ISCB Affiliated Group Logo

Stellenangebote

PhD Positions in Computational Cancer Research in Heidelberg

Are you interested in solving fascinating biological or medical questions computationally?

 

At the German Cancer Research Center (DKFZ) in Heidelberg, Germany’s largest biomedical research institute, computational scientists work at the forefront of cancer research. They combine inter­disciplinary approaches from physics, biology, bioinformatics and statistics to analyze and understand complex biological and medical data.

 

Main activities at the DKFZ involving big data:

•             Development and application of computa­tional methods for the integrative analysis of genomic, epigenomic, transcriptomic, proteomic, meta­bolomic and radiomic data

•             Development of methods for modeling and simulation of biological and medical processes

•             DNA mutation analysis by next-generation DNA sequencing of individual human cancer genomes

•             Application of state-of-the-art technologies in automated live-cell imaging and image analysis

•             Computer-assisted radiology and surgery

•             Biostatistical evaluation of experimental and clinical data

•             Integration and development of new methods for systems biology and systems medicine

 

More information about computational research at the DKFZ can be found at:

https://www.dkfz.de/en/forschung/schwerpunkte/fsp-e.php?campaign=phd/bioinf

and

https://www.dkfz.de/en/forschung/schwerpunkte/fsp-b.php?campaign=phd/bioinf

 

Full funding is provided for the duration of the PhD.

 

If you are interested in doing your PhD in the field of computational cancer research, why not join the International PhD Program at the DKFZ with more than 500 PhD students?

More information about the program at http://www.dkfz.de/en/phd-program/index.html?campaign=phd/bioinf

 

 

Application deadline: 5th January 2019

Postdoc: Bioinformatics, Cancer Genomics, Epigenomics, Precision Medicine

A full PDF version of this job posting is available from the following URL: http://www.medical-epigenomics.org/files/Postdoc_Bioinformatics_Genomics_Cancer.pdf 

 

Postdoc: Bioinformatics, Cancer Genomics, Epigenomics, Precision Medicine

 

We are recruiting an ambitious computational postdoc who wants to pursue groundbreaking research in bioinformatics and its applications in cancer research, including data analysis and methods development in the areas of genomics, epigenomics, and precision medicine. Our group at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences in Vienna combines wet-lab biology/medicine including massive-scale data production (cancer genomes/epigenomes, single-cell sequencing, CRISPR screens) with advanced bioinformatics including data science algorithms and deep learning. We work closely with physicians at the Vienna General Hospital & Medical University of Vienna to advance cancer therapy by precision medicine.

 

The Project

Our lab has pioneered the combined use of high-throughput epigenomics and advanced computational methods for dissecting the epigenetic basis of cancer, toward the goal of enabling new approaches to precision medicine (Nature Reviews Cancer 2012).  In recent projects, we have connected epigenome and clinical imaging data for brain tumor progression (Nature Medicine 2018), investigated epigenetic heterogeneity in a cancer of childhood (Nature Medicine 2017), identified clinically predictive chromatin signatures in leukemia (Nature Communications 2016), and modeled the time series dynamics in leukemia response to therapy (paper in revision). All four papers were spearheaded and first-authored by bioinformaticians. Furthermore, we have developed technology that enables large-scale functional dissection using CRISPR single-cell sequencing (Nature Methods 2017) and drug screening (Nature Chemical Biology, in press). In ongoing and future work, for which the successful candidate will play a leading role, we are studying cancer immunotherapies, the tumor microenvironment, and time series of therapy response.

 

The Candidate

We are looking for ambitious candidates who want to build a scientific career in bioinformatics and/or data science research with applications in biology and medicine. Candidate should have a strong background in the quantitative sciences (computer science, bioinformatics, statistics, mathematics physics, engineering, etc.). We will also consider applicants with a background in biology or medicine who have strong quantitative skills (including programming) and a keen interest in pursuing computational projects (a combination with wet-lab research is possible).

 

The Lab (http://epigenomics.cemm.oeaw.ac.at/)

The Medical Epigenomics Lab at CeMM pursues an interdisciplinary and highly collaborative research program aimed at understanding the cancer epigenome and establishing its utility for precision medicine. The lab is internationally well connected and active in several fields:

·         Bioinformatics. New computational methods enable the high-throughput analysis of disease mechanism and therapy responses. We develop algorithms for multi-omics data analysis, time series modeling, and clinical data integration.

·         Epigenomics. Many diseases show deregulation of epigenetic cell states. As members of the Human Cell Atlas and the International Human Epigenome Consortium, we use epigenome sequencing to dissect the epigenetic basis of cancer and immunity.

·         Technology. Groundbreaking biomedical research is frequently driven by new technologies. Our lab is therefore heavily invested into technology development, including single-cell sequencing, CRISPR screens, and deep neural networks.

·         Digital Medicine. New technologies in the area of genomics, imaging, and wearable sensors transform medicine into a ‘big data’ science. We employ machine learning / artificial intelligence to leverage such data for better patient care.

 

The Principal Investigator (https://scholar.google.com/citations?user=9qSsTcIAAAAJ)

Christoph Bock is a principal investigator at CeMM. His research focuses on bioinformatics, epigenetics, cancer biology, and high-throughput technology development. He is also a guest professor at the Medical University of Vienna, scientific coordinator of the Biomedical Sequencing Facility at CeMM, and adjunct group leader for bioinformatics at the Max Planck Institute for Informatics. He is a member of the Young Academy of the Austrian Academy of Sciences (since 2017) and recipient of several major research awards, including the Max Planck Society’s Otto Hahn Medal (2009), an ERC Starting Grant (2016-2021), and the Overton Prize of the International Society of Computational Biology (2017).

 

The Institute (http://www.cemm.at/)

CeMM is an international research institute of the Austrian Academy of Sciences and a founding member of EU-LIFE. It has an outstanding track record of top-notch science (last few years: >10 papers in Nature/Cell/Science/NEJM, >25 papers in Nature/Cell sister journals) and medical translation. With just over a hundred researchers, CeMM provides a truly collaborative and personal environment, while maintaining critical mass and all relevant technologies. Research at CeMM focuses on cancer, inflammation, and immune disorders. CeMM is located at the center of one of the largest medical campuses in Europe, within walking distance of Vienna’s historical city center. A study by “The Scientist” placed CeMM among the top-5 best places to work in academia world-wide (http://the-scientist.com/2012/08/01/best-places-to-work-academia-2012). Vienna is frequently ranked the world’s best city to live. It is a United Nations city with a large English-speaking community. The official language at CeMM is English, and more than 40 different nationalities are represented at the institute. CeMM promotes equal opportunity and harbors a mix of different talents, backgrounds, competences, and interests. Postdocs at CeMM are paid according to the Austrian Science Fund’s salary scheme, which amounts to an annual gross salary slightly above EUR 50,000.

 

Please apply online (https://cemm.jobbase.io/job/6c6xaqal) with cover letter, CV, academic transcripts, and contact details of three referees. Applications will be reviewed on a rolling basis. Any application received by 10 January 2019 will be considered. Start dates are flexible.

 

Research assistant/associate [University of Bonn]

In the frame of the collaborative research project DBAC (DNA-Barcode Analyzer for CITES Species), financed by the Federal Agency for Nature Conservation (BfN), the University of Bonn invites applications for a

 

Research assistant/associate (100%, TV-L E 13)

 

to begin on Febuary 1st, 2019 at the Nees Institute for Plant Biodiversity in the research group of Prof. Dr. Dietmar Quandt.

 

DBAC aims to develop a browser based open source analyses platform for DNA-barcode sequences generated via next generation sequencing (NGS). The standalone platform will also be embedded in the online resources of the West German Genome Center (WGGC) at the University of Bonn. Therefore, the applicant should be familiar with programming, NGS and bioinformatics. The research project runs in collaboration with the Institute for Human genetics, University Hospital Bonn (UKB), the Max Planck Institute (MPI) for Plant Breeding Research (MPIPZ), and the Institute for Evolutionary Biology, University of Münster.

 

The position's requirements are:

  • Diploma, or Master in (Bio)-Informatics or Biology, Plant Science, Evolutionary Biology, or related fields,

  • Preferably a PhD in one of the fields

  • Proven qualifications in programming and bioinformatics

  • Experience with next generation sequencing data and DNA-Barcoding

  • High motivation, active participation, commitment and interaction with the collaborative partners

  • Language skills: English (written and spoken)

 

Application documents:

  • Letter of motivation

  • Curriculum vitae

  • Transcripts of studies

  • Two letters of recommendation

 

The temporary position is limited to the duration of the research program and therefore restricted to a maximum duration of 12 months. Starting date of the position is February or latest March 1st, 2019.

 

The University of Bonn is an equal opportunities employer.

 

Applications in German or English should be sent in electronic form by December 10th, 2018 to Prof. Dr. Dietmar Quandt at the following e-mail address: Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein! (subject: DBAC Application).

Post-doc or Ph.D. Candidate in Single Cell Bioinformatics

The Institute for Computational Genomics RWTH Aachen  performs
research on computational methods for analysis of epigenomics and
transcriptomics data (www.costalab.org). Over the past years, we have
developed methods for prediction of cell specific binding sites from
open chromatin data (Gusmao et al., Bioinformatics, 2015; Nature
Methods, 2016), inference of regulatory networks driving cell
differentiation (Lin et al., NAR, 2015; Allhoff et al.,
Bioinformatics, 2015) and prediction of long noncoding RNA regulation
via DNA-RNA interaction (Kalwa et al., NAR, 2016). We invite
applicants for a Posdoc or Phd Candidate position in Machine learning
methods for the analysis of single cell data. Candidates will perform
research on methods for analysis of single cell epigenomics and
transcriptomics scATAC-Seq, scRNA-Seq and scBS-seq. The project will
be performed in collaboration with medical specialists from the RWTH
Aachen University to understanding cellular changes during
inflammation and fibrosis and their support to cancer. The Institute
of Computational Genomics is a partner of the Human Cell Atlas
Consortia.

Applicants should hold a M.Sc. (Ph.D.) in Bioinformatics or Computer
Science. Experience in the analysis of biological sequences,
regulatory genomics and/or machine learning is required. The candidate
should have solid programming skills (C, Python and/or R) and
acquaintance with Linux. Experience with high performance computing is
a plus. The working language of the group is English. 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!.

PostDoc Physics / Computer Science with a focus on Machine Learning / Deep Learning [Würzburg]

The Comprehensive Heart Failure Center Würzburg (CHFC) is an Integrated Research and Treatment Center supported by the German Ministry of Education and Research. More than 120 scientists conduct interdisciplinary basic, translational, and clinical research and provide innovative patient care in the field of prevention of heart failure and its medical complications. The CHFC’s vision is to improve the awareness of heart failure as an urgent health challenge in society, to connect existing excellent basic science and clinical research and to implement preventive strategies for diagnostics and management as well as new therapies. In 2017, the CHFC moved into a modern research building comprising four departments, i.e. imaging, translational research, genetics, and clinical research.

The PostDoc shall implement machine and deep learning algorithms for the image based prediction of heart diseases.

Successful candidates should have relevant experience in machine/deep learning, preferably in the area of medicine and/or image analysis and reconstruction.

Willingness to work in an interdisciplinary team of physicists, engineers, medical doctors and veterinarians as well as the active involvement in the continuation of the CHFC Imaging Facilities are absolute prerequisites. Previous experience in the field of magnetic resonance tomography and/or computational fluid dynamics would be greatly appreciated.

We offer an interesting and challenging task in a cutting-edge work environment with the possibility to contribute and extent your skills.

Payment will be according to individual qualification and the TV-L. Disabled applicants will be considered preferentially in case of equivalent qualifications.

Applicants should submit their complete application document (full CV including certificates, motivation letter, names and addresses of two references) in a single PDF file to:

Comprehensive Heart Failure Center, Am Schwarzenberg 15, Haus A15, 97078 Würzburg, preferably via email (all together in one single PDF document) to Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!. For further information please visit www.dzhi.de or contact Prof. Dr. Laura Schreiber (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!).

 

Links: www.dzhi.de

PhD and PostDoc position in computational cancer biology [European Institute of Oncoglogy (IEO) in Milan]

The lab of Martin Schaefer at the European Institute of Oncoglogy (IEO) in Milan is now recruiting two early-career scientists with a strong computational background. We are looking for one PhD student and one PostDoc.
The aim of the open positions is to further the understanding of cancer evolution by developing methods that allow to identify cancer driver events beyond point mutations (such as epigenetic changes or chromosomal rearrangements) and to apply these methods to experimental and clinical data. More details on the research interests of the lab can be found here: schaeferlab.org.
Candidates should have expertise in statistics, programming and the analysis of omics data. In particular, we encourage researchers with interest in either population genetics or network biology to apply.
The IEO is one of Europe’s leading cancer research institutes in a central location of Milan and hosts a vibrant, international research community. It provides postgraduate education through the European School of Molecular Medicine SEMM with a PhD program in Systems Medicine.
The positions are available immediately but the starting date can be negotiated. For more information see https://www.schaeferlab.org/misc/join/ or contact Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!.

Postdoc Position: Bioinformatics of Long Noncoding RNA Functional Elements

The “Genomics of Long Non-Coding RNAs in Disease” Laboratory (GOLD Lab) at the University of Bern has an opportunity for a Bioinformatics Postdoc.

The Project: Understanding how long noncoding RNA (lncRNA) functions are encoded in their sequence is a great challenge in biology. Our goal is to discover, classify and characterise lncRNA functional elements by means of an integrative bioinformatic / experimental approach. You will lead the bioinformatic component to develop novel methods for identifying lncRNA elements and predicting their functions. In collaboration our experimental team, you will have ample opportunities for experimental validation of in silico-generated hypotheses.

The Group: We are an international and interdisciplinary group of researchers with a passion for lncRNA research. We foster an open and collaborative working environment. Our work is funded by the Swiss National Center for Competence in Research (NCCR) “RNA & Disease” (nccr-rna-and-disease.ch), and we participate in the GENCODE project and International Cancer Genome Consortium (ICGC). We also have excellent biomedical links at the University Hospital of Bern. For more information about us: gold-lab.org / twitter.com/goldlab_bern

The City: Bern, the capital of Switzerland, has a vibrant international community, numerous outdoors and cultural activities, and ranks among the best cities worldwide for quality of life (https://tinyurl.com/y9vrtb7d).

The Person: We seek a dedicated and dynamic colleague to integrate into our diverse team. You should have strong background in bioinformatics or computer science, and specifically some/all of: Unix environment, R, perl/python, analysis of NGS data, webservers/databases. Experience in lncRNAs, CRISPR-Cas9 is a plus.

Details: Ideal start date will be Q1 of 2019. Project is fully funded for 4 years. Salary is according to (generous) University of Bern scales.

Recent publications:

Carlevaro-Fita et al. Biorxiv https://www.biorxiv.org/content/early/2017/10/23/189753

Uszczynska-Ratajczak B et al. Nat Rev Genet. 2018 Sep;19(9):535-548. doi: 10.1038/s41576-018-0017-y.

Lagarde J et al. Nat Genet. 2017 Dec;49(12):1731-1740. doi: 10.1038/ng.3988.

To apply: Please send a motivation letter, publications list, list of references, and CV to Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein! with subject title: “Job application Bioinformatics Postdoc”. Informal enquiries are also welcome.

W3-Professur für Bioinformatik [Heidelberg]

Am Institut für Pharmazie und Molekulare Biotechnologie (IPMB) der Universität Heidelberg ist eine

W3-Professur für Bioinformatik

zu besetzen.

Die Einbettung der Professur in das IPMB eröffnet die Möglichkeit, bioinformatische Methoden unmittelbar auf experimentellen, biologisch-therapeutischen und biotechnologischen Gebieten anzuwenden. Aufgrund der führenden Position der Universität Heidelberg und der benachbarten biomedizinischen Forschungseinrichtungen bestehen für die Professur darüber hinaus hervorragende Vernetzungs- und Entwicklungsmöglichkeiten im translational-bioinformatischen Bereich. Von der/dem Stelleninhaber/in werden ausgewiesene Forschungskompetenzen in der Bioinformatik mit Fokus auf Anwendungen in der Pharmakogenomik, der personalisierten Medizin oder Biotechnologie erwartet.

Von der/dem Stelleninhaber/in wird die Fähigkeit und Bereitschaft erwartet, die Lehrveranstaltungen in den Fächern Bioinformatik und Mathematik für die Bachelor- und Masterstudiengänge Molekulare Biotechnologie und den Staatsexamens-Studiengang Pharmazie persönlich abzuhalten. Der/die Stelleninhaber/in gestaltet die Lehre im Schwerpunkt Bioinformatik des BSc Studiengangs Molekulare Biotechnologie.

Die Einbindung der Professur in die vom IPMB verantworteten Studiengänge eröffnet die Möglichkeit zur forschungsorientierten Lehre, welche in den letzten Jahren beispielsweise durch die Erfolge im iGEM Wettbewerb eine erhebliche Sichtbarkeit erzielt hat.

Voraussetzung für die Bewerbung ist ein abgeschlossenes Hochschulstudium, sowie nach § 47 Abs. 2 Landeshochschulgesetz die Habilitation, die erfolgreich evaluierte Juniorprofessur oder eine vergleichbare Qualifikation, insbesondere die Leitung einer unabhängig evaluierten Nachwuchsgruppe. Die Universität Heidelberg strebt einen höheren Anteil von Frauen in den Bereichen, in denen sie unterrepräsentiert sind, an. Qualifizierte Wissenschaftlerinnen werden daher besonders um ihre Bewerbung gebeten. Schwerbehinderte werden bei gleicher Eignung bevorzugt.

Bewerbungen mit Lebenslauf, wissenschaftlichem Werdegang, Schriftenverzeichnis, Listen der bisherigen und laufenden Drittmittelprojekte und Lehrveranstaltungen, sowie einer kurzen Darstellung der zukünftigen Forschungsplanung werden, bevorzugt in elektronischer Form, zusammengefasst in einem einzelnen pdf-Dokument, bis zum 04.01.2019 erbeten an:
Frau Prof. Dr. Karin Schumacher, Dekanin der Fakultät für Biowissenschaften, Im Neuenheimer Feld 234, 69120 Heidelberg, e-mail:
Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!, unter dem Betreff: „Bioinformatik 2019“. 

Wir bitten um Verständnis, dass eingegangene Bewerbungsunterlagen nicht zurückgesandt werden.

Weitere Informationen zum Institut für Pharmazie und Molekulare Biotechnologie (IPMB) sind zu finden unter: https://www.ipmb.uni-heidelberg.de/ 

PhD and Post-doc position in Bioinformatics [Meyer lab]


(1) Post-doc position in RNA structure and transcriptome Bioinformatics at the BIMSB-MDC in Berlin, Germany

application deadline: Friday, 30. November 2018

for details see

https://www.mdc-berlin.de/career/jobs/post-doc-position-bioinformatics

and the Meyer lab web page

https://www.mdc-berlin.de/meyer#t-news

(2) PhD position in RNA structure Bioinformatics at the BIMSB-MDC in Berlin, Germany

application deadline: Friday, 30. November 2018

for details see

https://www.mdc-berlin.de/career/jobs/phd-position-bioinformatics

and the Meyer lab web page

https://www.mdc-berlin.de/meyer#t-news

Bioinformatician for translational cancer research (Saur lab)

The Klinikum rechts der Isar university hospital of the Technical University of Munich is a major European center of medical care and education. With over 1.161 beds and almost 5.500 employees, we treat 300.000 patients per year with state-of-the art care.

The “Department of Medicine II” of the Technical University of Munich (TUM) and the Institute of Translational Cancer Research at TUM and the German Cancer Research Center invites applications for a PhD Student/Post-doctoral fellow or Bioinformatician staff position in Bioinformatics and Cancer Biology 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 isolated a cohort of thousand PDAC primary cell cultures. Molecular characterization with multiple NGS methods has been performed. The advertised project is therefore focused on unraveling the molecular mechanisms of tumor development by analyzing the before mentioned annotated resources.

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

- Set up a bioinformatics platform and develop in-house computational pipelines for analysis of omics datasets, with particular focus on Next-Generation DNA Sequencing (NGS) platform for Whole Exome Sequencing, Whole Genome Sequencing and RNA-seq.

- Utilize available software and pipelines to generate and analyze NGS datasets from DNA- and RNA-based experiments;

- 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 projects.

 

The candidate will interact within a multidisciplinary environment of biologists, clinicians, computer scientists and mathematicians within the TranslaTUM. The successful candidate will work closely with a diverse team to formulate hypotheses and validate predictions using genomic assays. She/he will be exposed to cutting edge methods to study translational aspects of cancer (e.g. Cre/loxP and Flp/frt based dual- and triple recombinase systems, organoid culture, orthotopic transplantations of organoids, CRISPR/Cas9, in vivo imaging, in vivo transposon mutagenesis).

We are looking for a computational scientist with good record at the PhD or experienced MSc level. Previous exposure to and experience with bioinformatics as well interests in molecular aspects of cancer research is essential.

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

Please send your application including a letter of motivation, CV, certificates, recommendation letters in one pdf file to Prof. Dieter Saur (e-mail: Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!).]

Links: https://www.translatum.tum.de/