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20 nextflow jobs at 13 companies in San Francisco, CA

1mo
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Bioinformatics Engineer
San Jose, California, United States
HybridFull Time
AccuScan Sciences
AccuScan Sciences: Develops liquid biopsy and whole-genome sequencing for cancer diagnostics.
3+ YOEBachelor's degree in bioinformatics/computational biology/computer science, 3+ years experience, Nextflow workflow development, Python/Bash scripting, Docker/Kubernetes, AWS experience, testing and documentation skills.
Nextflow, Python, Bash, Docker, Kubernetes, AWS EC2, AWS S3, AWS Batch, AWS Lambda, GitHub, Terraform, CloudFormation
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1w
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Bioinformatics Scientist
Redwood City or Chicago
$100k-$175k/yr OnsiteFull Time
Tempus AI
Tempus AINASDAQ: TEM: Builds a data platform for AI-powered precision medicine diagnostics.
3+ YOEPhD or MS+3yrs in bioinformatics/computational biology or related field; deep NGS expertise; Python/R; cloud (AWS/GCP); Docker; Nextflow/Snakemake; ML/statistical modeling; publication or product contributions.
NGS, Python, R, AWS, GCP, Docker, Nextflow, Snakemake
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2d
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Principal Bioinformatics Scientist I
Santa Clara, California, United States
$121k-$225k/yr OnsiteFull Time
Roche
RocheSIX Swiss Exchange: ROG: Develops and manufactures pharmaceutical medicines and diagnostic solutions.
4+ YOEBachelor's plus 9 years, master's plus 7 years, or Ph.D. plus 4 years of related experience; CAP/CLIA diagnostic validation experience; Python, R, C++, Linux/Bash, Nextflow, and containerization expertise.
Nextflow, Docker, Singularity, Git, Python, R, C++, Linux, Bash
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1mo
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Senior Scientist, Computational Biology
South San Francisco or Seattle or London
$136k-$170k/yr OnsiteFull Time
Xaira Therapeutics
Xaira Therapeutics: Develops AI models for protein and antibody drug discovery.
5+ YOEPhD in a quantitative biology field, 5+ years industry/applied research, deep single-cell RNA‑seq and Perturb‑seq expertise, experience integrating large-scale datasets, production workflow development (Nextflow), Docker, AWS, Python (numpy, pandas, scanpy, scikit-learn), Unix, and GitHub.
Nextflow, Docker, AWS, Python, numpy, pandas, scanpy, scikit-learn, Unix, GitHub
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1w
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Open Source Research Software Engineer: Computational Infrastructure (0652) Job #87957 - Berkeley Institute for Data Science (BIDS)
Berkeley, California, United States
$102k-$190k/yr OnsiteFull Time
University of California, Berkeley
University of California, Berkeley: Public research university offering undergraduate and graduate education.
Advanced Python and software engineering skills, HPC and workflow system experience, containerization and CI knowledge, open source community participation, strong communication, and bachelor's degree or equivalent.
Python, SLURM, Docker, Apptainer, Singularity, Kubernetes, Snakemake, CWL, Dask, Nextflow, git, GitHub Actions, JupyterHub, Scientific Python, R, Project Jupyter
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5d
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Associate Director of Bioinformatics (Women's Health and Organ Health)
San Carlos, California, United States
$178k-$222k/yr RemoteFull Time
Natera
NateraNASDAQ: NTRA: Provides clinical genetic testing and diagnostics services.
7+ YOE3+ MgmtRequires Ph.D. or equivalent M.S. experience, 7+ years in bioinformatics, 3+ years leading scientists, diagnostic sequencing assay development, NGS analysis, Python, and regulated clinical product experience.
Python, R, Java, AWS, GCP, Snakemake, WDL, Nextflow, Cromwell, Docker, Kubernetes, PacBio HiFi, Oxford Nanopore, Illumina
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6d
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Member of Technical Staff: Research Software Engineer (0652) Job #88102 - BIDS
Berkeley, California, United States
$105k-$196k/yr OnsiteFull Time
University of California, Davis
University of California, Davis: A public research university providing higher education and clinical services.
Advanced Python and agentic AI/LLM coding experience; software engineering, GitHub, testing, CI/CD, secure development, project leadership, interdisciplinary collaboration, and a related bachelor's degree or equivalent experience.
Python, Claude, Codex, Git, GitHub Actions, GitHub, SLURM, Docker, Apptainer, Singularity, Kubernetes, Snakemake, CWL, Dask, Nextflow
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1mo
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Computational Scientist, Lung Transplant Immunology
San Francisco, California, United States
$64k-$195k/yr OnsiteFull Time
University of California
University of California: A public research university system providing education and healthcare.
5+ YOEAdvanced computational/statistical skills for end-to-end analysis of multimodal genomic datasets; strong R and Python proficiency; experience with reproducible workflows, HPC/cloud environments, and publication record in high-dimensional modalities.
R, Bioconductor, Seurat, Python, scanpy, anndata, scikit-learn, pandas, Linux, SLURM, Git, GitHub, conda, mamba, renv, Nextflow, Snakemake, Microsoft Visual Studio, AWS, GCP, UCSF Wynton, AWS HealthOmics
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3w
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Bioinformatics Scientist/Biostatistician Contractor
Menlo Park, California, United States
$75-$140/hr HybridContract, Full Time
MyOme
MyOme: Provides clinical whole genome analysis for personalized health insights.
3+ YOEMaster's (PhD preferred) in quantitative field, 3+ years analyzing NGS data, coding in R or Python, experience with bcftools/samtools/bedtools/plink, cloud (AWS/GCP), Linux/shell, and genomic databases.
R, Python, bcftools, samtools, bedtools, plink, Nextflow, AWS, GCP, Linux, shell scripting, UCSC, NCBI, dbSNP, Clinvar, Ensembl
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5d
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Advisor - Agent Research
San Francisco or Indianapolis or San Diego or Boston or South San Francisco
$152k-$222k/yr OnsiteFull Time
Eli Lilly and Company
Eli Lilly and CompanyNYSE: LLY: Researches and manufactures medicines for human health.
1+ YOEPhD, or equivalent master's or bachelor's experience, in ML, bioinformatics, cheminformatics, computer science, or related field; 1–2 years scientific AI/ML experience and hands-on AI model training.
Python, PyTorch, TensorFlow, JAX, Hugging Face, PPO, GRPO, DPO, RLHF, RLAIF, TRL, RDKit, MLflow, OpenAI Agent SDK, Anthropic Agent SDK, LangChain, Smol agents, AWS, Azure, Nextflow, Argo, Kubernetes, GitHub, NeurIPS, ICML, ICLR, ACL, EMNLP
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2mo
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Computational Biologist
Palo Alto, California, United States
OnsiteFull Time
Transcripta Bio
Transcripta Bio: AI-driven drug discovery platform leveraging high-resolution transcriptomic data.
3+ YOEPhD in Bioinformatics/Computational Biology with 3+ years of industry experience; extensive RNA-seq analysis and pipelines.
Python, R, Scanpy, Pandas, NumPy, DESeq2, ggplot2, Snakemake, Nextflow, Git
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1w
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Open Source Research Software Engineer: Computational Infrastructure (0652) Job #87957 - Berkeley Institute for Data Science (BIDS)
Berkeley, California, United States
$102k-$190k/yr OnsiteFull Time
University of California, Davis
University of California, Davis: Public research university and academic medical center.
Advanced Python and software engineering skills; HPC, containerization, workflow tools, git/GitHub Actions, open source community experience; ability to collaborate with interdisciplinary researchers.
Python, SLURM, Docker, Apptainer, Singularity, Kubernetes, Snakemake, CWL, Dask, Nextflow, git, GitHub Actions, JupyterHub, Jupyter, Scientific Python, R
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1w
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Principal Scientist, SOP & Workflow Automation Champion, AI for Drug Discovery (AIDD)
South San Francisco, California, United States
$201k-$374k/yr OnsiteFull Time
Roche
RocheSIX Swiss Exchange: ROG: Provides innovative pharmaceutical and diagnostic healthcare solutions.
8+ YOEPhD or equivalent advanced experience; 8+ years building computational systems; expertise in workflow orchestration, data pipelines, software architecture, Python, ML frameworks, drug discovery, and cross-functional technical leadership.
Python, PyTorch, TensorFlow, JAX, Nextflow, Snakemake, Airflow, CI/CD
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5d
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Senior Software Engineer I, Research Informatics
Brisbane, California, United States
$142k-$178k/yr HybridFull Time
Mammoth Biosciences: Developing CRISPR-based gene editing therapies and diagnostics.
7+ YOERequires a computer science or biological field degree, 7+ years of software engineering experience, Python, AWS, Docker, web development, SQL, AI coding tools, Git-based development, and onsite work two days weekly.
Benchling, Python, Amazon Web Services (AWS), Amazon S3, AWS Batch, Amazon RDS, Amazon EC2, AWS Lambda, Docker, ReactJS, HTML, CSS, SQL, Git, CI/CD, Prefect, Nextflow, CWL, Airflow, DBT, Terraform
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3d
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Senior Bioinformatician
Brisbane or San Francisco
$214k-$245k/yr OnsiteFull Time
Vivodyne
Vivodyne: Tests therapeutics on lab-grown human tissues using AI and robotics.
2+ YOEPh.D. in a quantitative biology field, 2–5 years post-Ph.D. experience, strong Python bioinformatics skills, scRNA-seq expertise, proteomics or secretomics experience, and Unix/Linux development proficiency.
Python, R, Scanpy, scverse, Seurat, Bioconductor, Monocle, Nextflow, Snakemake, git, containers, CI/CD, AWS, AnnData/H5AD, TileDB-SOMA
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1d
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Research Software Engineer, Brain Data Science Platform (24-Month Fixed-Term)
Stanford, California, United States
$110k-$205k/yr HybridFull Time, Contract
Stanford University
Stanford University: A private research university providing higher education and research.
3+ YOEBachelor's degree and 3 years relevant experience; production data pipelines, backend services, Python, cloud infrastructure, and healthcare data experience preferred.
Python, AWS, Amazon S3, AWS Lambda, AWS Batch, Amazon ECS, Amazon RDS, AWS IAM, Airflow, Prefect, Nextflow, Snakemake, Docker, Git, GitHub Actions, Epic, EDF, EDF+, DICOM, HL7, FHIR, OMOP, OHDSI, EEG, PSG, ECG, AWS-based platform
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