ISCB Affiliated Group Logo

Job Offers

2x PhD student pos., Comp. biochem./chem. or struct. bioinf., U of Duesseldorf, Gohlke group

Applications are invited for two PhD student positions in the Computational  Pharmaceutical Chemistry & Molecular Bioinformatics group of Prof. Dr. Holger Gohlke at the Heinrich-Heine-University, Duesseldorf, Germany.

PhD student position 1:

o    Topic: Development of novel modulators for the nicotinic acetylcholine receptor for the treatment of nerve agent poisoning

o    Availability: The position is available as of 01.10.2019.

PhD student position 2:

o    Topic: Overcoming lantibiotics resistance in bacterial pathogens: Nisin as a model system

o    Availability: The position is available as of 01.10.2019.

Please find more detailed information regarding the respective topic under: https://cpclab.uni-duesseldorf.de/index.php/Openings

Requirements

Ideal candidates will have a record of excellence and a strong background in computational biochemistry, molecular informatics, and computational structural biology as well as a high interest in working in an interdisciplinary research field, and profound knowledge in state-of-the-art molecular dynamics simulations (Amber) software and molecular modelling.

Application process

Applicants should submit applications (a one-page letter of motivation why they are interested in the respective project and how they can contribute to the project’s success, a current CV, and contact data of three references) by email to gohlke[at]uni-duesseldorf.de . Please provide all documents as one PDF file and specify for which position you are applying.

 

 

Postdoctoral Researcher (m/f/d) in botany/bioinformatics [Senckenberg Gesellschaft für Naturforschung ]

For over 200 years the Senckenberg Gesellschaft für Naturforschung (SGN) represents one of the most relevant institutions investigating nature and its diversity. Currently, scientists from more than 40 countries across 11 locations in Germany conduct research in the fields of biodiversity, earth system analysis and climate change. The head office of Senckenberg is Frankfurt am Main together with the Senckenberg Research Institute and Natural History Museum Frankfurt.

In the context of a research project on the phylogeny of Marcgraviaceae, we invite applications for a

Postdoctoral Researcher (m/f/d)
in botany / bioinformatics
(100%)

The project is funded by the German research foundation (DFG) and focusses on elucidating the evolutionary history of the neotropical plant family Marcgraviaceae which is diverse in its morphology, pollination syndromes and geography.

Your tasks:
- Managing and developing bioinformatic pipelines for editing and analyzing genomic sequence data (Gene Capture)
- Performing phylogenomic analyses, molecular dating, reconstructing trait and niche evolution and historical biogeography
- Lab work, especially DNA extraction, PCR, Next Generation Sequencing
- Writing scientific manuscripts and reports
- Presenting research results at conferences and in the relevant scientific journals
 
Your profile:
- University degree - preferably Ph.D.- in biology (systematics and evolution of seed plants) / bioinformatics (evolution/ sequence analysis) with
- Experiences with next generation sequencing and analysis of phylogenomic data
- Expertise with phylogenomic methods, reconstruction of trait evolution and molecular dating methods
- Good knowledge of seed plant systematics
- Active publication record in international journals
- Very good skills in managing scientific projects
- Excellent English (written/ oral)
 
We offer
- an interesting task in an international research project
- the possibility to build and extend your network with scientists at an international level and to attend national and international conferences
- a workplace in the city of Frankfurt, a lively and diverse city with high life quality
- flexible working hours – annual special payment – company pension scheme – Senckenberg badge for free entry in museums in Frankfurt – a family-conscious personnel policy (“audit berufundfamilie”)
Salary and benefits are in accordance with a public service position in Germany (collective agreement TV-H, payment category E13).
 
The contract shall start as soon as possible and will be limited to 24 months.
We look forward to your application!
Please send your application, mentioning the reference of this job offer (ref. #01-19030) by November 30th, 2019 (deadline) by e-mail (attachment in a single pdf document) and including
- a cover letter describing your suitability and motivation
- a detailed CV
- your credentials and certificates
- a list of publications
- and contact details of two potential referees to:
Senckenberg Gesellschaft für Naturforschung
Senckenberganlage 25
60325 Frankfurt
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 Dr. Stefan Dressler (This email address is being protected from spambots. You need JavaScript enabled to view it.).
 
Links:https://www.senckenberg.de/de/ueber-uns/stellenangebote/wissenschaftler/#content-0002_7
 

 

 

Entwickler (m/w/d) Webanwendungen

 

 

Stellenausschreibung Ref. #08-19011

Die Senckenberg Gesellschaft für Naturforschung (SGN) wurde 1817 gegründet und zählt zu den wichtigsten Forschungseinrichtungen rund um die biologische Vielfalt. An den elf Standorten in ganz Deutschland betreiben Wissenschaftlerinnen und Wissenschaftler aus über 40 Nationen modernste Forschung auf internationaler Ebene. Am Standort Görlitz befindet sich das Senckenberg Museum für Naturkunde inmitten der historischen Altstadt.

 

Zum nächstmöglichen Zeitpunkt suchen wir für unseren Standort in Görlitz "Museum für Naturkunde" in der Abteilung Botanik – vorbehaltlich der Bewilligung der finanziellen Mittel – im Rahmen des Projektes „FloraWebPlus: Weiterentwicklung der Fachinformationen zur Flora von Deutschland“  einen 

 

Entwickler (m/w/d) Webanwendungen

 

Das sind Ihre Herausforderungen:

Kern Ihrer Aufgaben ist die Entwicklung einer modularen Plattform zum Betrieb einer unbestimmten Zahl von Datenbanken und darauf basierenden Webportalen. Ziel ist die Vereinheitlichung einiger der im Laufe der Zeit entstandenen heterogenen Portale (Botanik, Citizen Science) im Senckenberg-Verbund und die Erstellung neuer Portale auf Basis dieser Plattform. Wichtige Aspekte der Arbeit umfassen:

·         Softwareentwicklung: Die Entwicklung (Planung und Umsetzung) der Software erfolgt eigenständig im Rahmen der gegebenen Anforderungen; eingesetzte Techniken: php, JavaScript, SQL (PostgreSQL), Linux (Debian)

·         Softwaredokumentation: Quellcode, API, Architektur, Anleitung zur Erstellung weiterer Module, Installationsanleitung

·         Erstellung eines Konzepts zur Migration bestehender Portale auf diese Plattformen

·         Vernetzung: Grundsätzlich sollen die erstellten Portale eigenständig laufen. Jedoch soll auch ein Datenaustausch zwischen diesen und verschiedenen anderen Portalen und Datenbanken über zu programmierende Schnittstellen möglich sein.

·         Kommunikationsfähigkeit: Um die tatsächlichen Anforderungen zu erfassen und bestmöglich umzusetzen, wird es notwendig sein, im regen Austausch mit den Mitarbeitern der Fachabteilungen und denen der hauseigenen und externen IT zu stehen.

 

Sie überzeugen uns mit:

·         einem abgeschlossenen Hochschulstudium (Uni, FH) oder einer vergleichbaren Qualifikation mit IT-relevantem Bezug

·         sehr guten Kenntnissen in den einzusetzenden Techniken (php, JavaScript, SQL (PostgreSQL), Linux (Debian))

·         fundierten Kenntnissen von Tools zur Versionskontrolle (z. B. Git, Subversion, Build-Werkzeuge)

·         guten Deutschkenntnissen zur effizienten Kommunikation mit den Mitarbeitenden

·         guten analytischen Fähigkeiten, einer selbstständige sowie service- und zielorientierten Arbeitsweise und wünschenswerterweise Interesse für Themen aus dem Bereich Umwelt / Biodiversität / Biologie / Ökologie

 

 

Die Stelle ist mit der Entgeltgruppe TV-L E 11 dotiert und bis zum 31.10.2022 befristet. Angestrebt ist zunächst eine Vollzeitbeschäftigung (100%) bis Ende Dezember 2020. Im Anschluss daran beträgt die Arbeitszeit bis zum Ende des Projektes voraussichtlich 80%. Arbeitsgeber ist die Senckenberg Gesellschaft für Naturforschung, Dienstort ist Görlitz. Senckenberg ist durch das „audit berufundfamilie“ zertifiziert. Bewerbungen von Menschen mit Behinderungen werden bei gleicher Eignung bevorzugt berücksichtigen.

 

Sie möchten sich bewerben?

Dann senden Sie bitte Ihre vollständigen und aussagefähigen Bewerbungsunterlagen, in elektronischer Form (vorzugsweise als einzelne PDF-Datei) unter der Angebe der Referenznummer #08-19011 bis zum 27.10.2019 an:

 

Senckenberg Gesellschaft für Naturforschung

Senckenberganlage 25

60325 Frankfurt a.M.

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

 

Ansprechpartner für fachliche Rückfragen ist Prof. Dr. Karsten Wesche (This email address is being protected from spambots. You need JavaScript enabled to view it.).

 

 


Links: https://www.senckenberg.de/de/ueber-uns/stellenangebote/fachkraefte/#content-0002_1

Postdoc Stelle in Data Science/Machine Learning [Universität Greifswald]

In der Arbeitsgruppe Bioinformatik  am Institut für Mathematik und Informatik der Universität Greifswald ist im Rahmen des durch das Ministerium für Bildung, Wissenschaft und Kultur Mecklenburg-Vorpommerns geförderten Projekts „Datenkompetenz“ folgende Stelle für die Dauer von vier Jahren zu besetzen:

Wissenschaftliche*r Mitarbeiter*in
(TV-L E 13, 100%)
 
Ziel des Projekts ist es, die fachliche Kompetenz Studierender aller Fachrichtungen beim Umgang mit großen Datensätzen durch die Konzeption und Durchführung neuer Lehrveranstaltungen zu verbessern, sowie Forschung im Bereich der angewandten Data Science zu leisten.

Ihr Profil:
    • Promotion in Data Science, Informatik, Mathematik, Statistik oder einem verwandten mathematischen oder naturwissenschaftlichen Fach
    • Kenntnisse in der Sprache Python und im Bereich des Maschinellen Lernens
    • Konzeptionelle Fähigkeiten
    • Erfahrung in der universitären Lehre

Kennziffer: 19/Sa37

Bewerbungsschluss: 01.12.2019

Den vollständigen Ausschreibungstext finden Sie unter: https://www.uni-greifswald.de/universitaet/information/stellenausschreibungen/oeffentliche-stellenausschreibungen/wissenschaftliches-personal/institut-fuer-mathematik-und-informatik-19sa37/"

Artifical Intelligence in Drug Discovery

Am Institut für Pharmazie und Molekulare Biotechnologie (IPMB) der Universität Heidelberg ist in der Abteilung Medizinische Chemie baldmöglichst eine Stelle als Akademische/r Mitarbeiter/in (Doktorand/in, m/w/d) zu besetzen. Thema: Maschinelles Lernen in der Wirkstoffentwicklung. Wünschenswert ist ein starkes Interesse und idealerweise Vorkenntnisse in instrumenteller Analytik (Massenspektrometrie) und Programmiersprachen (z.B. MATLAB, Python) sowie ein naturwissenschaftlich-technischer Studienabschluss (Chemie, Biotechnologie, Pharmazie, (Bio-) Informatik, Physik und vergleichbar). Die Vergütung erfolgt nach TV-L E13 50%. Die Stelle ist zunächst auf zwei Jahre befristet. Bewerbungsschluss ist der 31.10.2019. Weitere Informationen zu Thema und Bewerbungsprozess finden Sie online hier (https://adb.zuv.uni-heidelberg.de/info/INFO_FDB$.startup?MODUL=LS&M1=1&M2=0&M3=0&PRO=28025).


Links:
Weitere Informationen:
https://adb.zuv.uni-heidelberg.de/info/INFO_FDB$.startup?MODUL=LS&M1=1&M2=0&M3=0&PRO=28025

Postdoctoral Researcher in data analysis & methods development

For a project in crystallographic data analysis and methods development,
the Thorn Laboratory at the University of Würzburg, Germany, is looking
for a

POSTDOCTORAL RESEARCHER (m/f/d)

to uncover pitfalls in the measurement and processing of XFEL, neutron
and conventional single-crystal diffraction data. She or he will develop
new diagnostics in AUSPEX (www.auspex.de) using machine learning,
practical experiments and statistical analysis and establish new best
practices with major European diffraction facilities. We are looking for
someone with a good working knowledge of statistical analysis, Python
and C++ who is an excellent communicator and likes to travel. Previous
experience in crystallography and machine learning is a bonus.
We offer a position at the University of Würzburg, the birthplace of
X-rays, with a competitive salary, benefit package, career and family
support. Women are particularly encouraged to apply.

For more details, see:
https://www.uni-wuerzburg.de/fileadmin/43020000/2019/Stellenanzeige_PostdocThorn_Sep_2019_final_Auslage.pdf
https://www.uni-wuerzburg.de/rvz/forschung/assoziierte-forschungsgruppen/ag-thorn/

If you have any questions, please email This email address is being protected from spambots. You need JavaScript enabled to view it..

Links:
Full advertisement:
https://www.uni-wuerzburg.de/fileadmin/43020000/2019/Stellenanzeige_PostdocThorn_Sep_2019_final_Auslage.pdf
Group homepage:
https://www.uni-wuerzburg.de/rvz/forschung/assoziierte-forschungsgruppen/ag-thorn/

PhD candidate in crystallographic methods development

For a project in crystallographic methods development, the Thorn
Laboratory at the University of Würzburg, Germany, is looking for a

PHD CANDIDATE (m/f/d)

Our lab develops new methods for macromolecular X-ray crystallography
and Cryo-EM. In this exciting PhD project you will improve how well we
understand, measure and model macromolecular crystal structures using
practical experiments and big data analyses. We are looking for a good
communicator with skills in crystallography and programming. Any
previous experiences in machine learning, biochemistry, image or
statistical data analysis are a bonus. We offer a 36-month full- or
part-time position with a competitive salary, embedded in the Würzburg
Graduate School for Life Sciences (GSLS).

For more details, see:
https://www.uni-wuerzburg.de/fileadmin/43020000/2019/Stellenanzeige_PhD_Thorn_September_2019_final_Auslage.pdf
https://www.uni-wuerzburg.de/rvz/forschung/assoziierte-forschungsgruppen/ag-thorn/

If you have any questions, please email This email address is being protected from spambots. You need JavaScript enabled to view it..

Links:
Full advertisement:
https://www.uni-wuerzburg.de/fileadmin/43020000/2019/Stellenanzeige_PhD_Thorn_September_2019_final_Auslage.pdf
Group homepage:
https://www.uni-wuerzburg.de/rvz/forschung/assoziierte-forschungsgruppen/ag-thorn/

PhD student position (TVH-E13 65%) in Bioinformatics [the University of Marburg and the University of Giessen II]

The candidate will be responsible for the development of bioinformatics software to improve the comparability and reproducibility of state of the art methods to evaluate efficient data storage. That is to say, encoding information in biological molecules or chemical compounds. The action of encoding and decoding information is a process that we perform on a daily basis. Language is a great example as words carry different meanings. There exists many levels of processing information, the successful candidate will examine information theory metrics (e.g., compression ratio), error correction, and decoding accuracy (e.g., parity checks) for a quantitative assessment of information processing. A foundational aspect of this project is the creation of an evaluation framework that integrates state of the art methods for text mining (e.g., Markov chains, Long short-term memory or LSTM, etc). Her/His efforts include but are not limited to developing novel algorithms, implementing different state of the art methods into an open source framework, and maintaining a code base to benefit both the community and the research project. 

In the research project MOSLA, the University of Marburg and the University of Giessen will jointly develop novel approaches and solutions for long-time archives based on molecular and chemical stor-age systems. Besides the technical solutions of data storage, they will also research in (de-)coding of information for long-time storage, which will be achieved by a combination of genetic and chemical information encoding. The project is funded by the Hessian Ministry for Science and Arts. 

 

Links: https://synmikro.com/assets/content/Downloads/Ausschreibungen/fb12-0024-MOSLA-wmz-111019-engl.pdf

PhD student position (TVH-E13 65%) in Bioinformatics [University of Marburg and the University of Giessen]

The candidate will be responsible for the development of bioinformatics software, novel algorithms, and visualizations to depict the effect of weighing in reading frame and genomic patterns in the de-coding of information stored in biological molecules or chemical compounds. The desired end result is to visualize the qualitative and quantitative improvement of decoding when using different encod-ing/decoding strategies. The successful candidate will examine possible patterns that range from naturally occurring sequences to repeats, or functional patterns (secondary structure), and define successful strategies of encoding/decoding. In turn, these may be used as quality control checks once PCR amplification and sequencing have been completed. A foundational aspect of this project is the creation of adapted representations and algorithms to account for different encoding/decoding strategies. Her/His efforts include but are not limited to developing novel algorithms, implementing a visualization framework, and maintaining a documentation and a code base to benefit both the com-munity and the research project. 

In the research project MOSLA, the University of Marburg and the University of Giessen will jointly develop novel approaches and solutions for long-time archives based on molecular and chemical stor-age systems. Besides the technical solutions of data storage, they will also research in (de-)coding of information for long-time storage, which will be achieved by a combination of genetic and chemical information encoding. The project is funded by the Hessian Ministry for Science and Arts. 


Links: https://synmikro.com/assets/content/Downloads/Ausschreibungen/fb12-0023-MOSLA-wmz-111019-engl.pdf

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..

We use cookies on our website. Some of them are essential for the operation of the site, while others help us to improve this site and the user experience (tracking cookies). You can decide for yourself whether you want to allow cookies or not. Please note that if you reject them, you may not be able to use all the functionalities of the site.