Franz Arnold Ake

Franz Arnold Ake

Postdoctoral research scientist, Department of Pathology, Stanford University

You are an expert academic web designer and GitHub Pages/Jekyll developer.

I want you to fully customize and modernize my AcademicPages GitHub repository into a professional academic website suitable for a Stanford postdoctoral researcher in computational biology and bioinformatics.

Repository: https://github.com/franzake/franzake.github.io

The website should have:

  • a modern, minimal, elegant academic style
  • dark/light mode compatibility if possible
  • strong scientific branding
  • clean typography
  • professional research-focused structure
  • optimized SEO and metadata
  • responsive design
  • GitHub Pages compatibility preserved

My full identity: Franz Arnold Ake

Current position: Postdoctoral Researcher Department of Pathology Stanford University

Research domains:

  • Bioinformatics
  • Computational Genomics
  • Single-cell transcriptomics
  • Alternative polyadenylation
  • Differential isoform usage
  • RNA-seq analysis
  • Gene-fusion detection
  • Cancer genomics
  • Multi-omics integration
  • Reproducible workflow development
  • Nextflow / nf-core ecosystem

Scientific profile: I am a bioinformatician specialized in single-cell transcriptomics and transcript isoform analysis. My work focuses on alternative polyadenylation regulation, differential isoform usage, cancer transcriptomics, and scalable computational workflows for omics data analysis.

I develop reproducible Nextflow and nf-core pipelines for RNA-seq and single-cell analysis. I am particularly interested in computational methods for transcript quantification, fusion transcript detection, and post-transcriptional regulation.

Career background:

  • PhD in Bioinformatics at the University of Barcelona / IDIBELL
  • Program for Predictive and Personalized Medicine of Cancer
  • Plass Group
  • Current postdoctoral researcher at Stanford University

Technical expertise:

  • Nextflow
  • nf-core
  • R
  • Python
  • Linux/HPC
  • scRNA-seq
  • Bulk RNA-seq
  • Long-read transcriptomics
  • Workflow engineering
  • Cloud/HPC reproducibility

Projects to highlight:

  1. SCALPEL A Nextflow/nf-core-oriented pipeline focused on single-cell isoform quantification and alternative polyadenylation analysis.

  2. RNA-seq fusion analysis workflows Including STAR-Fusion and nf-core/rnafusion related developments.

  3. Reproducible workflow engineering Scalable omics pipelines using Nextflow and nf-core standards.

Website goals:

  • strong academic visibility
  • recruitment attractiveness
  • showcase computational biology expertise
  • showcase software/pipeline engineering
  • future industry AI/bioinformatics transition compatibility
  • polished professional online presence

Please perform the following modifications:

  1. Update _config.yml completely:
    • site title
    • biography
    • sidebar
    • author metadata
    • SEO metadata
    • social links placeholders
    • Stanford affiliation
    • GitHub username: franzake

  2. Replace all placeholder content.

  3. Create a professional homepage:
    • concise scientific introduction
    • research interests section
    • highlighted projects
    • selected publications placeholder
    • current affiliation
    • scientific mission statement
  4. Update navigation bar to:
    • About
    • Research
    • Publications
    • Software
    • Projects
    • CV
    • Contact
  5. Remove:
    • Blog
    • Generic teaching placeholders
    • Default academicpages demo content
  6. Create a polished Software/Projects section describing:
    • SCALPEL
    • nf-core contributions
    • RNA fusion workflows
    • Single-cell transcriptomics methods

  7. Modernize styling while remaining GitHub Pages compatible.

  8. Improve sidebar:
    • Stanford affiliation
    • Location: Stanford, California
    • GitHub
    • Google Scholar placeholder
    • ORCID placeholder
    • LinkedIn placeholder

  9. Generate concise but high-quality academic text throughout the website.

  10. Ensure all pages build correctly with Jekyll.

  11. Keep repository structure clean and maintainable.

  12. Provide all modifications directly as code/file edits.

  13. Suggest additional future improvements:
    • publication automation
    • ORCID sync
    • Google Scholar integration
    • project cards
    • timeline/CV improvements
    • research metrics
    • interactive visualizations

Tone:

  • rigorous
  • academic
  • concise
  • modern
  • high-level scientific profile
  • internationally competitive computational biology researcher

Avoid:

  • generic template text
  • overly verbose language
  • childish design
  • unnecessary animations

Goal: The final website should look like the personal website of a strong Stanford computational biology / AI-for-genomics researcher with expertise in single-cell transcriptomics and scalable bioinformatics workflow engineering.

Additional verified profile information:

Bio: Dr. Franz Arnold Ake is a computational biologist specializing in single-cell transcriptomics, alternative polyadenylation, and isoform regulation. His research focuses on developing computational methods and bioinformatic pipelines to characterize post-transcriptional regulation and differential isoform usage at single-cell resolution.

During his PhD under the mentorship of Dr. Mireya Plass at the University of Barcelona and IDIBELL Research Institute in Barcelona, Spain, he developed approaches for isoform quantification and differential isoform usage analysis in single-cell datasets.

He is currently a Postdoctoral Scholar in the Department of Pathology at Stanford University, sponsored by Dr. Vivek Charu. His current research focuses on multi-omics data integration, spatial transcriptomics, and cancer genomics to study tumor biology, tissue heterogeneity, and disease-associated molecular programs from high-dimensional sequencing data.

Contact:

  • Email: franzake@stanford.edu
  • Department: Pathology
  • Position: Postdoctoral Scholar
  • Institution: Stanford University
  • Location: Stanford, California
  • Mail Code: 5324
  • ORCID: https://orcid.org/0000-0003-0192-0370
  • GitHub: https://github.com/franzake

Education:

  • PhD in Bioinformatics, University of Barcelona / IDIBELL, 2025
  • MSc in Bioinformatics, Université Paris Diderot / Paris 7, 2019

Honors and Awards:

  • FPI Predoctoral Fellowship Grant, Ministry of Science and Innovation, Government of Spain, 2021–2025
  • Selected Nextflow Ambassador, Seqera, 2025
  • Keystone Symposia scholarship, Single Cell Biology: Pushing New Frontiers in the Life Sciences, April 2022
  • Winner Team, Meet-U Protein Prediction Program Competition, Université Sorbonne Paris Cité, 2019

Professional Organizations:

  • Member, International Society for Computational Biology, 2023–present
  • Contributor, nf-core Community / Seqera, 2021–present
  • Nextflow Ambassador, Seqera, 2025–present

Research emphasis for the website:

  • Single-cell transcriptomics
  • Alternative polyadenylation
  • Isoform regulation
  • Differential isoform usage
  • Spatial transcriptomics
  • Multi-omics integration
  • Cancer genomics
  • Tumor heterogeneity
  • Post-transcriptional regulation
  • Reproducible bioinformatics workflows
  • Nextflow / nf-core pipeline development

Please incorporate this information into:

  • the homepage
  • sidebar biography
  • research page
  • CV page
  • contact page
  • software/projects page
  • metadata/SEO descriptions

Use “Franz Arnold Ake” as the full professional name and “Dr. Ake” in formal third-person bios.