Full-Time GSSP Scholar­ships at Data Science in Hamburg — Helmholtz Graduate School for the Structure of Matter

DASHH is an inter­di­sci­plinary graduate school that supports challenging PhD topics at the interface of natural sciences or materials science and applied mathe­matics or computer science. DASHH involves several key research insti­tu­tions and univer­sities in the multi­faceted and vibrant city of Hamburg, Germany.

DASHH is looking for excellent and highly qualified PhD candi­dates outside Germany, interested in designing and working on inter­di­sci­plinary, data-driven research projects in accele­rator science, materials science, struc­tural biology, applied mathe­matics, computer science, or engineering. You are welcome to discuss and propose your own project ideas with our DASHH super­visors.

Our offer: two full-time GSSP scholar­ships by the German Academic Exchange Service DAAD for students outside Germany working on inter­di­sci­plinary research projects with super­visors from both fields

Our profile: world-leading large-scale research facilities (PETRA III, FLASH, EuXFEL), highly experi­enced super­visors from our nine partner insti­tu­tions (Deutsches Elektronen-Synchrotron DESY, University of Hamburg, Hamburg University of Technology, Helmut Schmidt University, Hamburg University of Applied Sciences, Helmholtz-Zentrum hereon, Helmholtz Centre for Infection Research, Max Planck Institute for the Structure and Dynamics of Matter, European XFEL) inspiring inter­na­tional environment in the Science City Hamburg Bahrenfeld, cutting-edge data science, excellent scien­tific training and soft skill & career develo­pment support

Candidate requi­re­ments: We are looking for highly motivated inter­na­tional students with an excellent academic background in accele­rator science, struc­tural biology, materials science, computer science, or applied mathe­matics. The candi­dates should bring a strong interest in working on highly inter­di­sci­plinary topics, be team-oriented, and have a strong background in programming.

For more infor­mation, see https://www.dashh.org/application/gssp_scholarships/index_eng.html

Bioin­for­matics scientist (m/f/d)

The MPI for Molecular Plant Physiology in Potsdam is looking for a Bioin­for­ma­tician (m/f/d) to join the Bioin­for­matics group, headed by Prof. Dirk Walther. The position is available immediately.

Background

The Bioin­for­matics group supports the experi­mental research activities at the institute by applying and developing bioin­for­matics methods and algorithms for the analysis of complex datasets. The rapid advancement and broad adoption of novel sequencing techno­logies have moved genomics research questions into the focus of our colla­bo­rative and our own research activities. In addition, the group pursues research questions in the fields of Struc­tural Bioin­for­matics, Quanti­tative Genetics, and Machine Learning, and develops databases, bioin­for­matics software, and data management solutions.

For further infor­mation: https://www.mpimp-golm.mpg.de/bioinformatics

We are looking for a broadly interested and experi­enced Bioin­for­ma­tician to help provide high-level Bioin­for­matics data analysis support to our experi­mental partner groups.

What we are looking for

• A PhD in Bioin­for­matics (or related disci­plines) or 3+ years of experience working as a Bioin­for­matics support scientist;
• Proven experience in OMICs data analysis, in parti­cular, Next Generation Sequencing (NGS) data analysis (RNAseq and the likes), in using associated software solutions, and a high-level familiarity with the under­lying algorithms;
• Solid knowledge of statistics;
• Familiarity with a broad range of standard Bioin­for­matics algorithms;
• Solid programming skills (R, Python, Perl, Java, C, or any subset thereof), in Linux/UNIX environ­ments;
• Experience in advanced Machine Learning methods is a strong plus;
• Interface programming experience is a plus, as is experience in high-perfor­­­mance computing;
• Prior specific experience in plant-related research is NOT required but is considered a plus, as is experience in relevant wetlab proce­dures (library construction etc.).
• Very good command of English (orally and in writing);
• Desired traits: self-motivated, well-organized, reliable, ability to effici­ently manage several parallel projects, ability to commu­nicate with experi­­­men­­­tally-oriented research colla­bo­rators, and a positive attitude towards inter­acting with colle­agues from different backgrounds and cultures;

The Max Planck Society strives for gender equality and diversity. We, therefore, welcome appli­ca­tions from people of all backgrounds.

What we offer

• Full-time position for two years, German public service pay scale (up to TVÖD Bund E13, commen­surate with prior experience and quali­fi­cation), including social benefits;
• Oppor­tu­nities to engage in scien­tific colla­bo­ra­tions with in-house scien­tists, the University of Potsdam, and other local research insti­tutes (Golm boasts three MPIs, two Fraun­hofer insti­tutes, the University of Potsdam, and several estab­lished and start-up companies in the applied sciences);
• Access to a state-of-the-art computing infra­structure;
• A welcoming and stimu­lating environment in a dynamic, inter­na­tional team of coope­rative and motivated scien­tists;
• Support and mentoring for scien­tific and career develo­pment;
• Working near the beautiful city of Potsdam and the exciting urban area of Berlin.

How to apply

Screening of appli­ca­tions will start immediately and will continue until a suitable candidate has been identified.

Please include the following documents in your appli­cation and send your appli­cation (merged into one PDF, please) to walther@mpimp-golm.mpg.de.

• CV;
• Publi­cation list;
• Contact infor­mation of a minimum of two references. Please specify the relati­onship to your reference (current/past super­visor, university teacher etc.);
• Motivation letter explaining why you are interested in assuming the role of a support scientist.

Description

Appli­ca­tions are invited for a full-time, fully funded four-year PhD position at the UCD Cancer Data Lab, University College Dublin, Ireland. The PhD studentship will cover EU tuition fees and a tax-free stipend of €22,000 per year.

Project overview:

Under­standing why the mutation of some genes causes pheno­typic defects while others are well tolerated is crucial both for under­standing the genetic variation observed in human popula­tions and for the develo­pment of new thera­peutic approaches for inherited disease. Parti­cu­larly important in this context are gene dupli­cates (paralogs). Because of their shared origin, pairs of paralogs often perform similar functions and therefore may compensate for each other’s loss. However 80% of Mendelian disease genes have identi­fiable paralogs. This suggests that the loss of these genes cannot be adequately compen­sated for by a paralog. The goal of the PhD will be to under­stand why certain paralogs cause disease when mutated and more generally how paralogs contribute to human genetic robustness. We are parti­cu­larly interested in integrative/systems approaches to address this.

In recent work we have explored how paralogs influence the response of cancer cells to genetic pertur­bation (De Kegel and Ryan, PLoS Genetics 2019) and how they shape the evolution of tumour genomes (De Kegel and Ryan, Molecular Systems Biology 2023). We have also explored, using proteomic approaches, how mutation/deletion of one paralog can alter the abundance of another (Venkatesh et al, Biorxiv 2024). This PhD project will move beyond cancer to look at the role of paralogs in inherited diseases.

About us:

We are a supportive and colla­bo­rative inter­di­sci­plinary research group based in the Conway Institute and associated with the School of Medicine in University College Dublin. We use large-scale data analysis and machine learning approaches to under­stand the conse­quences of genetic variation and to identify new thera­peutic targets. See cancerdata.ucd.ie/ for more details

Quali­fi­ca­tions

Due to the funding source, this position is only available to students from the EU/EEA/UK/Switzerland. This will be a fully dry-lab role and strong data analytics skills are required. Appli­cants should typically have a primary degree in genetics, bioin­for­matics, or computer science. If you’re not in this category, feel free to send me a mail to discuss.

Expertise in any of the below areas would be a plus:
— machine learning
— network biology
— systems biology
— analysing large scale genetics datasets
— evolu­tionary biology

Appli­cation

Please send an email to Colm Ryan (colm.ryan@ucd.ie) with CV and Cover Letter. Informal enquiries are also welcome.

IMB (www.imb.de) is a research institute on the campus of the Johannes Gutenberg University in Mainz, Germany.  It is generously funded by the Boehringer Ingelheim Foundation and the state of Rhineland-Palatinate. Our research focuses on the biology of the cell nucleus and ranges from the molecular level to systems and compu­ta­tional approaches. Resear­chers at IMB are supported by strong core facilities that offer state-of-the-art services in bioin­for­matics, cytometry, genomics, micro­scopy, proteomics, and protein production.

Background

Human brain develo­pment is spatially and tempo­rally tightly controlled, with sequential and precise orchestration of cellular and molecular programs. Any pertur­bation in these molecular programs can lead to detri­mental effects. For example, mutations in genes encoding epige­netic regulators, especially the BAF chromatin remodeling complexes, are frequently causative for neuro­de­ve­lo­p­mental disorders. These manifest in brain abnor­ma­lities, intellectual disabi­lities, and other physical aberra­tions. We still hardly under­stand the molecular mecha­nisms during human brain develo­pment mediated by these regulators and how their mutations manifest into the disease pheno­types.

BAF chromatin remodeler complexes are large multi-subunit complexes that can slide or eject nucle­osomes and thereby regulate chromatin acces­si­bility and gene expression. Recently, we have shown that the maintenance of chromatin acces­si­bility requires constant BAF complex activity and that pertur­bation of their function during brain develo­pment can result in severe molecular, cellular and pheno­typic altera­tions.

The position: Deciphering the role of BAF complexes in human brain develo­pment and neuro­de­ve­lo­p­mental disorders.

As part of the chromatin regulation group, you will work on a project addressing the cellular and molecular role of BAF chromatin remodelling complexes in human brain develo­pment and related diseases. For this project, the diffe­ren­tiation of human induced pluri­potent stem cell (hiPSC) into brain organoids in combi­nation with genetic and pharma­co­lo­gical pertur­ba­tions is used as a model system in combi­nation with advanced cell and molecular biology techniques, including bulk and single-cell genomics, proteomics, and micro­scopy. The project will include the analysis of the datasets, data integration and statis­tical analyses. Additio­nally, you will use machine learning and artificial intel­li­gence to make additional predic­tions from data by training available machine learning algorithms or deep learning models. The project is funded by the European Union (ERC Starting Grant).

Tasks and respon­si­bi­lities

• Compu­ta­tional analysis of transcrip­tomics and epige­nomic datasets, e.g. bulk and single cell (epi)genomics and proteomics data, and
• Multi-model data integration
• Feature selection and prediction using machine and deep learning models
• Data analysis, documen­tation and presen­tation
• Regularly parti­cipate and present at (internal) meetings
• Study of relevant scien­tific literature

 Requi­re­ments

• Highly motivated and creative researcher who enjoys compu­ta­tional analysis, data integration, and machine learning
• Experience in genomic and epige­nomic data analysis and integration is required
• Extensive experience in R/python, shell script and repro­du­cible research
• Strong statis­tical knowledge and knowledge of statis­tical modelling of multi-model datasets
• Knowledge of HPC or cloud-based systems
• Experience in machine learning will be highly beneficial
• Ability to work closely with wet-lab scien­tists
• Enthu­siasm about science, especially with regard to neuro­de­ve­lo­p­mental processes, gene regulation, and epige­netics
• Ability to work precisely and good attention to detail
• Ability to work independently as well as in a team
• Very good oral and written commu­ni­cation skills in English

Why joining us

We offer a stimu­lating, diverse, inter­na­tional research environment, a pleasant working atmosphere, and the oppor­tunity to perform state-of-the-art experi­ments and analyses. The institute is modern, well-equipped, and centrally located, with good public transport links and parking.

Our offer includes

• Compe­titive salary and favourable pension scheme
• Advanced training oppor­tu­nities
• Flexible working hours
• Job Ticket
• Employee events
• Being part of the ERC Starting Grant “SWItchFate”
• Co-super­­­vision by local and inter­na­tional experts in the field

What else you need to know

• Starting Date: January 2025 or later
• Duration: 2 years with option of extension
• Deadline: 30^th November 2024

Have we sparked your interest:

To apply, please upload your appli­cation containing your cover letter, CV, certi­fi­cates and contact infor­mation of at least two profes­sional references on our appli­cation form on www.imb.de. If you have questions relating to the appli­cation process, please send an email to hr@imb-mainz.de quoting the Ref. No. #SSPD02. Informal enquires should be addressed to Dr Sandra Schick-Nickolaus (s.schick@imb-mainz.de). IMB is an equal oppor­tunity employer.

Decla­ration of Consent and Data Protection

By sending us your appli­cation, you are consenting to us saving your personal data in order to carry out the selection process. You can find more infor­mation on data protection and retention periods at https://www.imb.de/jobs/data-protection.

The Hiller Lab at the Senckenberg Research Institute in Frankfurt, Germany has an opening for a Postdoc and a Bioin­for­ma­tician to work on our 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
Our 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.

The Bioin­for­ma­tician will assemble reference-quality genomes of ~150 bat species, for which we are currently generating PacBio HiFi and HiC data. For a few focal species, we will also generate a complete T2T assembly. The Bioin­for­ma­tician will also analyze transcrip­tomics data that we are sequencing in parallel for all target bat species, use this data and our homology-based methods (TOGA) to annotate the new genomes, generate whole genome alignments of bats and other mammals, and support the BATPROTECT project.

The Postdoc will contribute to analyzing these genomic and transcrip­tomic resources. Projects include compa­rative genomic screens to identify key adapt­a­tions in coding and non-coding genes as well as diffe­rences in gene expression patterns across the bat phylogeny, associating genomic and transcrip­tomics changes with longevity and viral reservoir traits, identi­fying novel bat genes, and inves­ti­gating the evolu­tionary history of endoge­nized viral elements.

Both new hires 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 and yearly retreats with all project members.

We provide

• cutting-edge compu­ta­tional (large HPC clusters, genome browser) and lab infra­structure to sequence and analyze genomes
• flexible working hours – oppor­tu­nities for mobile working – leave of absence due to family reasons (certified by “audit­be­ru­fund­fa­milie”) – parent-child office – annual special payment – company pension scheme – Senckenberg badge for free entry in museums in Frankfurt. – leave of 30 days/year
• Frankfurt is a vibrant and highly inter­na­tional city at the heart of Europe that combines a skyscraper skyline with ample parks and green areas. The Economist 2022 index ranked Frankfurt among the top 10 most livable cities worldwide.

How to apply

More infor­mation about these positions and how to apply can be found at https://tbg.senckenberg.de/hillerlab/jobs/

The initial appli­cation deadlines are middle of November, but we invite appli­ca­tions until the positions have been filled.

For more infor­mation about the lab and the project, please contact Prof. Dr. Michael Hiller (michael.hiller@senckenberg.de) or visit the lab webpage https://tbg.senckenberg.de/hillerlab/.

An overview of our publi­ca­tions is available here: https://tbg.senckenberg.de/hillerlab/publications/.