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Bioinformatics developer - database and web applications (m/f/d)

The division of Bioinformatics and Systems Cardiology at the Klaus Tschira Institute for Integrative Computational Cardiology develops software to study the role of RNA in cardiac disorders (https://github.com/dieterich-lab). The flow of genetic information from DNA to proteins has been traditionally seen as a linear pathway with an RNA intermediate. However, instead of just being an inert carrier of information, RNA performs a multitude of tasks and may even be transformed in the course of these events.

The position is initially limited to 1 year with option of further extension. The salary is paid according to the German TV-L system (the salary agreement for public service employees). The position is also suitable for part-time employment. Starting date is as soon as possible.

Tasks

The successful applicant will enter a collaborative research environment and contribute to the group’s bioinformatic software portfolio. He/She will have to work with common solution stacks (Linux, Apache, MySQL, Python) for web development application, implement data access management structures, and manage medium-to-large databases efficiently in cloud-based environments. We are specifically interested in implementing and customizing the gEAR portal solution for the DZHK Digitalization Initiative https://github.com/IGS/gEAR

Required Qualifications

Applicants should have a Master’s degree in computer science, bioinformatics, physics, engineering or a comparable relevant background and level of expertise. In addition to very good Linux administration skills (i.e. software management, shell and scripting languages), the ideal candidate has a proven record in database programming, web application development and/or high-level language programming in established software frameworks. The applicant is also expected to be familiar with team-based software development via GitHub. Fluent spoken and written English is expected. Required soft skills: ability to communicate and work in teams, flexibility and targeted action. Proficiency in handling large-scale scientific data sets, cluster and/or cloud computing, or virtualization is a plus.

What we offer

The Dieterich Lab (www.dieterichlab.org) offers a stimulating, diverse and international academic research environment. We are embedded in a vibrant community of cardiovascular research labs and collaborate with many experimentally or theoretically oriented labs in the Heidelberg area.

Additionally we offer:

  • Target-oriented individual further education and training opportunities
  • Targeted training on the job
  • Ticket for public transport
  • Possibility of child care (crèche and kindergarten) as well as subsidy for holiday care for school children
  • Active health promotion
  • Company pension scheme
  • Access to the university library and other university facilities (e.g. university sports)

Contact & Application

Please upload a covering letter/supporting statement, including a brief statement of research interests, CV and the details of two referees as part of your online application.

Please do not hesitate to contact us if you have any further questions.

Universitätsklinikum Heidelberg
Zentrum für Innere Medizin
Klinik für Kardiologie, Angiologie, Pneumologie (Innere Medizin III)
Section of Bioinformatics & Systems Cardiology, Prof. Dr. rer. nat. Christoph Dieterich 
Im Neuenheimer Feld 669
69120 Heidelberg
sekretariat.dieterich(at)med.uni-heidelberg.de


Research Assistant - Machine Learning for RNA analysis (m/f/d)

The Klaus Tschira Institute for Integrative Computational Cardiology / Internal Medicine III offers a full-time position for a postdoctoral researcher.

The Klaus Tschira Institute for Integrative Cardiology is active in three thematic areas. First: RNA maturation and processing. In particular, the development and physiology of the heart require strict control of RNA biology. Our laboratory has succeeded in publishing numerous software solutions for the investigation of the complex RNA world. Secondly, we have established the field of systems cardiology for in vitro and in vivo models of heart failure. Thirdly, we build a bridge into the field of clinical data science through the HiGHmed Consortium, as part of the German Medical Informatics Initiative. At this point, our AI work in the field of unstructured German texts from cardiological settings should be mentioned in particular. Further information is available at www.dieterichlab.org

The position is initially limited to 2 years with option of further extension. The salary is paid according to the German TV-L system (the salary agreement for public service employees). The position is also suitable for part-time employment. Starting date is as soon as possible.

Tasks

You will implement existing and develop new computational methods for the analysis and interpretation of RNA sequencing data and contribute to at least one of our research areas:

  • Direct RNA sequencing data: RNA modification detection
  • Single Cell RNA sequencing data: Hybrid approaches on the ONT platform
  • Predictive Machine Learning Models for RNA biology (Splicing, Translation, Decay)

Required Qualifications

The ideal candidates will have a diploma/master´s degree or equivalent in Bioinformatics, Data Science, Machine Learning, mathematics, physics, engineering science or a related discipline. You offer solid expertise in handling high-throughput data sets and are fully competent in managing the underlying statistical challenges. Moreover, you are happy to work in a highly interdisciplinary team. A proven competence in software engineering and development (i.e. at least two out of C/C++, R, Python, Java) is essential. Other relevant qualifications include a good understanding of RNA Biology. Experience working in Unix / Linux environments is required. Experience in developing and applying statistical, machine and/or deep learning-based computational methods is desired.

What we offer

The Dieterich Lab (www.dieterichlab.org) offers a stimulating, diverse and international research environment. We are embedded in a vibrant community of cardiovascular research labs and collaborate with many experimentally or theoretically oriented labs in the Heidelberg area. Our computer cluster consists of 26 dedicated computing nodes with main memory of up to one terabyte, which is needed for genome assembly or parallel analysis of large OMICS data sets, for example. In addition, the computer cluster has been equipped with dedicated servers that accommodates NVIDIA GPUs (Graphics Processing Units) for up-to-date machine learning approaches.

Additionally we offer:

  • Target-oriented individual further education and training opportunities
  • Targeted training on the job
  • Ticket for public transport
  • Possibility of child care (crèche and kindergarten) as well as subsidy for holiday care for school children
  • Active health promotion
  • Company pension scheme
  • Access to the university library and other university facilities (e.g. university sports)

Contact & Application

Please do not hesitate to contact us via e-mail: sekretariat.dieterich(at)med.uni-heidelberg.de if you have any further questions.

Interested?
 
Please upload a covering letter/supporting statement, including a brief statement of research interests, CV and the details of two referees as part of your online application until December 15th, 2021.

Universitätsklinikum Heidelberg
Zentrum für Innere Medizin
Klinik für Kardiologie, Angiologie, Pneumologie (Innere Medizin III)
Prof. Dr. rer. nat. Christoph Dieterich 
Im Neuenheimer Feld 669
69120 Heidelberg
sekretariat.dieterich(at)med.uni-heidelberg.de


Projektmanager HiGHmed und NUM (m/w/d)

zum nächstmöglichen Zeitpunkt für die Abteilung Bioinformatik und Systemkardiologie am Klaus Tschira Institute for Computational Cardiology / Klinik für Innere Medizin III gesucht.

Die Stelle ist befristet auf 1 Jahr. Die Vergütung erfolgt nach TV-L.

Der erfolgreiche Bewerber wird Teil eines gemeinschaftlichen Forschungsumfeldes innerhalb des HiGHMed-Konsortiums (http://www.highmed.org) und des Netzwerk Universitätsmedizin (NUM) sein. Er/Sie wird in der Arbeitsgruppe Bioinformatik und Systemkardiologie (www.dieterichlab.org) angestellt sein und den Standort Heidelberg (UKHD) als Projektmanager vertreten.

Ihre Aufgaben

  • Koordinierung und Kommunikation am Standort Heidelberg (UKHD) bzgl. der HiGHmed Use Cases und weiterer MI-I und NUM Aktivitäten
  • Selbstständige Leitung von Projekten mit dem Ziel, klinische Abläufe weiter zu entwickeln und in das digitale Zeitalter zu überführen
  • Statistische Auswertung von Patientendaten (Datenanalyse vorwiegende Excel, möglicherweise anderer geeigneter Software)
  • Überprüfung und Anpassung von Qualitätskriterien und Datenkuration
  • Mithilfe bei der Erstellung von Rekrutierungsmaterialien, Werbematerialien, Internetpräsenz etc.
  • Assistenz bei der Erstellung von Förderanträgen und Ethikanträgen
  • Berichterstattung für Förderorganisationen (Progress Reports bzgl. Meilenstein Erreichung)
  • Visuelle Aufbereitung der Prozesse, Daten etc. (z. B. PowerPoint)
  • Organisation, Leitung und Protokollierung von Projektmeetings

Ihre Qualifikationen

  • Idealerweise verfügen Sie über umfangreiche Erfahrungen (mehr als 3 Jahre) im Projektmanagement und haben bereits selbst Projekte erfolgreich geleitet
  • Sie verfügen über einschlägige Erfahrungen im Gesundheitswesen, im besten Fall in medizinischen Forschungsverbände
  • Sie haben einen Masterabschluss in der Betriebswirtschaft, der Wirtschafsinformatik, im Gesundheitsmanagement oder einem vergleichbaren Studienfach
  • Sie beherrschen Moderations- und Visualisierungstechniken
  • Sie überzeugen mit einer sehr guten Auffassungsgabe, sowie mit ihrem analytischen Denken in Verbindung mit ihrer hohen Sozialkompetenz
  • Grundkenntnisse in den Bereichen Statistik und Datenmanagement sind erforderlich
  • Selbstständige Arbeitsweise und proaktive detaillierte Berichtserstattung an den HiGHmed Standortsprecher

Wir bieten Ihnen

Das Dieterich Lab (www.dieterichlab.org) bietet ein anregendes, vielfältiges und internationales Forschungsumfeld. Wir sind eingebettet in eine lebendige Gemeinschaft von Herz-Kreislauf-Forschungslaboren und arbeiten mit vielen experimentell oder theoretisch ausgerichteten Laboren im Raum Heidelberg zusammen.

Zusätzlich bieten wir:

  • Zielorientierte, individuelle Fort- und Weiterbildungsmöglichkeiten
  • Gezielte Einarbeitung
  • Jobticket
  • Möglichkeit der Kinderbetreuung (Kinderkrippe und Kindergarten) sowie Zuschuss zur Ferienbetreuung für Schulkinder
  • Aktive Gesundheitsförderung
  • Betriebliche Altersvorsorge
  • Zugriff auf die Universitätsbibliothek und andere universitäre Einrichtungen (z. B. Universitätssport)

Kontakt & Bewerbung

Bitte laden Sie im Rahmen Ihrer Online-Bewerbung ein Begleitschreiben, einen Lebenslauf sowie Arbeitszeugnisse und/oder Referenzen hoch.

Die Stelle kann auch in Teilzeit besetzt werden.

Bewerbungen sollten über das Portal oder per E-Mail in einem PDF-File an sekretariat.dieterich(at)med.uni-heidelberg.de gesendet werden.

Universitätsklinikum Heidelberg
Zentrum für Innere Medizin
Klinik für Kardiologie, Angiologie, Pneumologie (Innere Medizin III)
Sektion für Bioinformatik und Systemkardiologie, Prof. Dr. rer. Nat. Christoph Dieterich 
Im Neuenheimer Feld 669
69120 Heidelberg
sekretariat.dieterich(at)med.uni-heidelberg.de


Research Assistant - Clinical NLP (m/f/d)

full time  – JobID: P0035V331

as soon as possible searched for The division of Bioinformatics and Systems Cardiology (www.dieterichlab.orgat the Klaus Tschira Institute for Integrative Computational Cardiology / Department of Internal Medicine III.

The position is initially limited to 2 years with option of further extension. The salary is paid according to the German TV-L system (the salary agreement for public service employees). The position is also suitable for part-time employment.

The Klaus Tschira Institute for Integrative Computational Cardiology / Internal Medicine III offers a full-time position for a research assistant in clinical natural language processing (NLP).

The Bioinformatics and Systems Cardiology Lab at the Klaus Tschira Institute for Integrative Computational Cardiology develops software to study the causes of cardiac disorders (https://github.com/dieterich-lab). In medicine in general and in cardiology in particular, much treatment-relevant information is still stored in unstructured free text. In this context we make use of recent advancements in NLP, applying deep neural networks for information extraction from unstructured texts.

Tasks

The successful applicant will enter a collaborative research environment and contribute to the group’s NLP portfolio. The successful applicant will basically work on noisy unstructured clinical data in German language, applying state-of-the-art NLP methods to extract clinical information.

  • Preparation and curation of data sets for clinical information extraction tasks
  • Data cleaning and data preprocessing
  • Designing and performing machine learning experiments using state-of-the-art NLP methods
  • Developing end-to-end information extraction pipelines, ready-to-use in clinical routine

Required Qualifications

  • BA/MA degree in computational linguistics, computer science or comparable relevant background and level of expertise
  • Strong Python programming skills
  • Proven record using the Python data science and NLP stack
  • Strong experiences using machine learning methods for information extraction tasks
  • Experience handling noisy and large-scale unstructured data sets
  • Good Linux administration skills (i.e. software management, shell and scripting languages)
  • Experience using deep learning libraries for NLP is a plus (i.e. PyTorch, huggingface)
  • Experience handling multi-user annotation projects is a plus (i.e. via WebAnno/brat)
  • Experience using MS Windows for software development is a plus
  • Familiar with agile software development tools (i.e. Github, Redmine)
  • Ability to communicate and collaborate with experts from various scientific domains
  • Good spoken and written German and English is expected

Your expertise is complemented by essential soft skills, the ability to communicate and work in teams, flexibility and targeted action.

We offer

The Dieterich Lab (www.dieterichlab.org) offers a stimulating, diverse and international research environment. We are embedded in a vibrant community of clinical NLP and collaborate with many NLP research teams in the Heidelberg area.

  • Target-oriented individual further education and training opportunities
  • Targeted training on the job
  • Ticket for public transport
  • Possibility of child care (crèche and kindergarten) as well as subsidy for holiday care for school children
  • Active health promotion
  • Company pension scheme
  • Access to the university library and other university facilities (e.g. university sports)

We are always looking for talented students and job application.

Contact & Application
Please upload a covering letter/supporting statement, including a brief statement of research interests, CV and the details of two referees as part of your online application.
Applications should be sent by email in ONE pdf-file to sekretariat.dieterich(at)med.uni-heidelberg.de

Please do not hesitate to contact us if you have any further questions.

University Hospital Heidelberg
Department of Internal Medicine III
Section of Bioinformatics & Systems Cardiology
Prof. Dr. rer. nat. Christoph Dieterich
Im Neuenheimer Feld 669
69120 Heidelberg
sekretariat.dieterich(at)med.uni-heidelberg.de

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