resume.json

{
  "$schema": "https://raw.githubusercontent.com/jsonresume/resume-schema/v1.0.0/schema.json",
  "basics": {
    "name": "Daniel Polanco",
    "label": "Bioinformatician | Software Developer | Cloud Engineer",
    "email": "[email protected]",
    "phone": "+1 (719) 422 3765",
    "url": "https://daniel.polanco.me",
    "summary": "Bioinformatician with over 10 years experience in automating pipelines and deploying production-ready applications. Skilled in cloud engineering, workflow automation, and software development. Dedicated to mentoring and leading software development teams, with a passion for public health genomics and clinical research collaboration.",
    "location": {
      "city": "Denver",
      "countryCode": "US",
      "region": "Colorado"
    },
    "profiles": [
      {
        "network": "GitHub",
        "username": "danpolanco",
        "url": "https://github.com/danpolanco"
      },
      {
        "network": "Linkedin",
        "username": "danpolanco",
        "url": "https://www.linkedin.com/in/danpolanco"
      }
    ],
    "meta": {
      "theme": "macchiato"
    }
  },
  "work": [
    {
      "name": "State of Colorado",
      "position": "Bioinformatician",
      "startDate": "2022-11-01",
      "summary": "Bioinformatician for the Colorado Department of Public Health and Environment (CDPHE) Genomics Surveillance Program (GSP). Focused on clinical pathogen sequencing, variant analysis, and automated epidemiological reporting for public health surveillance.",
      "highlights": [
        "Process and analyze over 7,000 COVID-19 patient samples using WDL workflows for pathogen detection and variant calling.",
        "Develop and implement RSV genomic surveillance workflow, analyzing 674 samples across three respiratory seasons for clinical insights.",
        "Support 23-person genomics surveillance team with 40TB+ cloud storage infrastructure growing at 0.5TB monthly.",
        "Design event-driven architecture with Pub/Sub for automatic load distribution and Cloud Functions auto-scaling to handle variable genomic data processing workloads.",
        "Implement Infracost cost estimation and storage lifecycle policies for cloud resource optimization and budget planning.",
        "Mentor team members on Terraform infrastructure development and provide code reviews for BigQuery/Dataform implementations.",
        "Perform quality control and variant interpretation using IGV, validating genomic data for clinical accuracy and GISAID repository submissions.",
        "Migrate weekly variant proportion reporting to cloud native solutions for public health decision-making and outbreak response.",
        "Submit pathogen genomes to clinical repositories including Biosample, SRA, GenBank, and GISAID following quality assurance protocols.",
        "Maintain compliance with PII/PHI protection standards and internal SOPs for clinical data handling and privacy protocols.",
        "Collaborate directly with clinicians on research projects, including RSV genomic diversity analysis presented at APHL conference.",
        "Collaborate with CDC and APHL on multiple projects including AIMS Influenza Sequencing Center and IT Security and Privacy white papers.",
        "Design, implement, and automate BigQuery data extract, load and transformation for disease surveillance using Dataform for reproducibility and stability.",
        "Configure and build out Google Cloud infrastructure with enhanced security protocols for clinical and wastewater data processing."
      ]
    },
    {
      "name": "Jonah Ventures",
      "position": "Software Engineer",
      "startDate": "2022-08-01",
      "endDate": "2022-11-01",
      "summary": "Worked as a software engineer for Jonah Ventures, a startup focused on developing innovative solutions for environmental genomics.",
      "highlights": [
        "Prototyped a sample management system for use by laboratory technicians.",
        "Expanded skills in R, R Markdown, R Shiny, AWS, SQL and related technologies to support environmental genomics projects."
      ]
    },
    {
      "name": "Atelier Circle",
      "position": "Founder & Software Engineer",
      "startDate": "2018-04-01",
      "endDate": "2022-10-01",
      "summary": "Founded Atelier Circle, a software company focused on innovative solutions for clinical research.",
      "highlights": [
        "Collaborated with the Colorado Center for Personalized Medicine to prototype iMTracker (lifestyle tracking app) on iOS for a pilot study.",
        "Reviewed project specifications and implemented industry standard solutions to met end user expectations.",
        "Worked with field experts to design user-interfaces that are engaging, simple, and informative for non-technical users while maintaining consent for research purposes.",
        "Introduced agile methodologies and development best practices to codebase to streamline product development."
      ]
    },
    {
      "name": "Stantec",
      "position": "Innovation Engineer",
      "startDate": "2016-10-01",
      "endDate": "2017-08-01",
      "summary": "Worked as an Innovation Engineer at Stantec, a global engineering and design firm. Focused on developing innovative solutions for environmental and infrastructure projects.",
      "highlights": [
        "Created a holographic mobile app for HoloLens using Git, Visual Studio Team Services, and Agile methodology.",
        "Built and deployed the app on Azure (Microsoft's cloud service) for Stantec while incorporating Practice Technology Director's feedback."
      ]
    },
    {
      "name": "University of Colorado",
      "position": "Teaching Assistant",
      "startDate": "2011-08-01",
      "endDate": "2013-04-01",
      "summary": "Worked at the University of Colorado Denver as a teaching and laboratory assistant.",
      "highlights": [
        "Assisted in teaching undergraduate courses in general biology and genetics.",
        "Lead laboratory sessions, helping students with experiments and data analysis.",
        "Graded assignments and provided feedback to students to enhance their learning experience."
      ]
    },
    {
      "name": "University of Colorado",
      "position": "Research Assistant",
      "startDate": "2010-08-01",
      "endDate": "2016-04-01",
      "summary": "Worked as a Research Assistant at the University of Colorado Anschutz Medical Campus, focusing on bioinformatics, evolutionary genomics, and computational biology.",
      "highlights": [
        "Conducted DNA/RNA laboratory work and bioinformatics programming for genomic data analysis on model organisms and clinical patient samples.",
        "Contributed to computational biology research that resulted in PNAS publication on Burmese python genome analysis."
      ]
    }
  ],
  "education": [
    {
      "institution": "University of Colorado",
      "url": "https://www.cuanschutz.edu/",
      "area": "Biomedical Sciences and Biotechnology",
      "studyType": "Master",
      "startDate": "2015-01-01",
      "endDate": "2017-01-01",
      "score": "3.7"
    },
    {
      "institution": "University of Colorado",
      "url": "https://www.ucdenver.edu/",
      "area": "Biology",
      "studyType": "Bachelor",
      "startDate": "2009-01-01",
      "endDate": "2013-01-01",
      "score": "3.9"
    },
    {
      "institution": "Arapahoe Community College",
      "url": "https://www.arapahoe.edu/",
      "area": "Arts",
      "studyType": "Associate",
      "startDate": "2005-01-01",
      "endDate": "2009-01-01",
      "score": "3.8"
    }
  ],
  "awards": [
    {
      "title": "Summa Cum Laude",
      "date": "2023-08-01",
      "awarder": "University of Colorado",
      "summary": "Bachelor of Science"
    }
  ],
  "certificates": [
    {
      "name": "Google Cloud Engineering Course",
      "issuer": "Google Cloud",
      "summary": "Currently completing Google Cloud Engineering course with planned certification exam"
    }
  ],
  "publications": [
    {
      "name": "Evaluation of RSV Genomic Diversity and Variant Prevalence Across Three Respiratory Seasons in Pediatric Cases in Colorado",
      "publisher": "APHL",
      "releaseDate": "2024-01-01",
      "url": "https://www.aphl.org/conferences/annualmeeting/Documents/AC24_Final_Program.pdf",
      "summary": "Optimized WGS method and analyzed 674 distinct RSV samples using bioinformatics workflow. Evaluated prevalence of A and B subtypes and clades across three respiratory seasons, performing phylogenetic comparisons to determine circulating variants in Colorado over time. Demonstrated seasonal subtype alternation: B dominant in 2021, A in 2022, returning to B in 2023."
    },
    {
      "name": "The Burmese python genome reveals the molecular basis for extreme adaptation in snakes",
      "publisher": "PNAS",
      "releaseDate": "2013-12-02",
      "url": "https://www.pnas.org/doi/10.1073/pnas.1314475110",
      "summary": "By analyzing the genomes and gene expression of the Burmese python and other snakes, we found that extensive genetic and transcriptional adaptations underlie snakes' extreme physiological traits, revealing system-wide changes in metabolism, organ function, and genome structure that provide insights relevant to vertebrate biology and medicine."
    }
  ],
  "skills": [
    {
      "name": "Bioinformatics",
      "level": "",
      "keywords": [
        "Clinical Genomics",
        "Data Visualization",
        "IGV",
        "Next-Generation Sequencing (NGS)",
        "Phylogenetic Analysis",
        "Pipeline Development",
        "Python",
        "Quality Control",
        "R",
        "Tableau",
        "Variant Analysis",
        "WDL Workflows"
      ]
    },
    {
      "name": "Cloud",
      "level": "",
      "keywords": [
        "Auto Scaling",
        "Cost Management",
        "Data Warehousing",
        "Disaster Recovery",
        "Google Cloud Platform (GCP)",
        "Load Balancing",
        "Microservices",
        "Monitoring",
        "Security",
        "Serverless",
        "Storage",
        "Terraform"
      ]
    },
    {
      "name": "General",
      "level": "",
      "keywords": [
        "AI",
        "Automation",
        "Bash",
        "Docker",
        "Git",
        "PowerShell",
        "Python",
        "R",
        "Shell Scripting"
      ]
    },
    {
      "name": "GitOps",
      "level": "",
      "keywords": [
        "GitHub Actions",
        "Continuous Deployment (CD)",
        "Continuous Integration (CI)",
        "Infrastructure as Code (IaC)"
      ]
    },
    {
      "name": "Statistical Analysis",
      "level": "",
      "keywords": [
        "Complex Data Manipulation",
        "Pandas",
        "Plotly",
        "Report Generation",
        "Statistical Graphics",
        "Data Analysis"
      ]
    }
  ],
  "languages": [
    {
      "language": "English",
      "fluency": "Native"
    },
    {
      "language": "Spanish",
      "fluency": "Elementary"
    }
  ],
  "interests": [
    {
      "name": "Culture",
      "keywords": [
        "Anime and Manga",
        "Electronic Music",
        "Indie Pop and Rock",
        "Food and Cuisine",
        "Science Fiction and Fantasy",
        "Cooperative Multiplayer Games"
      ]
    },
    {
      "name": "Weightlifting",
      "keywords": [
        "Balance and Coordination",
        "Functional Fitness",
        "Injury Prevention",
        "Mental Toughness",
        "Powerlifting",
        "Progressive Overload",
        "Strength and Conditioning",
        "Supplementation"
      ]
    }
  ],
  "projects": [
    {
      "name": "CDPHE GSP | GCP Infrastructure",
      "startDate": "2025-02-10",
      "description": "Automates and manages Google Cloud infrastructure with Terraform modules including integrated cost estimation. (Private repository)",
      "highlights": [
        "Designed and implemented modular Terraform infrastructure for a GCP-based sequencing data pipeline, supporting creation, ingestion, preparation, and processing stages.",
        "Developed secure, team-based access controls using IAM roles and Google Secret Manager for sensitive credentials and configuration.",
        "Automated provisioning and management of Google Cloud resources, including Cloud Storage buckets, Pub/Sub topics and subscriptions, Cloud Run jobs/services, and Cloud Scheduler jobs.",
        "Integrated external APIs (e.g., BaseSpace, workflow platforms) into cloud-native data workflows for scientific data processing.",
        "Enabled cost estimation and optimization using Infracost to provide detailed monthly breakdowns for cloud resources.",
        "Established a GitHub-based CI/CD workflow with automated versioning, PR checks, and release management using GitHub Actions.",
        "Documented infrastructure modules and workflows with clear diagrams (Mermaid) and compatibility matrices to support maintainability and cross-team collaboration.",
        "Implemented environment-specific (dev/prod) infrastructure with parameterized modules for flexible deployments."
      ]
    },
    {
      "name": "CDPHE GSP | Inbox Handler",
      "startDate": "2024-10-29",
      "description": "Automate processing raw instrument data into a cloud storage inbox.",
      "highlights": [
        "Developed and maintained cloud-native Python functions for automated sequencing data processing using Google Cloud Functions and Pub/Sub.",
        "Designed robust data ingestion pipelines for Illumina and Oxford Nanopore sequencing platforms, integrating with Google Cloud Storage and Firestore.",
        "Implemented dynamic workbook discovery and download logic from Google Cloud Storage, supporting both project and run-level organization.",
        "Built modular utilities for handling large-scale genomic data, including sample sheet creation, fastq file validation, renaming, and cloud uploads.",
        "Integrated Google Cloud Tasks for scalable, asynchronous sample processing workflows.",
        "Utilized environment-driven configuration management for seamless deployment across development and production environments.",
        "Leveraged pandas for efficient parsing and manipulation of sequencing metadata and sample workbooks.",
        "Implemented error handling and logging best practices to ensure traceability and reliability in cloud workflows.",
        "Collaborated on a multi-platform codebase supporting both Illumina BaseSpace and ONT instrument data extraction and transformation.",
        "Contributed to CI/CD and local testing workflows, including environment setup scripts and automated deployment pipelines."
      ],
      "url": "https://github.com/CDPHE-bioinformatics/inbox-handler"
    },
    {
      "name": "CDPHE GSP | Sequencer Utility",
      "startDate": "2024-08-27",
      "description": "Automate sequencing instrument import into the cloud environment.",
      "highlights": [
        "Designed and implemented modular Terraform infrastructure for a GCP-based sequencing data pipeline, supporting creation, ingestion, preparation, and processing stages.",
        "Developed secure, team-based access controls using IAM roles and Google Secret Manager for sensitive credentials and configuration.",
        "Automated provisioning and management of Google Cloud resources, including Cloud Storage buckets, Pub/Sub topics and subscriptions, Cloud Run jobs/services, and Cloud Scheduler jobs.",
        "Integrated external APIs (e.g., BaseSpace, workflow platforms) into cloud-native data workflows for scientific data processing.",
        "Enabled cost estimation and optimization using Infracost to provide detailed monthly breakdowns for cloud resources.",
        "Established a GitHub-based CI/CD workflow with automated versioning, PR checks, and release management using GitHub Actions.",
        "Documented infrastructure modules and workflows with clear diagrams (Mermaid) and compatibility matrices to support maintainability and cross-team collaboration.",
        "Implemented environment-specific (dev/prod) infrastructure with parameterized modules for flexible deployments."
      ],
      "url": "https://github.com/CDPHE-bioinformatics/sequencer-utility"
    },
    {
      "name": "CDPHE GSP | Workflow Operator",
      "startDate": "2024-04-30",
      "description": "Automate the analysis of sequencing data using cloud-native workflows.",
      "highlights": [
        "Developed and maintained a cloud-native bioinformatics workflow operator using Python and Google Cloud Functions.",
        "Designed and implemented robust REST API integrations with Google Cloud services, including Secret Manager, Storage, and Pub/Sub.",
        "Automated deployment pipelines using GitHub Actions, including version bumping, code analysis (mypy, ruff), and CI/CD workflows.",
        "Built modular, type-annotated Python code leveraging dataclasses, enums, and dependency injection for configuration management.",
        "Implemented secure handling of secrets and environment variables for multi-environment (dev/prod) deployments.",
        "Created reusable utility functions for dynamic dataset management, including creation, lookup, and upload to cloud platforms.",
        "Integrated with Google Cloud Storage for automated retrieval and processing of large-scale sequencing data files.",
        "Utilized pandas for efficient data manipulation and transformation within cloud functions.",
        "Enabled local and remote testing and deployment with custom Bash scripts and VS Code task automation.",
        "Documented development and deployment processes for team onboarding and operational transparency."
      ],
      "url": "https://github.com/CDPHE-bioinformatics/workflow-operator"
    }
  ]
}