Role overviewAs a Bioinformatics Scientist with a cellular reprogramming background, you will lead computational analysis of multi-modal genomics data (scRNA-seq, ATAC-seq) to identify transcription factor combinations driving desired cell state conversion. This role focuses on gene regulatory network inference, differential analysis of single-cell transcriptomics, and computational prioritization of TF cocktails for cellular reprogramming, requiring deep expertise in multi-platform scRNA-seq analysis and transcriptional regulation biology. You will collaborate closely with wet lab teams to translate computational predictions into experimental designs, while also exploring hybrid approaches that integrate foundation model insights into our reprogramming pipeline.
What you'll do- Lead end-to-end TF discovery for cellular reprogramming - from multi-platform single-cell genomics analysis (scRNA-seq, ATAC-seq) through GRN inference, differential analysis, and trajectory mapping - to nominate the regulators that flip cell fate.
>- Crack the combinatorial code of reprogramming by ranking TF cocktails as actionable combinations and decoding pooled perturbation and CRISPRa screens at single-cell resolution.
>- Read regulatory grammar straight off the chromatin - accessibility, motifs, synergy, repression - and build the data backbone that harmonizes modalities and platforms into something we can actually model on.
>- Sit shoulder-to-shoulder with wet lab teammates, closing the loop between predictions and screens: ingest fresh NGS readouts, retrain, re-prioritize, and pick the next experiment that teaches the model the most.
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Core requirements- PhD in Bioinformatics, Computational Biology, or related quantitative field (or MS with 5+ years relevant industry experience);
>- Demonstrated track record applying computational TF ranking and GRN inference to cellular reprogramming problems, transdifferentiation, directed differentiation, or iPSC systems;
>- Multi-platform single-cell RNA-seq expertise: hands-on analysis from at least two different platforms, including platform-specific troubleshooting and quality control;
>- Multi-modal genomics proficiency: ChIP-seq, CUT&RUN, or ATAC-seq analysis including peak calling, differential accessibility, and TF motif enrichment;
>- Hands-on experience with established GRN inference methods to nominate or rank regulators of cell state, beyond literature-curated lists;
>- Experience analyzing pooled perturbation screens (CRISPRa, CRISPR knockout, or barcoded TF overexpression) with single-cell or bulk readouts;
>- Working knowledge of trajectory inference and pseudotime methods for mapping cell state transitions;
>- Strong programming skills in Python and R, with proficiency in Scanpy/Seurat and statistical analysis for high-dimensional data;
>- Comfortable working in a modern computational environment: cloud platforms, workflow managers, containerization, and collaborative version control;
>- Strong publication record and demonstrated cross-functional collaboration with experimental biologists.
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You'll stand out with- Direct experience nominating or validating TF cocktails that successfully induced a cell state conversion (published or in preparation).
>- Experience with dynamical systems modeling for cell state transitions, or inverse problem approaches for TF combination ranking.
>- Background in advanced trajectory inference (optimal transport, GRN dynamics over pseudotime), Bayesian genomics, multi-omics integration, or cross-species comparative regulatory genomics.
>- Familiarity with transformer architectures in genomics and interest in hybrid classical/ML approaches to gene regulation.
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What we offer- Competitive salary + equity participation is considered
>- State-of-the-art facility in Portland metro area
>- Comprehensive Medical, Dental, Vision, and 401(k) with company match
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- 20 days PTO + 11 paid holidays
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DisclaimerThe above job description is intended to describe the general nature and level of work being performed by individuals assigned to this position. It is not intended to be an exhaustive list of all duties, responsibilities, and skills required. Responsibilities and duties may change or be adjusted to meet the needs of the company, and additional duties may be assigned as necessary. The job description is subject to change at any time at the discretion of e184.
We may use artificial intelligence (AI) tools to support parts of the hiring process, such as reviewing applications, analyzing resumes, or assessing responses. These tools assist our recruitment team but do not replace human judgment. Final hiring decisions are ultimately made by humans. If you would like more information about how your data is processed, please contact us.
