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GiatrasKon/README.md

💫 About Me:

  • 🔭 Pursuing a Master's in Data Science and Information Technologies with a specialization in Bioinformatics and Biomedical Data Science at the National and Kapodistrian University of Athens, Greece.
  • 🧬 Conducting my thesis in metagenomics under the supervision of Georgios Pavlopoulos and Fotis Baltoumas at the BSRC Alexander Fleming, Athens, Greece.
  • 🔬 Designed and implemented computational pipelines and machine learning approaches for analyzing biological data, including single-cell RNA sequencing, protein structure prediction, genetic variant detection, time series forecasting, and image analysis, with applications spanning cancer research, genomics, and data-driven healthcare solutions.
  • 🤝 Open to collaborating on innovative bioinformatics, data science, and machine learning projects.
  • 🌐 All of my projects are available here.

🌐 Socials:

LinkedInEmail

💻 Tech Stack:

  • Programming Languages:
    PythonShell ScriptRMATLABPerl
  • Development Tools:
    GitAnacondaNotionMicrosoft OfficeLaTeXMarkdown
  • Data Science & Machine Learning:
    NumPyPandasscikit-learnscikit-imageOptunaUMAP-learnSciPyTensorFlowKerasPyTorch
  • Data Visualization:
    PlotlyMatplotlibSeabornPillow
  • Operating Systems & Platforms:
    Windows TerminalLinuxMySQL

🧬 Bioinformatics Tools:

  • Sequence Analysis & Variant Calling:
    GATKSAMtoolsBCFtoolsBWAbedtoolssnpEff
  • Protein Structure Prediction:
    AlphaFoldRosetta Abinitio
  • Molecular Dynamics Simulation:
    NAMDVMDmdtraj
  • Multiple Sequence Alignment:
    MAFFTMUSCLE
  • Sequence Homology & Search:
    BLASTLASTDIAMONDHMMER
  • Sequence Search & Clustering:
    MMseqs2
  • Protein Structure Comparison & Search:
    Foldseek
  • Structural Visualization & Analysis:
    PyMOLChimeraXXMGraceMaestro Suite
  • Single-Cell RNA Analysis:
    anndatascanpy
  • Functional Enrichment & Profiling:
    gProfiler
  • Programming Libraries:
    Biopython

📊 GitHub Stats:





Pinned Loading

  1. Gastric-Cancer-scRNAseq-AnalysisGastric-Cancer-scRNAseq-AnalysisPublic

    Recreation and enrichment of the gastric (GC) cancer single-cell RNA-seq (scRNA-seq) data analysis pipeline described in the "Comprehensive analysis of metastatic gastric cancer tumour cells using …

    Jupyter Notebook 1 1

  2. Chromosome11-VariantCalling-GATKChromosome11-VariantCalling-GATKPublic

    A streamlined pipeline for germline variant calling on chromosome 11 using GATK. This repository includes workflows for data preprocessing, variant discovery, and annotation, with a focus on unders…

    R 1

  3. PTEN-MolecularDynamics-DrugDesignPTEN-MolecularDynamics-DrugDesignPublic

    Comprehensive molecular dynamics simulations and drug design analysis for PTEN protein: workflows include protein dynamics, binding site detection, ligand screening, and filtering for therapeutic d…

    Jupyter Notebook

  4. ProteinStructurePrediction-ComparativeStudyProteinStructurePrediction-ComparativeStudyPublic

    Comparison of protein structure prediction methods: Rosetta Ab Initio, which uses fragment assembly, Monte Carlo optimization and energy minimization, and a Linear Algebra Algorithm based on Cayley…

    Jupyter Notebook 1

  5. INDELseek-Optimized-ImplementationsINDELseek-Optimized-ImplementationsPublic

    Optimized Python and C++ implementations of INDELseek, a Perl tool for detecting complex genetic indels in NGS data, with performance improvements, validation, and benchmarking against other varian…

    C++

  6. Hyperspectral-Image-ClusteringHyperspectral-Image-ClusteringPublic

    Analysis of the Salinas hyperspectral image dataset using advanced clustering algorithms, focusing on identifying homogeneous regions in the image. Implementations of cost-function optimization and…

    MATLAB 1

, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '
Skip to content
View GiatrasKon's full-sized avatar

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GiatrasKon/README.md

💫 About Me:

  • 🔭 Pursuing a Master's in Data Science and Information Technologies with a specialization in Bioinformatics and Biomedical Data Science at the National and Kapodistrian University of Athens, Greece.
  • 🧬 Conducting my thesis in metagenomics under the supervision of Georgios Pavlopoulos and Fotis Baltoumas at the BSRC Alexander Fleming, Athens, Greece.
  • 🔬 Designed and implemented computational pipelines and machine learning approaches for analyzing biological data, including single-cell RNA sequencing, protein structure prediction, genetic variant detection, time series forecasting, and image analysis, with applications spanning cancer research, genomics, and data-driven healthcare solutions.
  • 🤝 Open to collaborating on innovative bioinformatics, data science, and machine learning projects.
  • 🌐 All of my projects are available here.

🌐 Socials:

LinkedInEmail

💻 Tech Stack:

  • Programming Languages:
    PythonShell ScriptRMATLABPerl
  • Development Tools:
    GitAnacondaNotionMicrosoft OfficeLaTeXMarkdown
  • Data Science & Machine Learning:
    NumPyPandasscikit-learnscikit-imageOptunaUMAP-learnSciPyTensorFlowKerasPyTorch
  • Data Visualization:
    PlotlyMatplotlibSeabornPillow
  • Operating Systems & Platforms:
    Windows TerminalLinuxMySQL

🧬 Bioinformatics Tools:

  • Sequence Analysis & Variant Calling:
    GATKSAMtoolsBCFtoolsBWAbedtoolssnpEff
  • Protein Structure Prediction:
    AlphaFoldRosetta Abinitio
  • Molecular Dynamics Simulation:
    NAMDVMDmdtraj
  • Multiple Sequence Alignment:
    MAFFTMUSCLE
  • Sequence Homology & Search:
    BLASTLASTDIAMONDHMMER
  • Sequence Search & Clustering:
    MMseqs2
  • Protein Structure Comparison & Search:
    Foldseek
  • Structural Visualization & Analysis:
    PyMOLChimeraXXMGraceMaestro Suite
  • Single-Cell RNA Analysis:
    anndatascanpy
  • Functional Enrichment & Profiling:
    gProfiler
  • Programming Libraries:
    Biopython

📊 GitHub Stats:





Pinned Loading

  1. Gastric-Cancer-scRNAseq-AnalysisGastric-Cancer-scRNAseq-AnalysisPublic

    Recreation and enrichment of the gastric (GC) cancer single-cell RNA-seq (scRNA-seq) data analysis pipeline described in the "Comprehensive analysis of metastatic gastric cancer tumour cells using …

    Jupyter Notebook 1 1

  2. Chromosome11-VariantCalling-GATKChromosome11-VariantCalling-GATKPublic

    A streamlined pipeline for germline variant calling on chromosome 11 using GATK. This repository includes workflows for data preprocessing, variant discovery, and annotation, with a focus on unders…

    R 1

  3. PTEN-MolecularDynamics-DrugDesignPTEN-MolecularDynamics-DrugDesignPublic

    Comprehensive molecular dynamics simulations and drug design analysis for PTEN protein: workflows include protein dynamics, binding site detection, ligand screening, and filtering for therapeutic d…

    Jupyter Notebook

  4. ProteinStructurePrediction-ComparativeStudyProteinStructurePrediction-ComparativeStudyPublic

    Comparison of protein structure prediction methods: Rosetta Ab Initio, which uses fragment assembly, Monte Carlo optimization and energy minimization, and a Linear Algebra Algorithm based on Cayley…

    Jupyter Notebook 1

  5. INDELseek-Optimized-ImplementationsINDELseek-Optimized-ImplementationsPublic

    Optimized Python and C++ implementations of INDELseek, a Perl tool for detecting complex genetic indels in NGS data, with performance improvements, validation, and benchmarking against other varian…

    C++

  6. Hyperspectral-Image-ClusteringHyperspectral-Image-ClusteringPublic

    Analysis of the Salinas hyperspectral image dataset using advanced clustering algorithms, focusing on identifying homogeneous regions in the image. Implementations of cost-function optimization and…

    MATLAB 1

, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix"); } } catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + '
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Content in all repositories owned by your account will be closed.
Maximum 250 characters. Please don’t include any personal information such as legal names or email addresses. Markdown is supported. This note will only be visible to you.
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GiatrasKon/README.md

💫 About Me:

  • 🔭 Pursuing a Master's in Data Science and Information Technologies with a specialization in Bioinformatics and Biomedical Data Science at the National and Kapodistrian University of Athens, Greece.
  • 🧬 Conducting my thesis in metagenomics under the supervision of Georgios Pavlopoulos and Fotis Baltoumas at the BSRC Alexander Fleming, Athens, Greece.
  • 🔬 Designed and implemented computational pipelines and machine learning approaches for analyzing biological data, including single-cell RNA sequencing, protein structure prediction, genetic variant detection, time series forecasting, and image analysis, with applications spanning cancer research, genomics, and data-driven healthcare solutions.
  • 🤝 Open to collaborating on innovative bioinformatics, data science, and machine learning projects.
  • 🌐 All of my projects are available here.

🌐 Socials:

LinkedInEmail

💻 Tech Stack:

  • Programming Languages:
    PythonShell ScriptRMATLABPerl
  • Development Tools:
    GitAnacondaNotionMicrosoft OfficeLaTeXMarkdown
  • Data Science & Machine Learning:
    NumPyPandasscikit-learnscikit-imageOptunaUMAP-learnSciPyTensorFlowKerasPyTorch
  • Data Visualization:
    PlotlyMatplotlibSeabornPillow
  • Operating Systems & Platforms:
    Windows TerminalLinuxMySQL

🧬 Bioinformatics Tools:

  • Sequence Analysis & Variant Calling:
    GATKSAMtoolsBCFtoolsBWAbedtoolssnpEff
  • Protein Structure Prediction:
    AlphaFoldRosetta Abinitio
  • Molecular Dynamics Simulation:
    NAMDVMDmdtraj
  • Multiple Sequence Alignment:
    MAFFTMUSCLE
  • Sequence Homology & Search:
    BLASTLASTDIAMONDHMMER
  • Sequence Search & Clustering:
    MMseqs2
  • Protein Structure Comparison & Search:
    Foldseek
  • Structural Visualization & Analysis:
    PyMOLChimeraXXMGraceMaestro Suite
  • Single-Cell RNA Analysis:
    anndatascanpy
  • Functional Enrichment & Profiling:
    gProfiler
  • Programming Libraries:
    Biopython

📊 GitHub Stats:





Pinned Loading

  1. Gastric-Cancer-scRNAseq-AnalysisGastric-Cancer-scRNAseq-AnalysisPublic

    Recreation and enrichment of the gastric (GC) cancer single-cell RNA-seq (scRNA-seq) data analysis pipeline described in the "Comprehensive analysis of metastatic gastric cancer tumour cells using …

    Jupyter Notebook 1 1

  2. Chromosome11-VariantCalling-GATKChromosome11-VariantCalling-GATKPublic

    A streamlined pipeline for germline variant calling on chromosome 11 using GATK. This repository includes workflows for data preprocessing, variant discovery, and annotation, with a focus on unders…

    R 1

  3. PTEN-MolecularDynamics-DrugDesignPTEN-MolecularDynamics-DrugDesignPublic

    Comprehensive molecular dynamics simulations and drug design analysis for PTEN protein: workflows include protein dynamics, binding site detection, ligand screening, and filtering for therapeutic d…

    Jupyter Notebook

  4. ProteinStructurePrediction-ComparativeStudyProteinStructurePrediction-ComparativeStudyPublic

    Comparison of protein structure prediction methods: Rosetta Ab Initio, which uses fragment assembly, Monte Carlo optimization and energy minimization, and a Linear Algebra Algorithm based on Cayley…

    Jupyter Notebook 1

  5. INDELseek-Optimized-ImplementationsINDELseek-Optimized-ImplementationsPublic

    Optimized Python and C++ implementations of INDELseek, a Perl tool for detecting complex genetic indels in NGS data, with performance improvements, validation, and benchmarking against other varian…

    C++

  6. Hyperspectral-Image-ClusteringHyperspectral-Image-ClusteringPublic

    Analysis of the Salinas hyperspectral image dataset using advanced clustering algorithms, focusing on identifying homogeneous regions in the image. Implementations of cost-function optimization and…

    MATLAB 1

, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms"); } } catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + '
Skip to content
View GiatrasKon's full-sized avatar

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Content in all repositories owned by your account will be closed.
Maximum 250 characters. Please don’t include any personal information such as legal names or email addresses. Markdown is supported. This note will only be visible to you.
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GiatrasKon/README.md

💫 About Me:

  • 🔭 Pursuing a Master's in Data Science and Information Technologies with a specialization in Bioinformatics and Biomedical Data Science at the National and Kapodistrian University of Athens, Greece.
  • 🧬 Conducting my thesis in metagenomics under the supervision of Georgios Pavlopoulos and Fotis Baltoumas at the BSRC Alexander Fleming, Athens, Greece.
  • 🔬 Designed and implemented computational pipelines and machine learning approaches for analyzing biological data, including single-cell RNA sequencing, protein structure prediction, genetic variant detection, time series forecasting, and image analysis, with applications spanning cancer research, genomics, and data-driven healthcare solutions.
  • 🤝 Open to collaborating on innovative bioinformatics, data science, and machine learning projects.
  • 🌐 All of my projects are available here.

🌐 Socials:

LinkedInEmail

💻 Tech Stack:

  • Programming Languages:
    PythonShell ScriptRMATLABPerl
  • Development Tools:
    GitAnacondaNotionMicrosoft OfficeLaTeXMarkdown
  • Data Science & Machine Learning:
    NumPyPandasscikit-learnscikit-imageOptunaUMAP-learnSciPyTensorFlowKerasPyTorch
  • Data Visualization:
    PlotlyMatplotlibSeabornPillow
  • Operating Systems & Platforms:
    Windows TerminalLinuxMySQL

🧬 Bioinformatics Tools:

  • Sequence Analysis & Variant Calling:
    GATKSAMtoolsBCFtoolsBWAbedtoolssnpEff
  • Protein Structure Prediction:
    AlphaFoldRosetta Abinitio
  • Molecular Dynamics Simulation:
    NAMDVMDmdtraj
  • Multiple Sequence Alignment:
    MAFFTMUSCLE
  • Sequence Homology & Search:
    BLASTLASTDIAMONDHMMER
  • Sequence Search & Clustering:
    MMseqs2
  • Protein Structure Comparison & Search:
    Foldseek
  • Structural Visualization & Analysis:
    PyMOLChimeraXXMGraceMaestro Suite
  • Single-Cell RNA Analysis:
    anndatascanpy
  • Functional Enrichment & Profiling:
    gProfiler
  • Programming Libraries:
    Biopython

📊 GitHub Stats:





Pinned Loading

  1. Gastric-Cancer-scRNAseq-AnalysisGastric-Cancer-scRNAseq-AnalysisPublic

    Recreation and enrichment of the gastric (GC) cancer single-cell RNA-seq (scRNA-seq) data analysis pipeline described in the "Comprehensive analysis of metastatic gastric cancer tumour cells using …

    Jupyter Notebook 1 1

  2. Chromosome11-VariantCalling-GATKChromosome11-VariantCalling-GATKPublic

    A streamlined pipeline for germline variant calling on chromosome 11 using GATK. This repository includes workflows for data preprocessing, variant discovery, and annotation, with a focus on unders…

    R 1

  3. PTEN-MolecularDynamics-DrugDesignPTEN-MolecularDynamics-DrugDesignPublic

    Comprehensive molecular dynamics simulations and drug design analysis for PTEN protein: workflows include protein dynamics, binding site detection, ligand screening, and filtering for therapeutic d…

    Jupyter Notebook

  4. ProteinStructurePrediction-ComparativeStudyProteinStructurePrediction-ComparativeStudyPublic

    Comparison of protein structure prediction methods: Rosetta Ab Initio, which uses fragment assembly, Monte Carlo optimization and energy minimization, and a Linear Algebra Algorithm based on Cayley…

    Jupyter Notebook 1

  5. INDELseek-Optimized-ImplementationsINDELseek-Optimized-ImplementationsPublic

    Optimized Python and C++ implementations of INDELseek, a Perl tool for detecting complex genetic indels in NGS data, with performance improvements, validation, and benchmarking against other varian…

    C++

  6. Hyperspectral-Image-ClusteringHyperspectral-Image-ClusteringPublic

    Analysis of the Salinas hyperspectral image dataset using advanced clustering algorithms, focusing on identifying homogeneous regions in the image. Implementations of cost-function optimization and…

    MATLAB 1

, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links"); } } catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); } })(); (function(){ try { var __m = "youtube.com"; var __re = new RegExp('^' + "youtube\\.com" + '
Skip to content
View GiatrasKon's full-sized avatar

Highlights

  • Pro

Block or report GiatrasKon

Block user

Prevent this user from interacting with your repositories and sending you notifications. Learn more about blocking users.

You must be logged in to block users.

Content in all repositories owned by your account will be closed.
Maximum 250 characters. Please don’t include any personal information such as legal names or email addresses. Markdown is supported. This note will only be visible to you.
Report abuse

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Report abuse
GiatrasKon/README.md

💫 About Me:

  • 🔭 Pursuing a Master's in Data Science and Information Technologies with a specialization in Bioinformatics and Biomedical Data Science at the National and Kapodistrian University of Athens, Greece.
  • 🧬 Conducting my thesis in metagenomics under the supervision of Georgios Pavlopoulos and Fotis Baltoumas at the BSRC Alexander Fleming, Athens, Greece.
  • 🔬 Designed and implemented computational pipelines and machine learning approaches for analyzing biological data, including single-cell RNA sequencing, protein structure prediction, genetic variant detection, time series forecasting, and image analysis, with applications spanning cancer research, genomics, and data-driven healthcare solutions.
  • 🤝 Open to collaborating on innovative bioinformatics, data science, and machine learning projects.
  • 🌐 All of my projects are available here.

🌐 Socials:

LinkedInEmail

💻 Tech Stack:

  • Programming Languages:
    PythonShell ScriptRMATLABPerl
  • Development Tools:
    GitAnacondaNotionMicrosoft OfficeLaTeXMarkdown
  • Data Science & Machine Learning:
    NumPyPandasscikit-learnscikit-imageOptunaUMAP-learnSciPyTensorFlowKerasPyTorch
  • Data Visualization:
    PlotlyMatplotlibSeabornPillow
  • Operating Systems & Platforms:
    Windows TerminalLinuxMySQL

🧬 Bioinformatics Tools:

  • Sequence Analysis & Variant Calling:
    GATKSAMtoolsBCFtoolsBWAbedtoolssnpEff
  • Protein Structure Prediction:
    AlphaFoldRosetta Abinitio
  • Molecular Dynamics Simulation:
    NAMDVMDmdtraj
  • Multiple Sequence Alignment:
    MAFFTMUSCLE
  • Sequence Homology & Search:
    BLASTLASTDIAMONDHMMER
  • Sequence Search & Clustering:
    MMseqs2
  • Protein Structure Comparison & Search:
    Foldseek
  • Structural Visualization & Analysis:
    PyMOLChimeraXXMGraceMaestro Suite
  • Single-Cell RNA Analysis:
    anndatascanpy
  • Functional Enrichment & Profiling:
    gProfiler
  • Programming Libraries:
    Biopython

📊 GitHub Stats:





Pinned Loading

  1. Gastric-Cancer-scRNAseq-AnalysisGastric-Cancer-scRNAseq-AnalysisPublic

    Recreation and enrichment of the gastric (GC) cancer single-cell RNA-seq (scRNA-seq) data analysis pipeline described in the "Comprehensive analysis of metastatic gastric cancer tumour cells using …

    Jupyter Notebook 1 1

  2. Chromosome11-VariantCalling-GATKChromosome11-VariantCalling-GATKPublic

    A streamlined pipeline for germline variant calling on chromosome 11 using GATK. This repository includes workflows for data preprocessing, variant discovery, and annotation, with a focus on unders…

    R 1

  3. PTEN-MolecularDynamics-DrugDesignPTEN-MolecularDynamics-DrugDesignPublic

    Comprehensive molecular dynamics simulations and drug design analysis for PTEN protein: workflows include protein dynamics, binding site detection, ligand screening, and filtering for therapeutic d…

    Jupyter Notebook

  4. ProteinStructurePrediction-ComparativeStudyProteinStructurePrediction-ComparativeStudyPublic

    Comparison of protein structure prediction methods: Rosetta Ab Initio, which uses fragment assembly, Monte Carlo optimization and energy minimization, and a Linear Algebra Algorithm based on Cayley…

    Jupyter Notebook 1

  5. INDELseek-Optimized-ImplementationsINDELseek-Optimized-ImplementationsPublic

    Optimized Python and C++ implementations of INDELseek, a Perl tool for detecting complex genetic indels in NGS data, with performance improvements, validation, and benchmarking against other varian…

    C++

  6. Hyperspectral-Image-ClusteringHyperspectral-Image-ClusteringPublic

    Analysis of the Salinas hyperspectral image dataset using advanced clustering algorithms, focusing on identifying homogeneous regions in the image. Implementations of cost-function optimization and…

    MATLAB 1

, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default"); } } catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + '
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GiatrasKon/README.md

💫 About Me:

  • 🔭 Pursuing a Master's in Data Science and Information Technologies with a specialization in Bioinformatics and Biomedical Data Science at the National and Kapodistrian University of Athens, Greece.
  • 🧬 Conducting my thesis in metagenomics under the supervision of Georgios Pavlopoulos and Fotis Baltoumas at the BSRC Alexander Fleming, Athens, Greece.
  • 🔬 Designed and implemented computational pipelines and machine learning approaches for analyzing biological data, including single-cell RNA sequencing, protein structure prediction, genetic variant detection, time series forecasting, and image analysis, with applications spanning cancer research, genomics, and data-driven healthcare solutions.
  • 🤝 Open to collaborating on innovative bioinformatics, data science, and machine learning projects.
  • 🌐 All of my projects are available here.

🌐 Socials:

LinkedInEmail

💻 Tech Stack:

  • Programming Languages:
    PythonShell ScriptRMATLABPerl
  • Development Tools:
    GitAnacondaNotionMicrosoft OfficeLaTeXMarkdown
  • Data Science & Machine Learning:
    NumPyPandasscikit-learnscikit-imageOptunaUMAP-learnSciPyTensorFlowKerasPyTorch
  • Data Visualization:
    PlotlyMatplotlibSeabornPillow
  • Operating Systems & Platforms:
    Windows TerminalLinuxMySQL

🧬 Bioinformatics Tools:

  • Sequence Analysis & Variant Calling:
    GATKSAMtoolsBCFtoolsBWAbedtoolssnpEff
  • Protein Structure Prediction:
    AlphaFoldRosetta Abinitio
  • Molecular Dynamics Simulation:
    NAMDVMDmdtraj
  • Multiple Sequence Alignment:
    MAFFTMUSCLE
  • Sequence Homology & Search:
    BLASTLASTDIAMONDHMMER
  • Sequence Search & Clustering:
    MMseqs2
  • Protein Structure Comparison & Search:
    Foldseek
  • Structural Visualization & Analysis:
    PyMOLChimeraXXMGraceMaestro Suite
  • Single-Cell RNA Analysis:
    anndatascanpy
  • Functional Enrichment & Profiling:
    gProfiler
  • Programming Libraries:
    Biopython

📊 GitHub Stats:





Pinned Loading

  1. Gastric-Cancer-scRNAseq-AnalysisGastric-Cancer-scRNAseq-AnalysisPublic

    Recreation and enrichment of the gastric (GC) cancer single-cell RNA-seq (scRNA-seq) data analysis pipeline described in the "Comprehensive analysis of metastatic gastric cancer tumour cells using …

    Jupyter Notebook 1 1

  2. Chromosome11-VariantCalling-GATKChromosome11-VariantCalling-GATKPublic

    A streamlined pipeline for germline variant calling on chromosome 11 using GATK. This repository includes workflows for data preprocessing, variant discovery, and annotation, with a focus on unders…

    R 1

  3. PTEN-MolecularDynamics-DrugDesignPTEN-MolecularDynamics-DrugDesignPublic

    Comprehensive molecular dynamics simulations and drug design analysis for PTEN protein: workflows include protein dynamics, binding site detection, ligand screening, and filtering for therapeutic d…

    Jupyter Notebook

  4. ProteinStructurePrediction-ComparativeStudyProteinStructurePrediction-ComparativeStudyPublic

    Comparison of protein structure prediction methods: Rosetta Ab Initio, which uses fragment assembly, Monte Carlo optimization and energy minimization, and a Linear Algebra Algorithm based on Cayley…

    Jupyter Notebook 1

  5. INDELseek-Optimized-ImplementationsINDELseek-Optimized-ImplementationsPublic

    Optimized Python and C++ implementations of INDELseek, a Perl tool for detecting complex genetic indels in NGS data, with performance improvements, validation, and benchmarking against other varian…

    C++

  6. Hyperspectral-Image-ClusteringHyperspectral-Image-ClusteringPublic

    Analysis of the Salinas hyperspectral image dataset using advanced clustering algorithms, focusing on identifying homogeneous regions in the image. Implementations of cost-function optimization and…

    MATLAB 1

, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers"); } } catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + '
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GiatrasKon/README.md

💫 About Me:

  • 🔭 Pursuing a Master's in Data Science and Information Technologies with a specialization in Bioinformatics and Biomedical Data Science at the National and Kapodistrian University of Athens, Greece.
  • 🧬 Conducting my thesis in metagenomics under the supervision of Georgios Pavlopoulos and Fotis Baltoumas at the BSRC Alexander Fleming, Athens, Greece.
  • 🔬 Designed and implemented computational pipelines and machine learning approaches for analyzing biological data, including single-cell RNA sequencing, protein structure prediction, genetic variant detection, time series forecasting, and image analysis, with applications spanning cancer research, genomics, and data-driven healthcare solutions.
  • 🤝 Open to collaborating on innovative bioinformatics, data science, and machine learning projects.
  • 🌐 All of my projects are available here.

🌐 Socials:

LinkedInEmail

💻 Tech Stack:

  • Programming Languages:
    PythonShell ScriptRMATLABPerl
  • Development Tools:
    GitAnacondaNotionMicrosoft OfficeLaTeXMarkdown
  • Data Science & Machine Learning:
    NumPyPandasscikit-learnscikit-imageOptunaUMAP-learnSciPyTensorFlowKerasPyTorch
  • Data Visualization:
    PlotlyMatplotlibSeabornPillow
  • Operating Systems & Platforms:
    Windows TerminalLinuxMySQL

🧬 Bioinformatics Tools:

  • Sequence Analysis & Variant Calling:
    GATKSAMtoolsBCFtoolsBWAbedtoolssnpEff
  • Protein Structure Prediction:
    AlphaFoldRosetta Abinitio
  • Molecular Dynamics Simulation:
    NAMDVMDmdtraj
  • Multiple Sequence Alignment:
    MAFFTMUSCLE
  • Sequence Homology & Search:
    BLASTLASTDIAMONDHMMER
  • Sequence Search & Clustering:
    MMseqs2
  • Protein Structure Comparison & Search:
    Foldseek
  • Structural Visualization & Analysis:
    PyMOLChimeraXXMGraceMaestro Suite
  • Single-Cell RNA Analysis:
    anndatascanpy
  • Functional Enrichment & Profiling:
    gProfiler
  • Programming Libraries:
    Biopython

📊 GitHub Stats:





Pinned Loading

  1. Gastric-Cancer-scRNAseq-AnalysisGastric-Cancer-scRNAseq-AnalysisPublic

    Recreation and enrichment of the gastric (GC) cancer single-cell RNA-seq (scRNA-seq) data analysis pipeline described in the "Comprehensive analysis of metastatic gastric cancer tumour cells using …

    Jupyter Notebook 1 1

  2. Chromosome11-VariantCalling-GATKChromosome11-VariantCalling-GATKPublic

    A streamlined pipeline for germline variant calling on chromosome 11 using GATK. This repository includes workflows for data preprocessing, variant discovery, and annotation, with a focus on unders…

    R 1

  3. PTEN-MolecularDynamics-DrugDesignPTEN-MolecularDynamics-DrugDesignPublic

    Comprehensive molecular dynamics simulations and drug design analysis for PTEN protein: workflows include protein dynamics, binding site detection, ligand screening, and filtering for therapeutic d…

    Jupyter Notebook

  4. ProteinStructurePrediction-ComparativeStudyProteinStructurePrediction-ComparativeStudyPublic

    Comparison of protein structure prediction methods: Rosetta Ab Initio, which uses fragment assembly, Monte Carlo optimization and energy minimization, and a Linear Algebra Algorithm based on Cayley…

    Jupyter Notebook 1

  5. INDELseek-Optimized-ImplementationsINDELseek-Optimized-ImplementationsPublic

    Optimized Python and C++ implementations of INDELseek, a Perl tool for detecting complex genetic indels in NGS data, with performance improvements, validation, and benchmarking against other varian…

    C++

  6. Hyperspectral-Image-ClusteringHyperspectral-Image-ClusteringPublic

    Analysis of the Salinas hyperspectral image dataset using advanced clustering algorithms, focusing on identifying homogeneous regions in the image. Implementations of cost-function optimization and…

    MATLAB 1

, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode"); } } catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); } })(); })();
Skip to content
View GiatrasKon's full-sized avatar

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GiatrasKon/README.md

💫 About Me:

  • 🔭 Pursuing a Master's in Data Science and Information Technologies with a specialization in Bioinformatics and Biomedical Data Science at the National and Kapodistrian University of Athens, Greece.
  • 🧬 Conducting my thesis in metagenomics under the supervision of Georgios Pavlopoulos and Fotis Baltoumas at the BSRC Alexander Fleming, Athens, Greece.
  • 🔬 Designed and implemented computational pipelines and machine learning approaches for analyzing biological data, including single-cell RNA sequencing, protein structure prediction, genetic variant detection, time series forecasting, and image analysis, with applications spanning cancer research, genomics, and data-driven healthcare solutions.
  • 🤝 Open to collaborating on innovative bioinformatics, data science, and machine learning projects.
  • 🌐 All of my projects are available here.

🌐 Socials:

LinkedInEmail

💻 Tech Stack:

  • Programming Languages:
    PythonShell ScriptRMATLABPerl
  • Development Tools:
    GitAnacondaNotionMicrosoft OfficeLaTeXMarkdown
  • Data Science & Machine Learning:
    NumPyPandasscikit-learnscikit-imageOptunaUMAP-learnSciPyTensorFlowKerasPyTorch
  • Data Visualization:
    PlotlyMatplotlibSeabornPillow
  • Operating Systems & Platforms:
    Windows TerminalLinuxMySQL

🧬 Bioinformatics Tools:

  • Sequence Analysis & Variant Calling:
    GATKSAMtoolsBCFtoolsBWAbedtoolssnpEff
  • Protein Structure Prediction:
    AlphaFoldRosetta Abinitio
  • Molecular Dynamics Simulation:
    NAMDVMDmdtraj
  • Multiple Sequence Alignment:
    MAFFTMUSCLE
  • Sequence Homology & Search:
    BLASTLASTDIAMONDHMMER
  • Sequence Search & Clustering:
    MMseqs2
  • Protein Structure Comparison & Search:
    Foldseek
  • Structural Visualization & Analysis:
    PyMOLChimeraXXMGraceMaestro Suite
  • Single-Cell RNA Analysis:
    anndatascanpy
  • Functional Enrichment & Profiling:
    gProfiler
  • Programming Libraries:
    Biopython

📊 GitHub Stats:





Pinned Loading

  1. Gastric-Cancer-scRNAseq-AnalysisGastric-Cancer-scRNAseq-AnalysisPublic

    Recreation and enrichment of the gastric (GC) cancer single-cell RNA-seq (scRNA-seq) data analysis pipeline described in the "Comprehensive analysis of metastatic gastric cancer tumour cells using …

    Jupyter Notebook 1 1

  2. Chromosome11-VariantCalling-GATKChromosome11-VariantCalling-GATKPublic

    A streamlined pipeline for germline variant calling on chromosome 11 using GATK. This repository includes workflows for data preprocessing, variant discovery, and annotation, with a focus on unders…

    R 1

  3. PTEN-MolecularDynamics-DrugDesignPTEN-MolecularDynamics-DrugDesignPublic

    Comprehensive molecular dynamics simulations and drug design analysis for PTEN protein: workflows include protein dynamics, binding site detection, ligand screening, and filtering for therapeutic d…

    Jupyter Notebook

  4. ProteinStructurePrediction-ComparativeStudyProteinStructurePrediction-ComparativeStudyPublic

    Comparison of protein structure prediction methods: Rosetta Ab Initio, which uses fragment assembly, Monte Carlo optimization and energy minimization, and a Linear Algebra Algorithm based on Cayley…

    Jupyter Notebook 1

  5. INDELseek-Optimized-ImplementationsINDELseek-Optimized-ImplementationsPublic

    Optimized Python and C++ implementations of INDELseek, a Perl tool for detecting complex genetic indels in NGS data, with performance improvements, validation, and benchmarking against other varian…

    C++

  6. Hyperspectral-Image-ClusteringHyperspectral-Image-ClusteringPublic

    Analysis of the Salinas hyperspectral image dataset using advanced clustering algorithms, focusing on identifying homogeneous regions in the image. Implementations of cost-function optimization and…

    MATLAB 1