PhD student in quantitative biology - Hiring in process/Finished, not possible to apply

Description of the workplace

The research group of Clinical Memory Research focuses on defining and understanding biological processes in Alzheimer’s disease and other neurodegenerative diseases. We work with large multimodal datasets composed of cohorts of patients and cognitively unimpaired volunteers, who undergo extensive testing with neuroimaging, biomarker measurements and neuropsychological evaluation. More information can be found here. We also work with large genomic, transcriptomic and proteomic datasets based on tissue extracted from humans, as well as from animal models. The lab is led by Dr. Jacob Vogel, and is nested within the larger research group led by Professor Oskar Hansson. This position will be placed at BMC in Lund.

We are committed to creating a positive, respectful and stimulating environment. We value communication and collaboration, and we strive for a workplace that promotes learning and development of all lab members. We are also committed to building a safe and positive environment for all lab members through mutual respect and toleration.

Project description

Alzheimer’s disease (AD) is thought to be caused by pathological misfolding and aggregation of β-amyloid and tau proteins. However, very little is known about the molecular changes that precede this protein aggregation, nor what molecular cascades lead from protein aggregation to cell death. Furthermore, much of what we do know about such molecular activity comes from animal studies, which are imperfect models of AD lacking many disease features that occur in humans. Recently, several datasets of human tissue have become available measuring gene transcriptomics) at the cellular level in elderly people who died with and without AD. In conjunction with proteomic data collected from cerebrospinal fluid (CSF) of healthy and cognitively impaired patients by our lab, these resources create an excellent dataset for probing molecular changes that precede, accompany and are precipitated by pathological protein aggregation in AD. This PhD project will use state-of-the-art disease modeling and statistical learning approaches to characterize the temporal landscape of the AD molecular cascade in humans. The project will involve modeling cell-specific molecular changes over the course of the disease, and will translate and monitor these changes in living, patients based on CSF proteomics

The PhD student will conduct research under the supervision of Dr. Jacob Vogel, Dr. Niklas Mattsson-Carlgren and Prof. Oskar Hansson.

Work duties and areas of responsibility

The main duties of the doctoral candidate are to conduct their research studies, which include participation in research projects and graduate courses. The doctoral candidate will perform data analysis combining multiple multi-omic and neuroimaging datasets, will write papers, and will present results locally and at national and international conferences. Other work responsibilities may include: data curation and processing; composition, editing, or executing of computational scripts; informal mentorship of and skill-sharing with other employees; or composition of grants and/or research fellowships. Other work duties may also occur. The majority of the research work will be done in collaboration with members of the research group.

Qualifications
The following are required for the position:

• Master of Science within engineering, neuroscience, statistics, quantitative biology, physics, mathematics or a related discipline OR a Bachelor's of Science in the same fields AND have acquired research experience largely equivalent to a Master’s degree (e.g. through paid employment in a research laboratory)
• Proficiency in oral and written communication in English
• Strong communication, presentation and writing skills
• Willingness to collaborate, but with ability to work independently
• Patient, detail-oriented and precise

The following are considered to be a merit:

• Specific interest in dementia and aging
• Fluency in computational programming, preferably using python or R
• Experience in statistical modeling and/or machine learning
• Experience with curation, preprocessing and/or analysis of neuroimaging, genomic, or other types of omics data
• Familiarity with git and GitHub and/or Datalad
• Familiarity with best practices in reproducibility and open science
• Individuals from diverse or underrepresented backgrounds are encouraged to apply

Eligibility
Students with basic eligibility for third-cycle studies are those who: have completed a second-cycle degree, have completed courses of at least 240 credits, of which at least 60 credits are from second-cycle courses, or have acquired largely equivalent knowledge in some other way, in Sweden or abroad.

Basis of assessment
The employment of doctoral students is regulated in the Swedish Code of Statues 1998: 80. Only those who are or have been admitted to PhD-studies may be appointed to doctoral studentships. When an appointment to a doctoral studentship is made, the ability of the student to benefit from PhD-studies shall primarily be taken into account. In addition to devoting themselves to their studies, those appointed to doctoral studentships may be required to work with educational tasks, research and administration, in accordance with specific regulations in the ordinance.

Further information

Employment is a full-time, fixed-term position of 4 years, in accordance with the Higher Education Ordinance, Chapter 5 Section 7. Start date should be between May 1st and September 5th, 2023, with a preference for an earlier start date

How to apply
Applications must include a personal motivation letter, a CV, contact information of two references, a diploma (including a grade transcript) and other documents you wish to be considered (e.g. letters of recommendation). Those applicants who will be called for interview, will likely be asked to perform a small test to demonstrate basic competence.