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Veröf­fent­licht: 17. May 2024

PhD student compu­ta­tional biology / bioin­for­matics (m/f/d)

Univer­si­täts­kli­nikum Schleswig-Holstein, Campus Lübeck

PhD student compu­ta­tional biology / bioin­for­matics (m/f/d) (fulltime)

The position will be hosted at the Institute of Human Genetics, in the workgroup “Regulatory Genomics” of Prof. Martin Kircher. The bioin­for­matics group performs research in the fields of sequence analysis, data mining, machine learning and functional genomics (https://kircherlab.github.io/). Our research focuses on compu­ta­tional approaches of identi­fying functionally relevant genetic changes in disease and adapt­ation as well as developing more sensitive methods in diagno­stics (especially exome, genome and cell-free DNA sequencing). For example, we devise compu­ta­tional approaches (e.g. CADD, CADD-SV, ReMM) to score and identify functional genetic changes in the human genome through Massively Parallel Reporter Assays and genome pertu­bation. Under­standing how gene regulation is encoded in our genomes across develo­pment and the diversity of cell-types is one of our funda­mental research questions.

Start in our team

The position is immediately available. The full-time contract will be issued for 3 years with the prospect of extension to finish the thesis work and prepa­ration of related publi­ca­tions.

We offer:

  • A colla­bo­rative research environment that encou­rages and supports scien­tific curiosity, innovation, and develo­pment of its team members
  • Training in compu­ta­tional biology and independent research, as well as receiving guidance on PhD requi­re­ments and thesis work
  • Career develo­pment and colla­bo­ration with internal and external partners
  • Parti­ci­pation in inter­na­tional meetings and scien­tific confe­rences
  • Salary based full-time payment on the German E13 TV‑L scale, if terms and condi­tions under collective bargaining law are fulfilled. This for example also includes 30 paid vacation days per year.
  • Flexible working hours and a family-friendly environment

Your respon­si­bi­lities:

  • Work on cutting-edge projects using state-of-the-art technology and gain insights into the sequence encoding of molecular function and its relation to disease as well as epige­netic and 3D genome annota­tions
  • Develop deep neural nets or classical machine learning models that integrate sequence features and molecular measures
  • Develop or improve methods to infer disease and regulatory mecha­nisms and develop data standards as well as prepare data for analysis or compu­ta­tional modeling
  • Analyze high-throughput sequencing data and develop custom compu­ta­tional tools,
  • Apply and improve methods for model inter­pre­tation, and actively contribute to the lab, institute and inter­na­tional colla­bo­ra­tions

Requi­re­ments:

  • Master degree or equivalent in bioin­for­matics, compu­ta­tional biology or similar, alter­na­tively in computer sciences with experience in molecular biology and large-scale data analysis
  • Basic knowledge of molecular biology, gene regulation and epige­netics as well as deep under­standing of sequence analysis, statis­tical concepts and machine learning
  • Highly skilled in a programming language such as Python, R, C++, or Java and inter­me­diate skills in a statis­tical modeling or analysis environment like R or Python scipy/scikit learn
  • Prior experience with Unix and bash scripting, previous exposure to HPC environ­ments is an advantage
  • Exposure to repro­du­cible work and FAIR principles
  • Highly motivated to expand knowledge and develop innovative approaches as well as diligent, goal-oriented and independent work attitude
  • Team-oriented with inter­di­sci­plinary commu­ni­cation skills and very good English language skills

We are looking forward to your appli­cation under the following Link: PhD student compu­ta­tional biology / bioin­for­matics (m/f/d) (uksh.de). Please submit your appli­cation until 05.06.2024, indicating your earliest possible starting date as well as the reference number 24264.

If you have any questions, do not hesitate to contact Prof. Martin Kircher: martin.kircher@uksh.de

We live diversity and strongly encourage qualified female scien­tists to apply. UKSH and the University of Lübeck aim to increase the number of women among faculty and staff. Appli­ca­tions from people with an immigrant background who meet the hiring requi­re­ments are encou­raged. Disabled candi­dates who are equally qualified will receive prefe­rence.

Veröf­fent­licht: 8. May 2024

Bioin­for­ma­tician as Statis­tical Data Scientist*

Immatics combines the discovery of true targets for cancer immuno­the­rapies with the develo­pment of the right T cell receptors with the goal of enabling a robust and specific T cell response against these targets. This deep know-how is the foundation for our pipeline of Adoptive Cell Therapies and TCR Bispe­cifics as well as our partner­ships with global leaders in the pharmaceu­tical industry. We are committed to delivering the power of T cells and to unlocking new avenues for patients in their fight against cancer.

We are currently seeking a full- or part-time

Bioin­for­ma­tician as Statis­tical Data Scientist* 

to support our R&D team to develop innovative immuno­the­ra­peutic products for next-generation cancer therapy.

You will work in Tübingen (Germany) in an inter­di­sci­plinary environment with colle­agues from research and clinical depart­ments and will contribute to our mission of developing new cancer immuno­the­rapies to improve clinical outcomes for patients. Tübingen is a vibrant University city close to Stuttgart in the south of Germany. This is a permanent position.

YOUR MISSION

Your main respon­si­bi­lities will include but are not limited to the following tasks:

  • Analyze clinical data and data from various assays with statistics or statis­tical learning methods, document and present your findings to guide and support scien­tific decisions.
  • Guide experi­mental design, under­standing the mecha­nisms of data generation and contri­buting statis­tical expertise.
  • Make suitable assump­tions and develop statis­tical models to infer relati­onships between variables or test hypotheses.
  • Contribute to our in-house platform for data analysis in that empowers your fellow scien­tists to develop innovative cancer immuno­the­rapies in a data-driven manner.
  • gainst relational databases to enable targeted analyses, develop tailored visua­liza­tions and support the publi­cation of clinical data, working closely with your colle­agues from Trans­la­tional Science and other scien­tific depart­ments.

YOUR PROFILE

  • You hold a PhD degree in Bioin­for­matics, Biosta­tistics or a related field. Ideally, you have gained two or more years of additional work experience in industry or academia.
  • You have a deep foundation in statistics and experience with biolo­gical and clinical data.
  • You are profi­cient in at least one scripting or programming language (e.g., R, Python) and are familiar with Linux based systems.
  • Knowledge of SQL databases, machine learning, pepti­domics, or immunology is an advantage.
  • You have excellent commu­ni­cation skills in English, a high degree of independent working and analy­tical reasoning, and you thrive in an inter­di­sci­plinary colla­bo­rative environment.

We kindly ask you to enclose with your appli­cation your transcripts of records (including all courses attended and grades earned) for all degrees (i.e., Bachelor, Master, PhD, if appli­cable) and to briefly mention which of your profes­sional skills are relevant for this position from your point of view as well as why you are interested in working at Immatics. 

WHY US?

We are a committed and inspired team and cherish the collegial, highly motivated, and family-friendly atmosphere within Immatics. Our culture allows for a high level of origi­nality, independent thinking, and initiative. We believe in supporting our employees’ profes­sional and social skills: We enable them to join confe­rences and trainings as well as to enjoy our Immatics benefits – e.g., job bike, job ticket, Health Programs, childcare benefits, relocation allowance, Company summer and winter events.

NOTICE

*We value diversity and inclusion. Immatics N.V. and all Immatics subsi­diaries are equal oppor­tunity employers that evaluate qualified appli­cants without regard to race, color, national origin, religion, sex, age, marital status, disability, veteran status, sexual orien­tation, gender identity, or other charac­te­ristics protected by law.

Interested? Please apply via our career page: Bioin­for­ma­tician as Statis­tical Data Scientist* | Immatics

 

 

 

 

Veröf­fent­licht: 8. May 2024

Bioin­for­ma­tician as Data Warehouse Architect*

Immatics combines the discovery of true targets for cancer immuno­the­rapies with the develo­pment of the right T cell receptors with the goal of enabling a robust and specific T cell response against these targets. This deep know-how is the foundation for our pipeline of Adoptive Cell Therapies and TCR Bispe­cifics as well as our partner­ships with global leaders in the pharmaceu­tical industry. We are committed to delivering the power of T cells and to unlocking new avenues for patients in their fight against cancer.

We are currently seeking a

Bioin­for­ma­tician as Data Warehouse Architect* 

to support our R&D team to develop innovative product candi­dates for cancer immuno­therapy. You will work in an inter­di­sci­plinary environment with colle­agues from research and clinical depart­ments at our site in Tuebingen (Germany) and will contribute to our mission of developing new cancer immuno­the­rapies to improve clinical outcomes for patients. Tuebingen is a vibrant University city close to Stuttgart in the south of Germany. This is a permanent position.

YOUR MISSION

You will support Immatics’ efforts to further digitalize the management of clinical data for cancer immuno­the­rapies. Your main respon­si­bi­lities will include but are not limited to the following tasks:

  • Integrate clinical data and life-science data from various sources into our clinical data warehouse as part of our immuno­in­for­matics platform, XCUBE™, to enable real-time access and facilitate inter­active analysis.
  • Contribute to the automatic data processing which empowers our scien­tists to work effici­ently and to improve cancer immuno­the­rapies for patients.
  • Design, implement, and maintain web inter­faces for our clinical data warehouse.
  • Colla­borate with life-science users to identify data silos, to create user requi­rement speci­fi­ca­tions to guide database develo­pment, and to integrate them into the clinical warehouse and our platform for data analysis.

YOUR PROFILE

  • You hold a PhD degree inBio­in­for­matics, Computer Science, or a related field, or have at least three years of relevant work experience.
  • You have relevant experience with database and software develo­pment in a biolo­gical or medical appli­cation context, demons­trated either through work experience or University courses. Knowledge of SQL databases, statistics or immunology is an advantage.
  • You are familiar with Linux-based systems and profi­cient in at least one scripting language (Python, Perl, or similar).
  • You have excellent commu­ni­cation skills in English, a high degree of independent working and analy­tical reasoning, and enjoy working in an inter­di­sci­plinary colla­bo­rative environment.

We kindly ask you to enclose with your appli­cation your transcripts of records (including all courses attended and grades earned) for all degrees (i.e., Bachelor, Master, PhD, if appli­cable) and to briefly mention which of your profes­sional skills are relevant for this position from your point of view as well as why you are interested in working at Immatics.

WHY US?

We are a committed and inspired team and cherish the collegial, highly motivated, and family-friendly atmosphere within Immatics. Our culture allows for a high level of origi­nality, independent thinking, and initiative. We believe in supporting our employees’ profes­sional and social skills: We enable them to join confe­rences and trainings as well as to enjoy our Immatics benefits – e.g., job bike, job ticket, Health Programs, childcare benefits, relocation allowance, Company summer and winter events.

NOTICE

*We value diversity and inclusion. Immatics N.V. and all Immatics subsi­diaries are equal oppor­tunity employers that evaluate qualified appli­cants without regard to race, color, national origin, religion, sex, age, marital status, disability, veteran status, sexual orien­tation, gender identity, or other charac­te­ristics protected by law.

Veröf­fent­licht: 6. May 2024

Postdoc (m,f,x) in Bioin­for­matics for 2 years with 39,83 hours per week, TV‑L E13

The Dept. of Molecular Immunology at the Ruhr-University Bochum invites appli­ca­tions from highly­mo­ti­vated candi­dates (m/f/x) with an interest in the regulation of gene expression influencing immune responses, the develo­pment of immune cells, and host-pathogen inter­ac­tions. The candidate (m/f/x) is
expected to work team-oriented in an inter­na­tional environment.

The Ruhr-Univer­­­­­sität Bochum is one of Germany’s leading research univer­sities, addressing the whole range of academic  disci­plines. A highly dynamic setting enables resear­chers and students to work across the tradi­tional boundaries of academic subjects and faculties. To create knowledge networks within
and beyond the university is RUB’s declared aim.
The Ruhr-Univer­­­­­sität Bochum stands for diversity and equal oppor­tu­nities. For this reason, we favour a working environment composed of hetero­ge­neous
teams, and seek to promote the careers of indivi­duals who are under­re­pre­sented in our respective profes­sional areas. The Ruhr-Univer­­­­­sität Bochum expressly requests job appli­ca­tions from women. In areas in which they are under­re­pre­sented they will be given prefe­rence in the case of equivalent quali­fi­ca­tions with male candi­dates. Appli­ca­tions from indivi­duals with disabi­lities are most welcome.

Your tasks:

  • Develo­pment and appli­cation of methods to analyze transcrip­tomics (e.g. RNAseq, scRNAseq), genomics (e.g. ATACseq, Cut&Run, micro­biota), and proteomics (e.g. mass spectro­metry) data
  • Pathway, Gene Ontology and similar analyses
  • Teaching and super­vision of Bachelor and Master students
  • Writing of publi­ca­tions and acqui­sition of third-party funding

Your profile:

  • PhD in bioin­for­matics, bioche­mistry, biology, or similar
  • Experience in programming in R, Python, Perl, and/or C++
  • Interest in developing techniques such as machine learning and/or artificial intel­li­gence
  • Excellent skills in commu­ni­cation (English and German) and work organization
  • Fluency in German (at least C1 level, in word and writing – required for an effective commu­ni­cation and for teaching in German) (nur bei Lehrver­pflichtung)

Our offerings:

  • challenging and varied tasks with a high degree of personal respon­si­bility
  • team-orien­­­tated coope­ration in a committed, inter­na­tional and appre­ciative team
  • a modern, well-equipped workplace
  • fair working hours and family-friendly working
  • other social benefits according to the TV‑L

Additional infor­mation:

  • At the request of the applicant (m,f,x), the staff council may be involved in selection inter­views. https://www.wpr.ruhr-uni-bochum.de/
  • The load of teaching will be calcu­lated according to § 3 of Lehrver­pflich­tungs­ver­ordnung (state of North Rhine-Westphalia).
  • German language courses are offered by the University Language Center (ZfA) in the field of German as a Foreign Language (DaF) https://www.daf.ruhr-uni-bochum.de/sbgk/index.html.en
  • You can find infor­mation about TVL at: https://oeffentlicher-dienst.info/

Contact details for your appli­cation:

  • Prof. Dr. Ingo Schmitz, Phone: +49234 32 21111
  • Travel expenses for inter­views cannot be refunded.
  • For infor­mation on the collection of personal data in the appli­cation process see: https://www.ruhr-unibochum.de/en/information-collection-personal-data-application-process.
  • We are looking forward to receiving your appli­cation with the speci­fi­cation ANR: 3254 until June 3rd 2024, send by e‑mail to the following address: ingo.schmitz@rub.de

Veröf­fent­licht: 6. May 2024

ERC-funded PhD and Postdoc Positions in Compa­rative Genomics on Bats

ERC-funded PhD and Postdoc Positions in Compa­rative Genomics
(full time / part-time options available)

The Hiller Lab at the LOEWE Center for Trans­la­tional Biodi­versity Genomics (TBG) in Frankfurt, Germany has two openings for a PhD student and/or a Postdoc to work on the BATPROTECT project to inves­tigate the genomic basis of long health­spans, disease resis­tance, and viral tolerance in bats.

BATPROTECT

is a 6‑year funded ERC synergy grant project that will use bats as natural models of healthy aging and disease tolerance to elucidate the molecular mecha­nisms behind bats’ excep­tional longevity and resis­tance to viral and age-related diseases. BATPROTECT brings together a team of global leaders in bat biology and ageing (Emma Teeling, Dublin), bat immunology and virology (Linfa Wang, Singapore), evolution and genomics (Michael Hiller, Frankfurt), and ageing model organisms (Bjoern Schumacher, Cologne) that will jointly inves­tigate aging and immune responses in bats from the wild and captive colonies, discover genes with evolu­tionary importance for longevity and disease resis­tance, and functionally validate longevity and immune regulators in stem and diffe­ren­tiated cells of bats and model organisms, with the ultimate goal to uncover new direc­tions to improve human healthspan and disease outcome.

The Project

The overall goal is to uncover the genomic basis of excep­tional health­spans and disease tolerance in bats, under­stand the evolution of these traits, and identify key molecular targets for functional validation. To this end, we will assemble ~150 new reference-quality bat genomes using HiFi and HiC sequencing to better cover the diversity of bats, generate compa­rative transcrip­tomic datasets, and analyze these data using our estab­lished methods reper­toire (TOGA and others). Work includes phylo­ge­nomics, performing compa­rative screens to identify key adapt­a­tions in coding and non-coding (miRNA) genes as well as diffe­rences in gene expression patterns across the bat phylogeny, associating genomic changes with longevity and viral reservoir status traits, identi­fying novel bat genes, and inves­ti­gating endoge­nized viral elements. The exact project will be defined based on the interests of the appli­cants.

The PhD student and postdoc will work closely with other members of the BATPROTECT team, the Hiller lab, and other Bat1K colla­bo­rators. We also offer exchanges with the other BATPROTECT labs as well as yearly retreats with all project members.

Your profile

  • Master or PhD degree in bioinformatics/computational biology, genomics or a related area
  • Solid programming skills in a Linux environment, experience with shell scripts and Unix tools
  • Strong interest in compa­rative genomics, experience in compa­rative genomics is an advantage
  • English in written and oral form

 

More infor­mation on our lab and how to apply can be found at https://sgn.one/46c
The appli­cation deadline is June 7.

Veröf­fent­licht: 6. May 2024

Postdoc-Stelle in Bioinformatik/Systembiologie in Jena

An der Professur Bioin­for­matik an der Fakultät für Biowis­sen­schaften (Prof. Stefan Schuster) ist zum 01.07.2024 oder später eine Stelle als Wissenschaftliche:r Mitarbeiter:in Bioin­for­matik in Teilzeit (90% / 36 Wochen­stunden) befristet für 4,5 Jahre zu besetzen.

Die Forschung an der o.g. Professur zielt auf ein Verständnis der komplexen Prozesse in lebenden Zellen und deren Inter­ak­tionen mittels mathe­ma­ti­scher Model­lierung und Compu­ter­si­mu­lation.

Ihre Aufgaben:

  • Bioin­for­ma­tische und system­bio­lo­gische Forschung
  • Koope­ration mit experi­mentell arbei­tenden Gruppen
  • Durch­führung von Lehrver­an­stal­tungen in Bioin­for­matik (Übungen, Prose­minare etc.)
  • Betreuung von Abschluss­ar­beiten im B.Sc. und M.Sc. Bioin­for­matik
  • Literatur- und Patent­re­cherchen
  • Arbeit an einem eigenen wissen­schaft­lichen Quali­fi­zie­rungs­projekt, i.d.R. Habili­tation

Ihr Profil:

Abgeschlossene Promotion (Dr. rer. nat. oder Dr. Ing.) oder zumindest einge­reichte Disser­tation in Bioin­for­matik, Infor­matik, Biologie, oder einem anderen natur­wis­sen­schaft­lichen Fach
Interesse an mathe­ma­ti­scher Model­lierung biolo­gi­scher Prozesse

Kennt­nisse in der Compu­ter­pro­gram­mierung

Bewerbung über das Online-Formular im unten angege­benen Link. Die Frist wird evtl. noch verlängert.

Link: Online-Stellen­­­markt der Univer­sität Jena, Wissenschaftliche:r Mitarbeiter:in Bioin­for­matik

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