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Postdoctoral Fellow - Computational Biologist

Job Description

The European Molecular Biology Laboratory (EMBL) is one of the highest ranked scientific research organisations in the world. The Headquarters Laboratory is located in Heidelberg (Germany), with additional sites in Grenoble (France), Hamburg (Germany), Hinxton (UK) and Monterotondo (Italy).

The Bork group seeks a Computational Biologist for the analysis of large-scale microbiomics data (metagenomics, metatranscriptomics etc). Focus will be on biological discovery by data integration. Data will come from various microbiome projects (e.g. human gut or ocean) and should be digested to gain functional understanding. The work will comprise technical as well as discovery aspects and will be carried out both independently and with internal and external collaborators.

Qualifications and Experience

The successful candidate should have a Ph.D. in a relevant field and is expected to have a sufficient background in both biology and bioinformatics; a profound knowledge in statistics is also desired. The position requires experience in scripting and the analysis of biological data, preferably in the areas where the Bork group is active in. The ability to work in a team is essential as EMBL offers a multicultural & interdisciplinary environment.

Application Instructions

Please apply online through www.embl.org/jobs

Additional Information

EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation.

Please note that appointments on fixed term contracts can be renewed, depending on circumstances at the time of the review.

Links: http://ig14.i-grasp.com//fe/tpl_embl01.asp?newms=jj&id=55148&aid=15470

 

Wissenschaftliche/r Mitarbeiter-/in Giessen

An der Professur für Systembiologie mit dem Schwerpunkt Genomik, Proteomik und Transkriptomik ist in einem drittmittelfinanzierten BMBF-Projekt zum nächstmöglichen Zeitpunkt befristet bis zum 28.02.2018 eine Vollzeitstelle mit einer/einem

Wissenschaftlichen Mitarbeiterin/Mitarbeiter

zu besetzen. Bei Vorliegen der tariflichen Voraussetzungen erfolgt die Vergütung nach Entgeltgruppe 13 Tarifvertrag Hessen (TV-H).

Aufgaben:

Im Projekt werden aktuelle Fragen in Bezug auf die Bereitstellung einer flexiblen Software-Plattform im Kontext der Genomforschung bearbeitet. Im Mittelpunkt des Projekts steht die bioinformatische Analyse von Hochdurchsatzdaten (Next-Generation-Sequencing) und deren systembiologische Interpretation und Visualisierung. Sie unterstützen den Aufbau und Betrieb einer Cloud-Computing-Plattform und die Anpassung dieser Plattform an die spezifischen Anforderungen im Bereich der mikrobiellen Bioinformatik .

Die Mit- und Weiterentwicklung der softwaretechnischen Cloud-Infrastruktur zur Erfassung, Verwaltung und Auswertung von Hochdurchsatzdaten bildet den Schwerpunkt Ihrer Tätigkeit.

Anforderungsprofil:

Sie verfügen über ein abgeschlossenes wissenschaftliches Hochschulstudium der (Bio-)Informatik oder einem vergleichbaren Fachgebiet sowie über Erfahrung im Bereich Cloud-Computing. Sie sind sicher in der Nutzung und Administration von Unix/Linux-Betriebssystemen und besitzen umfangreiche Kenntnisse im Bereich moderner Automatisierungs-, Virtualisierungs- und Monitoringtechnologien. Sie beherrschen sicher eine moderne objektorientierte Programmiersprache, mindestens eine Skriptsprache und verfügen über umfangreiche Kenntnisse im Einsatz von Datenbanksystemen.

Link zur kompletten Ausschreibung: http://www.inst.uni-giessen.de/stellenmarkt/pdf/stelle0008904.pdf

Bewerbungsfrist: 29.07.2016

Single-cell Sequencing and Bioinformatic Modeling of Cancer Heterogeneity (ERC-funded postdoc position)

On a new project funded by the European Research Council (ERC) we are recruiting a postdoc interested in single-cell sequencing technologies and/or bioinformatic algorithms for dissecting cancer heterogeneity.

Our group is part of the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences in Vienna. It combines a strong focus on biomedical technology (epigenomics, single-cell sequencing, drug screening, mass spectrometry, imaging, etc.) with a deep interest in computational modeling. We are also working closely with physicians at the Vienna General Hospital and the Medical University of Vienna, in order to advance precision medicine through the use of computation and high-throughput technology.


The Project

Cancer is the most heterogeneous of all diseases – a microcosm of tightly interlinked evolutionary and developmental processes. We want to understand this complexity at the level of single cells – including the cancer cells competing with each other for resources, but also the microenvironment that supports the cancer and the immune cells that try to fit the cancer. Using a combination of single-cell genome, epigenome, and transcriptome sequencing and computational modeling, we seek to establish a full evolutionary map of the dynamics underlying cancer development. Moreover, we pursue an engineering-inspired “build it to understand it” approach to cancer epigenetics, using CRISPR technology and computationally designed drug combinations to rationally reprogram normal cells into cancer cells and vice versa. This project seeks to establish a quantitative understanding of cancer heterogeneity and a predictive model for advancing precision therapies.

The Candidate

We are looking for highly motivated and academically outstanding candidates who want to pursue a scientific career in the field of computational and medical epigenomics. A strong candidate may have a background in the computational sciences (bioinformatics, statistics, physics, engineering, etc.) and some prior experience with collaborative research in high-throughput biology. In the same way, we are considering 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 systems medicine projects. We are fully equipped and experienced with both computational and wet-lab work, such that it is an option – but by no means mandatory – to build a unique skill set by combining and fully integrating these two approaches through own work and collaborations.
The Lab
(http://www.medical-epigenomics.org/)

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. We perform large-scale epigenome mapping in order to dissect the dynamics of cancer development and emerging drug resistance. This work is part of the European BLUEPRINT project and the International Human Epigenome Consortium.
- Technology. Exciting biomedical research is often driven by new technologies. Our lab is therefore heavily invested into technology development, including single-cell protocols, nanopore sequencing, CRISPR, and epigenome editing.
- Bioinformatics. New algorithms and advanced computational methods allow us to accurately infer epigenetic cell states from large-scale datasets, in order to reconstruct the epigenetic landscape that controls cellular differentiation and reprogramming.
- Diagnostics. Using large-scale DNA methylation mapping, bioinformatic prioritization, and functional characterization, we strive to develop clinically relevant biomarkers for informing personalized cancer therapy.

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

Christoph Bock is a principal investigator at CeMM, guest professor at the Medical University of Vienna, scientific coordinator of Vienna’s Biomedical Sequencing Facility, and adjunct group leader at the Max Planck Institute for Informatics. Previous appointments include the Max Planck Institute for Informatics (PhD studies) and the Broad Institute of MIT and Harvard (postdoctoral research). CB is a 2009 recipient of the Otto Hahn Medal by the Max Planck Society for pioneering work in computational epigenetics, and he recently received two major career development grants – a New Frontier Group award by the Austrian Academy of Sciences (EUR 1.4 million) and an ERC Starting Grant by the European Research Council (EUR 1.3 million). CB leads Genom Austria, which is the Austrian contribution to the International Network of Personal Genome Projects, and he is a member of several European and global initiatives on epigenetics & precision medicine.
The Institute

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

CeMM is an international research institute of the Austrian Academy of Sciences. Driven by medical needs, CeMM integrates basic research and medical expertise to pursue innovative approaches focused 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 30 different nationalities are represented at the institute. CeMM is an equal opportunity employer.

Applicants should please apply online (https://prescreen.io/j/0wzehooj) and submit cover letter, CV, academic transcripts, and contact details of three referees.

Applications will be reviewed on a rolling basis, and any application received by 15 August 2016 will be considered. Start dates are very flexible.

Bioinformatician/Data Scientist

To support a highly active and extremely productive team of twenty scientists with core computational analyses, statistical evaluation and expert visualization of complex data, we are seeking a computational scientist. The candidate should have a degree either in computational science/engineering or biology. The candidate needs to be able to adapt and expertly use existing bioinformatics tools, have good statistical and script programming skills/experience (e.g. R - bioconductor, python, MATLAB) and interest in developing data analysis protocols/pipelines for large screening experiments. Experience in developing more complex software and algorithms is a bonus. Good command of the English language and good interpersonal skills are a must.
 
The Laboratory

The Superti-Furga laboratory consists of a highly collaborative team of 22 scientists from 11 nations. In the last three years, we published about 70 papers, among which 10% in Nature, Science or Cell and 15 in Nature sister journals. Historically, 23 postdocs published on average 9,5 papers within our lab (0-25) that were on average cited 686 times. More than 50% of postdocs went on to independent positions, two went to work as clinicians. None abandoned research. You will enjoy a supportive mentoring from the PI and profit from a budding Postdoc training program both at CeMM, with the other life science institutes in Vienna and, internationally, within the highly active and unique network of excellence of the 13 EU-Life institutes: http://eu-life.eu/. Please visit our lab’s website: www.superti-furga-lab.at

References:

Köberlin MS, Snijder B, et al. Cell. 2015 Jul 2;162(1):170-83.
César-Razquin A, et al.  Cell. 2015 Jul 30;162(3):478-87.
Rebsamen M, et al. Nature. 2015 Mar 26;519(7544):477-81.
Huber KV, et al. Nature. 2014 Apr 10;508(7495):222-7.
Blomen VA, et al. Science, 2015 Nov 27;350(6264):1092-6.

The Institute

CeMM is a flagship institute for biomedical research in the heart of Europe, Vienna. CeMM is committed to highest scientific standards as exemplified by recent publications in top journals as well as by its top international scientific advisory board. The environment is very collaborative, dynamic and international. One of CeMM`s advantages is to be in close proximity to the Vienna Medical University Campus and the General Hospital (AKH). This allows the fruitful interaction of basic scientists with clinicians, and the use of models and cutting-edge technology to disease-relevant biological questions. According to a study by The Scientist, CeMM is ranked as the best European place to work in Academia 2012, internationally CeMM appears at the fourth place. For more information please visit: www.cemm.at

Application details

We offer a great working environment for passionate scientists and a generous employee benefits package.   Please click on the link below and apply online for this position:

https://prescreen.io/j/nmr9djus

At CeMM we are committed to increasing the percentage of female scientists working in life sciences, and thus we strongly encourage female applicants.

Closing date for applications: July 24th, 2016

Postdoc and PhD Positions in Bioinformatics and Genomics

The Research Group “Computational Biology and Evolutionary Genomics”
at the Max Planck Institute in Dresden has an opening for a computational biology
PhD and a Postdoc position.

We are hiring for two projects that will discover differences in the genome
that underlie phenotypic differences between species.
To this end, we will build high-quality genome alignments, apply comparative
methods that we have developed in the lab to discover functional genomic
differences, and use statistical approaches to associate genomic to phenotypic
differences. For promising candidate loci, we will experimentally test whether
editing these genomic loci in a model organism recapitulates natural phenotypic
differences.

Our Institute:

Our group is located at the Max Planck Institute of Molecular Cell Biology and
Genetics (MPI-CBG) and we are jointly affiliated with the Max Planck Institute
for the Physics of Complex Systems (MPI-PKS), both in Dresden. Both institutes
are highly interactive and interdisciplinary workplaces, provide an international
atmosphere with English as working language and access to cutting-edge
computational and experimental infrastructure and facilities. The MPI-CBG
was awarded one of the “Best Places To Work for Postdocs” in 2011.

Requirements:

Applicants should have a background in bioinformatics or computational biology.
Excellent programming skills (perl, python, or C/C++) in a Linux environment
as well as experience with shell scripting and Unix tools are required.
Previous experience in large-scale genomic data analysis is an advantage.

Interested candidates should please email
-  Your CV including publication list and contact information for at least two references
-  A summary of previous research experience (max 1 page)
to Michael Hiller (This email address is being protected from spambots. You need JavaScript enabled to view it.).


Links: Group page: http://www.mpi-cbg.de/research/michael-hiller.html

Tenured academic staff / Tenure track lecturer Statistical Bioinformatics

The Faculty of Sciences of Hasselt University (Belgium) seeks a (m/f)  Lecturer in Statistical Bioinformatics ( http://www.uhasselt.be/vacancies_detail?taal=04&vacid=1074)

Education task: The candidate will assume important teaching tasks in the field of bioinformatics and statistics, both at bachelor and master level, and in particular within the bioinformatics trajectory of the Master of Statistics program.

Research mission: It is expected that the candidate will strengthen and/or extend (both from a methodological and an application area perspective) the current research effort of the Center for Statistics (http://www.uhasselt.be/censtat) and Interuniversity Institute for Biostatistics and statistical Bioinformatics (http://ibiostat.be) the field of statistical bioinformatics.  The candidate will direct a part of his/her research interests towards scientific consulting endeavors (including service teaching for research institutions and industry) and ensure a fruitful interaction between the consulting, education, and research tasks.

Profile:

- PhD in statistical bioinformatics, (bio)statistics (or equivalent)
- You have got experience with respect to various aspects of academic education: coordination and organization of courses, development of teaching materials, and supervision of practical projects and dissertations.
- You are cooperative and can work well in teams.
- Academic staff must meet the statutory language requirements for knowledge of the language of instruction (Dutch). If necessary, Hasselt University offers concrete, tailored support measures to help achieve the required language level.
- You have proven (methodological and applied) scientific experience and have published in international and national scientific publications.
- You are involved in national/international partnerships.
- You have proven relevant practical experience in the statistical-bioinformatics field.
- A demonstrable experience in scientific consultation and contract research for industry is an added advantage.

Offer: We will offer either an appointment as a lecturer in the tenure track system during 5 years (this will lead to an immediate permanent contract as a senior lecturer, if the Board of Directors favorably assesses the party involved, based on previously set public grading criteria), or a fulltime appointment as a lecturer or higher, which will lead to tenure. In case of a first appointment as a member of the academic staff, the Board of Directors of the University can decide on a temporary appointment for a period up to 3 years. This will lead to a permanent contract if the Board of Directors favorably assesses the party involved.

Selection procedure: Pre-selection based on CV. Interview with and test lesson/presentation by the selected candidates.

Application: You can only apply online up to and including 15 June 2016.

Scientist in Computational Support for the CBB Unit in Image and Bio-Informatics

Job Description

The European Molecular Biology Laboratory (EMBL) is one of the highest ranked scientific research organisations in the world. The Headquarters Laboratory is located in Heidelberg (Germany), with additional sites in Grenoble (France), Hamburg (Germany), Hinxton (UK) and Monterotondo (Italy).

Research in the CBB Unit relies heavily on imaging technologies that produce very large volumes of complex quantitative data and molecular systems approaches that require the integration of image and biomolecular data and the integrative analysis of these different data types. This permanently requires setting up non-standard computational methods and workflows for data management, processing and analysis.

To address this need, we are seeking a scientist that will support the CBB Unit computationally to bridge the gap between imaging and molecular understanding of biological systems, combining image and bio-informatics. The candidate will develop and implement computational resources for the Unit, including web-based tools for recurrent bioinformatic analysis and reagent design tasks, custom databases for management and dissemination of data as well as data analysis workflows for using EMBL’s high performance compute cluster. The candidate will furthermore develop new methods for data mining using supervised and unsupervised machine learning methods, with a special focus on multidimensional imaging data from dynamic biological systems and their integration with more standard sequence based data types.

In addition to EMBL’s researchers, the candidate will also serve international visitors that aim to carry out projects with similar needs at EMBL. S/he will work in close collaboration with EMBL’s Microscopy and IT Service facilities as well as EMBL’s centres for statistical data and biomolecular network analysis. The candidate will furthermore be expected to actively engage in the general bioinformatics service and training activities of EMBL’s vibrant BioIT community.

Qualifications and Experience

The applicant holds a PhD in natural or computer science. (S)he should have extensive image processing as well as bioinformatics experience, including programming in Java, Perl, Python, MatLab or other modern programming languages (Applicants with a biology background should be able to demonstrate a record of programming skills, whereas applicants with computer science background should document a strong interest in biology at a research level). Familiarity with biological data repositories and web development is expected. Additional qualifications in the fields of database development and/or statistics would be an advantage.

Excellent organizational skills and the ability to work independently on multiple projects with interdisciplinary and international collaborators are expected. The post holder should have excellent communication and interpersonal skills and a strong dedication to enable front line life science research on the highest computational level.

Application Instructions

Please apply online through www.embl.org/jobs

Additional Information

EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation.

Please note that appointments on fixed term contracts can be renewed, depending on circumstances at the time of the review.

Links: http://ig14.i-grasp.com//fe/tpl_embl01.asp?newms=jj&id=55009&aid=15470

Senior IT Systems Engineer

We are looking for a Senior IT Systems Engineer with strong interest in High Performance Computing, experience in deploying and configuring complex open source packages, and in managing cluster schedulers. Solid background in UNIX, Linux, network architecture, scripting and parallel file systems is mandatory. You should have a Bachelor or Master degree in computer science or a related field or at least 5 years of hands-on experience. 

In this position you will be responsible for the maintenance and development of our scientific computing cluster. The main tasks on the cluster are related to genome-wide proteomics, human genome next generation sequencing, and large-scale statistical modeling. The work involves the interaction with several groups at CeMM including Michael Pilz (CeMM IT), Jörg Menche (bioinformatics, network theory) and Christoph Bock (bioinformatics, epigenomics, precision medicine).

Knowledge of BeeGFS - Parallel Cluster File System, Bright Cluster Manager, SLURM job scheduler and Azure cloud services would be an advantage. We take career development of our staff seriously at CeMM. Successful candidates get the opportunity to attend international HPC conferences like ISC High performance, EMiT (Emerging Technology) conference or the HPC Knowledge Meeting. As an international top research institute we encourage co-operations within our scientific networks in academia and industry.

Environment:

Supermicro SYS-F627G2-F73+ and IBM x3350 Nodes, Nehalem, Sandy Bridge and Hasswell based Xeon cpu’s 592 cores, 5,7 TB RAM, QDR and FDR Infiniband interconnect, SAS connected FhgFs 4 Fileservers 1 Metadata Server 715 TB net capacity, FC attached SAN 108 TB net capacity. Expected growth of 100% per year!

We offer:
- Excellent work environment

- Daily bonus for the in-house cafeteria

- Salary: This position is remunerated with a min. yearly salary (gross) of € 47,600 on a full time base. 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.

- Varied job in a meaningful, inspiring, international setting 

Application details:

Please send your application documents, referring to #ITSE by June 30 to: This email address is being protected from spambots. You need JavaScript enabled to view it.

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). 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, as more than 37 different nationalities are represented.

 

 

Phd Candidate position in Computational Epigenomics

The Bioinformatics Group RWTH Aachen University performs research on computational epigenomic methods. Over the past years, we have developed methods for prediction of cell specific binding sites from DNAse-Seq data (Gusmao et al., Bioinformatics, 2014; Gusmao et al., Nature Methods, 2016) and epigenetic and regulatory networks driving cell differentiation via integrative analysis of ChIP-Seq and RNA-Seq data (Allhoff et al., Bioinformatics, 2015; Lin et al., NAR, 2015).

We invite applicants for Phd Candidate positions in Computational Epigenomics. Candidates will perform research on methods for analysis of single cell epigenomics as ATAC-Seq, DNAse-seq and ChIP-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. 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. Interested candidates should send a brief statement of research interests, CV and the names of three references to This email address is being protected from spambots. You need JavaScript enabled to view it..

 

PhD student (f/m) in Neuroscience

The Hospital of the University of Munich, Germany, is one of the largest and most competitive university hospitals in Germany and Europe. 46 specialized hospitals, departments and institutions harbouring excellent research and education provide patient care at the highest medical level with approximately 10.000 employees. The Institute for Stroke and Dementia Research offers a fully funded position available immediately:

PhD student (f/m) in Neuroscience

The ISD is a research institute primarily financed by foundation funds bridging the traditional barriers between academic medicine and basic science in the area of stroke research and related dementias.

Description:

The candidate will work closely with the Principal Investigator to perform both experimental and computational approaches. This PhD position will be in an international, dynamic and “open-door” atmosphere, with access to state of the art laboratory facilities and structured training as part of the Graduate School for Systemic Neuroscience (GSN) (http://www.gsn.uni-muenchen.de/index.html), which is a part of Ludwig Maximilian University of Munich (LMU) (ranked as the top university in Germany according to
Times Higher Education World University Rankings).

Your profile:

Applicants should hold a diploma or Master’s degree in a quantitative discipline (e.g. physics, mathematics, computer science, engineering) or biological sciences, preferably with focus on bioinformatics (e.g. biology, medicine, bioengineering) is important. Experience in analysis of functional sequencing data and knowledge of R, Matlab or Python is strongly desired. Sound knowledge of the English language and team-oriented working is crucial for the applicant’s success. Suitable candidate should be highly motivated with an intrinsic interest in disease mechanisms.

Position:

We look for a talented individual to join the ISD (www.isd-muc.de). ISD has a modern infrastructure including: brand new fully equipped lab spaces and offices, an animal facility that is fully equipped with surgery rooms, state-of the art imaging equipment. Our group will integrate single-cell transcriptome profiling with in vivo imaging to focus basic research on clinically relevant questions on the prevention, diagnosis and treatment of stroke and cognitive decline.

The position is initially for 2 years, but has the possibility of extension. Salary will be based on German public employment guidelines (TV-L). The Ludwig-Maximilians-University/Klinikum der Universität München is an equal opportunity employer. Individuals of all nationalities, genders, ages, and those with disabilities are encouraged to apply. We give priority to applicants with a disability and essentially equal qualifications. Presentation costs cannot be refunded. Skype interviews for candidates from abroad are welcome for an initial interview.

Disabled persons will be preferentially considered in case of equal qualification. Presentation costs can’t be refunded.

Applicants should submit their complete application documents (including detailed CV, cover letter, copies of latest degree and transcripts, at least 1 references or the contact info of referee/s – all documents within a single PDF file) via email to:
E-Mail: This email address is being protected from spambots. You need JavaScript enabled to view it.

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