https://valentynbez.github.io/research/Sun, 21 Jun 2026 00:00:00 +0000https://valentynbez.github.io/research/<div class="relative rounded-3xl overflow-hidden bg-gradient-to-br from-indigo-950 via-slate-900 to-emerald-950 p-8 md:p-12 mb-12 border border-slate-800 shadow-2xl backdrop-blur-md"> <!-- Glowing gradient background orbs --> <div class="absolute -top-24 -right-24 w-96 h-96 bg-indigo-500/20 rounded-full filter blur-3xl opacity-30"></div> <div class="absolute -bottom-24 -left-24 w-96 h-96 bg-emerald-500/10 rounded-full filter blur-3xl opacity-20"></div> <div class="relative z-10 max-w-3xl"> <span class="inline-flex items-center px-3 py-1 rounded-full text-xs font-semibold bg-emerald-500/10 text-emerald-400 border border-emerald-500/20 mb-4"> 🧬 Research Vision </span> <h1 class="text-3xl md:text-5xl font-extrabold tracking-tight mb-4 leading-tight text-white"> Decoding Microbial Life with <span class="bg-gradient-to-r from-indigo-400 via-sky-400 to-emerald-400 bg-clip-text text-transparent">AI & Metagenomics</span> </h1> <p class="text-base md:text-lg text-slate-300 leading-relaxed font-light mb-6"> My research lies at the intersection of <strong class="text-white font-semibold">computational biology, machine learning, and microbiology</strong>. I develop and apply deep learning models to explore massive metagenomic datasets, with the goals of describing planetary viral diversity and elucidating functions of novel genes. </p> <div class="flex flex-wrap gap-2.5"> <span class="inline-flex items-center px-3 py-1.5 rounded-full text-xs font-semibold bg-rose-500/20 text-white border border-rose-500/30"> 🦠 Virology </span> <span class="inline-flex items-center px-3 py-1.5 rounded-full text-xs font-semibold bg-indigo-500/20 text-white border border-indigo-500/30"> 🏷️ Functional Annotation </span> <span class="inline-flex items-center px-3 py-1.5 rounded-full text-xs font-semibold bg-emerald-500/20 text-white border border-emerald-500/30"> 🧬 Microbiome </span> </div> </div> </div> <h2 class="text-2xl md:text-3xl font-bold text-slate-800 dark:text-slate-100 mb-8 flex items-center gap-2"> <span class="text-indigo-500">■</span> Core Research Directions </h2> <div class="grid grid-cols-1 lg:grid-cols-3 gap-8 mb-12"> <!-- Panel 1: Biological Sequence Analysis --> <div class="flex flex-col justify-between p-6 rounded-2xl bg-slate-50 dark:bg-slate-900/60 border border-slate-200 dark:border-slate-800/80 hover:border-indigo-500/50 dark:hover:border-indigo-400/50 transition-all duration-300 hover:shadow-xl group"> <div> <div class="w-10 h-10 rounded-xl bg-indigo-500/10 text-indigo-500 dark:text-indigo-400 flex items-center justify-center mb-4 group-hover:scale-110 transition-transform duration-300"> <svg class="w-5 h-5" fill="none" stroke="currentColor" viewBox="0 0 24 24"><path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M9 5H7a2 2 0 00-2 2v12a2 2 0 002 2h10a2 2 0 002-2V7a2 2 0 00-2-2h-2M9 5a2 2 0 002 2h2a2 2 0 002-2M9 5a2 2 0 012-2h2a2 2 0 012 2m-3 7h3m-3 4h3m-6-4h.01M9 16h.01"/></svg> </div> <h3 class="text-lg font-bold text-slate-800 dark:text-slate-100 mb-3">Biological Sequence Analysis</h3> <ul class="space-y-3 text-sm text-slate-600 dark:text-slate-400 leading-relaxed mb-6"> <li> <strong class="text-slate-800 dark:text-slate-200">CRISPR-PAM:</strong> Metagenomic mapping of PAM preferences across millions of Cas9 proteins to expand targeting options. </li> <li> <strong class="text-slate-800 dark:text-slate-200">DeepFRI:</strong> GNN-based function prediction directly from sequence-derived contact maps at database scale. </li> <li> <strong class="text-slate-800 dark:text-slate-200">scikit-bio:</strong> Contributions to Python's core bioinformatic library for sequence analysis and diversity metrics. </li> </ul> </div> <div class="flex flex-wrap gap-2 text-xs"> <a href="https://valentynbez.github.io/publications/cas9-pam-diversity-2026/" class="font-semibold text-indigo-500 hover:text-indigo-600 dark:hover:text-indigo-400">CRISPR-PAM ↗</a> <span class="text-slate-300 dark:text-slate-700">|</span> <a href="https://github.com/scikit-bio/scikit-bio" target="_blank" rel="noopener" class="font-semibold text-indigo-500 hover:text-indigo-600 dark:hover:text-indigo-400">scikit-bio ↗</a> </div> </div> <!-- Panel 2: Microbiome - Host Relationship --> <div class="flex flex-col justify-between p-6 rounded-2xl bg-slate-50 dark:bg-slate-900/60 border border-slate-200 dark:border-slate-800/80 hover:border-emerald-500/50 dark:hover:border-emerald-400/50 transition-all duration-300 hover:shadow-xl group"> <div> <div class="w-10 h-10 rounded-xl bg-emerald-500/10 text-emerald-500 dark:text-emerald-400 flex items-center justify-center mb-4 group-hover:scale-110 transition-transform duration-300"> <svg class="w-5 h-5" fill="none" stroke="currentColor" viewBox="0 0 24 24"><path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M19.428 15.428a2 2 0 00-1.022-.547l-2.387-.477a6 6 0 00-3.86.517l-.318.158a6 6 0 01-3.86.517L6.05 15.21a2 2 0 00-1.806.547M8 4h8l-1 1v5.172a2 2 0 00.586 1.414l5 5c1.26 1.26.367 3.414-1.415 3.414H4.828c-1.782 0-2.674-2.154-1.414-3.414l5-5A2 2 0 009 10.172V5L8 4z"/></svg> </div> <h3 class="text-lg font-bold text-slate-800 dark:text-slate-100 mb-3">Microbiome - Host Relationship</h3> <ul class="space-y-3 text-sm text-slate-600 dark:text-slate-400 leading-relaxed mb-6"> <li> <strong class="text-slate-800 dark:text-slate-200">Probiotics:</strong> Clinical trial mapping multi-species probiotics response on gut microbiota functions in obese postmenopausal women. </li> <li> <strong class="text-slate-800 dark:text-slate-200">Rhinosinusitis:</strong> Investigating spatial variability in chronic rhinosinusitis sinus microbiome, highlighting patient-specific differences. </li> </ul> </div> <div class="flex flex-wrap gap-2 text-xs"> <a href="https://valentynbez.github.io/publications/probiotics-2022/" class="font-semibold text-emerald-500 hover:text-emerald-600 dark:hover:text-emerald-400">Probiotics ↗</a> <span class="text-slate-300 dark:text-slate-700">|</span> <a href="https://valentynbez.github.io/publications/determinants-microbiome-rhinosinusitis-2024/" class="font-semibold text-emerald-500 hover:text-emerald-600 dark:hover:text-emerald-400">Rhinosinusitis ↗</a> </div> </div> <!-- Panel 3: Machine Learning --> <div class="flex flex-col justify-between p-6 rounded-2xl bg-slate-50 dark:bg-slate-900/60 border border-slate-200 dark:border-slate-800/80 hover:border-sky-500/50 dark:hover:border-sky-400/50 transition-all duration-300 hover:shadow-xl group"> <div> <div class="w-10 h-10 rounded-xl bg-sky-500/10 text-sky-500 dark:text-sky-400 flex items-center justify-center mb-4 group-hover:scale-110 transition-transform duration-300"> <svg class="w-5 h-5" fill="none" stroke="currentColor" viewBox="0 0 24 24"><path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M9.75 17L9 20l-1 1h8l-1-1-.75-3M3 13h18M5 17h14a2 2 0 002-2V5a2 2 0 00-2-2H5a2 2 0 00-2 2v10a2 2 0 002 2z"/></svg> </div> <h3 class="text-lg font-bold text-slate-800 dark:text-slate-100 mb-3">Machine Learning</h3> <ul class="space-y-3 text-sm text-slate-600 dark:text-slate-400 leading-relaxed mb-6"> <li> <strong class="text-slate-800 dark:text-slate-200">Metagenomic DeepFRI:</strong> Integrating deep-learning GNNs into bioinformatics pipelines to annotate novel gut microbial genes. </li> <li> <strong class="text-slate-800 dark:text-slate-200">TM-Vec2:</strong> Lightweight sequence embedder trained via knowledge distillation to predict protein structure similarity (TM-scores) at scale. </li> </ul> </div> <div class="flex flex-wrap gap-2 text-xs"> <a href="https://github.com/bioinf-mcb/Metagenomic-DeepFRI" target="_blank" rel="noopener" class="font-semibold text-sky-500 hover:text-sky-600 dark:hover:text-sky-400">DeepFRI ↗</a> </div> </div> </div>https://valentynbez.github.io/social-projects/Sun, 21 Jun 2026 00:00:00 +0000https://valentynbez.github.io/social-projects/<div class="relative rounded-3xl overflow-hidden bg-gradient-to-br from-amber-950/60 via-slate-900 to-orange-950/40 p-8 md:p-12 mb-12 border border-slate-800 shadow-2xl backdrop-blur-md"> <!-- Glowing gradient background orbs --> <div class="absolute -top-24 -right-24 w-96 h-96 bg-amber-500/10 rounded-full filter blur-3xl opacity-30"></div> <div class="absolute -bottom-24 -left-24 w-96 h-96 bg-orange-500/10 rounded-full filter blur-3xl opacity-20"></div> <div class="relative z-10 max-w-3xl"> <span class="inline-flex items-center px-3 py-1 rounded-full text-xs font-semibold bg-amber-500/10 text-amber-400 border border-amber-500/20 mb-4"> 🤝 Social Impact </span> <h1 class="text-3xl md:text-5xl font-extrabold tracking-tight mb-4 leading-tight text-white"> Building Community & <span class="bg-gradient-to-r from-amber-400 via-orange-400 to-yellow-400 bg-clip-text text-transparent">Supporting Education</span> </h1> <p class="text-base md:text-lg text-slate-300 leading-relaxed font-light"> Beyond academic research, I am committed to social projects that empower local communities, support children's education in conflict-affected regions, and cultivate spaces for open, offline intellectual discourse. </p> </div> </div> <div class="grid grid-cols-1 md:grid-cols-2 gap-8 mb-12"> <!-- Project 1: Ukrainian Charity Alliance --> <div class="flex flex-col justify-between p-8 rounded-2xl bg-slate-50 dark:bg-slate-900/60 border border-slate-200 dark:border-slate-800/80 hover:border-amber-500/50 dark:hover:border-amber-400/50 transition-all duration-300 hover:shadow-xl group"> <div> <div class="w-12 h-12 rounded-xl bg-amber-500/10 text-amber-500 dark:text-amber-400 flex items-center justify-center mb-5 group-hover:scale-110 transition-transform duration-300"> <svg class="w-6 h-6" fill="none" stroke="currentColor" viewBox="0 0 24 24"><path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M12 6.253v13m0-13C10.832 5.477 9.246 5 7.5 5S4.168 5.477 3 6.253v13C4.168 18.477 5.754 18 7.5 18s3.332.477 4.5 1.253m0-13C13.168 5.477 14.754 5 16.5 5c1.747 0 3.332.477 4.5 1.253v13C19.832 18.477 18.247 18 16.5 18c-1.746 0-3.332.477-4.5 1.253"/></svg> </div> <span class="text-xs font-bold text-amber-500 dark:text-amber-400 uppercase tracking-wider block mb-1">Role: Ambassador</span> <h3 class="text-2xl font-bold text-slate-800 dark:text-slate-100 mb-3">Ukrainian Charity Alliance</h3> <p class="text-sm text-slate-600 dark:text-slate-400 leading-relaxed mb-6"> As an ambassador for this Kharkiv-based charity, I support efforts dedicated to children's education and welfare in war-affected regions of Ukraine. The organization focuses on establishing safe learning environments, and providing educational resources. Besides, the project leads a veteran reeducation and integration programme with a goal of strengthening and rebuilding Kharkiv region. </p> </div> <div> <div class="flex flex-col gap-4"> <div class="flex flex-wrap items-center gap-2"> <span class="px-2.5 py-0.5 rounded-full text-xs font-medium bg-amber-500/10 text-amber-600 dark:text-amber-400">Children's Education</span> <span class="px-2.5 py-0.5 rounded-full text-xs font-medium bg-amber-500/10 text-amber-600 dark:text-amber-400">Veteran Reintegration</span> <span class="px-2.5 py-0.5 rounded-full text-xs font-medium bg-slate-500/10 text-slate-600 dark:text-slate-400">📍 Zurich, CH & Kharkiv, UA</span> </div> <a href="https://en.uba.com.ua/" target="_blank" rel="noopener" class="inline-flex items-center text-sm font-semibold text-amber-500 hover:text-amber-600 dark:hover:text-amber-400 group/link"> Visit uba.com.ua <svg class="w-4 h-4 ml-1.5 transform group-hover/link:translate-x-1 transition-transform" fill="none" stroke="currentColor" viewBox="0 0 24 24"><path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M14 5l7 7m0 0l-7 7m7-7H3"/></svg> </a> </div> </div> </div> <!-- Project 2: Coffeehouse Conference --> <div class="flex flex-col justify-between p-8 rounded-2xl bg-slate-50 dark:bg-slate-900/60 border border-slate-200 dark:border-slate-800/80 hover:border-orange-500/50 dark:hover:border-orange-400/50 transition-all duration-300 hover:shadow-xl group"> <div> <div class="w-12 h-12 rounded-xl bg-orange-500/10 text-orange-500 dark:text-orange-400 flex items-center justify-center mb-5 group-hover:scale-110 transition-transform duration-300"> <svg class="w-6 h-6" fill="none" stroke="currentColor" viewBox="0 0 24 24"><path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M17 20h5v-2a3 3 0 00-5.356-1.857M17 20H7m10 0v-2c0-.656-.126-1.283-.356-1.857M7 20H2v-2a3 3 0 015.356-1.857M7 20v-2c0-.656.126-1.283.356-1.857m0 0a5.002 5.002 0 019.288 0M15 7a3 3 0 11-6 0 3 3 0 016 0zm6 3a2 2 0 11-4 0 2 2 0 014 0zM7 10a2 2 0 11-4 0 2 2 0 014 0z"/></svg> </div> <span class="text-xs font-bold text-orange-500 dark:text-orange-400 uppercase tracking-wider block mb-1">Role: Advisory Board</span> <h3 class="text-2xl font-bold text-slate-800 dark:text-slate-100 mb-3">Coffeehouse Conference</h3> <p class="text-sm text-slate-600 dark:text-slate-400 leading-relaxed mb-6"> I serve on the advisory board of the Coffeehouse Conference, an organization hosting curated, offline gatherings designed to revive the historical coffeehouse tradition as centers of deep intellectual sharing and active debate. </p> </div> <div> <div class="flex flex-col gap-4"> <div class="flex flex-wrap items-center gap-2"> <span class="px-2.5 py-0.5 rounded-full text-xs font-medium bg-orange-500/10 text-orange-600 dark:text-orange-400">Curated Gatherings</span> <span class="px-2.5 py-0.5 rounded-full text-xs font-medium bg-slate-500/10 text-slate-600 dark:text-slate-400">📍 Zurich, CH</span> </div> <a href="https://coffeehouseconf.com" target="_blank" rel="noopener" class="inline-flex items-center text-sm font-semibold text-orange-500 hover:text-orange-600 dark:hover:text-orange-400 group/link"> Visit coffeehouseconf.com <svg class="w-4 h-4 ml-1.5 transform group-hover/link:translate-x-1 transition-transform" fill="none" stroke="currentColor" viewBox="0 0 24 24"><path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M14 5l7 7m0 0l-7 7m7-7H3"/></svg> </a> </div> </div> </div> </div>https://valentynbez.github.io/invited-talks/ai-impact-summit-2026/Wed, 18 Feb 2026 00:00:00 +0000https://valentynbez.github.io/invited-talks/ai-impact-summit-2026/<p>Presented on the intersection of deep learning and microbiology, demonstrating how to leverage generative AI models alongside metagenomic mining to design novel antimicrobial peptides. We explored pipelines that automate the identification of active sequences from environmental datasets, helping to address global challenges in antibiotic resistance.</p>https://valentynbez.github.io/publications/cas9-pam-diversity-2026/Sun, 08 Feb 2026 00:00:00 +0000https://valentynbez.github.io/publications/cas9-pam-diversity-2026/https://valentynbez.github.io/publications/scikit-bio-2025/Thu, 11 Dec 2025 00:00:00 +0000https://valentynbez.github.io/publications/scikit-bio-2025/https://valentynbez.github.io/invited-talks/usp-2024/Tue, 27 May 2025 00:00:00 +0000https://valentynbez.github.io/invited-talks/usp-2024/<p>Presented our research describing the diversity and functional potential of circularized phages discovered in various environments, utilizing metagenomic assembly and annotation. Hosted by Professor Arthur Gruber at the Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo.</p>https://valentynbez.github.io/invited-talks/ismb-2024/Fri, 12 Jul 2024 00:00:00 +0000https://valentynbez.github.io/invited-talks/ismb-2024/<p>Led the training session covering sequence analysis workflows, data structures, and algorithms within , a fundamental Python library for biological omics data. The tutorial walked participants through workflow on using protein embeddings for sequence analysis within the library.</p>https://valentynbez.github.io/publications/predictors-vip2-2024/Fri, 29 Mar 2024 00:00:00 +0000https://valentynbez.github.io/publications/predictors-vip2-2024/https://valentynbez.github.io/publications/determinants-microbiome-rhinosinusitis-2024/Thu, 01 Feb 2024 00:00:00 +0000https://valentynbez.github.io/publications/determinants-microbiome-rhinosinusitis-2024/https://valentynbez.github.io/publications/diagnostic-accuracy-bladder-2023/Wed, 03 May 2023 00:00:00 +0000https://valentynbez.github.io/publications/diagnostic-accuracy-bladder-2023/https://valentynbez.github.io/publications/msystems-2023/Thu, 27 Apr 2023 00:00:00 +0000https://valentynbez.github.io/publications/msystems-2023/https://valentynbez.github.io/publications/probiotics-2022/Fri, 11 Mar 2022 00:00:00 +0000https://valentynbez.github.io/publications/probiotics-2022/https://valentynbez.github.io/invited-talks/ismb-eccb-2021/Tue, 27 Jul 2021 00:00:00 +0000https://valentynbez.github.io/invited-talks/ismb-eccb-2021/<p>Presented my award-winning machine learning pipeline for the CAMDA 2021 &ldquo;Literature AI for Drug Induced Liver Injury&rdquo; (DILI) challenge. Discussed utilizing transformer models (RoBERTa) to automatically classify and extract liver pathology articles from large-scale PubMed datasets.</p>https://valentynbez.github.io/skills/Mon, 01 Jan 0001 00:00:00 +0000https://valentynbez.github.io/skills/