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Lead Bioinformatician (m/f/d) for high-throughput genome assembly and annotation [Job offer ref. # 12-19005]

Job offer ref. # 12-19005

The Senckenberg Gesellschaft für Naturforschung (SGN) is a member of the Leibniz Association and is based in Frankfurt am Main, Germany. LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG) is a joint venture of the Senckenberg Gesellschaft für Naturforschung (SGN), Goethe-University Frankfurt, Justus-Liebig-University Giessen and Fraunhofer Institute for Molecular Biology and Applied Ecology IME aiming to intensify biodiversity genomics in basic and applied research. We will establish a new and taxonomically broad genome collection to study genomic and functional diversity across the tree of life and make genomic resources accessible for societal-demand driven applied research.

The Senckenberg Gesellschaft für Naturforschung and the LOEWE-TBG invite applications for a

 

Lead Bioinformatician (m/f/d)

for high-throughput genome assembly and annotation

(100%)

 

Your tasks:

·         Lead a team of bioinformaticians to develop, maintain and run high-throughput pipelines for the assembly and annotation of de novo genomes from diverse eukaryotes

·         Implementing and documenting the work-flow from receiving data, issue assembled genomes to users and archiving data in public databases

·         Communication with user groups, service providers and external database managers

 

Your profile:

·         PhD in Bioinformatics or related subjects

·         Experience with de novo genome assembly of non-model organisms and developing large scale, high-throughput procedures for de novo genome assembly and annotation

·         Proven understanding of comparative genomics or evolutionary biology research preferably in non-model organisms

·         Familiarity in leading a service orientated unit and excellent communication skills

 

What is awaiting for you?

·         A central role in an innovative large-scale genomics project with the opportunity to create an own research profile

·         A motivated and dynamic team of international researchers at an internationally recognized biodiversity research institution

·         An opportunity to build a central research and service unit within LOEWE-TBG and Senckenberg

·         Excellent opportunities to expand your scientific network across disciplines

·         Flexible working hours – annual special payment – company pension scheme – 30 days holidays

 

Salary and benefits are according to a full time public service position in Germany                   (TV-H E14/15 according to qualification and experience). The contract should start as soon as possible and will initially be limited to December 31th, 2021. The Senckenberg Gesellschaft für Naturforschung 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. #12-19005) before July 28th, 2019 by e-mail (attachment in a single pdf document) and including a cover letter detailing research interests and experience, a detailed CV and a copy of your certification to:

 

Senckenberg Gesellschaft für Naturforschung

Senckenberganlage 25

60325 Frankfurt am Main

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

 
 

 

 

Wissenschaftlicher Mitarbeiter (w/m/d) im Bereich Bioinformatik [Tierärztliche Hochschule Hannover]

Am Institut für Tierzucht und Vererbungsforschung der Tierärztlichen Hochschule Hannover ist ab dem 01. Oktober 2019 eine Stelle als

wissenschaftlicher Mitarbeiter (w/m/d) im Bereich Bioinformatik

mit 65% 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 Bioinformatik, Biostatistik oder einem vergleichbaren Fach. Darüber hinaus werden Kenntnisse in der Shell-Programmierung unter Linux sowie in der Programmierumgebung R

erwartet.

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 31.07.2019 an Herrn Prof. Dr. Klaus Jung (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!), 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).]

2 PhD and 1 postdoc position in computational chemistry / machine learning [Norway.]

Two PhD positions and one postdoc position are available at the University of Bergen and , Western Norway University of Applied Sciences . All positions are associated with the RESPOND3 project “Towards better computational approaches and responsible innovation strategies in early drug discovery: application to antibiotics and COPD”. The project is a cross disciplinary collaboration between research groups at the Centre for Advanced studies in Biomedical Innovation Law at the University of Copenhagen, the Department of Computing, Mathematics and Physics at the Western Norway University of Applied Sciences as well as the Department of Biomedicine and the Department of Chemistry at University of Bergen. The main focus of RESPOND3 will be hit and lead optimization for targets for antibiotics (SAM riboswitch) and chronic obstructive pulmonary disease (proteinase 3) guided by the use of computational methods as well as the development of new scoring functions using machine learning. The entire project is embedded in a responsible research and innovation strategy.

One of the available PhD positions is in the group of Prof. Nathalie Reuter at the Department of Chemistry, University of Bergen. The main tasks of this position are:

- Modelling of target-compound interactions for compounds targeting serine proteases, and compounds targeting riboswitches;

- Quantification, through the use of molecular dynamics simulations and free energy calculations, of the relative affinity of datasets of compounds for the two above-mentioned targets;

- Contributions to development and validation of multi-site lambda dynamics, using experimental affinity data generated by the project.

- Application of multi-site lambda dynamics to ligand discovery and design for the targets noted above.

More details about this position and information on how to apply can be found here: https://www.jobbnorge.no/en/available-jobs/job/172204/phd-position-in-computational-chemistry

 

The other PhD position is in the group of Prof. Ruth Brenk at the Department of Biomedicine, University of Bergen.

The main objectives of this position are:

- to derive data sets for the development of new scoring functions for protein-ligand interactions with machine learning methods

- to retro- and prospectively evaluate the derived scoring functions

- to design ligands with improved affinities for the targets in the RESPOND3 project

- to supervise master students

More details about this position and information on how to apply can be found here: https://www.jobbnorge.no/en/available-jobs/job/172060/phd-structure-based-design-machine-learning

 

The postdoc position is in the group of Prof. Alexander Selvikvåg Lundervold, Faculty of Engineering and Science, Western Norway University of Applied Sciences.

The main objectives of this position are:

- Development of new scoring functions for protein-ligand interactions using both in-house data and publicly available data sets.

- Attempts at combatting the tendency for scoring functions to exploit uninteresting features in the training data (data leakage) using e.g. various debiasing techniques. The improved scoring functions will be evaluated prospectively.

- Investigation of the the potential for machine learning methods in de novo structure generation (e.g. using variants of generative adversarial networks).

- Assist in the supervision of MSc students and PhD candidates.

More details about this position and information on how to apply can be found here: https://www.jobbnorge.no/en/available-jobs/job/172249/postdoctoral-fellow-in-drug-discovery-and-machine-learning

 

Scientific Programmer / Bioinformatician [EMBL, Heidelberg]

We are seeking a highly motivated scientific programmer and data manager to join the new Zimmermann research group in the Structural and Computational Biology unit. The Zimmermann group combines high-throughput mass spectrometry, bacterial genetics, multi-omics analyses and computational models to investigate the interactions within microbial communities and between microbes and their environment. Your role would be to develop analysis pipelines, infrastructure and data management systems within the group and externally. It includes the development and maintenance of bioinformatics software for different research projects, adaptation of existing code and pipelines, and providing programming and statistics support to the group. The position involves large scale data handling from mass-spectrometry and sequencing experiments (metabolomics, NGS). The duties range from generic bioinformatics and IT support to development of own independent research projects.

Requirements:

—a Ph.D. degree in bioinformatics, computational biology, statistics, or related subjects

—substantial experience in software development and/or scientific computing

—experience with large-scale data analysis and management

—experience with the Linux/Unix shell

—advanced skills in a high level programming language (>2 years of experience)

—ability to work independently and in a team, and at the interface between life sciences and informatics

—willingness to learn new skills and programming languages as projects require

—good communication, interpersonal and English language skills

 

Links: https://www.embl.de/jobs/apply_page/?jobId=QHPFK026203F3VBQB688N79SB-1098&langCode=en_GB. 

MitoIntegrOMICS - Verbesserung der Diagnostik bei mitochondrialen Erkrankungen - PhD Projekt in Nizza/Frankreich

Mitochondriale Erkrankungen (MD) sind seltene Erkrankungen, die durch einen Mangel der mitochondrialen Atmungskette verursacht werden, die in jeder Zelle Energie liefert. MD werden durch Veränderungen (Varianten) an Genen verursacht, die an mitochondrialen Funktionen beteiligt sind. Die Diagnose von MD basiert auf der Identifizierung des/der krankheitsverantwortlichen Gene(s), die es ermöglichen, genetische Beratung, pränatale Diagnostik, Therapieansätze und eine bessere Versorgung der Patienten anbieten zu können. Die heute verwendeten Technologien zur Erkennung der verursachenden Varianten liegen bei 25-50%. Durch MultiOmics DatenIntegration und maschinellem Lernen soll die diagnotische Erfolgsrate in diesem PhD Projekt verbessert werden.

Link: http://univ-cotedazur.fr/fr/recherche/boosturcareer

 

Postdoc - Systems Biology of Infection [Uni Greifswald]

We have an opening for a Postdoc in Systems Biology of infection within the KoInfekt project: Elucidation of Pathomechanisms of Bacterial-Viral Co-infections with new Biomedical Models .

Applicants should have a strong research record in theoretical Systems Biology or related fields, ideally with experience in machine learning in systems biology, in multi-OMICs data integration, or modeling of biological processes using differential equations, and with a strong algorithmical and mathematical background. We expect the applicant to be willing to collaborate closely with both theory and experimental collaboration partners within the KoInfect consortium.

The position is paid according to the German TV-L salary scale (E-13), and is available immediately until December 2020, with possible extension. 

Links: http://www.kaderali.org/jobs.html

Scientific Programmer / Bioinformatician [ Zimmermann research group, EMBL]

We are seeking a highly motivated scientific programmer and data manager to join the new Zimmermann research group in the Structural and Computational Biology unit. The Zimmermann group combines high-throughput mass spectrometry, bacterial genetics, multi-omics analyses and computational models to investigate the interactions within microbial communities and between microbes and their environment. Your role would be to develop analysis pipelines, infrastructure and data management systems within the group and externally. It includes the development and maintenance of bioinformatics software for different research projects, adaptation of existing code and pipelines, and providing programming and statistics support to the group. The position involves large scale data handling from mass-spectrometry and sequencing experiments (metabolomics, NGS). The duties range from generic bioinformatics and IT support to development of own independent research projects.

Requirements:

—a Ph.D. degree in bioinformatics, computational biology, statistics, or related subjects

—substantial experience in software development and/or scientific computing

—experience with large-scale data analysis and management

—experience with the Linux/Unix shell

—advanced skills in a high level programming language (>2 years of experience)

—ability to work independently and in a team, and at the interface between life sciences and informatics

—willingness to learn new skills and programming languages as projects require

—good communication, interpersonal and English language skills 

Links: https://www.embl.de/jobs/apply_page/?jobId=QHPFK026203F3VBQB688N79SB-1098&langCode=en_GB

2 Phd positions in Computational Biology [Center for Molecular Medicine, Frankfurt]

The group of Prof. Marcel Schulz  is looking to fill the position of two Phd students (E13 TV-G-U, 65%) to start as early as possible at the Computational Epigenomics & Systems Cardiology group at the Institute for Cardiovascular Regeneration, Center for Molecular Medicine, Frankfurt (https://schulzlab.github.io).

Exact payment is based on previous research experience according to the work laws of Goethe University (TV-G-U).

Tasks:

We offer a Phd position for method development for integrative analysis methods targeted for analysis of single cell assays that are conducted with multiple assays simultaneously, for example RNA-seq and DNA methylation or ATAC-seq. Another position is about method development of novel approaches for the prediction of gene expression. Different approaches from Machine Learning should be tested and novel approaches for the interpretability of complex non-linear methods or Deep Learning based approaches should be developed to unravel gene-specific regulatory codes from a large catalogoue of epigenomics data.

Requirements:

·       Masters degree in Bioinformatics, Machine Learning, Computer Science or a related discipline

·       good programming skills

·       experience in the application of machine learning methods is advantageous

·       experience in the analysis of sequencing data is advantageous

·       we are working in an interdisciplinary team and are looking for people with good organizational and communication skills, as well as high creativity to address novel research problems

·       good knowledge of the English language

Please send your application with CV and two names of references latest until 15.06.2019 (preferably by email) to:

Prof. Marcel Schulz, Institut für Kardiovaskuläre Regeneration, Zentrum für Molekulare Medizin, Goethe-Universität Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, E-Mail: marcel.schulz AT em.uni-frankfurt.de

Please do not send original documents by mail, because there will be no return of such documents. All electronic documents should be combined into one pdf document. Travel and application costs are not being reimbursed.

Goethe University is comitted to increase the amount of female researchers and we encourage their application. Applicants with a disability and equal qualifications will be favoured.

 

Postdoc Computational Biology [Frankfurt]

In der Computational Epigenomics & Systems Cardiology Gruppe von Prof. Marcel Schulz (https://schulzlab.github.io) am Institut für Kardiovaskuläre Regeneration, Zentrum für Molekulare Medizin ist  schnellstmöglich die Stelle einer/s

Postdoktorandin /Postdoc (E13 TV-G-U, 100%)  befristet zu besetzen.

Die Eingruppierung erfolgt nach den Tätigkeitsmerkmalen des für die Goethe-Universität geltenden Tarifvertrags.

Aufgaben:

·       Mitarbeit im Projekt „Analyse hochdimensionaler Daten zur Vorhersage der Genregulation im Kontext von Herz-Kreislauf Erkrankungen“ im besonderen Anwendung von Methoden des Maschinellen Lernens für die Vorhersage von Aspekten der Genregulation oder Modellierung von Heterogenität in single cell Daten.

Voraussetzungen:

·       abgeschlossenes Hochschulstudium (Master) in der Bioinformatik, Machine Learning oder Informatik

·       Phd in Bioinformatics, Computational Biology, oder Machine Learning,

·       gute Programmierkenntnisse in C++ und einer Skriptsprache wie Python

·       Erfahrung in der Anwendung von Methoden des Maschinellen Lernens

·       Erfahrung in der Analyse von NGS-Daten sind wünschenswert

·       Organisations- und Teamfähigkeit, Flexibilität, Aufgeschlossenheit, Kommunikationsfähigkeit

·       sehr gute Englischkenntnisse

Ihre Bewerbung mit den üblichen Unterlagen richten Sie bitte bis spätestens den 15.06.2019  an:

Dr. Marcel Schulz, Institut für Kardiovaskuläre Regeneration, Zentrum für Molekulare Medizin, Goethe-Universität Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, E-Mail: marcel.schulz AT em.uni-frankfurt.de

Bitte senden Sie uns keine Originalunterlagen zu, da eine Rücksendung der Bewerbungsunterlagen nicht erfolgt. Sollten Sie sich per Mail bewerben, bitten wir Sie um Zusammenfassung der Unterlagen in einem pdf-Dokument. Fahrt- und Bewerbungskosten können nicht erstattet werden.

 

13 positions for PhD students available including a computational molecular design topic

Within the Research Training Group "Chemical Biology of Ion Channels (Chembion)" funded by the Deutsche Forschungsgemeinschaft (DFG) and established at the Westfälische Wilhelms-Universität in Münster 13 positions for PhD students, 13 TV-L (65 %) are available.

13 scientists of the Westfälische Wilhelms-Universität Münster have teamed up with their complementary expertise to focus on the chemical biology of ion channels. The interdisciplinary research activities are centered on five topics: ligand recognition, subtype specific modulation, molecular imaging, molecular and cellular physiology, integrative (patho)physiology. Our vision of this interdisciplinary project is to solve physiological questions in the field of ion channels with innovative chemical methods, to bring together the molecular world of chemistry/pharmacy with the function-centered world of medicine and to develop the internationalization of our doctoral students.

One topic is of special interest for the bioinformatics/cheminformatics community: "In-silico studies of ion channels and their modulators using computational molecular design".

Further details can be obtained from the Chembion homepage: www.uni-muenster.de/chembion