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PhD position in algorithmic bioinformatics [Canzar lab, Munich]

The Canzar lab at the Gene Center of the University of Munich (LMU) is recruiting a PhD student in algorithmic bioinformatics, to start in spring/summer 2017. The position provides a competitive salary for a period of 4 years.

We develop algorithms for the analysis of high-throughput sequencing data like (single-cell) RNA-seq as well as for third-generation technologies like PacBio and Oxford Nanopore. Supporting the lab's agenda, the successful candidate will use tools and techniques from large-scale optimization and machine learning to develop and engineer efficient algorithms that leverage large numbers of publicly available sequencing data sets. Translated into scalable and usable software, they will facilitate the systematic exploration of important biological or biomedical questions, such as the functional impact of alternative splicing.

The Canzar lab is embedded in the stimulating, interdisciplinary environment of the Graduate School for Quantitative Biosciences Munich (QBM), which integrates approaches ranging from bioinformatics and theoretical biophysics to molecular systems biology. The lab is housed in the new Research Center for Molecular Biosystems (BioSysM) at the life sciences campus Grosshadern/ Martinsried, with excellent access to other parts of Munich via public transport.

We are seeking motivated candidates with an excellent Master’s degree (or equivalent) in computer science, (applied) mathematics, or bioinformatics to join our lab. We expect the candidate to have a solid background in algorithm design and good programming skills as well as an interest in interdisciplinary work (biology, medicine).

To apply, send your application materials, including a motivation letter, your CV, and names of two referees in a single pdf file to Stefan Canzar (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!), who can also supply further information about this position. For more information about our lab at LMU, please visit our website at https://canzarlab.github.io/.

Applications will be reviewed starting from April 17, 2017   

Manager m|f Bioinformatics/Biostatistics [Miltenyi Biotec GmbH]

Your Role:
-You develop new methods and algorithms in collaboration with R&D members and software engineers for the analysis of high content type of data, such as microscopy, flow cytometry, and single cell sequencing
-You establish and maintain databases for biomarker discovery and functional interpretation
-You serve as an expert in selecting the right and innovative statistical methods for data analysis, experimental design and conducting the actual analysis
-As part of the R&D department you lead a team of 3-4 research professionals and manage the interface to other departments and key persons critical for project success, i.e. clinical development, engineering and marketing

Your Profile:
-You have successfully finished an academic education in computer science, natural scientific (e.g. Bioinformatics, Mathematics, Physics, Statistics) or similar
-You have profound experience in programming (e.g. R, Python, C++, Java, Linux shell scripting, and/or other languages) and statistics applied to life-sciences
-You have proven competences in database construction, development of biological classifiers and algorithm
-You bring along a proven track record of driving innovation and strategic change processes
-Basic knowledge in cell biology, immunology or cancer biology is advantageous
-Ideally you are experienced with working on Phase I- IV study trials within the medical device and/or pharmaceutical industry

What we offer:
-Flexible working hours for a family-friendly career
-Personal and professional development in our in-house academy
-Intercultural and cross-border collaboration
-A modern workplace and a role you can help shape
-Short communication lines and a collegial company culture

Who we are:
-Our innovative solutions in the area of biomedical research and biomedicine make us a pioneer for the therapy of serious diseases
-Today we are an interdisciplinary team of more than 1800 employees
-Based in Germany near Cologne and with 14 additional, international locations we are a multicultural team
-We develop innovative cell and gene therapy solutions – together, we want to make cancer history

Contact us:
Miltenyi Biotec GmbH
Benjamin Malik
HR Specialist | Talent Acquistion
Friedrich-Ebert-Straße 68
51429 Bergisch Gladbach
Phone: +49 2204 8306-2430
www.miltenyibiotec.com

Apply online:
https://miltenyibiotec.softgarden.io/job/897406?l=de

Research Scientist Bioinformatics Machine Learning/Deep Learning (m/f) [Bayer, Berlin]

Your tasks and responsibilities
• Leveraging Bayer’s unique position in Life Sciences: Research at the interface of human, animal and plant health.
• Be an active member (m/f) of a highly interdisciplinary and cross-organizational team, including scientists from our divisions across Europe
• Contribute to the implementation of a deep learning platform to leverage data in computational chemistry, pharmacokinetics, toxicology using deep learning
• Extensively validate and further improve the deep learning platform for various property predictions of crop science and drug development compounds
• Research, design, and implement deep learning algorithms for analysis problems related to high-throughput image analysis, for prediction of properties of molecules, and for analysis of complex genomic data
• Generate direct impact on our discovery projects to help patients and ensure proper nutrition of an ever growing population

Who you are

• PhD degree in bioinformatics, computational biology or chemistry, computer science or related fields and a solid background in chemistry or biology
• Experience with state of the art machine learning methods and model selection concepts
• Previous experience with deep learning is of advantage
• Excellent programming skills in Python are essential, additional skills in R or C++ is of advantage
• Proficiency in writing code and using a Linux high performance environment
• Expertise in handling, processing, integrating and analyzing data sets related to research in the pharmaceutical industry
• Highly creative personality with outstanding problem solving ability and the willingness to undertake challenging analysis tasks
• Strong interpersonal skills, excellent written and verbal communication, and the ability to work effectively both independently and in cross-functional teams • Willingness to travel between research sites
• Spoken and written proficiency in English is mandatory

Your application

This is a fixed-term contract for two years. We offer a competitive salary and benefits package and support both individual and professional development. Applications for this position should be made online at www.career.bayer.de, submitting a cover letter, your CV and references as well as your salary expectations.

Bayer welcomes applications from all individuals, regardless of race, national origin, gender, age, physical characteristics, social origin, disability, union membership, religion, family status, pregnancy, sexual orientation, gender identity, gender expression or any unlawful criterion under applicable law. We are committed to treating all applicants fairly and avoiding discrimination.

Country: Germany
Location: Berlin
Reference Code: 0000190819

Apply online
https://karriere.bayer.de/de/job/Research-Scientist-Bioinformatics-Machine-Learning-Deep-Learning-m-f--0000190819.html

Contact us:
Info-Hotline: +49 214 30 99779

Statistikerin / Statistiker [Ruhr-Universität Bochum]

Die Medizinische Bioinformatik des MPC sucht zum nächstmöglichen Zeitpunkt eine Statistikerin / einen Statistiker für die Auswertung quantitativer Proteomik-Daten (Auswertungs- / Experimentplanung, Anwendung und Anpassung von Methoden).

Anforderungsprofil:
Sie haben Kenntnisse und / oder Erfahrungen in den folgenden Bereichen der Statistik / Bioinformatik:
•Auswertungs-- / Experimentplanung (z. B. abhängige Variablen, Umgang mit bekannten und unbekannten Kovariablen, Fallzahlabschätzung)
•Univariate Methoden zur Datencharakterisierung und Biomarker-Detektion (z. B. statistische Testtheorie, nichtparametrische Tests, parametrische Tests wie z. B.t-Test oder ANOVA, Korrektur bei multiplem Testen)
•Multivariate Methoden zur Datensatzcharakterisierung, Komplexitätsreduktion und variable / feature selection (Hauptkomponentenanalyse, Methoden des hierarchischen Clustering, Klassifikationsmethoden wie z. B. random forest oder support vector machines)
•Expertenwissen in R (Funktionen anwenden und programmieren, Erfahrung mit einer Entwicklungsumgebung wie z. B. RStudio)
•Kooperationsfähigkeit mit fachfremden Wissenschaftlern (z. B. Naturwissenschaftler, klinische Forscher)

Tätigkeiten:
•Planung von Auswertungen / Experimenten zusammen mit den datengenerierenden Wissenschaftlern (z. B. Naturwissenschaftler, klinische Forscher)
•Anwendung adäquater Methoden
•Anpassung von vorhandenen Methoden an spezifische wissenschaftliche Fragestellungen
•Darstellung der statistischen Arbeiten in Publikationen, Berichten, Anträgen

Art der Beschäftigung: Vollzeit
Vergütung: TV-L E13 (100%)
Zeitraum der Beschäftigung: 15. Mai 2017 – 31. Dezember 2018 (Verlängerung des Drittmittelprojekts nach Zwischenevaluierung bis Februar 2020 möglich)

Bewerbungsfristende: Freitag, 31. März 2017 - 23:59
weitere Informationen und Kontakt: https://www.stellenwerk-bochum.de/jobboerse/wissenschaftl-mitarbeiterin-statistikerin-statistiker-bo-2017-02-22-105438

 

(Bio-)Informatikerin / (Bio-)Informatiker [Ruhr-Universität Bochum]

Die Medizinische Bioinformatik am Medizinischen Proteom-Center sucht zum nächstmöglichen Zeitpunkt:

eine (Bio‑)Informatikerin / einen (Bio‑)Informatiker für die Anpassung / Weiterentwicklung wissenschaftlicher Auswerte-Software für cloud computing.

Die Medizinische Bioinformatik realisiert unter anderem das BMBF-drittmittelgeförderte Service-Center „Bioinformatik der Proteomik – BioInfra.Prot“ des Deutschen Netzwerks für Bioinformatik Infrastruktur (www.denbi.de) und ist beteiligt am Europäischen Proteinforschungskonsortium PURE (http://www.pure.rub.de/) sowie an einem DGUV-geförderten Projekt zur Verifizierung von neuen molekularen Markern für die Frühdiagnose asbestassoziierter Lungentumoren.

Anforderungsprofil:
Sie haben Kenntnisse und / oder Erfahrungen in den folgenden Bereichen der Informatik / Bioinformatik:
•Administration von Linux-Betriebssystemen, Linux Skript-Programmierung
•OpenStack
•Verteiltes Rechnen und Virtualisierung
•Bioinformatik-Algorithmen / Auswerte-Software für Hochdurchsatz- / Omics-Daten

Tätigkeiten:
•Anpassen / Weiterentwickeln von wissenschaftlicher Auswerte-Software aus dem Bereich ‚Bioinformatik der Proteomik‘ für die Benutzung in cloud-Infrastrukturen (z. B. de.NBI-cloud)
•Unterstützung bei der Etablierung der wissenschaftlichen cloud-Infrastruktur (z. B. Anmelde- und Authentifizierungs-Service, Ressourcenverteilung / governance)
•Technische Unterstützung von Wissenschaftlern bei der Anwendung von Auswerte-Software in der cloud

Art der Beschäftigung: Teilzeit
Vergütung: 50% TV-L E13
Zeitraum der Beschäftigung: 15. Mai 2017 – 28. Februar 2018 (Verlängerung des Drittmittelprojekts nach Zwischenevaluierung bis Februar 2020 möglich)

Bewerbungsfristende: Freitag, 31. März 2017 - 23:59

weitere Informationen und Kontakt: https://www.stellenwerk-bochum.de/jobboerse/wissenschaftl-mitarbeiterin-bio-informatikerin-bio-informatiker-bo-2017-02-17-104803

Bioinformatics student project [Schulte lab, Charité, Berlin]

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

Identifying circRNAs in Neuroblastoma

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

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

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

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

How to apply?
Please send applications, as well as informal requests, to Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!.

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

 

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

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

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

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

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

Bitte senden Sie Ihre aussagekräftigen Bewerbungsunterlagen unter Hinweis auf die Ausschreibungsnummer 387 innerhalb von 2 Wochen nach Erscheinen dieser Anzeige per E-mail an Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein! (auch bei Rückfragen).

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

10 Ph.D. Student Positions (Code Number 16-17)

The International Max Planck Research School (IMPRS) for Genome Science is offering

10 Ph.D. Student Positions
(Code Number 16-17)

The IMPRS for Genome Science is a new graduate program established as a cooperation between the University of Göttingen and several other research institutions at the Göttingen Campus, including the Max Planck Institutes. Our research school aims at qualifying young scientists in the analysis of large data sets and research at the interface between experimental and theoretical disciplines in genome science. The students will be able to work in different fields of research, including experimental disciplines like genomics, transcriptomics, proteomics, metabolomics, and bioimaging as well as theoretical disciplines such as stochastics, bioinformatics, theoretical physics, and computational biology. Positions offered are to pursue Ph.D. projects in the areas of the life and computational sciences or related fields.

Requirements:
Candidates typically hold an outstanding Master's (or equivalent) degree in the life sciences or computational sciences, and have an interest in interdisciplinary projects. Criteria for admission include academic skills and experience, motivation and commitment, communication skills, knowledge of the English language, and creativity.

Application Process:
Applications can only be submitted online until April 15, 2017 via this website:

http://imprs-gs.uni-goettingen.de

Applicants must additionally submit a single pdf-file including a motivation letter, CV, and academic records. Letters of recommendation from two referees familiar with the work of the applicant must be sent independently to Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!.

Contact:
International Max Planck Research School for Genome Science
Prof. Dr. Patrick Cramer (Spokesperson)
Dr. Henriette Irmer (Coordinator)
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11
37077 Göttingen, Germany

Phone: +49 551 201-2821
For further information about the program please visit imprs-gs.uni-goettingen.de.
Informal enquires may be sent to Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!.

The Max Planck Society and the University of Göttingen are committed to increasing the number of individuals with disabilities in its workforce and therefore encourages applications from such qualified individuals. Furthermore, the Max Planck Society and the University of Göttingen seeks to increase the number of women in those areas where they are underrepresented and therefore explicitly encourages women to apply.

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

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

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

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

Prerequisites

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

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

Location                                Braunschweig (Germany)

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

Probation period                  6 months

Salary                                    TVöD E14

Published on                         13.02.2017

Closing date                          26.03.2017


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

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

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

All documents and information should be provided in English.

For questions regarding the bioinformatics projects, please contact Prof. Alice McHardy  (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!).
Entitle your email with the subject line ‘DZIF postdoc application’.

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


Links:

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

 

Postdoctoral position - Bioinformatics for Next Generation Sequence Analysis

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

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

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

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

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

Location                                Braunschweig (Germany)

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

Probation period                  6 months

Salary                                    TVöD E14

Published on                         13.02.2017

Closing date                          26.03.2017


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

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

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

All documents and information should be provided in English.

For questions regarding the bioinformatics projects, please contact Prof. Alice McHardy  (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!).
Entitle your email with the subject line ‘DZIF postdoc application’.

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