Open positions at EMBL

Postdoctoral Fellow – Bioinformatics
(Application deadline 1 April 2022)

The Steinmetz group at EMBL Heidelberg is looking for an ambitious computational fellow (postdoc or research scientist, depending on the level of experience) interested in developing novel computational tools to explore exciting large-scale sequencing datasets of different cellular modalities and biological applications. We offer unique opportunities to develop your own research directions using a multitude of data types that are generated in our lab on a daily basis. Our interest focusses but is not limited to the following areas:

• integrating data from different of single-cell modalities (genomes, transcriptomes, phenotypes) to understand the genetic basis of complex diseases

• explore long-read sequencing of genomes and transcriptomes of synthetic organisms and develop computational tools to understand the structure and evolution of genomes

• developing novel tools to analyze long-read and short-read sequencing data with isoform specificity of complex in vitro and in vivo disease model systems

• analyzing data from large-scale Perturb-seq/TAP-seq datasets by developing novel computational tools for causal inference and by leveraging the power of AI/ML

Our lab works across model organisms and systems, including yeast, human cells, complex 3D cell culture models, and animal models. We also work with synthetic organisms, such as the world’s first fully-synthetic eukaryote, Saccharomyces cerevisiae 2.0, which features an on-demand genome-wide recombination system engineered into its genome, to discover principles of genome design within an evolutionary context. Our lab has both wet lab and computational scientists, and works in long-standing collaborations with leading computational labs!

Apply now via EMBL’s e-recruitment portal

Open positions at Stanford

The Steinmetz Lab at Stanford is searching for 3 postdoctoral fellows to work on the following projects:

• Understanding Transcriptional Heterogeneity in the Human Heart
• Determining Immunological Basis of Myalgic Encephalomyelitis / Chronic Fatigue Syndrome
• Developing Precision CRISPR Editing Technologies in Human Cells

Transcriptional Heterogeneity in the Human Heart
We are actively looking for both wet and dry-lab postdocs to join our DCM team working on understanding transcriptional heterogeneity in human heart with state-of-art sequencing technologies. Much progress has been made in understanding the genetics of cardiovascular diseases like Dilated Cardiomyopathy, but developing targeted therapies will require a better understanding of how genetics affects heart function. Due to technical limitations, it remains challenging to unravel the whole repertoire of different isoforms expressed in a population of cells. Our project therefore aims to map all full-length transcript isoforms in single heart cells.   To overcome this we are developing  methods for the detection of full-length transcript isoforms at single cell resolution (Zhu et al. Nature Communications, 2021.)

In addition, we aim to add a read-out for CRISPR-mediated perturbations in order to obtain a systems analysis of the function of splice factors in single cells of the heart. We are looking for talented experimental biologists to lead the development of novel single-cell transcriptomics methods based on long-read sequencing, as well as experienced computational candidates to build on our existing pipelines for the analysis of our long-read data.

Candidates should have a Ph.D. in a relevant field with strong expertise in RNA biology and sequencing technologies. Experience in cardiac biology and in cultivating or isolating heart cells will be a bonus but is not a requirement.

Precision CRISPR Editing Technologies
We are looking for a postdoctoral fellow to lead our work on developing precision genome editing methods and other novel CRISPR tools in yeast and human model systems in our lab at the Stanford Genome Technology Center (SGTC). Recently, we have developed a system which improves the efficiency of homology directed repair (HDR) by an order of magnitude through actively recruiting donor DNA to CRISPR-mediated double strand breaks (Roy, Smith, Vonesch et al. Nat Biotech. 2018). We seek a candidate that will lead our efforts to make gene editing more precise, predictable, efficient, and scalable. The appointed candidate will use these tools for multiplexed, systematic genome editing to uncover the genetic basis of complex traits and map the causative variants underlying disease phenotypes by measuring the phenotypic consequences for tens to hundreds of thousands of genetic variants in parallel.

For this work, we seek a candidate interested in technology development and high throughput screening applications. You will start by working closely with an experienced team who established the donor recruitment and multiplexed editing technologies in our lab. You will be given independence to adapt these mechanisms to different cell types, including human cells, and apply them to assay genetic variants at a genome-wide scale. We offer state-of-the art systems biology tools and broad expertise in novel omics readouts for functional genomics screens. The research will be conducted at the SGTC which houses a comprehensive platform of automation systems for large scale screening experiments. Your work will be constantly supported by an experienced research technician and a bioinformatician.

Candidates should have a Ph.D. in a relevant field with experience in genome editing (CRISPR nucleases, base editors, prime editors, TALENs, zinc finger nucleases, etc), yeast and/or human tissue culture, transfection, cell line construction, and vector construction. Experience in next generation sequencing analysis, automation and/or a background in DNA repair would be beneficial.

Immunological Basis of ME/CFS
Many studies, including work from our lab (see Huang et al., PNAS, 2019), have shown that the immune system is affected in ME/CFS patients (e.g., low activity of NK cells, altered levels of cytokines) with microbial infections often preceding the illness. The project aims to understand ME/CFS etiology, and to identify novel strategies for disease prevention and treatment.

Within an interdisciplinary team of leading scientists in the field, including the laboratories of Ronald Davis and Mark Davis and clinical partners, you will develop state-of-the-art single-cell omics methods, which can be applied to characterize T cells isolated from ME/CFS patient blood samples. A major goal is to understand how T cell behavior may be different in ME/CFS and contribute to disease development. You will lead study design and perform experiments, including large-scale single-cell transcriptomics experiments in human T cells and other cells of the immune system, and be given the opportunity to establish new research directions in the field.

Candidates should have a Ph.D. in a relevant field with strong expertise in immunology and/or single-cell omics technologies. Knowledge and skills in analyzing next-generation sequencing data will be a bonus but is not required.

PhD and Master students

Students will have the opportunity to learn and help develop a variety of experimental and bioinformatic tools. For our research, we use diverse model systems, ranging from patient-derived cell lines to budding yeast. A theoretical background and / or interest in either functional genomics/genetics, transcription, disease models or bioinformatics is beneficial. Students are expected to be highly motivated to work on challenging research projects in an international team.

PhD applicants: Please apply through the EMBL International PhD Programme.

Master students: Please have a look at the pages for Visitors and Undergraduates and send your CV and a brief motivation letter to Lars Steinmetz directly.