ISCB Affiliated Group Logo

Stellenangebote

Phd Candidate/Postdoctoral position in Single Cell Computational Epigenomics [RWTH Aachen]

The Bioinformatics Group RWTH Aachen University performs research on computational methods for analysis of epigenomics and transcriptomics data. 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 Phd Candidate/Postdoctoral position in one of the following topics:

1) Machine learning methods for the analysis of single cell epigenomics data.

2) Sequence analysis algorithms for detection of interactions of long non-coding RNAs with DNA.

Candidates will perform research on methods for analysis of single cell epigenomics and transcriptomics scATAC-Seq, scRNA-Seq and scBS-seq. These projects will be performed in collaboration with stem cell and medical specialists from the RWTH Aachen University.

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!.

 The Bioinformatics Research Group (costalab.rwth-aachen.de) is supported by the Interdisciplinary Center for Clinical Research Aachen (IZKF) and hosted by the Institute for Biomedical Engineering, Department of Cell Biology, RWTH Aachen University Hospital and the Helmholtz Institute for Biomedical Engineering, RWTH Aachen.

 

Computational Biologist / Bioinformatician ( Charité Universitätsmedizin Berlin)

The Pediatric Oncology Reseach Institute of the Department of Pediatric Hematology, Oncology and SCT at the Charité – Universitätsmedizin Berlin is a multidisciplinary research institute closely affiliated to the Helmholtz Institute, Max Delbrück Center for Molecular Medicine (MDC) and the Berlin Institute of Health (BIH).

The goals of the research group of Prof. Johannes Schulte are an improved understanding of tumor biology and development of new therapeutic options for neuroblastoma, a highly devastating childhood cancer.

Investigating primary and relapse tumors as well as tumor model systems, we seek to identify key factors of tumor pathogenesis, tumor progression and tumor evolution. The research strategy of our interdisciplinary team includes multi-omics and wet lab approaches. Concepts identified in high-throughput analyses are validated in vitro and in vivo. To this end, we use cell culture model systems, patient-derived tumor xenografts and genetically engineered mouse models. Furthermore, we participate in major European Systems Biology consortia for generating and analyzing high-throughput sequencing data.

We are looking for a computational biologist / bioinformatician to develop and apply new analytical approaches for the study of neuroblastoma genomics. This research position is embedded into an interdisciplinary team of clinicians, biologists, biotechnologists and bioinformaticians and into the dynamic intellectual environment of the Charité and the BIH. The successful applicant will 1) set up analytical pipelines for diagnostic targeted resequencing, 2) plan and perform analyses within neuroblastoma research projects, 3) structure and manage high-throughput data 4) support existing collaborations with other bioinformatics groups (e.g. Nils Blüthgen, Uwe Ohler, Altuna Akalin, Dieter Beule). In collaboration with these groups, the applicant will be able to pursue his/her own bioinformatics research projects.

Prerequisites

The ideal candidate has a Master's (MSc) or PhD degree in computer science, computational biology, bioinformatics, statistics or any other quantitative discipline and proven experience in the analysis of next-generation sequencing data.

Moreover, the candidate should have excellent programming skills for data analysis, preferably in R, and be familiar with Bash scripting and one other scripting language such as Perl/Python. In-depth knowledge of applied multivariate statistics and data visualization techniques are also required.

An advanced knowledge of tumor biology and a publication track record of genomics-based oncology research are highly desirable.

Excellent communication and project management skills as well as the motivation for a long-time commitment in our department are a requirement.

Conditions

The position is open from August 2017. Salary will be according to the Charité internal tariff TV-C E13 with regular working time of 39 h per week. The initial contract will be until 31st of July, 2019 with the option of extension depending on extramural funding resources. The Charité – Universitätsmedizin Berlin is an equal opportunity employer and supports gender equality. Persons with disabilities will be preferred if equally qualified. The Charité cannot reimburse any incurring travel expenses.

Please, submit your application by email, including a cover letter describing your interests, a current CV, and 2-3 letters of recommendation, by August 13, 2017, to Prof. Johannes Schulte and Dr. Joern Toedling (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein! and Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!) and indicate the registration number DM.127.17.

Machine Learning in BioMedicine (ERC-funded postdoc position) [CeMM]

 We are recruiting a computational postdoc who wants to pursue groundbreaking research on digital medicine, combining a strong background in machine learning with cutting-edge technologies such as single-cell sequencing, wearable devices, ubiquitous sensors, and augmented reality, and a keen interest in biomedical applications.

Our group is based at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences in Vienna, on the campus of one of the world’s largest hospitals and medical schools. We combine a strong background in computational methods with the expertise, collaborations, and funding to pioneer the use of advanced digital technology in biotechnology and personalized medicine.

The Project

The successful candidate will develop and apply advanced machine learning technology (e.g., deep neural networks, kernel methods, non-linear regression, and/or causal modeling) in order to discover fundamental mechanisms of biology and medicine and to advance personalized medicine. Potential applications may include (but are not limited to) single-cell sequencing of cancer, 3D reconstruction of tumors and epigenetic landscapes, mobile health technology for patients with brain cancer, and pattern discovery in heterogeneous biomedical datasets. Our location on one of the largest medical campuses in Europe ensures direct relevance to medicine, while our close collaboration with the Max Planck Institute for Informatics (Germany) provides first-hand access to a cutting-edge computer science environment.

The Candidate

We are looking for highly motivated and academically outstanding candidates who want to pursue a career in machine learning research and its 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 medicine or in biology (e.g., functional genomics, chemical biology, human genetics, molecular medicine, etc.) who have strong quantitative skills and a keen interest in pursuing computational projects with a major machine learning component.

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:

- Epigenomics. Many diseases show widespread deregulation of epigenetic cell states. As members of the International Human Epigenome Consortium, we use epigenome sequencing to dissect the epigenetic basis of cancer and immune disorders.
- Technology. Groundbreaking biomedical research is often driven by new technologies. Our lab is therefore heavily invested into technology development, including single-cell sequencing, CRISPR screens, and epigenome editing.
- Bioinformatics. New algorithms and advanced computational methods allow us to infer epigenetic cell states from large datasets, in order to reconstruct the epigenetic landscape of cellular differentiation and complex diseases.
- Diagnostics. New technologies (genome sequencing, mobile devices, etc.) provide important information for personalized medicine. We develop and validate assays and algorithms for translating the value of digital medicine into routine clinical practice.

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

Christoph Bock is a computational biologist and principal investigator at CeMM. He is also a guest professor at the Medical University of Vienna’s Department for Laboratory Medicine, scientific coordinator of the Biomedical Sequencing Facility at CeMM, and an adjunct group leader for bioinformatics at the Max Planck Institute for Informatics. Christoph Bock obtained his PhD summa cum laude from Saarland University and the Max Planck Institute for Informatics in 2008, followed by three years of postdoctoral research at the Broad Institute of MIT and Harvard, where he contributed to the NIH Roadmap Epigenomics project. He has been a principal investigator of BLUEPRINT (in the International Human Epigenome Consortium), and he co-founded Genom Austria, a citizen science project that is the Austrian partner in the International Network of Personal Genome Projects. He has received several major research awards, including the Max Planck Society’s Otto Hahn Medal (2009), a New Frontier Group grant by the Austrian Academy of Sciences (2015-2020), 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 five 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. We are convinced that diversity and a multicultural work environment are clear advantages for successful research and are committed to attract, develop, and advance the most talented individuals regardless of their gender, sexual orientation, religion, age, disability status or any other dimension of diversity.

 Please apply online (https://cemm.jobbase.io/job/2ikdvm1m) with cover letter, CV, academic transcripts, and contact details of three referees. Applications will be reviewed on a rolling basis. Any application received by 31 August 2017 will be considered. Start dates are very flexible.

 

2 Promotionsstellen am Zentrum für Bioinformatik Hamburg

Am Zentrum für Bioinformatik Hamburg (ZBH), Abteilung AMD (Prof. Rarey), sind ab dem 1. Oktober 2017 zwei Promotionsstellen zu besetzen. Forschungsschwerpunkt der Gruppe liegt in der Entwicklung neuer Methoden in den Bereichen Chemieinformatik, Wirkstoffentwurf und strukturelle Bioinformatik und deren Anwendungen. Wir zeichnen uns durch eine anwendungsnahe Forschung aus, die wir durch vielfältige Industriekontakte und -kooperationen stärken. Softwarekomponenten aus unserer Forschung werden weltweit in der akademischen und industriellen Forschung eingesetzt. Als Bio- oder Chemieinformatiker, naturwissenschaftlicher Informatiker oder Chemiker mit guten Programmierkenntnissen sind Sie bei uns genau richtig.

Nähere Informationen finden Sie unter http://www.zbh.uni-hamburg.de/service/stellen.html

Bioinformatiker / Informatiker (w/m) (MVZ Humangenetik Ulm)

Das MVZ Humangenetik Ulm versorgt niedergelassene Ärzte und Ärztinnen sowie Krankenhäuser mit dem kompletten Spektrum humangenetischer Untersuchungen. Für den Bereich Molekulargenetik/Next-Generation Sequencing (NGS) suchen wir zum nächstmöglichen Zeitpunkt in Vollzeit einen Bioinformatiker / Informatiker (w/m).

 

 

Aufgaben

 

·         Allgemeine bioinformatische Unterstützung der Abteilung Molekulargenetik durch die Entwicklung neuer Tools und Datenbanken zur Optimierung und Automatisierung von In-House-Prozessen

 

·         Aufbau des Workflows im Bereich der NGS-Datenprozessierung

 

·         Analyse und Validierung von Daten und QC-Parametern im Bereich Next-Generation Sequencing durch die Entwicklung neuer Algorithmen sowie durch die Zusammenarbeit mit Kooperationspartnern

 

 

 

Voraussetzungen

 

·         Hochschulabschluss (Bachelor/Master) im Bereich Bioinformatik oder ähnliche Fachrichtung

 

·         Fundierte Kenntnisse im Umgang mit Linuxsystemen

 

·         Programmiererfahrung (Perl, Java, Python o.ä.)

 

·         Molekulargenetische Kenntnisse erwünscht, insbesondere im Bereich NGS von Vorteil

 

·         Teamfähigkeit, Flexibilität und Kreativität

 

·         Zuverlässigkeit, Selbstständigkeit und hohes Qualitätsbewusstsein

 

 

 

Es erwartet Sie eine verantwortungsvolle und abwechslungsreiche Tätigkeit in enger Zusammenarbeit mit dem Team Molekulargenetik sowie eine kreative eigenständige Arbeitsweise in freundlicher Arbeitsatmosphäre mit langfristiger beruflicher Perspektive.

 

 

 

 

 

Wir freuen uns auf Ihre schriftliche Bewerbung an:

 

 

 

MVZ Humangenetik Ulm

 

Sekretariat

 

Karlstraße 33

 

89073 Ulm

 

Tel.: 0731-850773-0

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

Postdoctoral Position in Vienna (Systems Biology | Network Medicine | Bioinformatics)

The Boztug Lab at CeMM in Vienna is searching for a motivated postdoctoral fellow for a project within a productive scientific collaboration with the Menche Lab at CeMM. We joined forces to realize an ambitious project at the intersection of rare disease genetics, network biology and precision medicine that has the potential to have a lasting impact on each of these three fields.

The Project — There are more than 7,000 rare diseases and collectively they affect around 5% of the population. Many of them are caused by single-gene defects and thereby offer unique opportunities to establish clear mechanistic genotype-phenotype relationships. To establish the precise molecular mechanisms by which individual gene aberrations perturb cellular networks, systems biology approaches will be instrumental. Rare diseases thus have extraordinary potential to serve as a paradigm for precision medicine that bridges the gap between wholistic, systems based analyses and actionable insights for personalized therapy. The overarching goal of the joint project is to rationalize patient-specific workflows from gene discovery and underlying pathomechanisms to targeted therapy. The project lead by Kaan Boztug will focus on using network biology to more efficiently identify novel disease etiologies underlying immunodeficiencies and to systematically dissect rare disease clusters to compare to more common immune disorders and to predict drug responses. The project will also involve the development of multi-layer network approaches to integrate diverse genomic data into a predictive platform for personalized medicine. This research project is funded by WWTF (https://www.wwtf.at).

The Research Groups — Kaan Boztug (www.rare-diseases.at) is a leading immunologist and rare diseases researcher and director of the newly founded Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases (LBI-RUD). His lab is interested in the genetics of rare primary immunodeficiencies and rare diseases of hematopoiesis with a special focus on disorders with autoimmunity and/or autoinflammation (Dobbs et al., NEJM 2015; Salzer et al., Nat Immunol 2016). His goal is to identify targets for tailored molecular therapies and to develop precision medicine approaches for diagnostics and treatment. His group applies a combination of state-of-the-art genomic technologies including next generation sequencing, a wide range of cellular and molecular techniques and innovative systems biology to elucidate novel pathways important for hematopoiesis and immune system homeostasis, to make a real impact by translating concepts and tools to the clinic. Jörg Menche (http://www.tinyurl.com/joergmenche) leads a newly established computational network medicine group and is an expert in analyzing large datasets derived from post-genomic technologies through the lens of network science (Menche et al., Science 2015).

The Institute (www.cemm.at) — CeMM is a flagship institute for biomedical research in the heart of Europe, Vienna. We are committed to highest scientific standards as exemplified by recent publications in top journals including Nature, Science and Cell. CeMM offers a uniquely dynamic, interactive and international environment and is located in a beautiful building at the center of the Medical University campus, within walking distance of Vienna’s historical city center. CeMM has been ranked among the top-5 best places to work in academia (http://the-scientist.com/2012/08/01/best-places-to-work-academia-2012).

Vienna is frequently ranked the world’s best city to live in. 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.

We are convinced that diversity and a multicultural work environment are clear advantages for successful research and are committed to attract, develop, and advance the most talented individuals regardless of their gender, race, sexual orientation, religion, age, disability status or any other dimension of diversity.

Why you want to join our team:

·         You want to pursue meaningful research projects at the highest level in an inspiring and international working environment.

·         You want to be part of the next generation of scientists that shape the future of medicine and value our numerous possibilities for personal and professional growth.

·         You appreciate our young and dynamic working atmosphere and the possibility to join our cultural, social and sports activities.

·         We are happy to provide help and assistance to all our employees, their spouses and family members in terms of visa and relocation procedures, dual-career and childcare services, and others.

·         You wish to receive a competitive salary: your position will be remunerated according to FWF personnel costs (https://www.fwf.ac.at/en/research-funding/personnel-costs/) depending on qualifications and experience.

Why we want you to join our team:

·         You are a proactive and independent thinker with a background in Bioinformatics, Systems or Network Biology, Complex Systems, or similar.

·         You are enthusiastic and passionate about science.

·         You are motivated to find innovative, creative and free-spirited solutions to open research questions.

·         You love to communicate, to collaborate, to connect different scientific disciplines and to contribute to multidisciplinary and multicultural teams.


Application Details — Please apply online (https://cemm.jobbase.io/job/tarvvgt9)  with a cover letter describing your career goals and explaining why you are the ideal candidate for this position, your detailed curriculum vitae and contact details of 2-3 referees. Please upload your full application here:

Ideally, you should please submit one Pdf file containing all of your application documents. Initial application deadline is 4th of August 2017 but the call will remain open until the position is filled. Candidates will be contacted by us on a rolling basis.


 

Dezernent/in Bioinformatik [Landesamt für Verbraucherschutz Sachsen-Anhalt]

Im Landesamt für Verbraucherschutz Sachsen-Anhalt, Fachbereich Lebensmittelsicherheit, ist am Standort Halle zum nächstmöglichen Termin ein Arbeitsplatz als

Dezernent/in Bioinformatik im Dezernat 31 „Tierische Lebensmittel“

befristet für 2 Jahre zu besetzen.

Der Fachbereich Lebensmittelsicherheit im Landesamt für Verbraucherschutz Sachsen-Anhalt erfüllt die gesetzlichen Aufgaben der amtlichen Untersuchung und sachverständigen Beurteilung von Lebensmitteln, Bedarfsgegenständen, Kosmetika und Tabakwaren im Auftrag der obersten Landesbehörden des Landes Sachsen-Anhalt.

Das Aufgabengebiet umfasst:
- Bioinformatische Analyse von NGS-Daten auf den Gebieten der Lebensmittelhygiene, der Tierseuchen- und Humandiagnostik inklusive Molekularepidemiologie (z. B. Clusteranalysen)
- Installation und Administration der zum NGS gehörenden IT-Infrastruktur (Server)
- Schulung und Unterstützung des vorhandenen Personals bei der NGS-Datenauswertung
- Sachverständigentätigkeit/Gutachtenerstellung

Konstitutive Anforderungen an die Bewerberin/den Bewerber:
- naturwissenschaftliches Hochschulstudium (Diplom, Master oder vergleichbarer Abschluss) der Fachrichtungen Bioinformatik oder Informatik

Wünschenswerte Anforderungen an die Bewerberin/den Bewerber:
- sehr gute Kenntnisse der Installation und Konfiguration von Linux-Servern
- sehr gute Kenntnisse der Installation und Konfiguration von Linux-Software
- sicherer Umgang mit Script-Sprachen und den zugehörigen Tools (z.B. bash, sed, awk, …)
- Kenntnisse über HPC (high-performance computing)
- Erfahrungen und sicherer Umgang mit Workflowmanagementsystemen (z. B. Snakemake)
- Grundkenntnisse in der Anwendung von Software zur Auswertung von NGS-Daten einschließlich Clusteranalysen und grafischer Aufbereitung der Ergebnisse
- Grundkenntnisse in relevanten Programmiersprachen (z. B. Python, Perl, R)
- Grundkenntnisse im Umgang mit Datenbanken (MS-SQL-Server, MySql)
- Gute Englischkenntnisse
- Hohe Einsatzbereitschaft und Stressstabilität
- Durchhaltevermögen
- Möglichst Grundkenntnisse über molekularbiologische Nachweisverfahren(PCR, real-time PCR; DNA-Sequenzierung)
- Möglichst Erfahrung in neuen molekularen Technologien, wie Next Generation Sequencing

Vergütungsgrundlage ist der TV-L (Tarifgebiet Ost).
Die Eingruppierung erfolgt nach Entgeltgruppe 13.

Die Befristung des Arbeitsvertrages erfolgt nach § 14 Abs. 2 Teilzeit- und Befristungsgesetz. Die Ausschreibung richtet sich daher ausschließlich an Personen, die bisher weder in einem befristeten noch unbefristeten Arbeitsverhältnis mit dem Land Sachsen-Anhalt gestanden haben bzw. das Beschäftigungsverhältnis mehr als drei Jahre zurückliegt. Ausbildungszeiten stellen kein Arbeitsverhältnis in diesem Sinne dar.

Schwerbehinderte Menschen oder ihnen gleichgestellte Bewerberinnen und Bewerber werden bei gleicher Eignung und Befähigung bevorzugt berücksichtigt.

Ihre schriftliche Bewerbung mit tabellarischem Lebenslauf, Qualifikationsnachweisen sowie aussagefähigen Beurteilungen/Arbeitszeugnissen senden Sie bitte bis zum 14.07.2017 an folgende Adresse:
Landesamt für Verbraucherschutz Sachsen-Anhalt
Dezernat 11 – Personal
Stichwort: Bioinformatiker/in
Kühnauer Straße 70
06846 Dessau-Roßlau
Onlinebewerbungen sind nicht zugelassen.

Bewerbungskosten werden nicht erstattet. Die Unterlagen werden nur zurückgesandt, wenn ein ausreichend frankierter Rückumschlag beigefügt ist. Ansonsten werden die Unterlagen nicht berücksichtigter Personen nach Ablauf von drei Monaten nach ihrer Benachrichtigung über die Auswahlentscheidung vernichtet.

Weitere Informationen erteilen Herr Dr. Räbel (Tel.: 0340/6501-101), Herr Prof. Dr. Mäde (Tel.: 0345/5643-313) oder Herr Lenze (Tel.: 0340/6501-170).

Research Scientists Bioinformatics (m/f) [University Medical Center Hamburg-Eppendorf]

The University Medical Center Hamburg-Eppendorf is seeking scientists to join its Bioinformatics Core group. The group aims at supporting research and diagnostics throughout the UKE and related institutes by providing a comprehensive range of Bioinformatics services. Its main focus is on the analysis of high-throughput sequencing (NGS) data.

Main tasks:
- Analysis of high-throughput sequencing (NGS) data
- Development of workflows and tools for sequence data processing
- Consultation on issues of sequencing and sequence data analysis

Candidate profile:
- Successfully completed studies in Bioinformatics, Biostatistics or in a closely related scientific subject
- Good command of Linux and at least one of the following programming languages: Ruby, R, Python, Java, Perl
- Good oral and written communication skills; in particular good knowledge of English
- Ability to clearly explain methods and results to scientist of other disciplines
- Desirable skills: competent handling of various sequence data, good understanding of statistical methods and their application to large data sets, familiarity with workflow management systems, and knowledge of machine learning techniques

Appointments are made for an initial period of two years with possibility of extension. Salary is set according to scale E13 TV-KAH.

We offer a work environment which provides equal opportunities regardless of age, gender, sexual identity, disability, origin or religion. This commitment is confirmed by signing the “Diversity Charter of German Companies”. We explicitly strive for an increased proportion of women in leading positions, particularly for employees in research and education. Female applicants will be treated preferentially in case of equivalent qualification. The same applies in case of minor representation of a certain gender in the advertising section. Applicants with severe disability will be treated preferentially in case of equivalent suitability, qualification and professional performance.

We look forward to receiving your application by June 19th 2017.

Please send your complete application to: Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!, reference number: 2017-260

For further information please contact Malik Alawi (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!) or Dr. Anne Wulf (+49(40)7410 53041)

2 PhD Students: Graph Representations for Genome Annotation [University of Greifswald]

The University of Greifswald´s Institute for Mathematics and Computer Science offers subject to the budgetary authority for the period from 01/02/2018 limited for 30 months two part-time positions (50 %) as a Research Assistant.

Payment will be made according to pay group 13 TV-L Wissenschaft if the personal and pay group specific qualifications can be provided.

The project "Scalable Genome Graph Data Structures for Metagenomics and Genome Annotation" is funded by the Swiss National Science Foundation (SNF) and will be carried out in close collaboration with project partners at the ETH Zürich. The aim is to design and implement a distributed graph data structure that can be used to efficiently encode thousands of genome sequences. The k-mer based data structure can be efficiently used as an alignment target for high throughput sequencing reads. One important application of the graph and aim of the applicants project is the accurate gene structure annotation of closely related species, e.g. of vertebrate clades, by taking phylogenetic relationships into account and using the graph.

There position at University of Greifswald advertised here is associated with another position at ETH Zürich in the group of Prof. Dr. Gunnar Rätsch. The candidate will be able to begin working on this project at ETH Zürich starting in or after August 2017 for up to six months, regulated by a separate contract. Within the group of Prof. Gunnar Rätsch, the core data structure and algorithms are being developed.
Job Description: One major task is the development and implementation of efficient methods to extract syntenic (homologous) regions from the graph. This could be via the identification of "bundles" of paths through the graph that represent homologous regions of different genomes that share many k-mers. Another major task is the development and implementation of a multi-species gene annotation algorithm directly utilizing the graph structure and its attached taxonomic annotation and building on top of the AUGUSTUS code base.

Job Specification:
The candidate shall have a Master of Science or "Diplom" in Bioinformatics, Biomathematics, Mathematics, Computer Science or a related field. She or he must have experience in the implementation of efficient algorithms for large data. In particular, experience in C++ in a Linux environment is desired. He or she should have a good knowledge of tools for sequence analysis and molecular evolution, both in practice and on the algorithmic background.
The University would like to increase the proportion of women in areas in which they are underrepresented and thus applications from women are particularly welcome and will be treated with priority if they have the same qualifications and as long as there are no clear reasons which make a fellow applicant more suitable.
Severly disabled applicants with the same qualifications will be considered with preference.

This announcement is directed at all persons, no matter which gender.
The costs for applying cannot be reimbursed by the state of Mecklenburg-Vorpommern.
The complete application should be e-mailed by 18th June 2017 with reference of the job advertisement Number 17/Sa11 to Prof. Dr. Mario Stanke: Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!

Links: http://bioinf.uni-greifswald.de/bioinf/projects/

PhD Position in Cheminformatics [Universität Hamburg]

A Ph.D. position (3 years, fixed term) in cheminformatics is immediately
available in the research group of Professor Johannes Kirchmair at the
University of Hamburg, Center for Bioinformatics
(http://www.zbh.uni-hamburg.de/acm), for a joint industry project with
Beiersdorf AG. The Ph.D. student will be employed by HITeC e.V., the
cooperation partner of the University of Hamburg in this project. The
Ph.D. position is remunerated according to the salary level TV-L 13 and
calls for 50% of standard work hours per week. The term is fixed for a
period of three years.

The project is focused on the development and application of
computational approaches for the prediction of the physicochemical and
biological properties of bioactive small molecules, with emphasis on
statistical and machine learning approaches.

Interested candidates should possess a Master’s degree in
cheminformatics, chemistry, bioinformatics or a related field. A solid
background in chemistry is mandatory. Knowledge of quantum chemistry,
toxicity and biochemistry is advantageous. Familiarity with machine
learning and statistical methods, Python, Java, R and Linux is desirable
but not essential. Excellent communication skills in English are a
requirement. German language skills are advantageous but not essential.

Your application should include a motivation letter, CV, copies of
university certificates and the contact details of at least two academic
references. Please send your application preferably by email to

Prof. Dr. Johannes Kirchmair
Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!
Universität Hamburg
MIN Faculty
Center for Bioinformatics
Bundesstrasse 43
20146 Hamburg

The evaluation of candidates begins immediately and will continue until
the position is filled.