PhD Opportunity: Developing Innovative Algorithms for Joint Analysis of Single-Cell & Spatial Transcriptomics
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Odense M
The Department of Mathematics and Computer Science at the University of Southern Denmark for the Computational Biology group chaired by Professor Richard Röttger invites applications for a PhD position for the development of innovative algorithms for the joint analysis of single-cell & spatial transcriptomic data in the framework of the Novo Nordisk Foundation funded collaborative data science grant “MOPITAS” – Multi-omics profiling in time and space.
The role of cells in the tissue is largely defined by their differential gene expression, which unfolds both in space and in time. The methods recording this structural information, known as Spatial Transcriptomics (ST), suffer from low transcriptomic resolution, and they are prohibitively expensive to perform at scale. Conversely, single-cell RNA sequencing (scRNA-seq) is a mature, cost-effective technology that captures more RNA transcripts and identifies individual cells adequately. With this transformative project, we seek to bridge the gap between ST and scRNA-seq utilizing novel and innovative algorithms based on a complex interplay of deep neural networks by actually identifying the spatial relationship of the sequenced cells based on a ST map. Subsequently, we will derive statistical tests which can decipher location specific regulatory mechanisms, unravelling how tissues form and change over time and space.
The successful candidate will be part of a strong international consortium (University of Southern Denmark, University of Copenhagen, EMBL, Technical University of Munich) ranging from data-science driven wet-lab experimentation to cutting-edge algorithm development. It is envisioned that the involved researchers are also actively visiting the connected labs.
Within SDU, the candidate will be embedded in a highly international and powerful consortium as a member of the Computational Biology group which offers a wide expertise in machine learning of biomedical data, both in the realm of unsupervised and supervised learning. We also provide the candidate with direct access to state-of-the-art computing facilities optimized for deep learning and distributed computing.
We are seeking outstanding candidates with a completed Master’s degree in Computer Science, Bioinformatics, Molecular Biology or similar. Master’s candidates about to complete their graduate studies will also be considered and should attach a statement from their supervisors regarding their impending completion. Applications for a 4+4 PhD programme are also welcome.
The candidate should have strong analytical and problem-solving skills and be strong in written and oral communication (in English). Expertise in data analysis of single-cell sequencing data as well as spatial transcriptomics are welcome but not strictly required.
Place of work
Computational Biology Group, Department of Mathematics and Computer Science, located at the main campus of the University of Southern Denmark, Odense, Denmark.
For further information please contact Professor Richard Röttger, tel.: +45 6550 2337, e-mail: [email protected].
Application, salary etc.Appointment as a PhD Research Fellow is for three (students who have completed their MSc) or four years (students who have not yet completed their MSc). Employment stops automatically at the end of the period. The holder of the scholarship is not allowed to have other paid employment during the three-year period.
The successful applicant will be employed in accordance with the agreement on salaried PhD scholars between the Ministry of Finance and AC (the Danish Confederation of Professional Associations). Please check links for more information on salary and taxation.
The successful candidate will be enrolled at this university in accordance with faculty regulations and the Danish Ministerial Order on the PhD Programme at the Universities (PhD order).
The University wishes our staff to reflect the diversity of society and thus welcomes applications from all qualified candidates regardless of personal background.
Application must be in English and made in the form of a Declaration of Interest including the following:
Shortlisting may be used in the assessment process.
Further information about the PhD-study can be found at the homepage of the University.
Applications must be submitted electronically using the link “Apply online”. Attached files must be in Adobe PDF or Word format. Each box can only contain a single file of max. 10 Mb. We strongly recommend that you read How to apply before you apply.
Incomplete applications and applications received after the deadline will neither be considered nor evaluated. This also applies to reference letters.
Further information for international applicants about entering and working in Denmark.
The role of cells in the tissue is largely defined by their differential gene expression, which unfolds both in space and in time. The methods recording this structural information, known as Spatial Transcriptomics (ST), suffer from low transcriptomic resolution, and they are prohibitively expensive to perform at scale. Conversely, single-cell RNA sequencing (scRNA-seq) is a mature, cost-effective technology that captures more RNA transcripts and identifies individual cells adequately. With this transformative project, we seek to bridge the gap between ST and scRNA-seq utilizing novel and innovative algorithms based on a complex interplay of deep neural networks by actually identifying the spatial relationship of the sequenced cells based on a ST map. Subsequently, we will derive statistical tests which can decipher location specific regulatory mechanisms, unravelling how tissues form and change over time and space.
The successful candidate will be part of a strong international consortium (University of Southern Denmark, University of Copenhagen, EMBL, Technical University of Munich) ranging from data-science driven wet-lab experimentation to cutting-edge algorithm development. It is envisioned that the involved researchers are also actively visiting the connected labs.
Within SDU, the candidate will be embedded in a highly international and powerful consortium as a member of the Computational Biology group which offers a wide expertise in machine learning of biomedical data, both in the realm of unsupervised and supervised learning. We also provide the candidate with direct access to state-of-the-art computing facilities optimized for deep learning and distributed computing.
We are seeking outstanding candidates with a completed Master’s degree in Computer Science, Bioinformatics, Molecular Biology or similar. Master’s candidates about to complete their graduate studies will also be considered and should attach a statement from their supervisors regarding their impending completion. Applications for a 4+4 PhD programme are also welcome.
The candidate should have strong analytical and problem-solving skills and be strong in written and oral communication (in English). Expertise in data analysis of single-cell sequencing data as well as spatial transcriptomics are welcome but not strictly required.
Place of work
Computational Biology Group, Department of Mathematics and Computer Science, located at the main campus of the University of Southern Denmark, Odense, Denmark.
For further information please contact Professor Richard Röttger, tel.: +45 6550 2337, e-mail: [email protected].
Application, salary etc.Appointment as a PhD Research Fellow is for three (students who have completed their MSc) or four years (students who have not yet completed their MSc). Employment stops automatically at the end of the period. The holder of the scholarship is not allowed to have other paid employment during the three-year period.
The successful applicant will be employed in accordance with the agreement on salaried PhD scholars between the Ministry of Finance and AC (the Danish Confederation of Professional Associations). Please check links for more information on salary and taxation.
The successful candidate will be enrolled at this university in accordance with faculty regulations and the Danish Ministerial Order on the PhD Programme at the Universities (PhD order).
The University wishes our staff to reflect the diversity of society and thus welcomes applications from all qualified candidates regardless of personal background.
Application must be in English and made in the form of a Declaration of Interest including the following:
- A research proposal/description of your approach to the above project (max one page excluding references).
- A list of publications stating the scientific publication(s) on which the applicant wishes to rely (if available).
- A letter stating your specific interest, motivation, and qualifications for the project in question (max. two pages) (please attach this under box “Application form”).
- Detailed CV, including information on previous employment, list of programming skills mastered by the applicant, and teaching and supervision experience and also personal contact information.
- Copies of diplomas, Bachelor as well as Master’s degree, including transcript of records of the current status of the Master studies.
- At least two signed reference letters from supervisors or previous employers. Should your referees wish to send their letters directly to us, please have them use e-mail: [email protected] mentioning your name and the title of the position in the subject line. And please note that these also need to reach us before deadline.
Shortlisting may be used in the assessment process.
Further information about the PhD-study can be found at the homepage of the University.
Applications must be submitted electronically using the link “Apply online”. Attached files must be in Adobe PDF or Word format. Each box can only contain a single file of max. 10 Mb. We strongly recommend that you read How to apply before you apply.
Incomplete applications and applications received after the deadline will neither be considered nor evaluated. This also applies to reference letters.
Further information for international applicants about entering and working in Denmark.
Information og data
Denne ledige stilling har jobtypen "Forsker", og befinder sig i kategorien "Sundhed og forskning".
Arbejdsstedet er beliggende i Odense M.
Jobbet er oprettet på vores service den 22.3.2023, men kan have været deaktiveret og genaktiveret igen.
Dagligt opdateret: Dette job opdateres dagligt ud fra jobudbyderens hjemmeside via vores søgemaskineteknologi og er aktivt lige nu.
- Forsker
- Odense M
- Onsdag den 19. april 2023
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