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<!DOCTYPE html>
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<head>
  <meta charset="UTF-8">
  <title>Stéphanie Battini | Biomedical Data Scientist</title>
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<body>
  <div class="page">
    <!-- Sidebar -->
    <aside class="sidebar">
      <div class="profile">
        <img src="images/stephanie-profile.jpeg" alt="Stéphanie Battini" class="profile-image">
        <h1 class="name">Stéphanie Battini</h1>
        <p class="tagline">Senior Biomedical Data Scientist · Computational Neuroscience · Metabolomics</p>
      </div>

      <div class="contact-block">
        <p>Neuchâtel / Lausanne, Switzerland</p>
        <p><a href="mailto:stephaniebattini@gmail.com">stephaniebattini@gmail.com</a></p>
      </div>

      <div class="links-block">
        <a href="https://github.com/StephLisa" target="_blank">GitHub</a>
        <a href="https://scholar.google.fr/citations?user=UKfnGmIAAAAJ" target="_blank">Google Scholar</a>
        <a href="https://orcid.org/0000-0003-0839-4553" target="_blank">ORCID</a>
        <a href="https://www.linkedin.com/in/stephanie-battini-computational-neuroscientist-metabolomics/" target="_blank">LinkedIn</a>
      </div>

      <a href="CV_Stephanie_Battini.pdf" target="_blank" class="cv-button">
        Download CV (PDF)
      </a>


      <nav class="nav">
        <a href="#about">About</a>
        <a href="#education">Education and Career</a>
        <a href="#research">Research</a>
        <a href="#projects">Projects</a>
        <a href="#skills">Skills</a>
        <a href="#publications">Publications</a>
        <a href="#contact">Contact</a>
      </nav>
    </aside>

    <!-- Main content -->
    <main class="content">
      <!-- About -->
      <section id="about" class="card">
        <h2>About</h2>
        <p>
          I am a multidisciplinary biomedical data scientist with a <strong>Ph.D. in Medical Sciences</strong> and over six years of postdoctoral experience at
          </strong>EPFL's Blue Brain Project</strong>, where I specialized in computational neuroscience and neuro-glia-vasculature modeling. My research background spans metabolomics,
          clinical research, and bioinformatics, with a proven track record in developing reproducible workflows, FAIR-compliant data pipelines, and integrative
          computational models for complex biomedical datasets.
        </p>
        <p>
          Currently, I serve as a <strong>Senior Biomedical Data Scientist</strong> (FAIR Data and Open Science) in the Data Science for Biomedical Research Unit (DSBU) at the University of Lausanne (UNIL),
          where I support large-scale data integration and research data management across life sciences and clinical projects. I am passionate about building tools that make scientific data more accessible and
          reusable—including developing open-source Python packages for biomedical metadata extraction and standardization.
        </p>
        <p>
          <strong>My expertise bridges clinical research, computational biology, and software development, with proficiency in Python, and version control systems.</strong>
          I am particularly interested in creating solutions that help researchers adhere to FAIR principles, enhance reproducibility, and accelerate discovery through better data management practices.
        </p>
      </section>

      <!-- Education and Career -->
      <section id="education" class="card">
        <h2>Education and Career</h2>
        <div class="education-image-container">
          <img src="images/education-career.png" alt="Education and Career Timeline" class="education-image">
        </div>
        <p style="margin-top: 1rem;">
          For the full list of skills and experience, see or download the
          <a href="CV_Stephanie_Battini.pdf" target="_blank">CV</a>.
        </p>
      </section>

      <!-- Research -->
      <section id="research" class="card">
        <h2>Research</h2>

        <div class="research-grid">
          <!-- Research 1 -->
          <article class="research-card">
            <h3>Cerebrovascular simulation: fluid dynamics & astrocyte coupling</h3>
            <div class="research-image-container">
              <img src="images/astrovascpy.png" alt="AstroVascPy Blood Flow Modeling" class="research-image astrovascpy-image">
            </div>
            <p>
              How do brain cells control blood supply? This study reveals how astrocytes—the brain's support
              cells—regulate blood flow through localized vessel diameter changes. Our computational model shows capillaries
              as key players in cerebral perfusion, with layer-specific responses across cortical depths.
            </p>
            <p class="research-citation">
              [Battini et al., Biomedicines, 2025]
            </p>
          </article>

          <!-- Research 2 -->
          <article class="research-card">
            <h3>Metabolomics in pancreatic cancer: predicting clinical outcomes</h3>
            <div class="research-image-container">
              <img src="images/pancreas.jpg" alt="Pancreatic Cancer Research" class="research-image">
            </div>
            <p>
              Identified metabolic biomarkers to predict survival in pancreatic cancer patients using
              HRMAS NMR spectroscopy. Analyzed 106 tumor samples and discovered that ethanolamine levels distinguish
              long-term from short-term survivors—a potential clinical biomarker obtainable in 20 minutes during surgery.
              This publication demonstrates how metabolomics profiling can guide treatment decisions.
            </p>
            <p class="research-citation">
              [Battini et al., BMC Medicine, 2017]
            </p>
          </article>

          <!-- Research 3 -->
          <article class="research-card">
            <h3>Metabolomics of hyperfunctioning parathyroid glands</h3>
            <div class="research-image-container">
              <img src="images/fluoropara.jpg" alt="Parathyroid Research" class="research-image">
            </div>
            <p>
              Distinguished single-gland from multiglandular disease in primary hyperparathyroidism using HRMAS NMR metabolomics.
              Analyzed 43 samples from 32 patients, identifying a 9-metabolite signature (including phosphorylcholine, choline, and glucose)
              that accurately differentiates disease subtypes. Applied network analysis with the ADEMA algorithm for metabolite prediction,
              offering potential for intraoperative surgical guidance.
            </p>
            <p class="research-citation">
              [Battini et al., Surgery, 2016]
            </p>
          </article>
        </div>
      </section>

      <!-- Projects -->
      <section id="projects" class="card">
        <h2>Projects</h2>

        <div class="project-grid">
          <!-- Project 1 -->
          <article class="project-card">
            <h3>AstroVascPy</h3>
            <p class="project-meta">Python · Computational Neuroscience · HPC</p>
            <p>
              A Python library for multiscale neuro–glia–vascular blood flow modelling, developed at EPFL’s Blue Brain Project.
              Focus on graph-based vasculature representations, flow simulations, and integration with existing neuroscience tools.
            </p>
            <a href="https://github.com/BlueBrain/AstroVascPy" target="_blank" class="project-link">View on GitHub</a>
          </article>

          <!-- Project 2 -->
          <article class="project-card">
            <h3>FAIR Metadata Pipeline</h3>
            <p class="project-meta">Python · Snakemake · FAIR · Metadata Standards</p>
            <p>
              Automated Snakemake-based pipeline for harmonizing clinical and research metadata across multiple data sources.
              Implements FAIR principles for improved data interoperability and reusability in biomedical research.
            </p>
            <span class="project-link disabled">In Development</span>
          </article>

          <!-- Project 3 -->
          <article class="project-card">
            <h3>Biomedical Data Validation Suite</h3>
            <p class="project-meta">Python · PHP · Data Quality · Archival Standards</p>
            <p>
              Comprehensive toolkit for validating, extracting, and packaging clinical research data for long-term archiving.
              Ensures compliance with institutional data management standards and facilitates reproducible research workflows.
            </p>
            <span class="project-link disabled">In Development</span>
          </article>

          <!-- Project 4 -->
          <article class="project-card">
            <h3>Vascular Network Analysis</h3>
            <p class="project-meta">Python · Graph Theory · Computational Neuroscience</p>
            <p>
              Advanced graph-based analysis tools for modeling cerebrovascular blood flow dynamics.
              Combines time-series analysis with machine learning approaches to study neuro-vascular coupling mechanisms.
            </p>
            <span class="project-link disabled">In Development</span>
          </article>
        </div>
      </section>

      <!-- Skills -->
      <section id="skills" class="card">
        <h2>Skills</h2>

        <h3>Programming & Data</h3>
        <p>
          Python (NumPy, pandas, SciPy, scikit-learn, PyTorch, Matplotlib, Seaborn), R, Bash, LaTeX.
          Reproducible workflows with Snakemake, containers (Docker, Singularity), Git/GitHub/GitLab.
        </p>

        <div class="skill-badges">
          <a class="badge badge-python" href="https://github.com/StephLisa?tab=repositories&q=python" target="_blank" title="More repositories coming soon!">
            Python projects
          </a>

          <a class="badge badge-matlab" href="https://github.com/StephLisa?tab=repositories&q=matlab" target="_blank" title="Code will be published soon!">
            MATLAB & numerical tools
          </a>

          <a class="badge badge-bash" href="https://github.com/StephLisa?tab=repositories&q=bash" target="_blank" title="Code will be published soon!">
            Bash & HPC scripts
          </a>

          <a class="badge badge-r" href="https://github.com/StephLisa?tab=repositories&q=R" target="_blank" title="Code will be published soon!">
            R projects
          </a>
        </div>


        <h3>Data Management & FAIR</h3>
        <p>
          FAIR data principles, metadata standards, data stewardship, REDCap, clinical and research data registries,
          Agile project management (Scrum, Kanban), JIRA, Confluence, Trello, Slack.
        </p>
      </section>

      <!-- Publications -->
      <section id="publications" class="card">
        <h2>Selected Publications</h2>
        <ul class="pub-list">
          <li>
            <strong>Modeling of Blood Flow Dynamics in Rat Somatosensory Cortex</strong><br>
            Battini S, Cantarutti N, Kotsalos C, et al. Biomedicines, 2025.<br>
            <a href="https://www.mdpi.com/2227-9059/13/1/72" target="_blank">Read article</a>
          </li>
          <li>
            <strong>Metabolomics approaches in pancreatic adenocarcinoma: tumor metabolism profiling predicts clinical outcome of patients</strong><br>
            Battini S, Faitot F, Imperiale A, et al. BMC Medicine, 2017.<br>
            <a href="https://link.springer.com/article/10.1186/s12916-017-0810-z" target="_blank">Read article</a>
          </li>
          <li>
            <strong>High-resolution magic angle spinning 1H nuclear magnetic resonance spectroscopy metabolomics of hyperfunctioning parathyroid glands</strong><br>
            Battini S, Imperiale A, Taieb D, et al. Surgery, 2016.<br>
            <a href="https://www.sciencedirect.com/science/article/pii/S0039606016001641" target="_blank">Read article</a>
          </li>
        </ul>
        <p>
          For the full list of publications, see
          <a href="https://scholar.google.fr/citations?user=UKfnGmIAAAAJ" target="_blank">Google Scholar</a>.
        </p>
      </section>

      <!-- Contact -->
      <section id="contact" class="card">
        <h2>Contact</h2>
        <div class="contact-content">
          <div class="contact-images">
            <img src="images/contact-picture.jpeg" alt="Contact Stéphanie Battini" class="contact-image">
            <img src="images/contact.jpg" alt="Stéphanie Battini" class="contact-image">
          </div>
          <div class="contact-info">
            <p>
              For collaborations or opportunities in biomedical data science, FAIR data stewardship, or digital health
              research, feel free to reach out.
            </p>
            <p class="contact-links">
              <i class="fas fa-envelope"></i> <a href="mailto:stephaniebattini@gmail.com">stephaniebattini@gmail.com</a><br>
              <i class="fas fa-graduation-cap"></i> <a href="https://scholar.google.fr/citations?user=UKfnGmIAAAAJ" target="_blank">
                Google Scholar
              </a><br>
              <i class="fab fa-linkedin"></i> <a href="https://www.linkedin.com/in/stephanie-battini-computational-neuroscientist-metabolomics/" target="_blank">
                LinkedIn profile
              </a>
            </p>

            <div class="office-locations">
              <h3>Professional Locations</h3>
              <div class="location">
                <i class="fas fa-map-marker-alt"></i>
                <div class="location-details">
                  <strong>Epalinges – bâtiment SE-C</strong><br>
                  Rte de la Corniche 7, 1066 Lausanne<br>
                  Office: bureau SEC/01/084
                </div>
              </div>
              <div class="location">
                <i class="fas fa-map-marker-alt"></i>
                <div class="location-details">
                  <strong>Dorigny – bâtiment Génopode</strong><br>
                  1015 Lausanne<br>
                  Office: 2024.2
                </div>
              </div>
            </div>
          </div>
        </div>
      </section>
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