ISCB Affiliated Group Logo

Job Offers

Master internship in Bioinformatics

Location: EMBL Rome, Italy
Category: Master internship
Duration: Minimum of 6 months, up to one year
Closing Date: October 15th 2019
Starting Date: Can be arranged with the selected candidate
 
The EMBL Epigenetics and Neurobiology Unit in Monterotondo (near Rome, Italy) is seeking a highly motivated student to join the Bioinformatics Services of EMBL Rome and the Boulard group for a Master internship.

Project

Epigenetics define biochemical modifications that are independent of the DNA sequence such as DNA methylation and histone modifications. Methylation of specific histone residues has been shown to influence gene expression. Abnormalities in histone modifications or transcription factor (TF) binding are frequently observed in cancer.
Innovative clinical trials targeting writers or erasers of histone modifications are currently under development. However, the gold standard method for epigenomic profiling, namely ChIP-seq, has failed to show differences in chromatin modification upon treatment by these new epi-drugs. Over 30 years ago, the ChIP protocol was introduced and has been widely-used by the community to screen for TFs or histone modifications genome-wide without spike-in controls. Recent developments and enhancements of ChIP-seq with enzyme-tethering and spike-in methods such as DamID, ChEC-seq, or Cut&Run, both at bulk and single-cell level offer investigation of genomic loci at an unprecedent precision.
 
The recent genomic revolution arising from these technologies however still lack solid bioinformatics foundations and benchmarking due to their recent development. The selected candidate, under the supervision of Nicolas Descostes and Mathieu Boulard, will be in charge of developing methodologies for processing and analyzing Cut&Run and Cut&Tag data. The work will involve benchmarking and analysis of publicly available but also internally produced data sets. These methodologies will have to be integrated in a pipeline. The candidate will have the opportunity to learn how to perform bioinformatics using one of the most powerful High Performance Computing (HPC) system in Europe but also, according to progression, to be initiated to the use of singularity dockers and conda environment. The work will be performed with Snakemake.
 
Profile
 
Background in Bioinformatics, Physics, Mathematics, Computer Sciences or other related disciplines are welcome.
The Candidate should have a solid training in programming (at least two-three courses of 30 hours with equivalent time of coding). The candidate will have to demonstrate that he or she conducted projects (in Java, C, R, Python or others) within the context of classes at University. Experience in project in R will be a plus.
Knowledge in genome biology would be a key advantage.
Good communication skills in English is compulsory.

Benefit

The selected candidate will be provided a small stipend and accommodation.

Application

CV and motivation letter should be sent to This email address is being protected from spambots. You need JavaScript enabled to view it..

Interdisciplinary Ph.D. Positions in Scientific Computing, Data Science and Physics

DASHH is a recently established, interdisciplinary graduate school that offers challenging Ph.D. topics at the interface of the natural sciences, applied mathematics and data and computer science. DASHH involves several research institutions and universities in the multifaceted city of Hamburg, Germany.

DASHH is looking for excellent and highly qualified Ph.D. candidates, interested to work on data-driven research in physics, chemistry, applied mathematics, computer science or structural biology.

We offer:

  • Interdisciplinary research in the natural sciences and computer/data science or applied mathematics
  • Research at world leading large-scale research facilities (PETRA III, FLASH, European XFEL, LHC)
  • Attractive, interdisciplinary thesis topics
  • Excellent working conditions at an international, vibrant and inspiring research campus
  • Close supervision and support by a panel of established professors and scientists
  • Training in transferable skills and career development
  • Work contract at the level of the German TV-L13 (100%) salary scheme for 3 year

Requirements:

We are looking for highly motivated students with an excellent academic background in the natural sciences, engineering sciences, informatics or applied mathematics. The candidates should bring a strong interest to work on highly interdisciplinary topics, should be team oriented and have a strong background in programming. For more information see: https://www.dashh.org

Application Deadline:

December 1st, 2019

DASHH is a joint venture of the Deutsches Elektronen Synchrotron (DESY), the Universität Hamburg (UHH), the Technische Universität Hamburg (TUHH), the Helmut Schmidt Universität (HSU), the Helmholtz Zentrum Gesthacht (HZG), the Helmholtz Zentrum für Infektionsforschung (HZI), Max Planck Institut für Struktur und Dynamik der Materie (MPSD) and European XFEL GmbH.

Identification of genomic differences from whole-genome alignments (Klau/Schneeberger labs)

Genome sequences are key resources to understand functional processes and divergent trait evolution within and between different species. Within http://ceplas.eu, many high-quality genome assemblies of closely related species of the Brassicaceae and other plant families are being generated. This makes it possible, in principle, to reveal intra-family similarities and structural variations from pairwise whole-genome alignments (WGA) as a major step towards family pangenome representations. However, even though efficient whole-genome alignment solutions exist there are no computational approaches that would annotate all genomic differences including the obvious hierarchy ranging from small single nucleotide changes to large complex rearrangements. The project will therefore extend SyRI, an existing algorithm for genome-wide structural rearrangement identification to solve this efficiently.

Qualifications needed: good algorithmic background, programming skills, basic knowledge in bioinformatics, Plus: experience with genomic data and/or plant genomics

Contact persons: Gunnar Klau (HHU), Korbinian Schneeberger (MPI)

PhD position “Machine-learning approaches for data integration and patient stratification in schizophrenia and comorbid diseases”

The Health Data Science Unit (HDSU, www.hdsu.org) is a newly created unit of the BioQuant and medical Faculty of the University Heidelberg, which focuses on research topics related to digital health and the integration of clinical and genomic datasets.

The recently funded COMMITMENT project (COMorbidity Modeling via Integrative Transfer machine-learning in MENTal illness), in which HDSU is leading one work-package, will establish an interdisciplinary research consortium for the identification of molecular hallmarks of schizophrenia and comorbid somatic illnesses, such as diabetes or cardiovascular diseases. The identification of shared and distinct biological profiles will allow disentangling patient heterogeneity and provide the basis for objective tools for personalized clinical management of psychotic disorders.

The HDSU will lead the work-package on data integration, signature extraction and transfer learning over cohorts of

In this context, we are looking for a PhD student with a focus on the following points:

- Extension of existing matrix factorization (MF) approaches for the integration of heterogeneous datasets;
- Comparison of neural network models and MF methods for the definition of molecular signatures;
- Extraction of molecular signatures using transfer learning approaches

 

We are looking for a candidate with the following qualifications:

- A master degree in the field of computational biology or applied mathematics with a focus on statistical learning
- Good programming skills and first experiences in the field of machine-learning
- An interest in working in an interdisciplinary field involving clinicians, biologists, statisticians and computer scientists
- Good communication skills

We are offering

- An exciting, excellent and highly multi-disciplinary research environment on the campus of Heidelberg University, Germanys oldest university
- Payment according to German TV-L E13 (65%)
- A superb living environment in Heidelberg and surroundings.

Application letters and CVs (as pdfs), together with contact information of two referees should be sent by mail to This email address is being protected from spambots. You need JavaScript enabled to view it.

Links: https://www.hdsu.org

Wissenschaftlicher Mitarbeiter (w/m/d) Fachrichtung Biologie, Bioinformatik, Statistik [Tierärztliche Hochschule Hannover]

Am Institut für Tierzucht und Vererbungsforschung der Tierärztlichen Hochschule Hannover ist zum

nächst möglichen Termin eine Stelle als

 

wissenschaftlicher Mitarbeiter (w/m/d)

(Fachrichtung Biologie, Bioinformatik, Statistik)

 

mit 75% der vollen Arbeitszeit zu besetzen. Die Stelle ist auf drei Jahre befristet. Ein Promotionsvorhaben

auf der Stelle wird unterstützt und ausdrücklich erwünscht.

 

Aufgaben sind die die Mitarbeit in aktuellen Forschungsaktivitäten der Arbeitsgruppe „Genomics and

Bioinformatics of Infectious Diseases“. Dazu zählen vor allem die Weiterentwicklung und Anwendung

von statistisch-bioinformatischen Methoden für die Analyse von High-Throughput-Sequenzdaten und

High-Throughput-Genexpressionsdaten (NGS-, Microarrays-Daten).

 

Voraussetzung für eine Bewerbung ist ein abgeschlossenes wissenschaftliches Hochschulstudium

mit Masterabschluss in Biologie, Bioinformatik, Statistik oder einem vergleichbaren Fach.

Die Vergütung erfolgt nach E 13 TV-L.

 

Schwerbehinderte Bewerberinnen und Bewerber werden bei gleicher Eignung vorrangig berücksichtigt.

Bitte senden Sie Ihre aussagekräftige Bewerbung per E-Mail bis spätestens 20.10.2019 an Herrn Prof.

Dr. Klaus Jung (This email address is being protected from spambots. You need JavaScript enabled to view it.), Institut für Tierzucht und Vererbungsforschungs, Tierärztliche

Hochschule Hannover. Weitere Auskünfte zu der Stelle werden gerne über diese E-Mail-

Adresse erteilt.

 

Ihre personenbezogenen Daten werden vertraulich behandelt (www.tiho-hannover.de/ds-bew).

CompCancer PhD Programme in Berlin

4 PhD positions available in an exciting new DFG-funded Bioinformatics/Computational PhD programme in Berlin addressing cutting edge questions in cancer research and oncology. Topics range from computational modelling to sequence analysis and single cell methods.

Links: http://comp-cancer.de, @CompCancerRTG

Leitung Geschäftsstelle CampusInstitut Data Science Uni Göttingen

Am Campus-Institut Data Science (CIDAS) der Georg-August-Universität Göttingen ist die Position einer "Leitung der Geschäftsstelle" ab dem nächstmöglichen Termin mit der regelmäßigen wöchentlichen Arbeitszeit (zzt. 39,8 Stunden) für die Dauer von zwei Jahren zu besetzen. Die Entgeltzahlung erfolgt nach Entgeltgruppe 14 TV-L. Teilzeitbeschäftigung ist möglich.

Das CIDAS ist als zentrale wissenschaftliche Einrichtung der Universität Göttingen errichtet worden und dient dem Ziel, die fakultätsübergreifenden und universitären Forschungs-, Lehr- und Weiterbildungsaktivitäten an der Universität auf dem Gebiet der Data Sciences zu koordinieren, durchzuführen und weiterzuentwickeln. Zugleich dient es der Koordination von Forschungs-, Lehr- und Weiterbildungsaktivitäten mit den Partnern des Göttingen Campus auf dem Gebiet Data Science.

Im Göttingen Campus arbeiten Universität, Universitätsmedizin, fünf Max-Planck-Institute, die Akademie der Wissenschaften, das Deutsche Zentrum für Luft- und Raumfahrt (DLR) sowie das Deutsche Primatenzentrum zusammen. Das CIDAS liegt an der Schnittstelle von Informatik, Statistik, Mathematik und Anwendungsdisziplinen und soll neueste Methodenentwicklung in Bereichen von Data Science mit internationaler Spitzenforschung in Profilfeldern des Standorts verbinden.

Die Leitung der Geschäftsstelle berichtet an den Vorstand des CIDAS und trägt die organisatorische Verantwortung. Dazu gehören insbesondere
- Aktive Beteiligung an Auf- und Ausbau des CIDAS
- Kommunikation mit den beteiligten Akteur_innen an der Universität und bei den Campuspartnern
- Koordination und Weiterentwicklung der Lehrangebote für Data Science
- Verwaltung der CIDAS Ressourcen
- Unterstützung des Vorstands des CIDAS
- Unterstützung bei Beantragung und Einwerbung von Drittmitteln
- Organisation von interner Projektförderung
- Vorbereitung und Durchführung von Veranstaltungen, Workshops und Tagungen des CIDAS

- Unterstützung des Stellenbesetzungsprozesses im Bereich Data Science
- Ausbau von Wirtschaftskontakten und Netzwerke-Pflege

- Betreuung und Vernetzung der Arbeitsgruppen des CIDAS

Ihr Profil:
- Führungs- und Verwaltungserfahrung in einer wissenschaftlichen Einrichtung
- Erfahrung in Teamführung und -management
- Abgeschlossenes wissenschaftliches Hochschulstudium
- Von Vorteil ist der Nachweis eigener Forschungserfahrung durch eine abgeschlossene Promotion
- Gute Kommunikationsfähigkeiten mit unterschiedlichen Stakeholdern
- Verhandlungssichere Kenntnisse der deutschen und englischen Sprache

Die Universität Göttingen strebt in den Bereichen, in denen Frauen unterrepräsentiert sind, eine Erhöhung des Frauenanteils an und fordert daher qualifizierte Frauen nachdrücklich zur Bewerbung auf. Sie versteht sich als familienfreundliche Hochschule und fördert die Vereinbarkeit von Wissenschaft/Beruf und Familie. Die Universität hat sich zum Ziel gesetzt, mehr schwerbehinderte Menschen zu beschäftigen. Bewerbungen Schwerbehinderter erhalten bei gleicher Qualifikation den Vorzug. Die Stelle ist unter Umständen teilzeitgeeignet.

Bitte reichen Sie Ihre Bewerbung mit den üblichen Unterlagen in einem einzigen PDF bis zum 30.09.2019 über das Bewerbungsportal unter dem Link https://lotus2.gwdg.de/uni/uzdv/perso/knr_100605.nsf ein.

Für Rückfragen steht Ihnen Herr Prof. Dr. Yahyapour, E-Mail: This email address is being protected from spambots. You need JavaScript enabled to view it., zur Verfügung.


Links:

PostDoc Researcher (m/f/d) in Evolutionary Genomics of Mammals

 

Job offer ref. #11-19012

The Senckenberg Gesellschaft für Naturforschung (SGN) is a member of the Leibniz Association and is based in Frankfurt am Main, Germany. SGN conducts natural history research with almost 800 employees and research institutions in six federal states. Within SGN, the Senckenberg Biodiversity and Climate Research Centre (BiK-F) explores the interactions between biodiversity, climate, and society.

Senckenberg BiK-F invites applications for a

 PostDoc Researcher (m/f/d)

in Evolutionary Genomics of Mammals

(100 %)

There is an exciting opportunity for a talented and motivated applicant to join the working group of Prof. Dr. Axel Janke. The applicant will be closely involved in gene flow, evolutionary-population or phylo-genetics to study speciation in mammals (bears, giraffe, kangaroos or allies) at the genomic level.

 

Your profile:

·         - PhD in Biology, Genetics, Bioinformatics or a related field

·         - strong interest and proven skills in evolutionary, population or phylo-genetics, preferentially in gene-flow analyses

· -    - experience in genome assembly, annotation and programing of scripts, R

·          - very good written and oral communication skills in English

 

Salary and benefits are according to a full time public service position in Germany (TV-H E 13, 100%). The contract should start as soon as possible and will initially be limited for two years.

The Senckenberg Research Institutes support equal opportunity of men and women and therefore strongly invites women to apply. Equally qualified handicapped applicants will be given preference. The place of employment is in Frankfurt am Main, Germany. The employer is the Senckenberg Gesellschaft für Naturforschung.

Please send your application, mentioning the reference of this job offer (ref. #11-19012) before September 1st, 2019 by e-mail (attachment in a single pdf document) and including a cover letter describing your motivation to apply, a detailed CV, relevant credentials and certificates, two relevant publications and contact details of two potential references to:

 

Senckenberg Gesellschaft für Naturforschung

Senckenberganlage 25

60325 Frankfurt am Main

E-Mail: This email address is being protected from spambots. You need JavaScript enabled to view it.

For scientific enquiries please get in contact with Prof. Dr. Axel Janke, This email address is being protected from spambots. You need JavaScript enabled to view it.



Links: http://www.senckenberg.de/files/content/stellenausschreibungen/ref-11-19012_postdoc_position_verlangert.pdf

Computational Biologist [Bork group]

We are Europe’s flagship research laboratory for the life sciences – an intergovernmental organisation performing scientific research in disciplines including molecular biology, physics, chemistry and computer science. We are an international, innovative and interdisciplinary laboratory with more than 1600 employees from many nations, operating across six sites, in Heidelberg (HQ), Barcelona, Hinxton near Cambridge, Hamburg, Grenoble and Rome.

 

You will work in the Bork group, which harbours a wide range of intertwined activities in the area of computational biology. Many of these are currently applied to microbiomics, with the focus on the human gut, but increasingly also on other environments such as ocean or soil.  Metagenome-wide association studies are coupled with targeted approaches and also, in the context of local collaborations, with experimental analysis of synthetic and ex-vivo microbial communities.

 

Your role

 

The post holder will analyse and integrate new and existing datasets to study the microbiome of hosts and their global environments and the implications these have for human health. Particular focus areas will include high-resolution analyses of microbial communities (e.g. at sub-species or strain-level) as well as the infant microbiome, where questions such as microbial transmission and the effect of probiotics on microbiome and human development will be explored. The required tasks will involve developing and applying bioinformatics methods to mine large multi-‘omics datasets from various biological systems. The work will comprise technical as well as discovery aspects and will be carried out both independently and with internal and external collaborators. The post holder will also mentor trainees, provide hands-on guidance in their research, and teach technical and analytical skills.

 

You have

 

You should have a PhD in a field related to Computational Biology as well as a solid training in Microbial Ecology, Computer Science, and Microbiomics. At least 1.5 years of postdoctoral and practical experience analysing metagenomic datasets is required and you should at least have experience in 16S rRNA and shotgun metagenomics profiling.

 

Strong motivation, excellent scientific skills as well as willingness to work in a multicultural & interdisciplinary environment are essential. As part of the work involves international collaborations, project management, communication and presentation skills as well as the ability to work in a team are also required. You should be familiar with the UNIX environment and have advanced experience in programming. Excellent data analysis skills in R or python are also required.

 

For more information and to submit your application, please visit our website: https://www.embl.de/jobs/searchjobs/index.php?ref=HD01593&newlang=1&srch_trm=HD01593. Closing date: 1 Sep 2019.

Bio-IT Computational Support & Training

EMBL is Europe’s flagship research laboratory for the life sciences – an intergovernmental organisation performing scientific research in disciplines including molecular biology, physics, chemistry and computer science. We are an international, innovative and interdisciplinary laboratory with more than 1600 employees from many nations, operating across six sites, in Heidelberg (HQ), Barcelona, Hinxton near Cambridge, Hamburg, Grenoble and Rome. 

 

Applications are invited for the above post to join the Gibson Team. The Gibson team develops and applies biological software tools in the analysis of protein data. An important activity of the group is to interface with experimental research groups at EMBL. The post-holder will be the focal point in providing bioinformatics support to the experimental researchers at EMBL. In this context, it is expected that the post-holder will organise a minimum of 4 bioinformatics/computational training courses per year.

 

Your role

 

The position is part of the EMBL Bio-IT project, a community-driven initiative to support the development and technical capacity of the diverse bio-computational community at EMBL. As one of the key members of this project, the post-holder will work closely with other members of Bio-IT to develop and/or organise various bioinformatics training courses, community-oriented outreach activities, community assessment tasks, and consulting. Through active communication and collaboration with many bioinformatics service experts at EMBL Heidelberg (e.g. the Computational Centres covering statistics, networks, image analysis, and systems models), the post-holder will help expand and maintain a lively network of bioinformaticians throughout the institute.

In addition, EMBL is a partner in the de.NBI (German Network for Bioinformatics Infrastructure) consortium which constitutes the ELIXIR Germany node. The post-holder will interact with individuals from de.NBI/ELIXIR to collaborate and jointly organise training and outreach activities. The post-holder will also have opportunities to attend and present at relevant conferences and events.

This is a highly collaborative role that provides diverse opportunities to engage with and support the scientific community while developing your own leadership skills. As well as being able to communicate and work well within a team, initiative, flexibility and willingness to learn will complete your profile.

 

You have

·         Ph.D. in Bioinformatics, Computational Biology, or related fields, or equivalent experience

·         Knowledge of a range of bioinformatics tools to provide support and training

·         Familiarity with one or multiple programming/scripting languages such as Bash, Python, R

·         Excellent communication and interpersonal skills

·         Experience of working at the interface between biology and computation

·         Experience in organising and teaching scientific/technical workshops

·         Interest in learning from other research communities of practices

 

Find more information and apply through our website.