Bringing Chromatin Conformation and Spatial profiling into clinical researchApply
The past two decades have provided unprecedented growth in data modalities and data availability within the biomedical research. As a result, methodologies for the multi-omic analysis of bulk (average profiles derived from hundreds to millions of cells), single-cell data or both are in continuous development. Our team has been involved in such developments working on multi-omic frameworks (STATegra framework + STATEgRa Bioconductor package), multi-omic DeepLearning based analysis (LIBRA - BioarXiv) and specific tools such as GeneSetCluster. As a next step, we aim to integrate into current integrative pipelines additional data-types such as Chromatin Conformation and Spatial profiling. We are looking for highly motivated and skilled visiting students to work on one or several of the following challenges sub-projects: - Integrating Chromatin Conformation information (such as HiC) in clinical oriented research. Myeloma as a case study. Proprietary data is available for such integration. - Integrating Spatial Transcriptomics and Cell-to-cell interaction analysis as part of a multi-omic integrative framework. We have existing proprietary data to work in the context of the Bone Marrow. For any selected student, the project to be conducted will be decided based on the student's interest, technical proficiency, and level of study. We expect for any participant (a) to bring motivation, enthusiasm, creativity, and hard work, (b) give lab seminars on your work, (c) collaborate with other lab members, and (d) produce a final written report. The project relies on multi-skilled collaborations involving biologists, clinicians, bioinformaticians and computational biologists. References of interest: - STATegra framework: https://www.frontiersin.org/articles/10.3389/fgene.2021.620453/abstract - STATegRa package: https://www.bioconductor.org/packages/release/bioc/html/STATegRa.html - LIBRA single-cell multi-omic framework: https://www.biorxiv.org/content/10.1101/2021.01.27.428400v1 - 3D data: https://www.nature.com/articles/s41467-020-20849-y
Program - BioScience
Division - Biological and Environmental Sciences and Engineering
Faculty Lab Link - https://www.kaust.edu.sa/en/study/faculty/david-gomez-cabrero
Field of Study - Biomedicine
Desired Project Deliverables
Enhancing critical thinking, presentations skills, and scientific writing. The research, in collaboration and with support of team members, may lead to scientific publications. Obtaining a hands-on perspective at the frontier of bioinformatics, multi-omic analysis, and its applications in an interdisciplinary research group and environment.