Bioinformatics Scientist

The Laboratory for Biological Engineering (Prof. Randall J. Platt) at ETH Zurich in Basel, Switzerland develops technologies at the interface of biological engineering, molecular (DNA, RNA, protein) perturbation technologies, and functional genomics, and applies them to understand and treat disease.

In support of these efforts, we are seeking a Bioinformatics Scientist to work closely with Professor Platt, guide the group’s computational research, contribute to ongoing projects, and pursue independent research directions aligned with the laboratory’s goals.

Our group builds high-throughput experimental platforms that require the development of novel computational methods. Two example areas in which the candidate would contribute are described below.

CRISPR perturbation screens, such as Perturb-seq, are transforming how we study gene function  recently developed an AAV-based method for direct in vivo single-cell CRISPR screening (Santinha, Nature, 2023) and are now expanding this approach to generate in vivo cell-type perturbation atlases, interrogate disease mechanisms, and identify therapeutic targets.

These efforts produce large-scale, rich in vivo perturbation datasets. The computational challenges include building scalable and reproducible pipelines for guide demultiplexing and assignment, cell-type annotation using bespoke references, and downstream effect estimation at both the perturbation and gene levels, as well as developing biologically grounded perturbation prediction models incorporating machine learning.

2. Transcriptome Recording and Cellular History Reconstruction

We are advancing our CRISPR-based transcriptional recording method (Schmidt, Nature, 2018; Tanna, Nature Protocols, 2020) that encodes transient cellular events into DNA and reads them out by sequencing.

Computational challenges include detecting biological signals when applying Record-seq to complex in vivo environments (Schmidt, Science, 2022) — especially in the context of drug–host microbiome interactions — and developing dedicated tools and analytic workflows for the novel data modalities generated by Record-seq and related molecular technologies.

• Working closely with Professor Platt and members of the laboratory — both experimental and computational — the successful candidate will play a central role in planning projects and experiments, developing computational methods, analyzing multi-omic datasets (including transcriptomics, metagenomics, metabolomics, and proteomics), reviewing results, and interpreting findings
• Beyond contributing to ongoing projects, the candidate will be expected to develop independent research directions aligned with the laboratory’s goals
• Responsibilities will also include publishing, grant writing, peer review, academic collaborations, industry partnerships, departmental service, research dissemination, and education
• The percentage of working time spent in any area will fluctuate based on priorities, but should on average be: research (70%), supervision of trainees (20%), service (10%)

It is anticipated that the candidate will be hired at the Established Researcher (Oberassistent) level (see Scientific Functions at ETH Zurich). Further career progression to a permanent position is possible, and a career development plan with clear milestones and timelines will be put in place.

The ideal candidate will hold a PhD or equivalent in bioinformatics, computational biology, computer science, applied statistics, or a related field, with substantial (>6 years) postdoctoral or equivalent experience developing and applying computational methods to large-scale biological datasets.

We are looking for someone who brings:

• Deep methodological expertise. A broad and current understanding of methods in bioinformatics and computational biology — including their strengths, limitations, and where the field is heading — along with the technical skills to independently design and execute projects that push these frontiers forward. Desirable technical skills are detailed in the application questionnaire
• Software development. A track record of developing and releasing well-documented…