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1322 lines (1236 loc) · 71.1 KB
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="google-site-verification" content="ItDwRylUvbJUrPSDTNFuMNykSKiSqeZxlg4Zxss-FaM" />
<title>Mallikarjuna Thippana, PhD — Computational Biologist</title>
<meta name="description" content="Portfolio of Mallikarjuna Thippana, PhD — Computational Biologist specializing in genomics & epigenomics (bulk RNA-seq, ChIP-seq, ATAC-seq, CUT&RUN), single-cell & spatial multi-omics, and statistical ML for biological data.">
<meta property="og:title" content="Mallikarjuna Thippana, PhD — Computational Biologist">
<meta property="og:description" content="Genomics & epigenomics (ChIP-seq, ATAC-seq, CUT&RUN, bulk RNA-seq) · Single-cell & spatial multi-omics · Statistical ML for biological data. Postdoctoral researcher at Karolinska Institutet.">
<meta property="og:type" content="website">
<meta property="og:url" content="https://arjunbioinfo.github.io/">
<meta property="og:site_name" content="Mallikarjuna Thippana, PhD">
<meta property="og:image" content="https://arjunbioinfo.github.io/profile.jpg">
<meta property="og:image:width" content="500">
<meta property="og:image:height" content="616">
<meta name="twitter:card" content="summary_large_image">
<meta name="twitter:image" content="https://arjunbioinfo.github.io/profile.jpg">
<link rel="canonical" href="https://arjunbioinfo.github.io/">
<link rel="icon" href="data:image/svg+xml,%3Csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 100 100'%3E%3Crect width='100' height='100' rx='20' fill='%23080b10'/%3E%3Ctext x='50' y='68' font-family='Arial,sans-serif' font-size='52' font-weight='700' fill='%234fd6c7' text-anchor='middle'%3EMT%3C/text%3E%3C/svg%3E">
<link rel="preconnect" href="https://fonts.googleapis.com">
<link rel="preconnect" href="https://fonts.gstatic.com" crossorigin>
<link href="https://fonts.googleapis.com/css2?family=Space+Grotesk:wght@400;500;600;700&family=Inter:wght@400;500;600;700;800&family=JetBrains+Mono:wght@400;500&display=swap" rel="stylesheet">
<style>
:root{
--bg:#080b10;
--bg-alt:#0d1219;
--card:#111823;
--card-hover:#141d2b;
--border:#1e2836;
--text:#e8edf3;
--text-dim:#8b98a9;
--text-faint:#5a6675;
--accent:#4fd6c7;
--accent-soft:rgba(79,214,199,0.12);
--accent2:#f2b134;
--accent2-soft:rgba(242,177,52,0.12);
--radius:14px;
--maxw:1120px;
}
*{margin:0;padding:0;box-sizing:border-box;}
html{scroll-behavior:smooth;}
body{
background:var(--bg);
color:var(--text);
font-family:'Inter',-apple-system,BlinkMacSystemFont,'Segoe UI',sans-serif;
line-height:1.6;
overflow-x:hidden;
}
h1,h2,h3,h4,.mono{font-family:'Space Grotesk',-apple-system,sans-serif;}
.mono-code{font-family:'JetBrains Mono',monospace;}
a{color:inherit;text-decoration:none;}
::selection{background:var(--accent);color:#04110f;}
.bg-grid{
position:fixed;inset:0;z-index:0;pointer-events:none;
width:100%;height:100%;display:block;
mask-image:radial-gradient(ellipse 90% 70% at 50% 15%, #000 30%, transparent 85%);
-webkit-mask-image:radial-gradient(ellipse 90% 70% at 50% 15%, #000 30%, transparent 85%);
}
/* NAV */
nav{
position:fixed;top:0;left:0;right:0;z-index:100;
display:flex;align-items:center;justify-content:space-between;
padding:18px 6vw;
background:rgba(8,11,16,0.72);
backdrop-filter:blur(14px);
border-bottom:1px solid var(--border);
transition:padding .3s ease;
}
.logo{font-weight:700;font-size:19px;letter-spacing:0.5px;display:flex;align-items:center;gap:8px;}
.logo .dot{color:var(--accent);}
.nav-links{display:flex;gap:34px;list-style:none;}
.nav-links a{
font-size:14px;color:var(--text-dim);font-weight:500;letter-spacing:.2px;
position:relative;padding:4px 0;transition:color .25s ease;
}
.nav-links a::after{
content:'';position:absolute;left:0;bottom:-3px;width:0;height:1.5px;background:var(--accent);
transition:width .25s ease;
}
.nav-links a:hover{color:var(--text);}
.nav-links a:hover::after{width:100%;}
.nav-cta{
font-size:13px;font-weight:600;padding:9px 18px;border-radius:8px;
border:1px solid var(--accent);color:var(--accent);
transition:all .25s ease;white-space:nowrap;
}
.nav-cta:hover{background:var(--accent);color:#04120f;}
.burger{display:none;flex-direction:column;gap:5px;cursor:pointer;z-index:110;}
.burger span{width:24px;height:2px;background:var(--text);border-radius:2px;transition:.3s;}
/* HERO */
.hero{
position:relative;min-height:100vh;display:flex;flex-direction:column;
align-items:center;justify-content:center;text-align:center;
padding:120px 6vw 80px;overflow:hidden;
}
#particles{position:absolute;inset:0;z-index:0;opacity:0.55;}
.hero-glow{
position:absolute;width:640px;height:640px;border-radius:50%;
background:radial-gradient(circle, rgba(79,214,199,0.16), transparent 70%);
top:-180px;left:50%;transform:translateX(-50%);z-index:0;pointer-events:none;
}
.eyebrow{
position:relative;z-index:2;
display:inline-flex;align-items:center;gap:8px;
font-size:12.5px;font-weight:600;letter-spacing:1.6px;text-transform:uppercase;
color:var(--accent);background:var(--accent-soft);
border:1px solid rgba(79,214,199,0.3);
padding:7px 16px;border-radius:100px;margin-bottom:28px;
}
.eyebrow .pulse{width:7px;height:7px;border-radius:50%;background:var(--accent);
box-shadow:0 0 0 0 rgba(79,214,199,.6);animation:pulse 2s infinite;}
@keyframes pulse{
0%{box-shadow:0 0 0 0 rgba(79,214,199,.55);}
70%{box-shadow:0 0 0 10px rgba(79,214,199,0);}
100%{box-shadow:0 0 0 0 rgba(79,214,199,0);}
}
.hero h1{
position:relative;z-index:2;
font-size:clamp(38px,7vw,80px);font-weight:700;line-height:1.03;letter-spacing:-1.5px;
margin-bottom:20px;
}
.hero h1 span{
background:linear-gradient(120deg,var(--accent) 10%,#7ee8dc 50%, var(--accent2) 100%);
-webkit-background-clip:text;background-clip:text;color:transparent;
}
.hero .role{
position:relative;z-index:2;
font-size:clamp(15px,2.4vw,20px);color:var(--text-dim);font-weight:500;
max-width:720px;margin-bottom:14px;
}
.hero .role b{color:var(--text);font-weight:600;}
.hero p.summary{
position:relative;z-index:2;
max-width:660px;color:var(--text-faint);font-size:15px;margin-bottom:38px;
}
.hero-actions{position:relative;z-index:2;display:flex;gap:14px;flex-wrap:wrap;justify-content:center;margin-bottom:46px;}
.btn{
padding:13px 26px;border-radius:9px;font-weight:600;font-size:14.5px;
display:inline-flex;align-items:center;gap:8px;transition:all .25s ease;cursor:pointer;
}
.btn-primary{background:var(--accent);color:#04120f;}
.btn-primary:hover{transform:translateY(-2px);box-shadow:0 10px 30px -8px rgba(79,214,199,0.5);}
.btn-ghost{border:1px solid var(--border);color:var(--text);}
.btn-ghost:hover{border-color:var(--accent);color:var(--accent);transform:translateY(-2px);}
.hero-meta{
position:relative;z-index:2;
display:flex;gap:28px;flex-wrap:wrap;justify-content:center;
font-size:13.5px;color:var(--text-dim);
}
.hero-meta span{display:flex;align-items:center;gap:7px;}
.hero-meta svg{width:15px;height:15px;stroke:var(--accent);flex-shrink:0;}
.scroll-cue{
position:absolute;bottom:34px;left:50%;transform:translateX(-50%);z-index:2;
display:flex;flex-direction:column;align-items:center;gap:8px;
color:var(--text-faint);font-size:11px;letter-spacing:2px;text-transform:uppercase;
animation:bob 2.4s ease-in-out infinite;
}
@keyframes bob{0%,100%{transform:translate(-50%,0);}50%{transform:translate(-50%,8px);}}
/* SECTION shared */
section{position:relative;z-index:1;padding:110px 6vw;}
.wrap{max-width:var(--maxw);margin:0 auto;}
.section-tag{
font-size:12.5px;font-weight:700;letter-spacing:2px;text-transform:uppercase;color:var(--accent);
margin-bottom:14px;display:flex;align-items:center;gap:10px;
}
.section-tag::before{content:'';width:26px;height:2px;background:var(--accent);display:inline-block;}
.section-title{font-size:clamp(26px,4vw,40px);font-weight:700;letter-spacing:-0.8px;margin-bottom:18px;}
.section-lead{color:var(--text-dim);font-size:15.5px;max-width:660px;margin-bottom:56px;}
.reveal{opacity:0;transform:translateY(28px);transition:opacity .7s ease, transform .7s ease;}
.reveal.visible{opacity:1;transform:translateY(0);}
/* ABOUT */
.about-grid{display:grid;grid-template-columns:1.3fr 1fr;gap:60px;align-items:start;}
.about-grid p{color:var(--text-dim);font-size:15.5px;margin-bottom:18px;}
.about-grid p b{color:var(--text);font-weight:600;}
.stat-card{
background:var(--card);border:1px solid var(--border);border-radius:var(--radius);
padding:22px 24px;margin-bottom:14px;
display:flex;align-items:center;justify-content:space-between;
transition:border-color .25s ease, transform .25s ease;
}
.stat-card:hover{border-color:var(--accent);transform:translateX(4px);}
.stat-card .num{font-family:'Space Grotesk';font-size:30px;font-weight:700;color:var(--accent);}
.stat-card .label{font-size:13px;color:var(--text-dim);text-align:right;max-width:170px;}
/* FOCUS CARDS */
.focus-grid{display:grid;grid-template-columns:repeat(4,1fr);gap:20px;}
.focus-card{
background:var(--card);border:1px solid var(--border);border-radius:var(--radius);
padding:28px 22px;transition:all .3s ease;position:relative;overflow:hidden;
}
.focus-card::before{
content:'';position:absolute;top:0;left:0;right:0;height:2px;
background:linear-gradient(90deg,var(--accent),var(--accent2));
transform:scaleX(0);transform-origin:left;transition:transform .35s ease;
}
.focus-card:hover{transform:translateY(-6px);border-color:transparent;background:var(--card-hover);
box-shadow:0 20px 40px -20px rgba(0,0,0,.6);}
.focus-card:hover::before{transform:scaleX(1);}
.focus-icon{
width:44px;height:44px;border-radius:10px;background:var(--accent-soft);
display:flex;align-items:center;justify-content:center;margin-bottom:18px;
}
.focus-icon svg{width:22px;height:22px;stroke:var(--accent);}
.focus-card h3{font-size:17px;margin-bottom:10px;font-weight:600;}
.focus-card p{font-size:13.8px;color:var(--text-dim);}
/* EXPERIENCE TIMELINE */
.timeline{position:relative;padding-left:36px;}
.timeline::before{content:'';position:absolute;left:6px;top:8px;bottom:8px;width:1.5px;
background:linear-gradient(var(--accent), var(--border) 90%);}
.t-item{position:relative;padding-bottom:52px;}
.t-item:last-child{padding-bottom:0;}
.t-dot{position:absolute;left:-36px;top:4px;width:13px;height:13px;border-radius:50%;
background:var(--bg);border:2px solid var(--accent);}
.t-item.current .t-dot{background:var(--accent);box-shadow:0 0 0 4px var(--accent-soft);}
.t-head{display:flex;flex-wrap:wrap;align-items:baseline;justify-content:space-between;gap:10px;margin-bottom:6px;}
.t-role{font-size:19px;font-weight:600;font-family:'Space Grotesk';}
.t-date{font-size:12.5px;color:var(--accent);font-weight:600;letter-spacing:.4px;
background:var(--accent-soft);padding:4px 12px;border-radius:100px;white-space:nowrap;}
.t-org{font-size:14px;color:var(--text-dim);margin-bottom:14px;font-style:italic;}
.t-proj{margin-bottom:16px;}
.t-proj h4{font-size:13.5px;color:var(--accent2);font-weight:600;margin-bottom:6px;letter-spacing:.2px;}
.t-item ul{list-style:none;}
.t-item li{
font-size:14.3px;color:var(--text-dim);padding-left:18px;position:relative;margin-bottom:7px;
}
.t-item li::before{content:'▸';position:absolute;left:0;color:var(--accent);}
/* PUBLICATIONS */
.pub-tabs{display:flex;gap:10px;margin-bottom:32px;flex-wrap:wrap;}
.pub-tab{
padding:8px 18px;border-radius:100px;border:1px solid var(--border);font-size:13px;
font-weight:600;color:var(--text-dim);cursor:pointer;transition:all .2s ease;
}
.pub-tab.active,.pub-tab:hover{border-color:var(--accent);color:var(--accent);background:var(--accent-soft);}
.pub-list{display:flex;flex-direction:column;gap:12px;}
.pub-item{
display:grid;grid-template-columns:44px 1fr auto;gap:20px;align-items:center;
background:var(--card);border:1px solid var(--border);border-radius:12px;
padding:20px 24px;transition:all .25s ease;
}
.pub-item:hover{border-color:var(--accent);transform:translateX(4px);}
.pub-num{font-family:'JetBrains Mono';color:var(--text-faint);font-size:15px;font-weight:500;}
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<div class="avatar"><img src="profile.jpg" alt="Mallikarjuna Thippana" onerror="this.style.display='none'"><span>MT</span></div>
<div class="eyebrow"><span class="pulse"></span> Open to Bioinformatics Scientist / Computational Biology roles</div>
<h1>Mallikarjuna <span>Thippana</span>, PhD</h1>
<p class="role">Computational Biologist — <b>Genomics, Epigenomics & Data Science</b></p>
<p class="summary">7+ years turning large-scale genomic and epigenomic data — from bulk to single-cell and spatial multi-omics — into reproducible pipelines and biological insight. Postdoctoral researcher at Karolinska Institutet, working at the intersection of chromatin biology, genomics, and machine learning.</p>
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<a href="CV_Thippana_2026.pdf" class="btn btn-primary" download>Download CV</a>
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<div class="updates">
<div class="u-label"><span class="pulse"></span> Latest</div>
<div class="u-track">
<span class="u-item"><b>2026</b> Co-authored CTCF/MYC study under review at Nucleic Acids Research (IF ~23.5)</span>
<span class="u-item"><b>2025</b> New first-author preprint & journal paper on lung squamous cell carcinoma</span>
<span class="u-item"><b>Dec 2024</b> Joined Karolinska Institutet as Postdoctoral Researcher, Dept. of Oncology-Pathology</span>
<span class="u-item"><b>2024</b> Completed PhD in Computational Systems Biology, University of Hyderabad</span>
</div>
</div>
<section id="about">
<div class="wrap reveal">
<div class="section-tag">Profile</div>
<h2 class="section-title">Bridging wet-lab biology<br>and computational rigor</h2>
<div class="about-grid">
<div>
<p>I'm a <b>PhD-level computational biologist</b> with a specialization in Computational Systems Biology and 7+ years analysing large-scale multi-omics datasets in cancer genomics, chromatin biology, and, more recently, single-cell and spatial biology.</p>
<p>Across postdoctoral and doctoral research, I've built <b>end-to-end reproducible pipelines</b> — from raw NGS reads to publication-ready figures — spanning bulk and single-cell RNA-seq, ChIP-seq, ATAC-seq/scATAC-seq, CUT&RUN, GRO-seq, WGS/WES variant calling, and spatial transcriptomics, deployed on Linux HPC infrastructure with Nextflow and Snakemake.</p>
<p>At <b>Karolinska Institutet</b> I work on 3D genome organisation, chromatin remodelling in metastasis, and patient stratification using single-nucleus RNA-seq — applying statistical and machine learning methods to high-dimensional biological data and translating results for clinicians and molecular biologists alike.</p>
</div>
<div>
<div class="stat-card"><span class="num">7+</span><span class="label">Years in computational biology & genomics</span></div>
<div class="stat-card"><span class="num">11</span><span class="label">Peer-reviewed publications + preprints</span></div>
<div class="stat-card"><span class="num">6</span><span class="label">Competitive fellowships & travel awards</span></div>
<div class="stat-card"><span class="num">5+</span><span class="label">Cross-institutional research collaborations</span></div>
</div>
</div>
</div>
</section>
<section id="focus" style="background:var(--bg-alt);border-top:1px solid var(--border);border-bottom:1px solid var(--border);">
<div class="wrap reveal">
<div class="section-tag">Research Focus</div>
<h2 class="section-title">What I work on</h2>
<p class="section-lead">Four interconnected areas spanning bulk & single-cell genomics, chromatin biology, and applied machine learning.</p>
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<h3>Genomics & Single-Cell Multi-Omics</h3>
<p>Bulk & single-cell RNA-seq, scATAC-seq, multiome, and 10x Visium spatial workflows — from alignment and QC to differential expression, clustering, and deconvolution.</p>
</div>
<div class="focus-card">
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<h3>Cancer Epigenomics</h3>
<p>ChIP-seq, ATAC-seq, CUT&RUN, GRO-seq and 3D genome integration to map enhancers, CTCF-driven regulatory loops, and chromatin remodelling in metastatic progression.</p>
</div>
<div class="focus-card">
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<h3>Statistical ML for Biology</h3>
<p>Supervised & unsupervised learning, dimensionality reduction, latent variable models, and gene regulatory network inference on high-dimensional biological data.</p>
</div>
<div class="focus-card">
<div class="focus-icon"><svg viewBox="0 0 24 24" fill="none" stroke-width="2"><path d="M20 7h-9M14 17H5"/><circle cx="17" cy="17" r="3"/><circle cx="7" cy="7" r="3"/></svg></div>
<h3>Reproducible Pipelines</h3>
<p>Version-controlled, HPC-deployed Nextflow & Snakemake workflows engineered for reproducibility, automation, and cross-team reuse.</p>
</div>
</div>
</div>
</section>
<section id="experience">
<div class="wrap reveal">
<div class="section-tag">Experience</div>
<h2 class="section-title">Research Experience</h2>
<p class="section-lead">From cancer network biology to single-cell multi-omics in a clinical epigenomics group.</p>
<div class="timeline">
<div class="t-item current">
<div class="t-dot"></div>
<div class="t-head">
<span class="t-role">Postdoctoral Researcher — Computational Cancer Epigenomics</span>
<span class="t-date">Dec 2024 – Present</span>
</div>
<div class="t-org">Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden</div>
<div class="t-proj">
<h4>3D genome organisation & transcriptional regulation in cancer</h4>
<ul>
<li>Integrate GRO-seq, ATAC-seq & RNA-seq to characterise chromatin accessibility and transcriptional dynamics; built reproducible HPC pipelines for multi-omics processing</li>
<li>Co-author on a study (Nucleic Acids Research, 2026, under review, IF ~23.5) resolving how a distal CTCF-binding site controls MYC expression plasticity via a negative feed-forward loop</li>
</ul>
</div>
<div class="t-proj">
<h4>p60AmotL2, mechanotransduction & chromatin remodelling in metastasis</h4>
<ul>
<li>Integrative ATAC-seq & multi-omics analysis of chromatin accessibility changes driving invasive, metastatic cancer phenotypes</li>
<li>Applied statistical inference & dimensionality reduction to identify differential regulatory elements and TF activity across cancer cell states</li>
</ul>
</div>
<div class="t-proj">
<h4>snRNA-seq — human endometrium in PCOS</h4>
<ul>
<li>Full snRNA-seq workflow: ambient RNA removal, doublet detection, Harmony multi-donor integration, Leiden clustering, cell-type annotation</li>
<li>Patient-level stratification: PCOS vs. control differential expression, CTCF binding-site enrichment near TSS, cohort variability analysis</li>
</ul>
</div>
<div class="t-proj">
<h4>Transcriptomic dissection of HIV–cancer pathway crosstalk</h4>
<ul>
<li>Bulk RNA-seq of HIV-positive patient cohorts to identify candidate genes and map crosstalk with oncogenic pathways</li>
</ul>
</div>
</div>
<div class="t-item">
<div class="t-dot"></div>
<div class="t-head">
<span class="t-role">IoE Postdoctoral Fellow — Computational Drug Discovery</span>
<span class="t-date">Jul – Nov 2024</span>
</div>
<div class="t-org">Computational Chemistry/Bioinformatics Group, University of Hyderabad, India</div>
<ul>
<li>Applied structural bioinformatics, cheminformatics, molecular docking, pharmacophore modelling & ADMET profiling to identify novel Tyrosine Kinase inhibitor candidates</li>
</ul>
</div>
<div class="t-item">
<div class="t-dot"></div>
<div class="t-head">
<span class="t-role">PhD Researcher — Cancer Multi-Omics & Network Biology</span>
<span class="t-date">2018 – 2024</span>
</div>
<div class="t-org">Dept. of Biotechnology & Bioinformatics, University of Hyderabad — ICMR-funded</div>
<ul>
<li>Integrated transcriptomics, genomics & protein interaction networks (TCGA/GEO) to identify driver genes in cervical squamous cell carcinoma</li>
<li>Developed two novel ML-informed gene-prioritisation algorithms — fractal/chaos game representation and moment-of-inertia tensor analysis — both published in peer-reviewed journals</li>
<li>Five first/co-author publications; presentations at ISMB/ECCB 2023, GIW/ISCB-Asia 2022, SACB 2022</li>
<li>Mentored 5 postgraduate students and served as Graduate Teaching Assistant</li>
</ul>
</div>
<div class="t-item">
<div class="t-dot"></div>
<div class="t-head">
<span class="t-role">Junior Research Fellow — Disease Target Discovery</span>
<span class="t-date">2018 – 2019</span>
</div>
<div class="t-org">CRRao AIMSCS & School of Physics, University of Hyderabad — DST-SERB-funded</div>
<ul>
<li>Integrative network & systems biology to prioritise disease drug targets; applied statistical models to graph-structured biological data</li>
</ul>
</div>
</div>
</div>
</section>
<section id="publications" style="background:var(--bg-alt);border-top:1px solid var(--border);border-bottom:1px solid var(--border);">
<div class="wrap reveal">
<div class="section-tag">Publications</div>
<h2 class="section-title">9 Peer-Reviewed Papers + 2 Preprints</h2>
<p class="section-lead">Spanning cancer genomics, network biology, and computational method development.</p>
<div class="pub-tabs" role="tablist" aria-label="Filter publications">
<button class="pub-tab active" data-filter="all" type="button">All (11)</button>
<button class="pub-tab" data-filter="journal" type="button">Journal Articles (9)</button>
<button class="pub-tab" data-filter="preprint" type="button">Preprints (2)</button>
</div>
<div class="pub-list" id="pubList">
<div class="pub-item" data-type="journal">
<span class="pub-num">01</span>
<div>
<div class="pub-title">A distal CTCF-binding site drives MYC expression plasticity in a negative feed-forward loop</div>
<div class="pub-meta">Gao C, ... Thippana M, et al., Göndör A. <span class="pub-journal">Nucleic Acids Research</span> · 2026 <span class="pub-if">IF ~23.5</span> <span class="pub-badge">Under Review</span></div>
</div>
<a class="pub-link" href="https://doi.org/10.64898/2026.01.28.702300" target="_blank" rel="noopener" aria-label="Open DOI"><svg viewBox="0 0 24 24" fill="none" stroke-width="2"><path d="M18 13v6a2 2 0 0 1-2 2H5a2 2 0 0 1-2-2V8a2 2 0 0 1 2-2h6"/><path d="M15 3h6v6M10 14 21 3"/></svg></a>
</div>
<div class="pub-item" data-type="journal">
<span class="pub-num">02</span>
<div>
<div class="pub-title">Unraveling the gender-specific molecular landscape of lung squamous cell carcinoma progression</div>
<div class="pub-meta">Dwivedi A, Thippana M, Khammampalli S, Cholleti SN, Vindal V. <span class="pub-journal">J Biomolecular Structure & Dynamics</span> · 2025 <span class="pub-if">IF 3.4</span></div>
</div>
<a class="pub-link" href="https://doi.org/10.1080/07391102.2025.2460069" target="_blank" rel="noopener" aria-label="Open DOI"><svg viewBox="0 0 24 24" fill="none" stroke-width="2"><path d="M18 13v6a2 2 0 0 1-2 2H5a2 2 0 0 1-2-2V8a2 2 0 0 1 2-2h6"/><path d="M15 3h6v6M10 14 21 3"/></svg></a>
</div>
<div class="pub-item" data-type="journal">
<span class="pub-num">03</span>
<div>
<div class="pub-title">Prioritizing cervical cancer candidate genes using chaos game and fractal-based time series approach</div>
<div class="pub-meta">Mallikarjuna T, Thummadi NB, Vindal V, et al. <span class="pub-journal">Theory in Biosciences</span> · 2024 <span class="pub-if">IF 1.8</span></div>
</div>
<div class="pub-links">
<a class="pub-link" href="https://doi.org/10.1007/s12064-024-00418-3" target="_blank" rel="noopener" aria-label="Open DOI"><svg viewBox="0 0 24 24" fill="none" stroke-width="2"><path d="M18 13v6a2 2 0 0 1-2 2H5a2 2 0 0 1-2-2V8a2 2 0 0 1 2-2h6"/><path d="M15 3h6v6M10 14 21 3"/></svg></a>
<a class="pub-link" href="https://github.com/arjunbioinfo/cgr-mfxdfa-gene-prioritization" target="_blank" rel="noopener" aria-label="View code"><svg viewBox="0 0 24 24" fill="none" stroke-width="2"><path d="M9 19c-5 1.5-5-2.5-7-3m14 6v-3.87a3.37 3.37 0 0 0-.94-2.61c3.14-.35 6.44-1.54 6.44-7A5.44 5.44 0 0 0 20 4.77 5.07 5.07 0 0 0 19.91 1S18.73.65 16 2.48a13.38 13.38 0 0 0-7 0C6.27.65 5.09 1 5.09 1A5.07 5.07 0 0 0 5 4.77a5.44 5.44 0 0 0-1.5 3.78c0 5.42 3.3 6.61 6.44 7A3.37 3.37 0 0 0 9 18.13V22"/></svg></a>
</div>
</div>
<div class="pub-item" data-type="journal">
<span class="pub-num">04</span>
<div>
<div class="pub-title">Identification of key molecular players and associated pathways in cervical squamous cell carcinoma progression through network analysis</div>
<div class="pub-meta">Thippana M, Dwivedi A, Das A, Palanisamy M, Vindal V. <span class="pub-journal">Proteins</span> · 2023 <span class="pub-if">IF 3.8</span></div>
</div>
<a class="pub-link" href="https://doi.org/10.1002/prot.26502" target="_blank" rel="noopener" aria-label="Open DOI"><svg viewBox="0 0 24 24" fill="none" stroke-width="2"><path d="M18 13v6a2 2 0 0 1-2 2H5a2 2 0 0 1-2-2V8a2 2 0 0 1 2-2h6"/><path d="M15 3h6v6M10 14 21 3"/></svg></a>
</div>
<div class="pub-item" data-type="journal">
<span class="pub-num">05</span>
<div>
<div class="pub-title">Fused toes homolog, a potential molecular regulator of human papillomavirus type 16 E6 and E7 oncoproteins in cervical cancer</div>
<div class="pub-meta">D.S.P, Chaturvedi PK, Krishnamoorthy D, Seo YS, Thippana M, et al. <span class="pub-journal">PLOS ONE</span> · 2022 <span class="pub-if">IF 3.7</span></div>
</div>
<a class="pub-link" href="https://doi.org/10.1371/journal.pone.0266532" target="_blank" rel="noopener" aria-label="Open DOI"><svg viewBox="0 0 24 24" fill="none" stroke-width="2"><path d="M18 13v6a2 2 0 0 1-2 2H5a2 2 0 0 1-2-2V8a2 2 0 0 1 2-2h6"/><path d="M15 3h6v6M10 14 21 3"/></svg></a>
</div>
<div class="pub-item" data-type="journal">
<span class="pub-num">06</span>
<div>
<div class="pub-title">Prioritizing the candidate genes related to cervical cancer using the moment of inertia tensor</div>
<div class="pub-meta">Thummadi NB, Thippana M, Vindal V, P.M. <span class="pub-journal">Proteins</span> · 2022 <span class="pub-if">IF 3.8</span></div>
</div>
<div class="pub-links">
<a class="pub-link" href="https://doi.org/10.1002/prot.26226" target="_blank" rel="noopener" aria-label="Open DOI"><svg viewBox="0 0 24 24" fill="none" stroke-width="2"><path d="M18 13v6a2 2 0 0 1-2 2H5a2 2 0 0 1-2-2V8a2 2 0 0 1 2-2h6"/><path d="M15 3h6v6M10 14 21 3"/></svg></a>
<a class="pub-link" href="https://github.com/arjunbioinfo/moment-of-inertia-tensor-gene-prioritization" target="_blank" rel="noopener" aria-label="View code"><svg viewBox="0 0 24 24" fill="none" stroke-width="2"><path d="M9 19c-5 1.5-5-2.5-7-3m14 6v-3.87a3.37 3.37 0 0 0-.94-2.61c3.14-.35 6.44-1.54 6.44-7A5.44 5.44 0 0 0 20 4.77 5.07 5.07 0 0 0 19.91 1S18.73.65 16 2.48a13.38 13.38 0 0 0-7 0C6.27.65 5.09 1 5.09 1A5.07 5.07 0 0 0 5 4.77a5.44 5.44 0 0 0-1.5 3.78c0 5.42 3.3 6.61 6.44 7A3.37 3.37 0 0 0 9 18.13V22"/></svg></a>
</div>
</div>
<div class="pub-item" data-type="journal">
<span class="pub-num">07</span>
<div>
<div class="pub-title">Synthesis of pyrazolo[3,4-d]pyrimidin-4(5H)-ones tethered to 1,2,3-triazoles and their evaluation as potential anticancer agents</div>
<div class="pub-meta">Allam M, Bhavani AKD, Mudiraj A, Ranjan N, Thippana M, Babu PP. <span class="pub-journal">European Journal of Medicinal Chemistry</span> · 2018 <span class="pub-if">IF 6.7</span></div>
</div>
<a class="pub-link" href="https://doi.org/10.1016/j.ejmech.2018.06.055" target="_blank" rel="noopener" aria-label="Open DOI"><svg viewBox="0 0 24 24" fill="none" stroke-width="2"><path d="M18 13v6a2 2 0 0 1-2 2H5a2 2 0 0 1-2-2V8a2 2 0 0 1 2-2h6"/><path d="M15 3h6v6M10 14 21 3"/></svg></a>
</div>
<div class="pub-item" data-type="journal">
<span class="pub-num">08</span>
<div>
<div class="pub-title">Total Synthesis of Penicinoline E, Marinamide and Methyl marinamide and its antimalarial activity</div>
<div class="pub-meta">Naveen B, Ommi NB, Mudiraj A, Mallikarjuna T, Babu PP, Nagarajan R. <span class="pub-journal">ChemistrySelect</span> · 2017 <span class="pub-if">IF 2.1</span></div>
</div>
<a class="pub-link" href="https://doi.org/10.1002/slct.201700242" target="_blank" rel="noopener" aria-label="Open DOI"><svg viewBox="0 0 24 24" fill="none" stroke-width="2"><path d="M18 13v6a2 2 0 0 1-2 2H5a2 2 0 0 1-2-2V8a2 2 0 0 1 2-2h6"/><path d="M15 3h6v6M10 14 21 3"/></svg></a>
</div>
<div class="pub-item" data-type="journal">
<span class="pub-num">09</span>
<div>
<div class="pub-title">A Homology Based Model and Virtual Screening of Inhibitors for Geranylgeranyl Transferase 1 (GGTase1)</div>
<div class="pub-meta">Thippanna M, et al. <span class="pub-journal">Bioinformation</span> · 2013 <span class="pub-if">IF 1.3</span></div>
</div>
<a class="pub-link" href="https://doi.org/10.6026/97320630009973" target="_blank" rel="noopener" aria-label="Open DOI"><svg viewBox="0 0 24 24" fill="none" stroke-width="2"><path d="M18 13v6a2 2 0 0 1-2 2H5a2 2 0 0 1-2-2V8a2 2 0 0 1 2-2h6"/><path d="M15 3h6v6M10 14 21 3"/></svg></a>
</div>
<div class="pub-item" data-type="preprint">
<span class="pub-num">10</span>
<div>
<div class="pub-title">LCLNCRdb: A Comprehensive Resource for Investigating long non-coding RNAs in Lung Cancer</div>
<div class="pub-meta">Dwivedi A, Zulfia SA, Thippana M, Cholleti SN, Vindal V. <span class="pub-journal">bioRxiv</span> · 2025 <span class="pub-badge">Preprint</span></div>
</div>
<a class="pub-link" href="https://doi.org/10.1101/2025.02.14.638263" target="_blank" rel="noopener" aria-label="Open DOI"><svg viewBox="0 0 24 24" fill="none" stroke-width="2"><path d="M18 13v6a2 2 0 0 1-2 2H5a2 2 0 0 1-2-2V8a2 2 0 0 1 2-2h6"/><path d="M15 3h6v6M10 14 21 3"/></svg></a>
</div>
<div class="pub-item" data-type="preprint">
<span class="pub-num">11</span>
<div>
<div class="pub-title">Prioritization of Lung Cancer Candidate Genes using Moment of Inertia Tensor Analysis</div>
<div class="pub-meta">Dwivedi A, Thippana M, Manimaran P, Vindal V. <span class="pub-journal">bioRxiv</span> · 2024 <span class="pub-badge">Preprint</span></div>
</div>
<a class="pub-link" href="https://doi.org/10.1101/2024.10.18.619023" target="_blank" rel="noopener" aria-label="Open DOI"><svg viewBox="0 0 24 24" fill="none" stroke-width="2"><path d="M18 13v6a2 2 0 0 1-2 2H5a2 2 0 0 1-2-2V8a2 2 0 0 1 2-2h6"/><path d="M15 3h6v6M10 14 21 3"/></svg></a>
</div>
</div>
<p class="pub-more">Full list on <a href="https://scholar.google.com/citations?user=NpLUj68AAAAJ&hl=en" target="_blank" rel="noopener">Google Scholar →</a></p>
</div>
</section>
<section id="skills">
<div class="wrap reveal">
<div class="section-tag">Technical Expertise</div>
<h2 class="section-title">Tools & Technologies</h2>
<p class="section-lead">The computational stack behind the research above.</p>
<div class="skills-grid">
<div class="skill-cat">
<h4>Python Ecosystem</h4>
<div class="chip-row">
<span class="chip">Scanpy</span><span class="chip">scverse</span><span class="chip">anndata</span><span class="chip">squidpy</span><span class="chip">scikit-learn</span><span class="chip">SciPy</span><span class="chip">pandas</span><span class="chip">NumPy</span><span class="chip">matplotlib</span><span class="chip">seaborn</span>
</div>
</div>
<div class="skill-cat">
<h4>R Ecosystem</h4>
<div class="chip-row">
<span class="chip">Seurat</span><span class="chip">Signac</span><span class="chip">Bioconductor</span><span class="chip">DESeq2</span><span class="chip">edgeR</span><span class="chip">ggplot2</span><span class="chip">Harmony</span><span class="chip">Monocle3</span>
</div>
</div>
<div class="skill-cat">
<h4>Single-Cell & Spatial</h4>
<div class="chip-row">
<span class="chip">CellRanger</span><span class="chip">STARsolo</span><span class="chip">SoupX</span><span class="chip">CellBender</span><span class="chip">Scrublet</span><span class="chip">DoubletFinder</span><span class="chip">10x Visium</span><span class="chip">SpatialDE</span><span class="chip">cell2location</span><span class="chip">RCTD</span>
</div>
</div>
<div class="skill-cat">
<h4>ML & Trajectory</h4>
<div class="chip-row">
<span class="chip">PCA / UMAP</span><span class="chip">Leiden / Louvain</span><span class="chip">Diffusion Maps</span><span class="chip">scVelo</span><span class="chip">SCENIC / pySCENIC</span><span class="chip">MOFA+</span>
</div>
</div>
<div class="skill-cat">
<h4>Genomics & Epigenomics</h4>
<div class="chip-row">
<span class="chip">Bulk RNA-seq</span><span class="chip">ChIP-seq</span><span class="chip">ATAC-seq</span><span class="chip">CUT&RUN</span><span class="chip">GATK</span><span class="chip">Samtools</span><span class="chip">Bedtools</span><span class="chip">deepTools</span><span class="chip">MACS2</span><span class="chip">ArchR</span><span class="chip">IGV</span><span class="chip">GRO-seq</span><span class="chip">WGS/WES</span>
</div>
</div>
<div class="skill-cat">
<h4>Workflow, HPC & Databases</h4>
<div class="chip-row">
<span class="chip">Nextflow</span><span class="chip">Snakemake</span><span class="chip">Git</span><span class="chip">Linux HPC</span><span class="chip">Jupyter</span><span class="chip">TCGA</span><span class="chip">GEO</span><span class="chip">GTEx</span><span class="chip">Ensembl</span><span class="chip">Human Cell Atlas</span>
</div>
</div>
</div>
</div>
</section>
<section id="awards" style="background:var(--bg-alt);border-top:1px solid var(--border);border-bottom:1px solid var(--border);">
<div class="wrap reveal">
<div class="section-tag">Recognition & Education</div>
<h2 class="section-title">Awards & Academic Background</h2>
<div class="two-col">
<div>
<h3 style="font-size:15px;color:var(--text-dim);margin-bottom:6px;font-weight:600;text-transform:uppercase;letter-spacing:1px;">Honours & Awards</h3>
<div class="award-row"><span class="award-date">Jun 2023</span><span class="award-text"><b>DST-SERB International Travel Support</b><span>ISMB/ECCB 2023, Lyon, France</span></span></div>
<div class="award-row"><span class="award-date">May 2023</span><span class="award-text"><b>ISCB Travel Fellowship</b><span>ISMB/ECCB 2023, Lyon, France</span></span></div>
<div class="award-row"><span class="award-date">Apr 2023</span><span class="award-text"><b>NUS–Temasek Foundation Travel Grant</b><span>RNA Society Annual Meeting, Singapore</span></span></div>
<div class="award-row"><span class="award-date">Oct 2022</span><span class="award-text"><b>DBT-CTEP Travel Grant</b><span>SACB 2022, Woods Hole, USA</span></span></div>
<div class="award-row"><span class="award-date">Jun 2019</span><span class="award-text"><b>ICMR Senior Research Fellowship</b><span>Indian Council of Medical Research, Govt. of India</span></span></div>
<div class="award-row"><span class="award-date">2015</span><span class="award-text"><b>GATE 2015</b><span>Graduate Aptitude Test in Engineering (Biotechnology)</span></span></div>
</div>
<div>
<h3 style="font-size:15px;color:var(--text-dim);margin-bottom:16px;font-weight:600;text-transform:uppercase;letter-spacing:1px;">Education</h3>
<div class="edu-item">
<div class="deg">PhD, Biotechnology — Computational Systems Biology</div>
<div class="school">University of Hyderabad, India</div>
<div class="thesis">"Integrative studies to explore key molecular players involved in cervical squamous cell carcinoma"</div>
<div class="yrs">Aug 2018 – May 2024</div>
</div>
<div class="edu-item">
<div class="deg">M.Tech, Bioinformatics</div>
<div class="school">University of Hyderabad, India · GATE 2015 qualified</div>
<div class="yrs">2015 – 2017</div>
</div>
</div>
</div>
</div>
</section>
<section id="conferences">
<div class="wrap reveal">
<div class="section-tag">Community</div>
<h2 class="section-title">Conferences & Memberships</h2>
<p class="section-lead">Presenting research internationally and staying active in the computational biology community.</p>
<div class="conf-grid">
<div>
<h3 style="font-size:15px;color:var(--text-dim);margin-bottom:16px;font-weight:600;text-transform:uppercase;letter-spacing:1px;">Conferences Attended</h3>
<div class="conf-card">
<div class="conf-icon"><svg viewBox="0 0 24 24" fill="none" stroke-width="2"><path d="M12 21s-7-6.2-7-11a7 7 0 1 1 14 0c0 4.8-7 11-7 11z"/><circle cx="12" cy="10" r="2.5"/></svg></div>
<div>
<div class="conf-name">ISMB/ECCB 2023</div>
<div class="conf-meta"><span>Lyon, France</span><span class="sep">·</span><span>Jun 2023</span><span class="sep">·</span><span>Oral & poster presentation</span></div>
</div>
</div>
<div class="conf-card">
<div class="conf-icon"><svg viewBox="0 0 24 24" fill="none" stroke-width="2"><path d="M12 21s-7-6.2-7-11a7 7 0 1 1 14 0c0 4.8-7 11-7 11z"/><circle cx="12" cy="10" r="2.5"/></svg></div>
<div>
<div class="conf-name">RNA Society Annual Meeting</div>
<div class="conf-meta"><span>Singapore</span><span class="sep">·</span><span>Apr 2023</span></div>
</div>
</div>
<div class="conf-card">
<div class="conf-icon"><svg viewBox="0 0 24 24" fill="none" stroke-width="2"><path d="M12 21s-7-6.2-7-11a7 7 0 1 1 14 0c0 4.8-7 11-7 11z"/><circle cx="12" cy="10" r="2.5"/></svg></div>
<div>
<div class="conf-name">SACB — Systems Approaches to Cancer Biology 2022</div>
<div class="conf-meta"><span>Woods Hole, USA</span><span class="sep">·</span><span>Oct 2022</span></div>
</div>
</div>
<div class="conf-card">
<div class="conf-icon"><svg viewBox="0 0 24 24" fill="none" stroke-width="2"><path d="M12 21s-7-6.2-7-11a7 7 0 1 1 14 0c0 4.8-7 11-7 11z"/><circle cx="12" cy="10" r="2.5"/></svg></div>
<div>
<div class="conf-name">GIW/ISCB-Asia 2022</div>
<div class="conf-meta"><span>Tainan, Taiwan</span><span class="sep">·</span><span>2022</span><span class="sep">·</span><span>Oral & poster presentation</span></div>
</div>
</div>
<p style="font-size:13px;color:var(--text-faint);margin-top:6px;">7 international conference presentations in total across the above and additional venues.</p>
</div>
<div>
<h3 style="font-size:15px;color:var(--text-dim);margin-bottom:16px;font-weight:600;text-transform:uppercase;letter-spacing:1px;">Professional Memberships</h3>
<div class="mem-card">
<span class="mem-name">RNA Society</span>
<span class="mem-since">2024 – present</span>
</div>
<div class="mem-card">
<span class="mem-name">ISCB — International Society for Computational Biology</span>
<span class="mem-since">2022 – present</span>
</div>
<div class="mem-card">
<span class="mem-name">FABA</span>
<span class="mem-since">2022 – present</span>
</div>
</div>
</div>
</div>
</section>
<section class="contact-cta" id="contact">
<div class="wrap reveal">
<div class="section-tag" style="justify-content:center;">Get In Touch</div>
<h2>Let's talk <span>science</span>, data,<br>or opportunities.</h2>
<p>Open to bioinformatics scientist and computational biology roles in industry and academia — drug discovery, biomarker research, precision medicine, and genomics/epigenomics from bulk to single-cell.</p>
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