and human cell lineages within individual patients, to further personalize medicine in infection research. The methods that we employ or develop in our research are related to the fields of machine learning, phylogenetics and population genetics-. The lab co-organizes the Critical Assessment of Metagenome Interpretation challenge (CAMI; Sczyrba et al., Nature Methods 2017), hosts the bioinformatics unit of the German Center for Infection Research (DZIF; https://www.dzif.de), is part of the new German excellence cluster RESIST (www.dfg.de) and a priority programme on CRISPR-Cas (https://gepris.dfg.de/gepris/projekt/405892038) and collaborates locally, nationally and internationally with biologists and medical experts. The lab’s projects offer plenty of opportunity for an excellent bioinformatics postdoc to shine.

Requirements: The candidate should have a PhD degree in bioinformatics, computational biology, machine learning, biomathematics, computer science, statistics or similar and a competitive publication record. A commitment to reproducible research, the ability to work in a highly interdisciplinary research field and very good programming skills are obligatory. Prior experience in meta’omics, infection research, statistical learning or with the analysis of NGS data sets is advantageous, but not required.

 

 

 

Assistenzprofessor*in mit Qualifizierungsvereinbarung im Bereich Bioinformatik

Am Fachbereich Biowissenschaften gelangt die Stelle
e. wissenschaftlichen Mitarbeit*er/in im Forschungs- und Lehrbetrieb
gemäß UG und Angestelltengesetz mit e. Assistenzprofessor*in mit
Qualifizierungsvereinbarung (gemäß § 27 Kollektivvertrag der
Universitäten) zur Besetzung.  Nach Erreichen des vereinbarten
Qualifizierungszieles wird das Vertragsverhältnis entfristet
(assoz. Professor*in). Gehaltsschema: Gehaltsgruppe A2 gem. § 49 (2)
KV; das monatliche Entgelt für diese Verwendung beträgt € 4.498,40
brutto (14× jährlich). Sollte die Qualifizierungsvereinbarung nicht
bereits zu Dienstbeginn abgeschlossen werden, erfolgt bis zum
Abschluss dieser Vereinbarung die Einstufung in die Gehaltsgruppe B1
gem. § 49 (3) lit. b KV. Das monatliche Entgelt für diese Verwendung
beträgt € 3.803,90 brutto (14× jährlich).


Vorgesehener Dienstantritt: 1. März 2020
Beschäftigungsdauer: 6 Jahre (nach Erfüllung der Qualifizierungsvereinbarung unbefristet)
Beschäftigungsausmaß in Wochenstunden: 40
Arbeitszeit: Rahmendienstzeit

Aufgabenbereiche: facheinschlägige Habilitation innerhalb eines
arbeitsvertraglich festgelegten Zeitraums (maximal 4 Jahre) oder in
besonders begründeten Ausnahmefällen andere festgelegte
Qualifizierungsziele; eigene wissenschaftliche Forschung und Lehre,
Aufund Ausbau von Kooperationen im Forschungs- und Lehrbetrieb des FB
Biowissenschaften sowie Mitwirkung an universitären
Verwaltungsaufgaben; Einwerbung von Drittmitteln, Durchführung und
Entwicklung von selbständiger Lehre in deutscher und englischer
Sprache im Umfang von vier Semesterwochenstunden (nach dem Erreichen
des Qualifikationszieles acht Semesterwochenstunden); Entwicklung und
Anwendung von bioinformatischen Methoden zur Integration, Analyse und
Interpretation von *omics Daten (Genom, Epigenom, Exom, Transkriptom
und Proteom) im Kontext biologischer und biomedizinischer Forschung,
Betreuung von Bachelor-, Master- und Dissertationsarbeiten

Anstellungsvoraussetzungen: abgeschlossenes Doktoratsstudium im
Bereich Computational Biology, Bioinformatik, Data Science,
Biostatistik oder einem dazu verwandten Forschungsfeld; Nachweis der
Publikationstätigkeit in hochrangigen wissenschaftlichen
Zeitschriften, sowie nachweisliche Erfahrung in der Analyse und
Interpretation von großen Datensätzen, beispielsweise solchen aus der
Hochdurchsatzsequenzierung. Erfahrung in der universitären Lehre sowie
in der Drittmittelbeantragung, eine – nach Möglichkeit im Ausland
erfolgte – zumindest einjährige externe wissenschaftliche Tätigkeit

Erwünschte Zusatzqualifikationen: Kenntnisse in Programmiersprachen
(z.B. C++, Python), R, Unix/Linux, Datenbanksystemen, Code-Management;
sehr gute Deutsch- und Englischkenntnisse; Bereitschaft und Fähigkeit
zur interdisziplinären Zusammenarbeit Gewünschte persönliche
Eigenschaften: hohe Motivation und Sozialkompetenz; Teamfähigkeit;
Bereitschaft zur Anleitung von Studierenden

Die Bewerbung hat in elektronischer Form (unter Angabe der
Geschäftszahl der Stellenausschreibung per E-Mail an
Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!) zu erfolgen und neben den üblichen Unterlagen
Folgendes zu enthalten:
a. Darstellung der Leistungen in der Wissenschaft und Forschung
b. Darstellung der Erfahrungen und Tätigkeiten in der Lehre (und allenfalls in der Betreuung von wissenschaftlichen Nachwuchskräften)
c. Konzept für künftige Pläne in Forschung und Lehre und für den Beitrag zum wissenschaftlichen Profil des Fachbereichs
d. Konzept für Wissenstransfer und Wissenschaftsmanagement
e. Darstellung der sozialen und anderen Kompetenzen
Auskünfte werden gerne von Prof.in Angela Risch (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!) oder telefonisch unter
Tel. Nr. +43 662 8044 7220 gegeben.
Bewerbungsfrist bis 12. Juni 2019

Bioinformatikerin/Bioinformatiker für methodologische Entwicklungen in Bereich der Einzelzellgenomik

Die Health Data Science Unit (HDSU, www.hdsu.org) ist eine neue Abteilung am BioQuant – Heidelberg  und an der Medizinischen Fakultät der Universität Heidelberg, die sich auf Forschungsthemen im Zusammenhang mit digitaler Gesundheit und der Integration von klinischen und genomischen Datensätzen fokusiert. HDSU ist einer der wichtigsten Partner des HighMed-Konsortiums für medizinische Informatik (www.highmed.org) und leitet die Entwicklung und Einrichtung von Systemen für die Integration klinischer Daten. Weitere Forschungsthemen sind die Analyse von (epi)genomischen und einzelligen Datensätzen. Wir wollen neue Ansätze für die Integration von Multi-Omics-Datensätzen entwickeln, insbesondere für die  Einzelzellengenomik.

Innerhalb des von der DFG geförderten Transregio-Projekts „Determinanten und Dynamik der Elimination versus Persistenz der Hepatitis-Virus-Infektion“ (www.trr179.de) plant die Gruppe von Dr. Carl Herrmann den Aufbau einer zentralen Einzelzellanalyse-Einrichtung in Zusammenarbeit  mit dem Single Cell Open Lab am BioQuant Heidelberg (https://malone.bioquant.uni-heidelberg.de/scopenlab/). Insbesondere sollen die Ursachen der Variabilität in der zellulären Reaktion auf eine Virusinfektion, insbesondere das HCV-Virus, untersucht werden, indem mehrere Datentypen  (scRNA-seq / scATAC-seq) in verschiedenen Zellpopulationen kombiniert werden.

In diesem Zusammenhang suchen wir eine/einen Bioinformatikerin/Bioinformatiker, die/der diese Bemühungen unterstützt und koordiniert, wobei folgende Schwerpunkte im Vordergrund stehen:

• Entwicklung und Implementierung von Standard-Einzelzellanalyse-Workflows für scRNA-seq- und scATAC-seq-Datensätze in einer HPC-Umgebung;

• Implementierung solcher Workflows in einer Cloud-Infrastruktur (de.NBI-Cloud, ELIXIR,…);

• Entwicklung von Datenintegrationsmethoden und -strategien für Single-Cell-Datensätze (scRNA-seq / scATAC-seq)

• Analyse von Einzelzelldatensätzen (scRNA-seq / scATAC-seq / CITE-seq), die im Rahmen des DFG-Konsortiums erstellt wurden;

• Beitrag zu Schulungen und Dokumentation für externe Benutzer dieser Workflows.

Wir suchen eine/einen Kandidatin/Kandidaten mit Erfahrung in der Analyse von Hochdurchsatz-Sequenzierung (RNA-seq / ChIP-seq / ATAC-seq)  sowie der Möglichkeit, Analyse-Workflows einzurichten (vorzugsweise mit Snakemake). Erste Erfahrungen mit Einzelzell-Datensätzen sowie ein solider statistischer Hintergrund wären ein starkes Plus.

Die Stelle ist zunächst auf zwei Jahre befristet und kann möglicherweise weiter verlängert werden.

Bewerbungsschreiben und Lebensläufe (als PDF) sowie Kontaktinformationen von zwei Gutachtern sind per Email an Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein! zu senden

 

Wissenschaftlicher Mitarbeiter (m/w/d) im Bereich Bioinformatik (TV-H E13 100%)

An der Professur für Systembiologie an der Justus-Liebig-Universität Gießen ist im Rahmen eines drittmittelfinanzierten BMBF-Projekt zum nächstmöglichen Zeitpunkt eine Vollzeitstelle mit einer/einem Wissenschaftlichen Mitarbeiter/in zu besetzen.

 

Aufgaben:

·         zentrale Aufgaben zur Zertifizierung einer Cloud-Computing-Infrastruktur sowie die Einführung der entsprechend erforderlichen Managementsysteme

·         Planung und Überwachung der Implementierung und Bereitstellung Cloud-basierter Services.

·         Erstellung Benutzer-orientierter Sammlung von zumeist bioinformatischen Software-Tools inklusive Installation und Funktionstest in OpenStack- und Kubernetes-basierten Umgebungen.

·         Pflege einer zugehörigen umfassenden Benutzerdokumentation

·         Teilprojekt-spezifische Unterstützung bei der Datenanalyse als auch die Entwicklung neuer Softwaretools für die Analyse und Visualisierung von Hochdurchsatzdaten.

 

Anforderungsprofil:

·         Abgeschlossenes wissenschaftliches Hochschulstudium in der Bioinformatik / Informatik oder einem anderen IT-nahen Fach

·         Umfangreiche Erfahrung im Bereich der Systemadministration, insbesondere mit Linux-Betriebssystemen

·         Grundlegende Kenntnis der Anforderungen an Zertifizierungsprozesse im IT-Bereich

·         Vorkenntnisse im Bereich der Administration von Infrastruktur-Systemen sowie relevanter bioinformatischer Applikationen und deren Wartung und Installation

·         Solide Kenntnisse im Bereich der Netzwerkinfrastruktur

·         Erfahrungen mit der effektiven Nutzung von Cloud-Computing Plattformen wie OpenStack oder Kubernetes

·         Sichere und nachweisbare Erfahrung mit mindestens einer Programmiersprache, z.B. Perl, Java, Python

 

Link zur kompletten Ausschreibung: [http://www.inst.uni-giessen.de/stellenmarkt/pdf/stelle0011800.pdf

Wissenschaftlicher MitarbeiterIn (m/w/d) (DoktorandIn oder Postdoc, TV-L E13/100%) in Bioinformatik

In der Arbeitsgruppe von Prof. Dr. Caroline Friedel an der Ludwigs-Maximilians-Universität München ist frühestens zum 1.7.2019 die Stelle einer/s

Wissenschaftlichen Mitarbeiter/in (TV-L 13, 100%)

als Promotions- oder Postdoc-Stelle zu besetzen.

Diese Stelle ist Teil des durch die DFG geförderten Projektes „Large-scale investigation of short read archives for disruption of transcription termination and circular splicing“.  

Ziel dieses Projektes ist dabei die Entwicklung und Anwendung von neuen Methoden zum Durchsuchen großer Read-Datenbanken wie die NCBI SRA nach Evidenz für Störungen in der Transkriptionsterminierung und speziellen Splicing-Ereignissen.

Kandidatinnen und Kandidaten sollten ein Hochschulstudium (Master/Diplom) bzw. eine Promotion für die Postdoc-Stelle in Bioinformatik oder einem nahe verwandten Fachgebiet absolviert haben oder kurz vor dem Abschluss stehen. Vorausgesetzt werden gute Programmierkenntnisse (Java, Python und/oder Perl) und Interesse an quantitativer Datenanalyse und bioinformatischer Methodenentwicklung. Erfahrungen mit der Analyse von Hochdurchsatz-Daten, insbesondere Next-Generation Sequencing-Daten, wären von Vorteil.

Bewerbungen mit den üblichen Unterlagen (Lebenslauf, Zeugniskopien, Master/Diplom-Arbeit bzw. Doktorarbeit als PDF per Email) bzw. Fragen zur Stellenausschreibung sind zu richten an:

Prof. Dr. Caroline Friedel
Lehr- und Forschungseinheit für Bioinformatik
Institut für Informatik
Ludwig-Maximilians-Universität München
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Full Professorship in Medical Data Science and Services (W3 BBesO grade post)

We are one of the youngest universities in Germany and think in terms of unlimited possibilities instead of possible limitations. Located in the heart of the Ruhr metropolis, our 11 faculties develop ideas for the future. We are strong in research and teaching, we embrace diversity, promote academic potential, and we are highly committed to educational equality.

University Medicine Essen is on its way to becoming a SMART Hospital, where digital technologies will enable employees to further improve patient care, research and education. We are convinced that truly personalized medicine can only be realized, if we combine digitization in medicine with artificial intelligence. We have therefore decided to establish an Institute for Artificial Intelligence (AI) in Medicine. In its founding stage, this institute will be staffed with four professorships dealing with different aspects of AI in medicine. We envision these professorships to synergistically lead the successful development of our innovative concept. It is our aim to identify highly motivated individuals with a broad and complementary range of expertise with whom we undertake this journey.

The Medical Faculty of the

University of Duisburg-Essen

is inviting applications for a

Full Professorship in

Medical Data Science and Services

(W3 BBesO grade post)

The position is newly established and will work in concert with three additional professorship positions (two of them within the framework of the Cancer Research Center Cologne Essen (CCCE)), all related to the use of artificial intelligence in medicine. Upon successful development perpetuation of the professorship is envisioned.

Core tasks of the applicant are (i) enhancing the potential of medical data by enabling interoperability between different systems and locations by means of structurization, harmonization, and annotation (ii) data aggregation of next generation information systems like bioimaging, outputs from multi-omics analyses, and others (iii) strategies for anonymization and nationwide valid patient's consent and data access management (iv) data protection-compliant distributed analytics over multiple national and international sites.

The future job holder should have several years of professional experience in the field of data analysis. Excellent knowledge of relational and non-relational database systems is desirable. Further prerequisites are experience in the development and implementation of cooperations with industry as well as scientific productivity. The applicant should have experience with AI techniques and neuronal networks. Ideally, the applicant is familiar with NLP and related methods.

The future chair will also contribute to the main research focuses of the Medical Faculty and will collaborate with and contribute to ongoing and evolving research consortia. Furthermore, the future chair will possess dedicated teaching skills and use innovative methods in teaching and post-graduate qualification.

Qualifications according to § 36 Hochschulgesetz NRW are required and successful experience with competitive third-party funding applications are mandatory. As the University of Duisburg-Essen puts special emphasis on the quality of academic teaching, concepts on the participation in teaching activities with regard to the profile of the University Duisburg-Essen should be provided.

The Medical Faculty in Essen promotes research particularly in the following areas: Cardiovascular Disease, Oncology, Transplantation Medicine and Translational Neuro- and Behavior Sciences, as well as the bridging disciplines of Immunology and Infectious Diseases. This position is dedicated to the area of Oncology.

The position will be available at the earliest.

Application deadline: 13.06.2019

The University of Duisburg-Essen aims to increase diversity among its faculty members (see http://uni-due.de/diversity) and strives to increase the number of women in such positions; therefore, we especially encourage women with relevant qualifications to apply. Women with the appropriate qualifications will receive preferential consideration. Applications from severely disabled candidates according to § 2 Abs. 3 SGB IX are welcome.

Applications with the usual supporting documents [curriculum vitae, list of scientific publications (see http://www.uni-due.de/imperia /md/content/medizin/formblatt_aufbau_schriftenverzeichnis.pdf)], documents on scientific and professional career, certificate copies, information on third-party funding, participation in academic self-administration, past teaching experience and concepts for teaching, and 5 key publications should be submitted by email (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!) to Univ.-Prof. Dr. J. Buer, Dekan der Medizinischen Fakultät, Universitätsklinikum Essen, Hufelandstr. 55, 45147 Essen.

Furthermore, we need you to fill in our application form at https://www.uni-due.de/med/de/organisation/bewerbungsbogen.php. Further information on the position and its embedding in the University of Duisburg-Essen as well as in the Faculty can be found at https://www.uni-due.de/med/de/organisation/berufungen.php. For general information please visit: https://ai.uk-essen.de.

 

Full Professorship in Translational Image-Guided Oncology (W3 BBesO grade post, initially limited to 5 years)

We are one of the youngest universities in Germany and think in terms of unlimited possibilities instead of possible limitations. Located in the heart of the Ruhr metropolis, our 11 faculties develop ideas for the future. We are strong in research and teaching, we embrace diversity, promote academic potential, and we are highly committed to educational equality.

University Medicine Essen is on its way to becoming a SMART Hospital, where digital technologies will enable employees to further improve patient care, research and education. We are convinced that truly personalized medicine can only be realized, if we combine digitization in medicine with artificial intelligence. We have therefore decided to establish an Institute for Artificial Intelligence (AI) in Medicine. In its founding stage, this institute will be staffed with four professorships dealing with different aspects of AI in medicine. We envision these professorships to synergistically lead the successful development of our innovative concept. It is our aim to identify highly motivated individuals with a broad and complementary range of expertise with whom we undertake this journey.

The Medical Faculty of the

University of Duisburg-Essen

is inviting applications for a

Full Professorship in

Translational Image-Guided Oncology

(W3 BBesO grade post, initially limited to 5 years)

The position is newly established within the framework of the Cancer Research Center Cologne Essen (CCCE), in which the University Hospital Essen and the University Hospital Cologne join forces to advance translational cancer research and computational cancer biology. Generous funding is provided by the state of Nordrhein-Westfalen for 5 years; following successful development of the CCCE perpetuation of the professorship is envisioned.

The holder of this position will contribute to research and teaching in the field of Image-guided Oncology at the Medical Faculty and University Hospital Essen. She or he will interact within the framework of the the West German Cancer Center (WTZ), a leading comprehensive cancer center designated as Oncology Center of Excellence by the German Cancer Aid. As partner site of the federally funded German Cancer Consortium (DKTK), formed by seven excellent university medical centers and the German Cancer Research Center Heidelberg (DKFZ), the West German Cancer Center offers a highly competitive and stimulating scientific environment including access to core facilities, biobanks and datasets from large patient cohorts. Collaborative research with basic science is fostered through the Center for Medical Biotechnology integrating the Faculties of Biology, Chemistry and Medicine of the University of Duisburg-Essen.

The future chair should be an internationally acknowledged scientist with broad, outstanding track record in the technical aspects of image-guided oncology. The future chair is expected to establish research lines that translate innovative image guidance concepts for a range of interventions, including, but not limited, to precision surgery, focal and molecularly targeted systemic therapies, into clinical exploration and application in cancer patients. Particular focus areas are the realization of improved procedural planning, real-time intraprocedural diagnostics, imaging-based therapy delivery or theranostics. The future chair will also contribute to the main research focuses of the Medical Faculty and will collaborate with and contribute to ongoing and evolving research consortia. Furthermore, the future chair will possess dedicated teaching skills and use innovative methods in teaching.

Qualifications according to § 36 Hochschulgesetz NRW are required. Publications in peer-reviewed journals and successful experience with competitive third-party funding applications are mandatory. Involvement in teaching activities of the university with emphasis on postgraduate education is mandatory. Concepts on the participation in teaching activities with regard to the profile of the Medical Faculty of the University of Duisburg-Essen should be provided.

The Medical Faculty in Essen promotes research particularly in the following areas: Cardiovascular Disease, Oncology, Transplantation Medicine and Translational Neuro- and Behavior Sciences, as well as the bridging disciplines of Immunology and Infectious Diseases. This position is dedicated to the area of Oncology.

The position will be available at the earliest.

Application deadline: 13.06.2019

The University of Duisburg-Essen aims to increase diversity among its faculty members (see http://uni-due.de/diversity) and strives to increase the number of women in such positions; therefore, we especially encourage women with relevant qualifications to apply. Women with the appropriate qualifications will receive preferential consideration. Applications from severely disabled candidates according to § 2 Abs. 3 SGB IX are welcome.

Applications with the usual supporting documents [curriculum vitae, list of scientific publications (see http://www.uni-due.de/imperia /md/content/medizin/formblatt_aufbau_schriftenverzeichnis.pdf)], documents on scientific and professional career, certificate copies, information on third-party funding, participation in academic self-administration, past teaching experience and concepts for teaching, and 5 key publications should be submitted by email (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!) to Univ.-Prof. Dr. J. Buer, Dekan der Medizinischen Fakultät, Universitätsklinikum Essen, Hufelandstr. 55, 45147 Essen.

 

Furthermore, we need you to fill in our application form at https://www.uni-due.de/med/de/organisation/bewerbungsbogen.php. Further information on the position and its embedding in the University of Duisburg-Essen as well as in the Faculty can be found at https://www.uni-due.de/med/de/organisation/berufungen.php. For general information please visit: https://ai.uk-essen.de.


 

 

 

WEB UI DEVELOPER / BIOINFORMATICIAN

EMBL is seeking a highly motivated web UI developer/(bio)informatician to work in the Genome Biology Computational Support (GBCS). The GBCS team develops and maintains data management and analysis solutions used by EMBL scientists across various EMBL sites. Among these services, STOCKS is a web-based application offering solutions for the management of lab collections (consumables, specimen, samples ...) and *omics data produced by high-throughput assays (in particular NGS data). STOCKS is also an Electronic Lab Notebook allowing scientists to link between their collection items, samples, assays and protocols. STOCKS user front-end is written in Vue.js while the server back end (and the administration interface) is developed using the Python Django framework.

The position primarily involves the maintenance and development of the STOCKS User Interface (Vue.js). The position also involves the maintainance of different tools (e.g. Galaxy & RStudio Server Pro), the installation of scientific libraries (on unix servers) and the production of analysis pipelines for standard NGS protocols using Galaxy, Snakemake or nextflow. The successful applicant supports users on a daily basis, assembles training materials (e.g. writing of wiki-based documentation/how-to) and organizes tutorials.

Applicants should have an appropriate university degree in computer science or bioinformatics (master degree with 3+ years of experience or PhD).

Demonstrated experience in web application development/deployment with modern javascript frameworks (e.g. Vue.js), experience in python development and the use of collaborative tools (git) are a must.

The successful applicant is organized (documentation and communication is an important aspect of the job), open-minded, able to work on different projects in parallel, proactive (problem solving skills are essential) and have a user-oriented spirit.  

The candidate should be able to work independently and also interact well within a team environment. A working knowledge of English is a must.

EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation with a very collegial and family friendly working environment. The remuneration package comprises from a competitive salary, a comprehensive pension scheme, medical, educational and other social benefits, as well as financial support for relocation and installation, including your family and the availability of an excellent child care facility on campus. EMBL has a large thriving community of bioinformaticians, working in close collaboration with experimental scientists and with strong links to other local scientists and institutions.

Links: https://www.embl.de/jobs/searchjobs/index.php?ref=HD01530&newlang=1&srch_trm=we

Translational Artificial Intelligence (W3 BBesO grade post, initially limited to 5 years)

We are one of the youngest universities in Germany and think in terms of unlimited possibilities instead of possible limitations. Located in the heart of the Ruhr metropolis, our 11 faculties develop ideas for the future. We are strong in research and teaching, we embrace diversity, promote academic potential, and we are highly committed to educational equality.

University Medicine Essen is on its way to becoming a SMART Hospital, where digital technologies will enable employees to further improve patient care, research and education. We are convinced that truly personalized medicine can only be realized, if we combine digitization in medicine with artificial intelligence. We have therefore decided to establish an Institute for Artificial Intelligence (AI) in Medicine. In its founding stage, this institute will be staffed with four professorships dealing with different aspects of AI in medicine. We envision these professorships to synergistically lead the successful development of our innovative concept. It is our aim to identify highly motivated individuals with a broad and complementary range of expertise with whom we undertake this journey.

The Medical Faculty of the

University of Duisburg-Essen

is inviting applications for a

Full Professorship in

Translational Artificial Intelligence

(W3 BBesO grade post, initially limited to 5 years)

 

The position is newly established and will work in concert with three additional professorship positions (two of them within the framework of the Cancer Research Center Cologne Essen (CCCE)), all related to the use of artificial intelligence in medicine.

Core tasks of the applicant are (i) the analysis of clinical processes with regard to improvement potential through AI systems (ii) the design and implementation of corresponding systems and (iii) the seamless integration of these systems into clinical processes. For this purpose, the applicant must have a deep understanding of practical clinical medicine and the technical competence to process clinical data on a large scale, to train AI systems using classical machine learning and deep learning, and to finally integrate these systems back into the hospital infrastructure. Special emphasis will be placed on the suitability of such systems for routine clinical use, in particular with regard to user interaction.

The future job holder should have several years of professional experience as a physician in a diagnostic field, ideally radiology, nuclear medicine or digital pathology. In addition, good knowledge and practical experience with standards for data exchange in healthcare (in particular DICOM, HL7, FHIR, SNOMED-CT and LOINC) are required. Practical skills in the areas of Machine Learning and Deep Learning are also required. Proven practical skills in programming distributed systems, microservices and big data architectures as well as many years of experience in dealing with relational and non-relational database systems are desirable. Practical previous experience in dealing with web technologies, especially with regard to the creation of web-based user interfaces, is also desirable. Further prerequisites are previous experience in the development and implementation of industrial cooperations as well as intensive scientific activity that can be proven by scientific publications.

The future chair will also contribute to the main research focuses of the Medical Faculty and will collaborate with and contribute to ongoing and evolving research consortia. As the University of Duisburg-Essen puts special emphasis on the quality of academic teaching, concepts on the participation in teaching activities with regard to the profile of the University Duisburg-Essen should be provided. Furthermore, the future chair will possess dedicated teaching skills and use innovative methods in teaching and qualified post graduates qualification.

Qualifications according to § 36 Hochschulgesetz NRW are required. Publications in peer-reviewed journals and successful experience with competitive third-party funding applications are mandatory. Involvement in teaching activities of the university with emphasis on postgraduate education is mandatory.

The Medical Faculty in Essen promotes research particularly in the following areas: Cardiovascular Disease, Oncology, Transplantation Medicine and Translational Neuro- and Behavior Sciences, as well as the bridging disciplines of Immunology and Infectious Diseases.

The position will be available at the earliest.

Application deadline: 13.06.2019

The University of Duisburg-Essen aims to increase diversity among its faculty members (see http://uni-due.de/diversity) and strives to increase the number of women in such positions; therefore, we especially encourage women with relevant qualifications to apply. Women with the appropriate qualifications will receive preferential consideration. Applications from severely disabled candidates according to § 2 Abs. 3 SGB IX are welcome.

Applications with the usual supporting documents [curriculum vitae, list of scientific publications (see http://www.uni-due.de/imperia /md/content/medizin/formblatt_aufbau_schriftenverzeichnis.pdf)], documents on scientific and professional career, certificate copies, information on third-party funding, participation in academic self-administration, past teaching experience and concepts for teaching, and 5 key publications should be submitted by email (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!) to Univ.-Prof. Dr. J. Buer, Dekan der Medizinischen Fakultät, Universitätsklinikum Essen, Hufelandstr. 55, 45147 Essen.

Furthermore, we need you to fill in our application form at https://www.uni-due.de/med/de/organisation/bewerbungsbogen.php. Further information on the position and its embedding in the University of Duisburg-Essen as well as in the Faculty can be found at https://www.uni-due.de/med/de/organisation/berufungen.php. For general information please visit: https://ai.uk-essen.de.