Allen Institute

Associate

• Lead breakthrough research and deployment of state-of-the-art methods in cellular and circuit neuroscience
• Contribute to discovery science efforts to understand the cellular, molecular and circuit basis of neurodegenerative diseases
• Advise and mentor scientists and technicians performing proteomic and connectomic studies in human brain tissues
• Contribute to Alzheimer’s research as part of the Seattle Alzheimer’s Disease Brain Cell Atlas (SEA-AD)
• Work collaboratively across teams in related technological or disease-centric areas
• Develop and establish scalable methods for cleared and/or expanded techniques in human tissues
• Develop high-affinity reagents for specific labeling of relevant targets
• Seek and evaluate new cutting-edge techniques
• Work synergistically with bioinformaticians and data scientists
• Publish and present findings in peer-reviewed journals and scientific meetings
• Present periodic progress summaries to the research community, Institute executive leadership, and external advisors
• Pursue external funding through grant writing and submission to federal and private foundation funding agencies

Associate Investigator – Brain Disease Proteomics, Connectomics

Scientist

• Develop mechanistic models of many interacting neurons fit directly to connectivity and neural activity data
• Derive coarse-grained descriptions of models to identify connectivity features governing neural dynamics
• Characterize models consistent with datasets and determine how connectivity constrains them
• Develop theories explaining how perturbations narrow the model space
• Identify the most informative experiments to perform next
• Collaborate with experimentalists to turn theory into testable hypotheses about neural computation
• Present results to collaborators and the wider scientific community through talks, conferences, and publications
• Use large-scale connectivity atlases, brain-wide recordings, spike trains, and targeted activity perturbations to study neural computation and flexible behavior

Scientist I – Neural Circuits Theory

Data Scientist

• Design and implement ML/DL pipelines for microscopy image analysis
• Preprocess and clean large-scale microscopy datasets
• Develop, optimize, and fine-tune classical and deep learning models for segmentation, feature extraction, and classification
• Integrate and scale image analysis protocols into high-throughput computational pipelines
• Participate in code reviews and contribute to efficient, maintainable, well-documented codebases
• Maintain reproducible analysis records, version-controlled code, documented parameters, and traceable results
• Coordinate with experimental scientists on data collection and study design
• Track developments in machine learning and image analysis and evaluate promising methods
• Work with large-scale microscopy datasets on dedicated HPC computing infrastructure
• Collaborate with multidisciplinary computational and experimental research teams

Data Scientist II, Deep Learning, Image Analysis

Artificial Intelligence

• Lead the Proteome Editor team in building and running a rapid, repeatable design-test-learn pipeline focused on proteome editor screening
• Design and oversee library screening and degrader evaluation experiments to generate high-quality, model-ready datasets
• Partner with machine learning colleagues to define next targets, curate data, and implement active-learning strategies
• Optimize flywheel performance by improving turnaround time, throughput, cost, and per-cycle model lift
• Identify and remove experimental bottlenecks
• Coordinate with other flywheel leads and AI BioDesign stakeholders to align priorities, timelines, and dependencies
• Mentor and manage a high-performing team
• Foster a collaborative culture and clear communication
• Present scientific results and complex concepts internally in talks and progress reports
• Present results to the external community at conferences and in publications

Scientist III – Proteome Editor Design, AI BioDesign

• Help lead a research project to establish foundational knowledge of mammalian neuromodulatory cell types
• Develop conceptual and quantitative frameworks for understanding how neuronal properties across modalities relate to cell type identity and function
• Conduct in-depth analyses and modeling of neuronal morphology using single neuron reconstruction data
• Develop and apply methods to integrate transcriptomic, morphological, and connectivity data
• Collaborate closely with experimentalists and computational scientists
• Lead multimodal integration and analysis efforts
• Produce foundational knowledge and openly shared datasets on the structural organization of neuromodulation
• Communicate project progress and present findings to internal stakeholders and the broader scientific community
• Help draft reports and manuscripts
• Attend occasional national and international conferences

Associate Investigator – Brain Disease Proteomics, Connectomics

Scientist I – Neural Circuits Theory

Data Scientist II, Deep Learning, Image Analysis

Scientist III – Proteome Editor Design, AI BioDesign

Scientist I – Neuromodulation Anatomy, Multimodal Data Integration