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Phd candidate in bioinformatics of single cell epigenomics

The Computational Biology Group of Interdisciplinary Center for Clinical Research (IZKF) Aachen, RWTH Aachen University Hospital, Aachen, invites applicants for a PhD candidate in bioinformatics methods for statistical methods for the analysis of single cell epigenomics data.

The project is based on the development of computational methods for analysis and integration of single cell ATAC-Seq, ChIP-Seq and RNA-Seq. This project will be performed in collaboration with stem cell specialists from the RWTH Aachen University Medical Faculty and includes the analysis of in-house generated data.

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

The expected starting date is May 2016. 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 Computational Biology Group 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.

PhD program in Bioinformatics in Berlin

The International Max Planck Research School for Computational Biology and Scientific Computing (IMPRS-CBSC) at the Max Planck Institute for Molecular Genetics (MPIMG) in Berlin invites applications to their graduate program in bioinformatics.

We offer cutting edge computer science, secure funding and travel programs, a student community and vivid exchange, and comprehensive scientific and transferable skills training! The graduate school with a reputable faculty and a world-wide Alumni network focuses on molecular dynamics and modeling, biological networks, genomics and proteomics, and stochastic processes. Candidates should have a prominent background in computer science with a strong interest in biology. Join our team in this exciting and disruptive field of research in the vibrant capital of Germany!

Apply now on www.molgen.mpg.de/IMPRS/application before February 22, 2016!
For more information visit our website, find us on LinkedIn, or follow us on Twitter.

Werkstudent im Bereich Data Science [m/w] für Health Care Daten in München

Die Gesundheitsforen Leipzig bilden als Wissensdienstleister auf dem Gesundheitsmarkt eine wichtige Schnittstelle zwischen Wissenschaft und Praxis. Wir vernetzen Fach- und Führungskräfte, unterstützen Unternehmen aus der Gesundheitswirtschaft bei Forschungs- und Projektarbeiten sowie Veranstaltungsmanagement und bieten Software-Anwendungen für verschiedenste fachliche Fragestellungen im Krankenkassengeschäft.

Ihre Tätigkeiten umfassen:

§  medizinischen und ökonomischen Analysen auf der Forschungsdatenbank

§  die Unterstützung bei der Entwicklung von analytischen Modellen

§  die Weiterentwicklung einer Software zur Visualisierung von Sequenzen und Musteranalyse

§  die Unterstützung in der Pflege und Weiterentwicklung der Forschungsdatenbank

Wir erwarten von Ihnen:

§  ein fortgeschrittenes Studium der Informatik/Statistik/Bioinformatik

§  gute Datenbankkenntnisse (MySQL/TSQL) und Programmiererfahrung (Java, Perl)

§  Interesse am Gesundheitswesen.

§  Data Mining Kenntnisse sind von Vorteil (R/Weka/Knime)

§  Sehr gute Deutsch und Englischkenntnisse in Wort und Schrift

Wir bieten Ihnen:

§  eine anspruchsvolle und verantwortungsvolle Tätigkeit in einem dynamischen Team

§  eine angemessene Vergütung und flexible Arbeitszeiten

§  die Möglichkeit, neben dem Studium praktische Erfahrungen zu sammeln und die im Studium erworbenen Kenntnisse einzubringen und zu vertiefen

§  eine Referenz für den (späteren) Berufseinstieg und ein Netzwerk für die zukünftige Karriere

Links: http://www.gesundheitsforen.net/portal/de/geschaeftsfelder/medizin_und_versorgung/startseite_medizin_und_versorgung.xhtml

 

Haben wir Ihr Interesse geweckt?

Dann senden Sie bitte Ihre vollständigen Bewerbungsunterlagen unter Angabe Ihres frühestmöglichen Einstiegstermins in elektronischer Form an:

Jana Hapfelmeier

Gesundheitsforen Leipzig GmbH | Büro München | Landsberger Str. 154| 80339 München

Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein! | www.gesundheitsforen.net

Two postdoctoral positions in viral metagenomics / methods development

The Soeding lab (quantitative and computational biology) at the MPI for biophysical chemistry is looking to fill two positions for postdocs (E13 TVoeD Bund,  three years, each starting ~04/2016) in methods development and data analysis in metagenomics. 
 

The Virus-X project runs for four years starting around April 2016 and is a collaboration of academic labs and companies from Iceland, France, Belgium, Poland, Norway, Sweden, the Netherlands and Germany that is financed through the Horizon2020 framework of the ERC. The goal is to develop experimental and bioinformatic methods for the high-thoughput discovery of novel viral genes for biotechnological applications by focusing in particular on extreme (hot, salty, deep vent) environments. 

Our part, planned for the first 3 years of Virus-X, is the prediction of genes from the partly assembled contigs and their function prediction and prioritisation for further experimental studies. Our planned work involves both methods development, e.g. extensions of our software packages MMseqs2 and HH-suite and a new method for finding gene discovery particularly suitable for viruses, and building pipelines for function prediction and automatic structure prediction for the large metagenomics datasets produces in the project. The goal is to have marketable proteins after 4 years.

 
If you are interested I would be happy to hear from you!
Johannes Soeding <Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!>

Medical Geneticist or Next Generation Sequencing Bioinformatician

The Boztug lab at CeMM is searching for a Medical Geneticist or Next Generation Sequencing Bioinformatician to optimize data processing of high-throughput genomic data arising from various sequencing applications including exome, genome and transcriptome sequencing data, with the overall goal to fuel research on monogenic human diseases.

 

The Opportunity:

In this role you would be responsible for establishing and maintaining data processing pipelines for a variety of next-generation sequencing applications, with a focus on DNA sequencing, in particular, identification of single-nucleotide variants and small chromosomal mutations leading to the aberrant gene function. Wet-lab experience would be a plus but not a prerequisite. In addition, you would develop novel custom-designed algorithms for analysis of phenotype-based patient cohorts to identify underlying mutations and pathways.

 

The Candidate:

We are looking for a highly motivated candidate (bioinformatics or biomedical science background) with a strong interest in contributing to the genomics revolution of biomedicine and with an interest in research on rare and undiagnosed Mendelian diseases. Excellent communication skills will enable intensive exchange with both wet lab scientists and other bioinformaticians at CeMM. Any previous experience with clinical patient data and/or biobanking would be of value. Intellectual curiosity, flexibility and dedication to science will be key success factors in this exciting new role.

 

The Boztug Lab:

The main research interest of the Boztug Lab is molecular understanding of Mendelian disorders including inherited defects of the immune system (so-termed primary immunodeficiency disorders, see Salzer E et al JACI 2014, Boztug K et al Nature Genet 2014, Willmann K*, Klaver S* et al Nature Comm 2014, Dobbs K*, Dominguez Conde C*, Zhang S-Y*, Parolini S* et al New Eng J Med 2015). The group has accumulated a large collection of informative pedigrees and is performing state-of-the-art genomic analyses combined with functional assays to identify and validate novel disease-causing mutations. The genomic research comprises high throughput genetics/genomics such as high-resolution SNP arrays and deep sequencing as well as functional proteomics of protein complexes. Candidate genes are then studied in detail using an array of biochemical, immunological and imaging technologies to obtain molecular gene-to-phenotype relationships.

 

The Institute:

The CeMM Research Center for Molecular Medicine is an international and interdisciplinary research institute of the Austrian Academy of Sciences. Driven by medical needs, CeMM integrates basic research and clinical expertise to pursue innovative diagnostic and therapeutic approaches focused on cancer, inflammation and immune disorders. CeMM is located in a new tailor-made building at the center of the Vienna Medical University campus, within walking distance of Vienna’s historical city center. According to a study by “The Scientist”, CeMM is 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).

 

To apply, please submit: a cover letter, curriculum vitae, and the contact details of at least two referees to Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!. Please refer to "Boztug lab Medical Geneticist/Bioinformatician" in the subject line.

Application deadline: 31st December 2015.

PhD student positions on "Functional state modulation of membrane proteins by dynamic association and dissociation"

Applications are invited for two PhD student positions available 1.1.2016 in the Computational Pharmaceutical Chemistry & Molecular Bioinformatics group (Prof. Dr. Holger Gohlke; http://cpclab.uni-duesseldorf.de) at the Heinrich-Heine-University, Düsseldorf, Germany.

Background: The central question we intend to investigate within the newly established Collaborative Research Center (CRC) 1208 (“Identity and dynamics of membrane systems – From molecules to cellular function”) is how dynamic association and dissociation modulates the functional state of membrane proteins under the condition of conserving their molecular identity.
We will address this question on two systems: I) molecular components central for ethylene perception in plants, which are located at the ER and Golgi membranes (Binder, Chang, Schaller, Annu Plant Rev 44, 117-145, (2012)); II) PlbF, a novel phospholipase A from P. aeruginosa suggested to be a virulence factor, which is anchored in the inner bacterial membrane and exposed to the periplasm (http://docserv.uni-duesseldorf.de/servlets/DerivateServlet/Derivate-19673/PhD%20Thesis%20Filip%20Kovacic.pdf). In both cases, (multi)membrane systems play a crucial role for spatial coordination of dynamic association and dissociation.
By molecular simulation and modeling studies at an atomic level in close connection with experimental validation studies, we intend to provide insights on I) the role and transport of the copper cofactor for ethylene receptor biogenesis and ethylene perception in plants and II) the molecular mechanism of monomerization/dimerization-dependent PlbF activation.
As for both systems either almost none or only static atomic-level information is available, it is mandatory to develop a conceptual framework of adequate computational approaches for model building and hypothesis generation and high-content experimental platforms for validation and providing feedback. The molecular simulation and modeling studies will be performed by the PhD students in the Gohlke lab. The PhD students will furthermore work closely together with scientists of the Groth (http://www.biochemplant.hhu.de/) and Jaeger (http://www.iet.uni-duesseldorf.de/) labs for experimentally validating the established models and generated hypothesis.

Requirements: Ideal candidates will have a record of excellence and a strong background in computational biochemistry/chemistry or structural bioinformatics, a high interest in working in an interdisciplinary collaboration, and profound knowledge in state-of-the-art molecular dynamics simulations (Amber) software, molecular modeling (in particular, protein-protein docking), and QM/MM calculations.

Applicants should submit applications (a one-page letter of motivation why they are interested in the respective project and how they can contribute to the project’s success, a current CV, and contact data of three references) by email to Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein! . Please provide all documents as one PDF file.

Detailed information about living and studying in Düsseldorf is provided here: http://www.uni-duesseldorf.de/home/leben-in-duesseldorf.html

Postdoc positions on "Identification of and Virtual Screening on Novel Allosteric Sites using Constraint Network Analysis"

Applications are invited for two Postdoc positions available in spring 2016 in the Computational Pharmaceutical Chemistry & Molecular Bioinformatics group (Prof. Dr. Holger Gohlke; http://cpclab.uni-duesseldorf.de) at the Heinrich-Heine-University, Düsseldorf, Germany.

Background: A quantitative description of allostery is fundamental to an understanding of processes in living systems and of practical relevance when developing allosteric modulators. The Gohlke group has developed Constraint Network Analysis (CNA) as a framework to analyze and predict allosteric sites in proteins.[1-3] The CNA approach analyzes the network coupling between putative binding sites by rigidity theory.
CNA applies concepts grounded in rigidity theory to analyze biomolecular flexibility [4] and how it might be perturbed by compound binding. The approach works on conformational ensembles [5] or ensembles of network topologies, [6] considering dynamics of molecules in an efficient way based on key intramolecular and intermolecular interactions (hydrophobic, H-bond, salt bridge constraints), without the need for very long molecular dynamics simulations. CNA is applied in a perturbation approach to gain structure-based insights into allosteric signaling and coupling in dynamic proteins. It is fast enough, for example, that one could perform an Alanine scan across the entire protein to identify which residues’ mutations might show the greatest perturbation at a given active site.
The Gohlke group already validated this approach against several targets. Thus, CNA is a useful tool for identifying novel allosteric sites and analyzing the effects of compound binding at these sites.

Objective: In collaboration with a major pharmaceutical company, we aim to extend and integrate the CNA approach into a virtual screening workflow to find novel chemical matter that would bind and appropriately perturb the identified allosteric sites to achieve desired pharmacological effects. In doing so, we will also fill a major gap in ligand-based virtual screening and enable automatic structure-based pharmacophore searches for targets.

Requirements: Ideal candidates will have a record of excellence (PhD plus publications in highly visible journals) and a high interest in working in an industrial collaboration. Postdoc 1 is required to have a strong chemoinformatics background and application-based skills; Postdoc 2 is required to have a strong structural bioinformatics / computational biochemistry-based background and programming skills in Python and C++.

Applicants should submit applications (a one-page letter of motivation why they are interested in the respective project and how they can contribute to the project’s success, a current CV, and contact data of three references) by email to Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein! . Please provide all documents as one PDF file and specify for which position you apply.

Detailed information about living and studying in Düsseldorf is provided here: http://www.uni-duesseldorf.de/home/leben-in-duesseldorf.html

References
[1]    Pfleger, C., Rathi, P. C., Klein, D. L., Radestock, S. & Gohlke, H. Constraint Network Analysis (CNA): A Python Software Package for Efficiently Linking Biomacromolecular Structure, Flexibility, (Thermo-) Stability, and Function. J. Chem. Inf. Model. 53, 1007-1015 (2013).
[2]    Rathi, P. C., Mulnaes, D. & Gohlke, H. VisualCNA: A GUI for interactive Constraint Network Analysis and protein engineering for improving thermostability. Bioinformatics 31, 2394-2396 (2015).
[3]    Kruger, D. M., Rathi, P. C., Pfleger, C. & Gohlke, H. CNA web server: rigidity theory-based thermal unfolding simulations of proteins for linking structure, (thermo-)stability, and function. Nucleic Acids Res. 41, W340-348 (2013).
[4]    Pfleger, C., Radestock, S., Schmidt, E. & Gohlke, H. Global and local indices for characterizing biomolecular flexibility and rigidity. J. Comput. Chem. 34, 220-233 (2012).
[5]    Rathi, P. C., Radestock, S. & Gohlke, H. Thermostabilizing mutations preferentially occur at structural weak spots with a high mutation ratio. J. Biotechnol. 159, 135-144 (2012).
[6]    Pfleger, C. & Gohlke, H. Efficient and robust analysis of biomacromolecular flexibility using ensembles of network topologies based on fuzzy noncovalent constraints. Structure 21, 1725-1734 (2013).

Making and Breaking Cancer Cells (ERC-funded Postdoc & PhD Positions)

A more complete PDF version of this job posting is available from the following URL:

http://epigenomics.cemm.oeaw.ac.at/files/Job_Posting_Making_and_Breaking_Cancer_Cells.pdf

For a recently awarded European Research Council (ERC) grant we are recruiting a postdoc and a PhD student who want to develop and apply advanced genomics and screening technology. We aim to explore whether epigenetic alterations alone may suffice to convert a normal cell into a cancer cell and vice versa. Progress along these lines will answer a fundamental question of cancer biology and provide a broadly useful platform technology for developing a new generation of epigenetic cancer drugs.

Our lab is based at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences in Vienna. It combines advanced technologies (epigenomics, single-cell sequencing, drug screening, mass spectrometry, imaging, etc.) with a deep interest in computational modeling and relevant clinical collaborations. We are working to advance cancer therapy through systems-level research focusing on the cancer epigenome.

The Project

Epigenetic alterations can be detected in all cancers and in essentially every patient. Despite their prevalence, the concrete functional roles of these alterations are not well understood. In this project, we aim to develop and apply epigenome programming technology that will allow us to precisely manipulate the epigenome and to rationally reprogram normal cells into cancer cells and vice versa. We will adapt CRISPR technology and combinatorial use of epigenetic drugs to high-throughput epigenome editing, develop suitable screening assays, and ultimately engineer and erase a cancer from scratch through a defined series of epigenetic modifications. This project will establish a broadly applicable methodology and toolbox for dissecting the functional roles of epigenetic alterations in cancer, and it will introduce a “build it to understand it” paradigm into cancer epigenetics, which will challenge our understanding of cancer as a (mainly) genetic disease.

The Candidate

We are looking for highly motivated and academically outstanding candidates who want to pursue a scientific career in the emerging field of medical epigenomics. An ideal candidate would have a background in molecular biology (including functional genomics, chemical biology, biotechnology, human genetics, molecular medicine, etc.) or in the computational sciences (bioinformatics, physics, statistics, etc.) and a strong interest in collaboration and teamwork at the interdisciplinary interface of cancer epigenetics, systems biology, and medicine.

Postdoc applicants should submit cover letter, curriculum vitae, academic transcripts, and contact details of three referees to Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!. Applications will be reviewed on a rolling basis, and any application received by 10 January 2016 will be considered. Start dates are very flexible. PhD candidates are asked to apply for the CeMM PhD program (http://www.cemm.oeaw.ac.at/phd-program).

Data Analyst / Bioinformatician

Short Summary: The Bergthaler laboratory at CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences offers an exciting position for a Data Analyst / Bioinformatician. Candidates with a background in computational biology who are ready to take on the challenge of integrating and analyzing systems-level data from complementary global experiments in the context of infectious diseases, inflammation and metabolism will be considered.

 

 

 

The Challenge: The successful applicant will integrate and analyze large data sets derived from different techniques including next-generation sequencing (RNA-seq, ChIP-seq, genomics) and mass-spectrometry (quantitative proteomics, protein-interaction networks, metabolomics). These data are generated in-house and may be complemented by additional data sets from public repositories. On top of such collaborations, the candidate is encouraged to drive her/his own research project and has the opportunity to perform experiments in the wet lab.

 

 

 

The Candidate: You should have a background in Computational Biology (Bachelor, Master or PhD degree), and a track record of successful data integration, global data analyses and the application of biomathematical and statistical methods. Expertise in data visualization is of advantage. Your publication record demonstrates your successful collaboration with biologists and highlights your expertise in programs such as R, Python, Matlab and/or systems biology tools such as Cytoscape. You bring to the job a creative mindset and the ability to think outside the box. Interdisciplinary and network thinking and strong communication skills as well as the ability to work independently and in a team would round off your profile. You are a self-motivated individual who is prepared to tackle the complexity of immunology and to make a difference within our quest on fundamental questions of infectious diseases.

 

 

 

The Lab: Our aim is to unravel novel molecular mechanisms of infectious diseases and inflammation. We employ an integrative approach comprising experimentally tractable infection models and state-of-the-art tools of virology, immunology, genetics, pathology, metabolomics and systems biology. A particular emphasis lies on chronic infections, superinfections and the crosstalk of metabolism and inflammation. The principal investigator has received training in premier laboratories at the University of Tokyo, University/ETH Zurich and at the Institute for Systems Biology in Seattle. The current group consists of 8 members from 7 countries, who closely collaborate across projects as a team and have published two recent high impact studies. Scientific and social interactions are promoted by weekly lab meetings, journal clubs, CeMMinars with internationally renowned guest speakers as well as by annual lab retreats. Lab websites: http://www.bergthaler1.at, http://goo.gl/a95KyW.

 

References: Bhattacharya*, Hegazy* et al. Immunity 2015, Johnson*, Bergthaler* et al. Journal of Immunology 2015, Schliehe C. et al. Nature Immunology 2014, Litvak V. et al. Nature 2012.

 

 

 

The Institute: CeMM is a flagship institute for biomedical research in the heart of Europe, Vienna. Our work is focused on unraveling the molecular basis of diseases in infections, inflammation and cancer. We are committed to highest scientific standards and provide a dynamic, interactive and international environment. Working language is English. CeMM has been repeatedly ranked by The Scientist as one of the Best Places to Work Academia worldwide (link: http://goo.gl/51VMO). The institute is situated within the medical campus of Vienna, which facilitates collaborations between basic scientists and clinicians. CeMM operates cutting-edge technology platforms and hosts two bioinformatics groups, offering an intellectually challenging and interdisciplinary environment for computational biologists.

 

 

 

Salary: The salary is compliant with the applicable collective agreement including an overpayment depending on the qualifications of the applicant. The definite salary agreement will be made during the personal interview.

 

 

 

Contact details: Interested candidates should please send their applications (including a cover letter, a CV and names and contact details of at least 2 referees) using the reference code #DA-AB1 to Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!. This call will remain open until the position is filled.

 

Bioinformatics position

The Medical Faculty of RWTH Aachen University operates a Genomics Facility at the Interdisciplinary Center for Clinical Research (IZKF) Aachen. The mission of the Genomics Facility is to carry out and support internationally outstanding research on DNA Microarrays and Next Generation Sequencing.

The open position is for a talented and motivated bioinformatics scientist to establish bioinformatics pipelines and perform data analyses (e.g. DNA-Seq, Chip-Seq, RNA-Seq) of NGS data generated in the Genomics Facility. The applicant is also encouraged to develop own research driven activities and to implement up-to-date methodology for data analysis. This will be done to support and in collaboration with the life science institutes and clinical departments of Medical Faculty of RWTH Aachen University. The opportunity to receive a PhD is given.

Your tasks:

• Understand scientific goals, and identify and implement bioinformatics solutions
• Deliver impactful bioinformatics support
• Work with scientists, clinicians, PhD students and postdocs to translate NGS analysis into research and clinical practice
• Proactively engage in knowledge sharing and peer support to build expertise in the tools and techniques
• Maintain the core facility computational servers

Your profile:

• M.Sc. degree (or Ph.D./Postdoc) in bioinformatics or related fields with at least 3 years of research experience in bioinformatics
• Demonstrated experience in bioinformatics methods for analysis of NGS data and management of large data sets
• Proficiency in programming languages such as shell script, R, Python or similar
• Acquaintance with Linux operation system administration and experience with web based bioinformatics environments (i.e. Galaxy) is a plus
• Skilled in effective communication of complex genomic data to a non-expert
• Interest to work in interdisciplinary teams

Salary and benefits are according to a public service position in Germany (TV-L E13).

The position shall be filled as soon as possible and is initially for 5 years with the possibility for extension.

RWTH Aachen University is certified as a "Family-Friendly University". We particularly welcome and encourage applications from women, disabled persons and ethnic minority groups, recognizing they are underrepresented across RWTH Aachen University. The principles of fair and open competition apply and appointments will be made on merit.

Please send your electronic application before 15.12.2015 to: Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!.