CRG - BGI Joint International PhD Programme

The Al Jord's lab at CRG Mechanics of Organelle Remodeling conducts interdisciplinary research aimed at understanding how cytoskeletal forces impact nuclear dynamics at various scales, both in health and disease. The group focuses on the mechano-regulation of nuclear biomolecular condensates and RNA-processing.

The Lian's group at the “Cell Omics Research and Development Centre” plans to develop pioneering new technologies for single-cell-full-length transcript sequencing and mapping transcript distribution at subcellular resolution. These advanced technologies will be applied to elucidate how cytoskeletal forces affect RNA processing and localization dynamics within cells.

PhD Project

How do cytoplasmic forces relate to RNA processing and distribution in the nucleus? This essential mechanobiology question, with significant implications for health and therapeutics, remains largely unexplored and will be the focus of this interdisciplinary project. As a PhD candidate, your main objectives will be to i) investigate how cytoskeletal forces influence the kinetics of nuclear RNA splicing in a spatiotemporal manner using advanced live imaging techniques, and ii) develop and apply cutting-edge single-cell spatial transcriptomics approaches to uncover how the cytoskeleton regulates splicing dynamics.

What are we looking for?

The ideal candidate should be a motivated and curious scientist ready to engage in cross-disciplinary and international research in biology and omics technology development. A background in Cell Biology, Molecular Biology, and/or Biophysics is essential. The candidate should share an enthusiasm for investigating the mechanisms of mechanobiology, biomolecular condensates, and RNA. Creativity, independence, and strong communication skills in English are important, as well collaborative spirit to thrive in a diverse research environment.

The T2T Genomics Team at the BGI led by Chentao Yang, specializes in constructing high-quality reference genomes for vertebrates, with a particular focus on telomere-to-telomere (T2T) genomes, employs multi-omics sequencing tools and utilizes comparative genomics and population genetics methods to analyze various biological issues, including genetic variation, genome evolution, and complex regions.

The Repetitive DNA Biology (REPBIO) lab at the CRG, led by Bernardo Rodríguez-Martin, utilizes the latest advances to decode nucleotide sequences, and develops algorithms for examining the role of repetitive DNA in genome function and evolution. Utilizing advanced long-read sequencing and creating computational tools, the lab strives to understand these repeats and their contributions to structural variations, including cancer-related processes and polymorphic structural variants.

PhD Project

This PhD project aims to gain insight into the impact of structural variation in genome chromatin conformation and gene function through long-read multiomics and computational methods development.

What are we looking for?

The ideal candidate for this PhD project should have a strong background in genomics, molecular biology, or bioinformatics, with a particular interest in structural variation and its functional impact on the genome. Proficiency in long-read sequencing technologies and multi-omics data analysis is essential as well as advanced computational and programming skills (e.g., Python, R). The candidate should be highly motivated, possess strong analytical and problem-solving skills, and be able to efficiently communicate in English (oral and written).

The Ya lab at the BGI focuses on multi-omics research on maternal and child health by conducting two aspects of studies. One aspect involves multi-omics studies in prospective birth cohorts for establishing biomarkers for gestational diseases and birth defects. Another aspect involves the transcriptome atlas of early human embryogenesis and disease using spatial transcriptome, single cell/nuclei RNA transcriptome, single cell/nuclei ATAC, etc.

The Irimia lab at the CRG/UPF investigates how transcriptomic diversification through various mechanisms contributes to embryogenesis and evolution. Their research blends computational and experimental biology, and uses different models, from early mammalian development to neurogenesis and pancreatic cell maturation.

PhD Project

In each cell type, genes can be expressed using alternative promoters, often generating different protein isoforms. How the use of alternative promoters during human embryogenesis is regulated and its functional impact remain largely unknown. Here, we will identify alternative promoters that are differentially regulated during development with cell type resolution. We will produce single-cell 5' RNA-seq data at different developmental stages, and combine it with available matched single-nucleus ATAC-seq data to identify regulatory elements. Comparison with similar mouse datasets will provide insights into the conservation of transcriptional regulation during evolution.

What are we looking for?

Candidate needs to be familiar with high-throughput sequencing technologies, ideally focused on single-cell omics studies and proficient in at least one programming language such as Python, Perl or C/C++, R, with rich programming and plotting experience and good background on statistics. He/she should have strong sense of responsibility, be good at independent thinking and have good communication skills in English, as well as team organization skills.

Di Croce's lab at CRG focuses on understanding the mechanisms of gene regulation and epigenetics, particularly in the context of chromatin dynamics and transcriptional control in stem cells and cancer. The lab combines molecular biology, genomics, and cutting-edge epigenomic technologies to reveal key pathways involved in cell fate decisions and cancer progression.

Wu's lab at BGI Research focus on developing high-throughput single-cell omics technologies, as well as underlying the key states or features of malignant cells and microenvironmental components during tumor growth, relapse and metastasis, and drug resistance, using cutting-edge single-cell omics and spatial omics technologies.

PhD Project

Diffuse Midline Glioma (DMG) is an incurable paediatric brain cancer. In our lab, we have identified several potential targets that, when inhibited, halt cancer growth. The PhD student will use single-cell analysis and spatial transcriptomics to investigate: (1) the mechanisms of tumor initiation and progression in patient-derived brain organoids developed in our labs, and (2) the pathways involved in tumor regression following inhibition of our top-priority target.

What are we looking for?

A highly motivated student who works closely together with wet lab scientists. The tasks include analysis, interpretation and integration of comprehensive, state-of-the-art genome-wide datasets such as RNA-seq, ATAC-seq and ChIP-seq and development and implementation of analysis pipelines. Applicants are expected to hold an academic degree (BSc, MSc, PhD in Bioinformatics, Biostatistics, or Life Sciences) and be proficient in NGS data analysis (e.g. transcriptome profiling data sets), including scripting, programming, statistical analyses and applying common standard analysis tools and algorithms (R/Bioconductor, python, etc). Experience in epigenetic mechanisms of gene regulation and analysis of circadian rhythms is welcome.

Mara Dierssen's lab at the CRG focuses on understanding the neural and molecular mechanisms underlying cognitive function and dysfunction, particularly in relation to intellectual disabilities, Down syndrome, and neurodegenerative diseases like Alzheimer’s. The lab employs interdisciplinary approaches, including genetics, neurobiology, and behavioral analysis, to explore how genetic and transcriptomic changes impact brain circuits and cognitive processes.

Miguel Esteban's lab at BGI focuses on regenerative medicine, stem cell biology, and reprogramming technologies to understand cellular mechanisms underlying tissue regeneration and disease. The lab investigates how stem cells and induced pluripotent stem cells (iPSCs) can be used to model and potentially treat age-related diseases and neurodegenerative disorders.

PhD Project

This project investigates circuit-specific and molecular mechanisms driving cognitive impairment and neurodegeneration in Down syndrome (DS), Alzheimer’s disease (AD), and age-related decline. Key outcomes include insights into pathology spread in DS and AD, and transcriptomic changes associated with accelerated aging and disease in both affected and healthy populations.

What are we looking for?

The candidate needs to have a strong interdisciplinary background. This includes Neuroscience and Neurobiology with in-depth knowledge of brain anatomy, neurodegeneration, and disease mechanisms (especially Alzheimer’s and Down syndrome) to interpret circuit-specific and molecular findings. Molecular Biology and Genomics experience is needed, focusing on molecular mechanisms, gene expression, and transcriptomics to identify pathology drivers and changes related to disease and aging. Proficiency in Bioinformatics and Computational Biology is also essential, involving the use of bioinformatics tools for analyzing large transcriptomic datasets (e.g., RNA sequencing) and experience with statistical software (e.g., R, Python) for data interpretation.

Yue Zheng Lab at the BGI is focusing on both protein engineering technologies studies and novel protein tools exploration in research fields of gene editing tools, molecular biological enzymes, and antibodies. The gene editing projects aim to improve the editing efficiency and editing precision of target gene editing tools.

Noelia Ferruz Lab at the CRG is focusing on the implementation and training of large AI models for protein design, in particular language models. We are interested in multimodality, reinforcement learning and explainability techniques with the specific goal of designing new-to-nature enzymes.

PhD Project

The student will primarily focus on the de novo design of deaminases, with the specific goal of improving the editing efficiency and narrowing of the editing windows for the application in base editing. The student will learn AI modeling and ultra-high-throughput screening.

What are we looking for?

Candidate should have strong coding experience, preferably in Python, and previous experience in training neural networks. Basic scientific training in biochemistry, molecular biology or protein engineering is necessary, as well as good communication skills in English.

The research group of the Zhouchung Shang at the BGI investigates stem cell biology and regenerative medicine in the context of aging and disease. The lab extensively uses single cell and spatial multi-omics approaches.

The group of Pia Cosma at the CRG investigate the mechanisms and factors that regulate somatic cell reprogramming and tissue regeneration in mammals. The lab extensively utilizes super-resolution microscopy to explore the functional organisation of genome in cells and tissues.

PhD Project

Retinal regeneration is highly efficient in zebrafish and chicken but remains limited in mammals. The student will employ state-of-the-art methods, such as spatial transcriptomics and super-resolution microscopy, to uncover the specific cellular mechanisms controlling regeneration in lower vertebrates. The ultimate aim is to enhance endogenous regeneration in mammals. Data integration using computational biology methods will be conducted across multiple species.

What are we looking for?

The ideal PhD applicant should have a strong background in molecular and cellular biology, with a keen interest in regenerative medicine and developmental biology. Proficiency in advanced microscopy techniques and experience in bioinformatics or computational biology for data analysis are highly desirable. Prior experience working with model organisms such as zebrafish, chicken, or mouse would be beneficial.