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Postdoctoral Fellow - Bioinformatician with experience in biological data analysis

The research group of Wolfgang Huber (www.huber.embl.de) at EMBL works on biological data science and mathematical / computational method development. The interdisciplinary and international team uses statistical data analysis and modelling to discover and understand biological principles and biomedical applications and has strong collaborations with researchers in basic biology and cancer research.

About the project SMART-CARE

The SMART-CARE consortium is a collaboration between EMBL, the German Cancer Research Centre, the University Hospital Heidelberg, Heidelberg University and Mannheim University of Applied Sciences, that aims to develop new systems medicine approaches to battle cancer recurrence, using the integration of proteome and metabolome mass spectrometry approaches with other ‘omics and clinical data. The consortium brings together clinical, mass spectrometry and computational expertise. 

Cancer recurrence is the main determinant of cancer related death and therefore a  major global health problem. The surge of genomic technologies in clinical practice has brought great benefit in disease stratification, however genomic information alone is often insufficient to accurately predict or identify the dynamic process of disease progression. Systematic analyses of proteins and metabolites using mass spectrometry in combination with statistical data analysis and mathematical modelling promise a new generation of biomarkers that could be used to tailor personalized cancer therapy. There is a need to develop and establish powerful and standardizable pipelines for proteome and metabolome analysis in the clinical setting. The aim of the SMART-CARE project is to firmly establish mass spectrometry-based systems medicine technologies and data analysis methods and apply these to predict cancer recurrence across paradigmatic tumor entities and thus improve patient stratification.

Your role

You will be part of the Huber group at EMBL’s Heidelberg site, participate in the SMART-CARE project and shape your own research profile by pursuing research in method development and collaborative analysis of novel datasets. Your activities will comprise the following: 

·       Advanced statistical inference and biological model building: Compare the information content of the different data types, in terms of their ability to map patient and disease heterogeneity, and predict tumor recurrence and treatment response. Use and adapt methods for data integration developed within the group, e.g. the Multi Omics Factor Analysis (MOFA) or further develop state of the art methods from statistical learning.

·       Data-type specific “preprocessing” and feature engineering.

·       Automated data quality assessment / control (QA/QC) and  visualization.

·       Publish computational methods and biological discoveries in scientific articles, and publish scientific software as, e.g., R/Bioconductor packages.

You have

A PhD or equivalent qualification in a quantitative science (mathematics, statistics, physics, computer science, computational biology). We are looking for a range of talents, which should include some of the following: solid training in mathematical statistics, understanding of high-dimensional statistics, machine learning and Bayesian approaches; experience in biological data science and data-driven discovery; scientific programming, and good software engineering skills. Applications from “newcomers” into biology are welcome.

You might also have

You are excited by making or contributing to biological discoveries, you are interested in interdisciplinary science, enjoy collaborative work and like to communicate concepts and results to other scientists in different fields of research. You are interested in understanding and comparing methods in computational biology and in pushing them forward with your own ideas.

 

 

Genomic Data Analysis - Bioinformatician

Location:

Heidelberg, Germany

Staff Category:

Staff Member

Contract Duration:

3 years

Grading:

7

Closing Date:

29 February 2020

Reference Number:

HD01688

EMBL is seeking an expert in Computational Biology to join the Korbel research group in the Genome Biology Unit. The position holder will actively participate in the design, development, and implementation of interoperable workflows and pipelines to enable the analysis of data from the latest genomics sequencing platforms. The post holder will analyse large numbers of clinically relevant human genomes and single cell sequencing data using cloud technologies and high-performance compute clusters.  

Your role

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

·         Design, develop and implement cloud-based workflows for single-cell sequencing protocols such as Strand-Seq and 10X Genomics

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

·         Provide support for cutting-edge research projects of the Korbel group by helping and advising researchers with their experimental design, data analysis and interpretation of results

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

You have

·         A PhD or equivalent qualification in a quantitative science (Computational Biology, Bioinformatics, Physics, Mathematics or Computer Science) with solid experience in handling large-scale genomics data

·         Strong interest in computational biology and genomics data analysis

·         Programming skills in a scripting language, R and a high-level programming language

·         An interest in cutting-edge molecular biology and its data-generating technologies

·         A basic understanding of molecular genetics and cancer research

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

You might also have

·         Prior expertise in the application of cloud computing in genomics

·         Practical knowledge in sequencing data analysis, statistics or machine learning

·         Experience in analysing single cell omics/genomics data sets

·         Experience as a software developer or package maintainer for genomics data analysis

·         Knowledge of scientific authoring frameworks, web service development or data management technologies

Why join us

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 a competitive salary, a comprehensive pension scheme, medical, educational and other social benefits, and the availability of an excellent child care facility on campus. You will be involved in cutting-edge projects and activities and will collaborate with experts from the scientific community and have the possibility to acquire new state-of-the-art skills.  

What else you need to know

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

 

PhD position in times series analysis at University of Greifswald

We are looking for a strong candidate to pursue a PhD in time series analysis at the University of Greifswald in the group of Prof. Dr. Joscha Diehl. The project involves joint collaboration with the group of Prof. Dr. Kurusch Ebrahimi-Fard (NTNU, Norway) as well as with researchers from the Greifswald Medical School. The position is for 3 years and involves 2 hours of teaching per week during the semester (SWS).

 Necessary are

- a Master's degree in mathematics, statistics, physics or computer science

- enthusiasm to work with real-life data

- interest in time series analysis from a theoretical perspective

- fluency in the English language

Beneficial are

- programming experience (python, R, ..)

- knowledge of algebra (commutative, noncommutative, representation theory, ..)

- knowledge of statistics

Application deadline: February 28th, 2020.

For the complete announcement, please visit https://diehlj.github.io

For any questions, please contact Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!.

 

Wissenschaftlicher Datenanalyst (m/w/d) im Bereich Wildtiergenetik

Die Senckenberg Gesellschaft für Naturforschung (SGN) wurde 1817 gegründet und zählt zu den wichtigsten Forschungseinrichtungen rund um die biologische Vielfalt. An den elf Standorten in ganz Deutschland betreiben Wissenschaftlerinnen und Wissenschaftler aus über 40 Nationen modernste Forschung auf internationaler Ebene. Hauptsitz der Gesellschaft ist die Mainmetropole Frankfurt im Herzen Deutschlands. Hier befindet sich auch eine der bekanntesten Senckenberg-Einrichtungen, das Senckenberg Naturmuseum.

 

Das Senckenberg-Zentrum für Wildtiergenetik am Standort Gelnhausen führt in enger Kooperation mit Umweltbehörden von Bund und Ländern sowie NGOs und anderen wissenschaftlichen Einrichtungen genetische Untersuchungen zum Bestandsmonitoring geschützter Wildtiere, wie Wildkatze, Luchs und Wolf durch und trägt so zur Erforschung und Bewahrung der Biodiversität bei.

 

Zum schnellstmöglichen Termin suchen wir für unseren Standort in Gelnhausen für das Fachgebiet Naturschutzgenetik einen

 

Wissenschaftlichen Datenanalysten (m/w/d)

im Bereich Wildtiergenetik

(Vollzeit)

Ihre Aufgaben:

·         Analyse von Genotyp- und Sequenzdaten im Rahmen der fortlaufenden Auftragsforschung im genetischen Wildtiermonitoring

·         Statistische und bioinformatische Auswertung genetischer Datensätze, z.B. hinsichtlich Populationsgröße, Genflussmustern, Inzucht und genetischer Diversität in Beständen geschützter Wildtiere

·         Erstellung von Berichten und Mitarbeit an wissenschaftlichen Fachartikeln

·         Mitarbeit bei der Datenbankentwicklung und -Instandhaltung

·         Kommunikation mit nationalen und internationalen Projektpartnern

 

 

Ihr Profil:

·         Abgeschlossenes Diplom- oder Masterstudium im Bereich Biologie, Bioinformatik oder einer ähnlichen Fachrichtung; Promotion ist erwünscht, jedoch nicht Voraussetzung

·         Sehr gute Kenntnisse im Bereich der statistischen Analyse populationsgenetischer Daten

·         Sehr gute IT-Kenntnisse inklusive Vorkenntnisse in Programmierung und bioinformatischer Analyse großer Datensätze

·         Sehr gute Deutsch- und Englischkenntnisse in Wort und Schrift

·         Teamgeist, Sorgfalt, Motivation und Engagement sowie ein hohes Maß an Eigeninitiative

 

Wir bieten Ihnen:

·         eine attraktive und herausfordernde Tätigkeit im Bereich Wildtierforschung und Artenschutz in

·         selbstständiges Handeln in einem internationalen und professionellen Umfeld

·         Flexible Arbeitszeiten – ein vergünstigtes Jobticket – Unterstützung bei Kinderbetreuung oder bei der Pflege von Familienangehörigen (zertifiziert durch das „audit berufundfamilie“) – Dienstausweis in Verbindung mit kostenfreiem Eintritt in alle städtischen Museen – Jahressonderzahlung – betriebliche Altersvorsorge

 

  

Ort:                                         Gelnhausen

Beschäftigungsumfang:      Vollzeit (40 Stunden/Woche)

Vertragsart:                           zunächst befristet für 2 Jahre mit anschließender Option auf Entfristung

Vergütung:                            Entgeltgruppe 13 TV-H

 

Senckenberg ist durch das „audit berufundfamilie“ zertifiziert. Schwerbehinderte Menschen werden bei gleicher Eignung besonders berücksichtigt.

 

Sie möchten sich bewerben?

 

Dann senden Sie Ihre vollständigen und aussagekräftigen Bewerbungsunterlagen (Motivationsschreiben, Lebenslauf, Ausbildungs- und Arbeitszeugnisse) in elektronischer Form (als eine zusammenhängende PDF-Datei) bitte unter Angabe der Referenznummer #04-20001 bis zum 01.03.2020 an Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein! oder bewerben Sie sich direkt auf unserer Homepage über das Online Bewerbungsformular.

 

 

Open (permanent) position in Bioinformatics at RKI/Berlin

We have a permanent position available as a principal investigator and head of our bioinformatics core facility at the Robert Koch Institute. 
The RKI is Germany's national public health institute and pursues research on human and zoonotic diseases within Germany and internationally. It accommodates the latest research infrastructure and utilizes it to detect disease outbreaks and defense against bioterroristic threats. As the head of the bioinformatics core facility you are conceptualizing and executing state of art methods and pipelines that make a real difference in public health. Currently, the bioinformatics core facility team is composed of 3 permanent researchers (E13), plus fixed term researchers and students. Please do not hesitate to call if you have questions about this opportunity. The application deadline is 09.Feb.2020. Kind regards, Max von Kleist, PhD Robert Koch Institut Acting head MF1 (Bioinformatics) Nordufer 20 13353 Berlin Germany Link: https://interamt.de/koop/app/stelle?id=562968

Doktorandenstelle am Zentrum für Bioinformatik

Am Zentrum für Bionformatik Hamburg ist ab dem 1. Mai 2020 eine Stelle als Wissenschaftliche Mitarbeiterin bzw. Wissenschaftlicher Mitarbeiter (M/W/D) zu besetzen. Den vollständigen Ausschreibungstext finden Sie hier.

PhD student (f/m/d) position in Computational Biology/Bioinformatics for translational cancer research with a focus on the analysis of single cell sequencing data

The Department of Internal Medicine II, at the Technische Universität München (TUM) and the Institute of Translational Cancer Research and Experimental Cancer Therapy at TUM and the German Cancer Research Center offers a

 

PhD student (f/m/d) position
in Computational Biology/Bioinformatics for translational cancer research with a focus on the analysis of single cell sequencing data

 

at the Center for Translational Cancer Research (TranslaTUM) in Munich.

 

We are deploying genetic models to study molecular, immunological and translational aspects of pancreatic cancer. We utilize these systems to uncover molecular mechanisms as well as inflammatory and immune pathways that are required for tumor initiation and -progression in vivo (e.g. Nature 2018, 554:62-68; Nat. Commun. 2016, 7:10770; Nat Med. 2014, 20:1340-7; Cancer Cell. 2013,24:15-29, Cancer Cell. 2013,23:406-20, Nat Commun. 2013;4:1630; PNAS 2011, 108:9945-50). During the past decade, our lab has generated a comprehensive resource of pancreatic primary tumors and primary cell cultures. Multiple NGS methods have been performed to decipher the molecular makeup of these tumors. The advertised project focuses on unraveling tumor heterogeneity and its impact on treatment response and resistance using single cell sequencing techniques and will be performed in close collaboration with the Floßdorf lab (Dr. rer. nat. Michael Floßdorf) at TUM.

 

We are an enthusiastic and international team and offer intensive training and mentoring. The successful candidate will have the opportunity to:

                Set up bioinformatics platforms and develop computational pipelines for the analysis of single cell RNA-sequencing and single cell DNA-sequencing datasets

                Integrate these datasets with molecular (WES, WGBS, lcWGS, ChIPseq, ATACseq), phenotypic (e.g. histology) and clinical information

                Apply bioinformatics techniques to published/unpublished data for the analysis and interpretation of omics datasets

                Aid researchers select and use computational and statistical tools relevant to their single cell sequencing projects

 

The successful candidate will interact within a multidisciplinary environment of biologists, clinicians, computational scientists and mathematicians within the TranslaTUM. She/he will work closely with a diverse team to formulate hypotheses and validate predictions using genomic and transcriptomic assays. She/he will be exposed to cutting edge experimental methods to study translational aspects of cancer.

 

We are looking for an exceptional self-motivated computational scientist with a strong analytical background. Previous exposure to and experience with bioinformatics as well interests in molecular aspects of cancer research are an asset, but not required. Due to the interdisciplinary framework and close collaboration with wet-lab scientists, communicative skills are essential.

 

We give priority to severely disabled applicants with essentially equal qualifications. Payment according to tariff (TV-L).

 

We are looking forward for you application!

 

Interested candidates should send a CV with cover letter, certificates, and letters of recommendation by e-mail to: Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!

 

Univ.-Prof. Dr. med Dieter Saur

Institut für Experimentelle Tumortherapie

Klinik und Poliklinik für Innere Medizin II

Klinikum rechts der Isar der Technischen Universität München

Ismaninger Straße 22

81675 München

 

 

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

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