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Stellenangebote

Wissenschaftlicher Mitarbeiter (m/w) im Bereich Bioinformatik (TV-H E13, 100%)

An der Professur für Systembiologie mit dem Schwerpunkt Genomik, Proteomik und Transkriptomik, Fachbereich Biologie und Chemie, ist im Rahmen des vom Land Hessen geförderten LOEWE-Schwerpunktes „Diffusible Signals – Impact on diffusible signals at human cell-microbe interfaces“ ab dem nächstmöglichen Zeitpunkt befristet bis zum 31.12.2024 eine Vollzeitstelle mit einer/einem Wissenschaftlichen Mitarbeiter/in zu besetzen. 

Aufgaben:

Im Rahmen des Teil-Projekts „Integrierte Modellierung der Mikroben-Wirts-Interaktion durch skalierbare bioinformatische Analyse-Workflows“ sind Sie verantwortlich für die

·         Software-Entwicklung zur Prozessierung und Visualisierung von umfangreichen Sequenz-Daten aus Genom und Transkriptom-Sequenzierungen inklusive der zugehörigen Metadaten

·         Entwicklung von sowohl verbesserten Auswertungsmethoden als auch adäquaten Datenstrukturen zur Speicherung und Integration der Analyseergebnisse und Metadaten um unterschiedlichste Datensätze untereinander vergleichen und kombiniert auswerten zu können

·         Entwicklung von benutzerfreundliche Visualisierungsverfahren, die eine interaktive und intuitive Exploration der Daten bis hin zur Darstellung von regulatorischen Netzwerken erlauben

·         Bearbeitung von aktuellen Fragen in Bezug auf die Bereitstellung einer flexiblen Software-Plattform zur systematischen und automatisierten Analyse von Hochdurchsatzdaten in Cloud-Computing-Umgebungen

·         bioinformatische Analyse von Hochdurchsatzdaten (Next-Generation-Sequencing, insbe­sondere RNA-Seq und Derivate) und deren systembiologische Interpretation und Visualisierung

·         Mit- und Weiterentwicklung der softwaretechnischen Infrastruktur zum Datenmanagement

·         Teilprojekt-spezifische Unterstützung bei der Datenanalyse als auch die Entwicklung neuer Softwaretools und einer web-basierten Plattform für die interaktive Visualisierung und Interpretation von Hochdurchsatzdaten

 

Anforderungsprofil:

·         Abgeschlossenes wissenschaftliches Hochschulstudium im Fach Bioinformatik oder Informatik oder einem verwandten Fachgebiet mit dokumentierten Erfahrungen in bioinformatischer Grundlagenforschung und Software-Programmierung in diesem Bereich

·         Ausgewiesene Kenntnisse in Fragestellungen der modernen Hochdurchsatz-Sequenzierungs­technologien (Next-Generation Sequencing)

·         Kenntnisse im Umgang mit relationalen Datenbanken und der Implementierung von web-basierten Schnittstellen für Benutzer

·         Fähigkeiten in der Datenanalyse mit Hilfe von Workflow-Systemen (z.B. CWL, Nextflow) Erfahrung im Umgang mit Unix/Linux-Betriebssystemen

·         Sicherer Umgang mit Java und einer der folgenden Skriptsprachen: Perl, Python, Groovy

·         Praktische Erfahrungen im High-Performance-Computing und Cloud-Computing sind von Vorteil

 

Für Fragen steht Ihnen Herr Prof. Dr. Goesmann gerne zur Verfügung (Tel. 0641/99-35801 oder per Mail Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!).

 

Ihre Bewerbung (keine E-Mail) richten Sie bitte unter Angabe der Referenznummer 148/08 mit den üblichen Unterlagen bis zum 23.02.2021 an Herrn Prof. Dr. Alexander Goesmann, Professur für Systembiologie, Heinrich-Buff-Ring 58, 35392 Gießen. Bewerbungen Schwerbehinderter werden - bei gleicher Eignung - bevorzugt. Wir bitten, Bewerbungen nur in Kopie und ohne Hefter/Hüllen vorzulegen, da diese nach Abschluss des Verfahrens nicht zurückgesandt werden.

 

Der Link zur kompletten Stellenausschreibung lautet:

https://www.uni-giessen.de/karriere/stellenangebote/ausschreibungen/wissenschaftliche-mitarbeiter/148-08

PhD position: Bioinformatics dissection of aberrant developmental progression during tumorigenesis using a single-cell multi-omics approach (INSERM, CNRS, AMU, Marseille)

We are proposing a PhD position to investigate, at the single cell level, the gene regulatory regions controlling brain development and tumorigenesis in Drosophila. For this purpose, we will use a single-cell multi-omics approach (RNA-seq and ATAC-seq).

Details of the project and host labs can be found here: https://centuri-livingsystems.org/phd2021-06

This PhD project is part of the PhD Programme of the Turing Centre for Living Systems (CENTURI). The deadline of application is: February 26, 2021 and the application procedure is explained here: https://centuri-livingsystems.org/recruitment/

Recent single-cell transcriptomics data have shown that brain cancers in children are driven by aberrantly redeployed developmental programs. However, it is still unclear how these developmental programs are coopted and regulated in the tumorigenic context. Brain development is understood in unmatched details in Drosophila where we have recently generated a model of brain tumors that recapitulates childhood tumors. New technologies now allow the simultaneous analysis of the transcriptome and regulome (regulatory regions) in single-cells. This project aims to generate and analyze single-cell data from neural progenitors isolated from the developing brain and tumors in Drosophila. The student will prepare tissues for high-throughput sequencing (HTS). He will then carry out a bioinformatics analysis to identify gene regulatory regions and infer gene regulatory networks involved during normal brain development and brain tumorigenesis. This project will shed light on how developmental programs can be coopted to promote tumorigenesis in children.

The PhD candidate should have a Master's degree in an area related to Bioinformatics, Biophysics, or Computer Science with a strong interest in data analysis. Previous experimental experience is not required but the student should be motivated to embark on a substantial amount of experimental work in order to generate the single-cell data to be analyzed.

Thank you for sharing this offer with motivated candidates.

Aitor González : https://tagc.univ-amu.fr/en/users/gonzalez-aitor; Cédric Maurange : http://www.ibdm.univ-mrs.fr/fr/equipe/plasticite-des-cellules-souches-neurales/

Student or scientific assistant (SHK/WHK): Support for virtual working group meetings & data mobilization in synthesis Postdoc projects

Working time: max. 19 hours per week until 30.9.2021

sDiv usually hosts 15 working groups a year and welcomes more than 20 participants each meeting from all parts of the world. Due to Covid-19, our working groups meet now fully virtually. To help them to be more productive and concentrate on science, we offer a student assistant position at the German Centre for Integrative Biodiversity Research (iDiv). A virtual meeting lasts between 2-4 days with several virtual meeting time blocks and due to the time difference among the participants, the support is mainly needed in the late afternoon until evening and potentially sometimes in early mornings. In times of less working group activity, the assistant will support biodiversity data (e.g. species traits) mobilisation in sDiv synthesis Postdoc projects (normal working hours).

The position is supervised by Dr. Marten Winter (head of sDiv).

Job description:

• technical support of the virtual working group meetings

o oversee virtual meeting platform functionalities (usually Zoom)

o help with break out room coordination

o support with audio, video problems of participants

o help setting up and oversee potential virtual whiteboards, slack channels etc

• support in meeting preparation

• note taking & synthesizing while and after the meetings

• potential help with meeting moderation/facilitation

Requirements / expected profile:

• You are currently a MSc student in a related research discipline (e.g., archaeology, zoology, ecology, palaeontology, geography, geology) or you already hold a Master’s or equivalent degree in a related field of research

• You should be familiar with at least one the following topics: Ecology, biodiversity research

• Fluent English language skills are a prerequisite and skills in other languages are beneficial.

• Your place of work is the German Centre for Integrative Biodiversity Research (iDiv) in Leipzig. Depending on the Corona-situation home office can be made.

You will be employed as student assistant via Leipzig University. The preferred starting data is 01 March 2021 or shortly thereafter. Applications should be directed to sDiv (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!) and should include a short motivation letter and a short curriculum vitae.]

 

Links: https://www.idiv.de/en/sdiv.html

Postdoc Position in Comparative Genomics

The Hiller Lab at the LOEWE Center for Translational Biodiversity Genomics (TBG) in Frankfurt, Germany is looking for an ambitious Postdoc to investigate the genomic basis of phenotypic differences between vertebrates.
 
Project:
The project aims at linking phenotypic adaptations to genomic differences, which is a central goal in the genomics era. The postdoc is expected to capitalize on a powerful repertoire of genomic methods as well as genome alignments and comparative data for several hundred mammals and birds that the lab has generated. A large list of interesting adaptations including metabolic, physiological and morphological traits in bats, dolphins, other mammals and vertebrates is available to be studied, and choices can be influenced by the preference of the postdoc.
 
Our lab:
The mission of our group is to understand how nature's fascinating phenotypic diversity has evolved and how it is encoded in the genome. Work in the lab includes genome sequencing and assembly, genome alignment and annotation, development and application of comparative genomic methods to discover differences in genes and cis-regulatory elements, and the use of statistical approaches to link phenotypic to genomic changes [1-8].
 
Our lab is part of TBG (https://tbg.senckenberg.de/) and Senckenberg Research Society, and is based near the city center of Frankfurt am Main, Germany. The TBG provides access to cutting-edge computational infrastructure (HPC, genome browser) and lab facilities to sequence genomes of diverse creatures. English is the working language in our lab. Frankfurt is a vibrant and highly-international city at the heart of Europe that combines a skyscraper skyline with ample park and green areas.
 
Requirements:
Applicants should have a degree in bioinformatics/computational biology, genomics or a related area, and a strong publication record. Solid programming skills in a Linux environment and experience with shell scripting and Unix tools are required. Previous experience in large-scale comparative genomic data analysis is an advantage.
 
How to apply:
If interested, please email (i) your CV including publication list and contact information for at least two references and (ii) a summary of previous research experience (max 1 page) to Michael Hiller (Michael.Hiller@sen­­­­ckenberg.de). Further information: https://tbg.senckenberg.de/personen/hiller/
 
 
The position is fully-funded. Salary and benefits are according to TV-H E13 100%. The position will be initially for 2 years, but funding is available to extend it further. The employer is the Senckenberg Society for Nature Research in Frankfurt am Main. Senckenberg supports equal opportunity of men and women and therefore strongly invites women to apply. Equally qualified handicapped applicants will be given preference.
 
Application deadline is March 15th 2021. The position is available immediately and the search continues until the position has been filled.
 
Recent publications:
[1] Jebb et al. Six reference-quality genomes reveal evolution of bat adaptations. Nature, 583, 578–584, 2020
[2] Huelsmann et al. Genes lost during the transition from land to water in cetaceans highlight genomic changes associated with aquatic adaptations. Science Adv, 5(9), eaaw6671, 2019
[3] Hecker et al. Convergent gene losses illuminate metabolic and physiological changes in herbivores and carnivores. PNAS, 116(8), 3036-3041, 2019
[4] Roscito et al. Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution. Nature Communications, 9:4737, 2018
[5] Langer et al. REforge associates transcription factor binding site divergence in regulatory elements with phenotypic differences between species. MBE, 35(12), 3027–3040, 2018
[6] Lee et al. Molecular parallelism in fast-twitch muscle proteins in echolocating mammals. Science Adv, 4(9), eaat9660, 2018
[7] Sharma et al. A genomics approach reveals insights into the importance of gene losses for mammalian adaptations. Nature Communications, 9(1), 1215, 2018
[8] Nowoshilow et al. The axolotl genome and the evolution of key tissue formation regulators. Nature, 554(7690), 50-55, 2018
 



W2-Professur Informatik mit Schwerpunkt Bioinformatik

Technische Hochschule Mittelhessen
Wiesenstraße, 14
35390 Gießen


Mit nahezu 18.000 Studierenden gehört die Technische Hochschule
Mittelhessen zu den größten Hochschulen für angewandte Wissenschaften in
Deutschland.

Zur Verstärkung unseres Kollegiums ist am Campus Gießen im Fachbereich
Mathematik, Naturwissenschaften und Informatik (MNI) zum nächstmöglichen
Zeitpunkt eine

  W2-Professur
  mit folgendem Fachgebiet
  Informatik mit Schwerpunkt Bioinformatik
  Bewerbungsende: 17. Februar 2021
  Ref. Nr. B 20-014

zu besetzen.

Detaillierte Informationen zu der zu besetzenden Professur –
insbesondere die sich aus den
§§ 61 und 62 HHG ergebenden Einstellungsvoraussetzungen des Landes
Hessen - entnehmen Sie bitte unserer Homepage unter:

  karriere.thm.de


Die Vereinbarkeit von Familie und Beruf ist uns ein Anliegen. Im Rahmen
des audits "familiengerechte Hochschule" arbeiten wir an der
Weiterentwicklung entsprechender Strukturen.

Bioinformatics Engineer (6 months) in Clinical Bioinformatics

Mission: 

In prevision of a maternity leave, a fixed-term contract of 6 months is available from April 2021 within the Clinical Bioinformatics Group included inside the Diagnostic and Theranostic Medecine Division of Curie Institute. 

Main activities: 

  • Implementation of analysis pipelines 

  • Developpement of custom tools for clinical diagnostic 

 

  • Calibration and validation of analysis pipelines 

  • Help to functionally interpret results using various databases 

  • Contribute to the evolution and maintenance of diagnostic pipelines: updates, bug reporting, validations 

  • Contribute to research projects associated with clinical trials 

  • Regular progress meetings with biologists 

 

  • Technological watch 

Required skills:  

  • Proficient with Unix/Linux environment 

  • Proficient in at least of the following programming languages (ideally with experience with several of them): python, java, R or any other object-oriented programming language 

  • Good knowledge of standard bioinformatics tools for analyzing and interpreting Next Generation Sequencing data (DNA and RNAseq) 

 

  • Have an interest for interactions with biologists 

  • Rigorous, dynamic, autonomous 

  • Excellent team work 

Desired skills: 

  • Good knowledge in algorithmics 

 

  • Code versioning using git 

  • Proficient in English (oral and written) 

  • Some skills in one or several of the following is highly advantageous: usage of calculation cluster (SGE / SLURM / LSF / MOAB, etc.), experience with distributed programming, usage of GPU, experience in machine learning / deep learning 

  • Some knowledge in oncology is advantageous 
     

Diploma: 

 

  • A PhD or MSc in Bioinformatics 

  • A first experience Next Generation data analysis is preferred

In order to apply, please send an email to bioinfo-clinique[AT]curie.fr

Bioinformatician [Collaborative Research Centre TRR 305]

In the framework of the newly funded Collaborative Research Centre TRR 305 „Striking a moving target: From mechanisms of metastatic organ colonisation to novel systemic therapies“, we are looking for a

Bioinformatician (m/f/d)

to support project partners in the bioinformatics analysis of omics data.

 

Your tasks will include:

  • setting up and maintaining pipelines for sequencing data analyses (bulk and single-cell RNA-Seq, ATAC-Seq, ChIP-Seq);
  • closely interacting with CRC project partners to support post-processing analyses of omics data (e.g. functional enrichment, visualisation and interpretation of results, data integration with publicly available datasets, preparation of publication-ready figures);

Your qualifications:

  • academic degree (MSc/PhD) in bioinformatics, computational or life sciences. A PhD is preferred but not essential.
  • prior experience in the analysis of next-generation sequencing data is advantageous;
  • familiarity with working in a Linux/Unix environment;
  • strong programming skills (e.g. Python, Perl, R);
  • excellent communication skills and fluency in English.

 

The position will initially be available for 4 years, with the possibility of further extension.

 

Applications should be sent to Dr. Fulvia Ferrazzi, Institute of Pathology, FAU Erlangen-Nürnberg (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!) and Wencke Wallusch (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!), and include a CV (containing a list of publications, if applicable), a brief description of research experience, as well as contact information of two references.

 

The EU funded International Training Network (ITN) "ALPACA" announces 14 PhD positions, to be filled in 2021

Please see https://alpaca-itn.eu/vacancies for a list of participating institutions / companies, and brief descriptions of the individual projects. Project start will generally be no later than September 2021, but depends on particular arrangements with the individual institution.

Applicants are asked to apply for up to a maximum of 5 positions. Applying for several positions is favorable, because applications may be discussed on a network wide level. However, applying for more than 5 positions may render the application ineligible.

Please apply directly at the institutions of your choice, following the links to the institutions listed at https://alpaca-itn.eu/vacancies.

Deadlines for submission of applications can vary by institution. As a general guideline, it is favorable to submit applications before 15th of February to receive full consideration.

Looking forward to receiving your application.

Ph.D. position in plant RNA bioinformatics

We are seeking a Ph.D. student for a project to discover and understand structured RNAs in plants. The position is in the research group of bioinformatician Dr. Zasha Weinberg (https://zashaweinberglab.org) at Leipzig University, and is a collaboration with Prof. Andreas Wachter (https://mps-imp.biologie.uni-mainz.de), whose lab studies plant biology at the University of Mainz.

The last 20 years have seen a revolution in our understanding of the impact and versatility of non-coding and cis-regulatory RNAs in biology, i.e., RNAs that do not function as a simple messenger. Our goal is to develop novel bioinformatics approaches to find new types of plant RNAs, and to study these RNAs to better understand plant biology, especially alternative splicing. Your role will be to design and program new computational methods, analyze the resulting predictions from a bioinformatic and biological perspective and interact with the Wachter lab.

More information and how to apply:  https://zashaweinberglab.org/plants/



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