REANNOUNCEMENT - Computational PhD Position in Enhancer Evolution and Synthetic Enhancer Design

The Madsen group at the Section for Data Science and Statistics, Department of Mathematics and Computer Science invites applications from outstanding PhD candidates who are interested in joining the team and the Human Gene Regulation Map, a part of the new Novo Nordisk Foundation Center for Genomic Mechanisms of Disease (NNFC), in a three-year PhD position. The position is available from 1 March 2023, or as soon as possible thereafter. Application deadline: 23 Janury 2023.

The Section for Data Science and Statistics
The Madsen group is located at the Section for Data Science and Statistics (DSS) at the Department of Mathematics and Computer Science, SDU. The DSS currently hosts sixteen independent research groups focusing on various aspects of data science, including three groups working with bioinformatics and computational biology. The Section constitutes an international, ambitious, highly dynamic, and well-equipped working environment having access to state-of-the-art computing facilities, including high performance computing systems.

In addition to the DSS, the Madsen group is a partner in ambitious national and international research centres, in which the successful candidates can actively participate and (net)work:

The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease (NNFC)
The Madsen group is a partner in the Human Gene Regulation Map (HGRM), a part of the new Novo Nordisk Foundation Center for Genomic Mechanisms of Disease (NNFC). The HGRM is an international joint research centre between four research groups at the Broad Institute of MIT and Harvard and four Danish research groups. The aim of HGRM is to build comprehensive maps of gene regulation in the human genome as a resource for uncovering biological mechanisms on common genetic diseases, with an initial focus on cell types relevant to cardiometabolic diseases including type 2 diabetes. We aim to combine recent advances in genomics, molecular biology, single-cell analysis, and stem cell models with approaches in computational biology and machine learning to identify fundamental rules of gene regulation.

The Center for Functional Genomics and Tissue Plasticity (ATLAS)
The Madsen group is a partner in the Center for Functional Genomics and Tissue Plasticity (ATLAS) at University of Southern Denmark which is supported by the Danish National Research Foundation. ATLAS is a national joint research centre between five research groups at the University of Southern Denmark and three research groups at Odense University Hospital (OUH). The aim of ATLAS is to obtain systems-level, mechanistic and cell type-resolved understanding of adipose and hepatic tissue plasticity in response to diet-induced obesity and regression in mouse models; and to translate this for in-depth understanding of the functional changes in human adipose and hepatic tissues in response to severe obesity and reversal. The centre applies a combination of functional genomics approaches including single cell sequencing, mouse models, proteomics, in vivo targeting, computational biology, and clinical studies.

Research Projects and Roles
As a PhD student in the Madsen group, you will be engaged in a highly ambitious project aimed at shedding new light on the regulatory and functional architecture of the human genome with the aim of furthering the understanding of how it contributes to health and disease. You will interact and collaborate closely with other researchers in the Madsen group as well as with members of the other research groups within the DSS, the department and the research centres.

The successful candidate will be embedded in the HGRM project with opportunities to collaborate closely with international partners in the centre. The candidate will be responsible for a project which aims to understand enhancer evolution and design optimized synthetic enhancers targeting specific cell types in the liver with therapeutic potential. To achieve those aims, the successful candidate will apply recent machine learning architectures to both public and in-house high-throughput datasets, and subsequently interpret these models to glean new insights into the rules underlying enhancer architecture and control of the human genome.

Qualifications/requirements
We are looking for highly motivated, dedicated, and ambitious candidates with:

• A Master’s degree in Applied Mathematics, Data Science, Bioinformatics, Computational Biology, or a closely related field.
• Documented experience with statistical programming (e.g. R or Python).
• Documented experience with (single-cell) -omics data analysis, e.g. (sn)ATAC-seq.
• Strong communication and collaborative skills and an interest in working in an interdisciplinary environment.
• Proficiency in spoken and written English.
Experience with liver biology is considered an advantage.

We offer:

• A three-year PhD position in a stimulating and supportive, international research environment.
• Access to state-of-the-art equipment, facilities, and infrastructure.
• Opportunity to interact with an extensive network of national and international collaborators.
• A competitive salary and social benefits (e.g. health coverage, parental leave, social security etc.).
• Dedicated assistance and support with various practical, social, and legal aspects (housing, visa, administration, tax etc.), especially for international candidates through our international staff office (ISO) and department.

For further information please contact Assistant Professor Jesper Grud Skat Madsen ([email protected]).

Application, salary etc.
Appointment as a PhD Research Fellow is for three years. 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 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 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 personal contact information
• Copies of diplomas, Bachelor as well as Master’s degree, including transcript of notes/grades
• At least two signed reference letters. 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.