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W1 Professorship for Biomedical Informatics

The Faculty of Medicine at Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) invites applications for a
 
W1 Professorship for Biomedical Informatics (Assistant Professor)
at the Institute of Medical Informatics, Biometry, and Epidemiology. The professorship is to be filled by the earliest possible starting date for an initial period of three years. Upon successful evaluation, the appointment will be extended for another three years. 
 
We seek to appoint a top early career scientist who will develop outstanding expertise in the field. The professorship is involved in the MIRACUM project, which unites ten university hospitals, two universities and a partner from the healthcare industry, with the aim of making clinical, image, molecular and genomic data available for use in innovative research projects via modular, scalable and federated data integration centres. Candidates should come from a biomedical informatics background and have experience in medical research data management (FAIR principles) to develop aspects of data engineering and data integration in a medical context in their own research. Experience of collaboration with clinical and pre-clinical working groups, international research and project and team management is an advantage. The successful candidate is expected to become actively involved in research networks at FAU and the Faculty of Medicine (Collaborative Research Centres, Research Training Groups, Interdisciplinary Centre for Clinical Research, leading-edge cluster Medical Valley, Graduate School in Advanced Optical Technologies [SAOT]) and collaborate with the Department of Artificial Intelligence in Biomedical Engineering (AIBE) at FAU, which is currently being established. The Faculty of Medicine offers degree programmes in medicine, dentistry, molecular medicine, medical process management and integrated immunology. The assistant professor will be expected to participate in teaching, which is mostly carried out in German, particularly in lectures for medicine and computer science (medical informatics as a minor subject).
 
Successful candidates demonstrate initial academic achievements and the capacity for independent research at the highest international standards. You have substantial research experience abroad and/or experience in managing research projects and in raising third-party funding. A university degree and an outstanding doctoral degree as well as a passion for education and pertinent teaching experience are also prerequisites. Candidates who are able and willing to teach in both English and German are desired.
 
FAU expects applicants to become actively involved in administering academic affairs and in developing strategic initiatives. FAU pursues a policy of intense student mentoring and therefore expects its teaching staff to be present during lecture periods.
 
FAU offers career development, mentoring and an attractive initial research budget. Based on international standards and transparent performance agreements, FAU ensures a fair evaluation process.
 
In its pursuit of academic excellence, FAU is committed to equality of opportunity and to a proactive and inclusive approach, which supports and encourages all under-represented groups, promotes an inclusive culture and values diversity. FAU is a family-friendly employer and is also responsive to the needs of dual career couples.
 
Please submit your complete application documents (CV, list of publications, list of lectures and courses taught, copies of certificates and degrees, list of third-party funding) online at https://berufungen.fau.de by 23. April 2021, addressed to the Dean of the Faculty of Medicine. Please contact Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein! with any questions.): Titel: Text:

PhD student in precision cancer bioinformatics

Ref. no.: BIH-42.21

 

The Digital Health Center, headed by Prof. Roland Eils, develops and applies state-of-the-art and innovative technologies to healthcare research with a strong focus on machine learning, bioinformatics, imaging and genomics. The department has a strong standing within international consortium (e.g. Human Cell Atlas, ICGC, de.NBI, ELIXIR, EOSC), and have exceptional computational resources (in-house HPC, cloud, Nvidia DGX and FPGA technology).

 

We have recently established a precision medicine genomics platform, which aims to use whole genome and transcriptome sequencing for cancer patients. Building on top of an excellent existing pipeline, we aim to further develop the computational analytics part of the pipeline in the upcoming years.

 

Your area of responsibility:

 

- Undertake and publish excellent scientific research

- Interacting with other members of the clinical genomics program including management, pathology, genomics and clinical partners

- Analyzing genome sequencing data for prospective patients, working closely with clinicians to identify actionable mutations

- Analyzing genome sequencing data for retrospective studies

- Development of new genomics workflows (e.g. supporting new genome references and genomics lesions such as STRs and enhancer hijacking) and interacting with our Data Management Platform team for deployment in a production environment

- Development and implementation of novel computational methods that aid genomics based diagnostics and prognosis

- Interacting with other collaborative sites, in particular the DKFZ and NCT in Heidelberg

 

Your profile:

 

- A PhD candidate with a recent masters degree in bioinformatics, cancer genomics, computer science, medicine, physics or similar

- Ambitious, self-driven, a thirst for answering scientific questions and aim to build a scientific career in biomedical data science research

- Excellent programming proficiency especially in Python, R, Julia, bash or similar

- Experience in designing and implementing data analysis pipelines

- Experience with next generation sequencing data processing and analysis

- Experience with linux based HPC or cloud environments

- Fluent in English (written and spoken)

 

Qualifications – desirable:

 

- Prior research experience in liquid biopsies, cancer genomics data, single cell ‘omics data, or spatial transcriptomics

- Knowledge of transcriptional regulation and epigenomics

- Knowledge of cancer immunology

- Experience with machine learning methods (e. g. RF, NMF, VAE) and frameworks (e. g. PyTorch, TensorFlow, Keras, sklearn)

- Experience with workflow management systems and similar paradigs (e. g. ELIXIR-WES, snakemake, NextFlow)

 

Start: Immediately

 

Length of employment: 3 years

 

Working time: 25,35 hrs./week

 

Pay scale: E13 acc. to collective agreement TVöD VKA – K

 

Contact person: For further information please contact Dr. Naveed Ishaque, E-Mail: Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!

Wissenschaftliche*r Mitarbeiter*in

Wir sind ein interdisziplinäres Team aus Naturwissenschaftlern, Texttechnologen sowie Bibliothekaren und entwickeln neue Text-Mining-Werkzeuge zur semantischen Erschließung der mitteleuropäischen Biodiversitätsliteratur des 19. und 20. Jahrhunderts (hauptsächlich in deutscher Sprache). Vorhandene, bisher schwer zugängliche Daten zur Systematik und Ökologie verschiedener Organismen können so mobilisiert und für weitere wissenschaftliche Studien genutzt werden. In unserer zweiten Projektphase konzentrieren wir uns auf Ökosystemleistungen im Sinne von Pflanzen-Bestäuber-Interaktionen und Bodeninvertebraten.
 
Ihre Aufgaben
  • Erweiterung, Vereinheitlichung und Strukturierung bestehender Vokabularien und Thesauri zu morphologischen und funktionellen Traits der Bodenfauna auf Basis des Data-Warehouse Edaphobase und in Zusammenarbeit mit einem internationalen Team
  • Unterstützung bei der Entwicklung einer Ontologie zu Arten-Traits der Bodenfauna und ihrer Verlinkung mit taxonomischen Ontologien
  • Evaluierung und Konsolidierung von Text-Mining-Technologien
  • Analyse und Veröffentlichung von projektbezogenen Daten
  • Projektpräsentationen auf nationalen und internationalen Konferenzen
  • Mitwirkung bei der Organisation von Workshops für Nutzergruppen
  • Berichterstattung gegenüber der DFG und dem wissenschaftlichen Beirat
 
Sie überzeugen uns mit
  • einem erfolgreich abgeschlossenen Hochschulstudium (idealerweise Promotion) in Biologie, Bio(diversitäts)informatik oder einem verwandten Fachgebiet
  • guten Kenntnissen von Terminologien und Nomenklaturen in der Biologie, insbesondere Morphologie, Systematik und Traits der Bodenfauna
 
 
 
 
Ort: Frankfurt am Main oder wahlweise Görlitz
 
Beschäftigungsumfang: Vollzeit (40 Stunden/Woche)
 
Vertragsart: zunächst für 12 Monate befristet (mit Option auf Verlängerung)
 
Vergütung: voraussichtlich nach TV-H / TV-L E 13
 
 
Senckenberg strebt an den Frauenanteil zu erhöhen. Qualifizierte Kandidatinnen werden daher besonders ermutigt, sich zu bewerben. Schwerbehinderte Menschen werden bei gleicher Eignung besonders berücksichtigt. Senckenberg ist durch das „audit berufundfamilie“ zertifiziert.
 
 
Sie möchten sich bewerben?
 
Dann senden Sie Ihre vollständigen und aussagekräftigen Bewerbungsunterlagen (Lebenslauf, Ausbildungs- und Arbeitszeugnisse, Motivationsschreiben, Angabe Ihres bevorzugten Arbeitsortes), vorzugsweise in elektronischer Form (als eine zusammenhängende PDF-Datei) bitte unter Angabe der Referenznummer #01-21012 bis zum 07.04.2021 an Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein! oder bewerben Sie sich direkt auf unserer Homepage über das Online Bewerbungsformular.

Postdoctoral position: Elucidating the gene regulatory network controlling oxidative phosphorylation (INSERM, CNRS, Marseille)

We are proposing a two-year Postdoctoral position in Bioinformatics to investigate the gene regulatory networks controlling OXPHOS gene expression in Drosophila. For this purpose, we will use a multiomics approach integrating DNA motifs, ChIPseq and RNAseq.

This Postdoctoral project is funded by the Turing Centre for Living Systems (CENTURI). Details of the project and host labs can be found here: https://centurilivingsystems.org/pdp202109/

- Application deadline: April 16, 2021 (CET)
- Information: https://centurilivingsystems.org/recruitment/
- Application form: https://centurilivingsystems.org/applicationformpdp202109/

Mitochondrial oxidative phosphorylation (OXPHOS) is an essential source of ATP for a cell's energy needs and is a highly dynamic and controlled process during cell differentiation and animal development and its dysfunction drives plethora human diseases and cancer. This project aims at identifying the gene regulatory network that underlies OXPHOS gene expression plasticity, an essential function of tissue development and stem cell differentiation. We have shown that the Drosophila transcription factor, M1BP, is responsible for basal level transcription of OXPHOS genes. The postdoc will integrate multiple "omics" datasets such as DNA motifs, interactomes, ChIPseq and transcriptomes to predict transcriptional cofactors of M1BP responsible for OXPHOS transcriptional plasticity. These predictions will be validated experimentally using RNAi and ChIPseq.

The postdoc candidate should have a PhD in bioinformatics, or related field, with interest in “omics” data analyses, genomics and gene regulation. Most of the projet work involves computational manipulation of large and highly multivariable datasets. Wet lab experience is a benefit, but not essential as these techniques are well established in the host lab.

Thank you for sharing this offer with motivated candidates.

- Andrew Saurin http://www.ibdm.univmrs.fr/equipe/mechanismsofgeneregulationbytranscriptionfactors
- Aitor González: https://tagc.univamu.fr/en/users/gonzalezaitor

Bioinformatician position available, Medical University of Vienna

We are looking for a bioinformatician in the fields of epigenetics, gene regulation & proteomics. This position is embedded in the special research program (SFB) “Histone deacetylases (HDACs) as regulators of T cell-mediated immunity in health and disease”. The ideal candidate has knowledge in the analysis of NGS dataset and pathway analysis. The candidate will be responsible for the computational analysis of NGS data and for basic pathway and network analysis. Throughout the project, the candidate will work in close collaboration with the whole research network.

 
ABOUT THE RESEARCH PROGRAM
The special research program (SFB) “Histone deacetylases (HDACs) as regulators of T cell-mediated immunity in health and disease” constitutes a major strategic grant, consortium and research network newly funded by the Austrian Science Fund (FWF). The overall aim of this 8-year SFB research program and consortium is to provide a mechanistic molecular rationale for the development and application of isoform-selective HDAC inhibitors for the treatment of T cell-mediated diseases, and to test essential regulatory roles of reversible lysine acetylation beyond histone modifications and epigenetic gene regulation in T helper cells. It comprises an interdisciplinary team of eight research groups, of which seven are located in Vienna and one in Salzburg, Austria. The project started in March 2019.
 
APPLICATION: Candidates have to demonstrate a strong motivation to engage in the SFB network. Previous research experience in Systems Biology, Bioinformatics, or another relevant discipline is desired. Electronic applications must include the following documents in a single PDF file:
1.   Academic Curriculum Vitae of no more than 2 -3 pages
2.   List of peer-reviewed publications (submitted papers must include the submission confirmation)
3.   Motivation letter explaining why you wish to start / continue a career in the field (1-page)

The job offer is open until March 31, 2021. The position will be filled as soon as suitable candidates have been identified and selected. Two reference letters must be e-mailed by mentors of applicants to Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!. Short-listed candidates will be invited for Zoom interviews in April 2021. The position (initially for up to 2 years) is open immediately; the actual start date is flexible.
 
Links: www.meduniwien.ac.at/HIThttp://www.meduniwien.ac.at/HIT/contact.html,
 


PostDoc Biostatistik/Epidemiologie/Bioinformatik

Wir suchen eine*n Wissenschaftler*in bzw. Postdoktorand*in am Institut für Medizinische Biometrie und Statistik an der Universität zu Lübeck.

Das erwartet Sie:
• Eigenverantwortliche statistische Auswertungen in klinisch-experimentellen und genetisch-epidemiologischen Projekten
• Methodische Forschung zu genetisch-epidemiologischen und / oder bioinformatischen Methoden mit einem Schwerpunkt auf Methoden des maschinellen Lernens
• Beteiligung an der biometrischen Beratung sowie an der Lehre in den verschiedenen Studiengängen unserer Universität
• Publikationstätigkeit und Einwerbung von Drittmitteln

Das bringen Sie mit:
• Ein abgeschlossenes Hochschulstudium sowie eine Promotion in Mathematik, Statistik, Epidemiologie, (Bio-)Informatik oder in einem vergleichbaren Fachgebiet
• Ausgewiesene Kenntnisse in Methodenentwicklung und angewandter Statistik
• Grundlagen zu Verfahren des Maschinellen Lernens
• Praktische Erfahrungen in der Auswertung genetisch-epidemiologischer oder anderer molekularbiologischer Datensätze
• Fundierte Programmierkenntnisse in R (inkl. Implementierung von statistischen Methoden)
• Engagierte, selbständige Arbeitsweise, wissenschaftliche Kreativität und Freude am Arbeiten in einem interdisziplinären Team
• Idealerweise Erfahrungen in der Lehre und der biometrischen Beratung
• Kenntnisse in der Durchführung von Simulationsstudien sind gewünscht

Das bieten wir Ihnen:
• Eingruppierung in die Entgeltgruppe E 13 TV-L, bei Erfüllung der tariflichen Voraussetzungen
• Eine Vollzeitbeschäftigung, zzt. 38,5 Stunden / Woche. Eine Teilzeittätigkeit kann im Rahmen bestimmter Arbeitszeitmodelle vereinbar sein.
• Ein attraktives Arbeitsumfeld
• Möglichkeit zur wissenschaftlichen Weiterqualifikation (z.B. Habilitation)
• Flexible Arbeitszeitgestaltung (Gleitzeit)
• Attraktive Fort- und Weiterbildungsmöglichkeiten

Auf ein Gespräch mit Ihnen über fachliche Details freuen sich Frau Prof. Inke König (0451-500 50601) und Frau Prof. Silke Szymczak (0451-500 50600).
Wir freuen uns auf Ihre Bewerbung bis zum 30.03.2021 unter Angabe der Ausschreibungsnummer 4459. Über diesen Link können Sie sich bewerben: https://jobs.uksh.de/job/L%C3%BCbeck-Schl-23538/656819901/

Links: https://jobs.uksh.de/job/L%C3%BCbeck-Schl-23538/656819901/

Leader (m/f/d) of our new junior research group “Artificial Intelligence-based image data analysis”

The Leibniz-Institut für Analytische Wissenschaften - ISAS - e. V. is a research institute dedicated to the development and improvement of analytical methods and tools for health research and related fields. The ISAS is a member of the Leibniz Association and is publicly funded by the Federal Republic of Germany and its federal states.

A new project area in the institute is the development of advanced imaging, especially light-sheet fluorescence microscopy (LSFM), for the analysis of whole organs under physiological and pathological conditions. LSFM generates extremely large data sets. Modern machine learning and artificial intelligence provide approaches to fully exploit these data sets and translate their rich information into a better understanding of the underlying biological mechanisms. Innovative machine learning approaches, for example based on explainable deep learning approaches, promise to make hidden structures of human cognition accessible and thus guide further experimental investigation and new hypotheses.

In the department of Biospectroscopy at the ISAS (Dortmund, Germany) you will setup your own research group that focuses on the following tasks:

• Devise and carry out an interdisciplinary research agenda that advances the use of LSFM and other microscopy approaches in life science research through the development of innovative machine learning approaches

• Exploit the advantages of an in-house IT infrastructure involving a high-performance GPU- cluster and petabyte-sized data storage facilities

• Build up a research infrastructure including large scale ground truth data sets and annotations of healthy and diseased organs in close cooperation with the biomedical research groups at ISAS and supported by appropriate artificial data enhancement techniques

• Develop open scientific software accompanying the research agenda, supporting data analysis, image segmentations, annotations and visualizations for biomedical research studies

• Establish a visible landmark in the computational life science research community through high ranking publications and successful third-party funding initiatives, as well as a regional, national and international network of interdisciplinary collaborators.

Your profile

• A PhD degree in computer science/statistics/physics/computer visualistics/data science or a related field

• Alternatively, a career changer, e.g. with biomedical PhD, who has acquired specialized IT knowledge over the years

• An excellent track record in computational biomedical research, ideally with a focus on microscopic image analysis

• Publications at top tier conferences in computer vision and machine learning, like NeurIPS, CVPR, MICCAI and ISBI.

• Excellent skills as communicator and team leader

• Fluent English (spoken and written)

• Good German communication skills are a plus

We offer

• A superbly equipped group funded initially for 5 years

• Scientific development opportunities in an international cooperative, interdisciplinary re-search environment and an excellent working atmosphere in a very dynamic and professional team

• Access to a research and teaching community at many nearby universities

• Extensive state-of-the-art equipment and infrastructure for the desired project

• A wide range of activities in skill enhancement and further qualification

 

Links: https://www.isas.de/news/042021-leader-mfd-of-our-new-junior-research-group-artificial-intelligence-based-image-data

Post-doctoral position / Scientist (m/f/d) in Bioinformatics

Das Leibniz-Institut für Analytische Wissenschaften - ISAS - e. V. ist ein Forschungsinstitut mit der Aufgabe der Entwicklung und Verbesserung von Analysemethoden und -instrumenten für die Gesundheitsforschung und angrenzende Bereiche. Das ISAS ist Mitglied der Leibniz-Gemeinschaft und wird durch die Bundesrepublik Deutschland und ihre Länder öffentlich gefördert.  Für die Abteilung Bioanalytics an unserem Standort in Dortmund suchen wir eine/n Post-doctoral position / Scientist (m/f/d) in Bioinformatics.

Nähere Informationen zur Stelle finden Sie unter www./isas.de/karriere.

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