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<!doctype html>
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<title>Arjun Patel, PhD — Genome-scale Modeling & Data Analytics</title>
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<span class="dot"></span><span>Arjun Patel, PhD</span>
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<a href="#about">About</a>
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<p class="kicker">Postdoctoral Scholar · San Diego State University</p>
<h1>Genome-scale modeling & data analytics for biology.</h1>
<p class="lead">I’m a computational systems biologist with 14 peer-reviewed publications and six years building predictive genome-scale models of microbial metabolism. I currently apply metabolism-and-expression (ME) modeling to plant rhizosphere bacteria for bioenergy applications, and I specialize in translating multi-omics data into models that guide strain engineering.</p>
<div class="cta">
<a class="btn" href="assets/Arjun_Patel_CV.pdf" target="_blank" rel="noopener noreferrer">Download CV</a>
<a class="btn ghost" href="#contact">Contact</a>
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<div class="social">
<a href="https://scholar.google.com/citations?user=5Ym5JKAAAAAJ&hl=en" target="_blank" rel="noopener noreferrer">Google Scholar</a>
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<img src="assets/arjun.jpg" alt="Arjun Patel, PhD" class="profile-img" width="420" height="420" />
<h2>Quick links</h2>
<ul class="quick">
<li><a href="https://www.cobrame.org" target="_blank" rel="noopener noreferrer">COBRAme.org <span aria-hidden="true">↗</span></a></li>
<li><a href="https://escholarship.org/uc/item/8k63h9cx" target="_blank" rel="noopener noreferrer">Dissertation <span aria-hidden="true">↗</span></a></li>
<li><a href="#services">Consulting services</a></li>
<li><a href="#publications">Publications</a></li>
</ul>
<p class="muted">Postdoctoral Scholar at San Diego State University. Alongside that work I take on selective independent contracting in genome-scale modeling and biological data analytics.</p>
</div>
</div>
</div>
</section>
<section id="about" class="section">
<div class="container">
<h2>About</h2>
<div class="prose">
<p>I’m a Postdoctoral Scholar in the Computational Biotechnology Research Group at San Diego State University, where I build metabolism-and-expression (ME) models for plant rhizosphere bacteria with integrated pH- and temperature-stress mechanisms. I validate these reconstructions against large-scale phenotypic screens across pH and temperature gradients, integrate model predictions with multi-omics and biogeochemical data from the Earth Microbiome Project, NMDC, and NEON, and contribute to federally funded research programs (DOE, NSF) on metabolic modeling of bioenergy-relevant microbial systems.</p><p>My PhD work at UC San Diego combined unsupervised machine learning on large multi-omics datasets with genome-scale metabolism and expression models to study proteome allocation and stress response in <em>E. coli</em>. I also built and deployed a web-based platform that makes ME-model tools accessible to the broader scientific community.</p><p>Alongside my postdoctoral position, I consult for academic research groups under an independent contractor agreement — ME-model reconstruction, constraint-based modeling methods, multi-omics analysis, and modeling infrastructure.</p>
</div>
</div>
</section>
<section id="services" class="section alt">
<div class="container">
<h2>Services</h2>
<p class="subhead">Selective independent contracting for academic labs, biotech, and industry R&D, taken on alongside my postdoctoral research.</p>
<div class="cards">
<div class="card"><h3>Genome-scale modeling</h3><p>Build, curate, and analyze GEMs and ME-models; condition-specific constraints; gene knockouts; and interpretable model-based predictions.</p></div>
<div class="card"><h3>Constraint-based analysis</h3><p>FBA / ME optimization, resource allocation analyses, and workflow automation with clear documentation and reproducible outputs.</p></div>
<div class="card"><h3>Multi-omics integration</h3><p>Integrate transcriptomics, proteomics, and metabolomics with modeling frameworks; quality control, normalization, and structured compendia.</p></div>
<div class="card"><h3>Data analytics</h3><p>Statistics and ML for high-dimensional biology (dimensionality reduction, clustering, regression) with an emphasis on interpretability.</p></div>
<div class="card"><h3>Reproducible pipelines</h3><p>Python + Git + Docker-based pipelines for analyses you can hand off to a team and maintain over time.</p></div>
</div>
<div class="engagement">
<h3>Engagement types</h3>
<ul class="bullets">
<li><strong>Short consult</strong> — one or two calls + written recommendations</li>
<li><strong>Fixed-scope project</strong> — defined deliverables and timeline</li>
<li><strong>Ongoing support</strong> — weekly hours for modeling/analytics work</li>
</ul>
</div>
</div>
</section>
<section id="work" class="section">
<div class="container">
<h2>Selected work</h2>
<p class="subhead">Representative artifacts that show capabilities end-to-end.</p>
<div class="cards">
<a class="card linkcard" href="https://www.cobrame.org" target="_blank" rel="noopener noreferrer"><h3>COBRAme.org</h3><p>A web platform I built and deployed to make ME-model tools accessible to outside research groups — run and explore genome-scale metabolism & expression workflows without a local install.</p><span class="arrow">↗</span></a>
<a class="card linkcard" href="https://escholarship.org/uc/item/8k63h9cx" target="_blank" rel="noopener noreferrer"><h3>PhD Dissertation</h3><p>UC San Diego, 2025. Integrating multi-omics knowledge with constraint-based modeling to improve predictive physiology — machine learning on transcriptomes and proteomes coupled to genome-scale ME-models of <em>E. coli</em>.</p><span class="arrow">↗</span></a>
<a class="card linkcard" href="https://scholar.google.com/citations?user=5Ym5JKAAAAAJ&hl=en" target="_blank" rel="noopener noreferrer"><h3>Google Scholar</h3><p>Complete publication list, citations, and links.</p><span class="arrow">↗</span></a>
<a class="card linkcard" href="https://github.com/arjunpatel96" target="_blank" rel="noopener noreferrer"><h3>GitHub</h3><p>Open-source tools, pipelines, and modeling code.</p><span class="arrow">↗</span></a>
</div>
</div>
</section>
<section id="publications" class="section alt">
<div class="container">
<h2>Publications</h2>
<p class="subhead">
14 peer-reviewed publications. Full metrics and links on <a href="https://scholar.google.com/citations?user=5Ym5JKAAAAAJ&hl=en" target="_blank" rel="noopener noreferrer">Google Scholar <span aria-hidden="true">↗</span></a>.
</p>
<div class="pubs">
<h3 class="pub-year" id="pub-2026">2026</h3>
<ol class="pub-list">
<li><span class="pub-authors">Shin J; <strong>Patel A</strong>; Lou XA; Catoiu EA; Krishnan J; Hefner Y; Szubin R; Sung J; Son HF; Zielinski DC; Palsson BO.</span> <span class="pub-title"><a class="pub-link" href="https://doi.org/10.1073/pnas.2531884123" target="_blank" rel="noopener noreferrer">A systems-level atlas of carbon-response transcriptional states in Escherichia coli.</a></span> <span class="pub-venue"><strong>Proceedings of the National Academy of Sciences</strong> 123(27), e2531884123.</span></li>
<li><span class="pub-authors"><strong>Patel A</strong>; Banwani N; Mink R; Prabhakaran DM; Khairnar SV; Feist AM; Palsson BO; Anand A.</span> <span class="pub-title"><a class="pub-link" href="https://doi.org/10.1016/j.isci.2026.114715" target="_blank" rel="noopener noreferrer">Aerobicity stimulon in Escherichia coli revealed using multi-scale computational systems biology of respiratory variants.</a></span> <span class="pub-venue"><strong>iScience</strong> 29(2), 114715.</span></li>
</ol>
<h3 class="pub-year" id="pub-2025">2025</h3>
<ol class="pub-list">
<li><span class="pub-authors">Rychel K; Chen K; Catoiu EA; Olson CA; Sandberg TE; Gao Y; Xu S; Hefner Y; Szubin R; <strong>Patel A</strong>; Feist AM; Palsson BO.</span> <span class="pub-title"><a class="pub-link" href="https://doi.org/10.1093/gbe/evaf171" target="_blank" rel="noopener noreferrer">Laboratory evolution reveals transcriptional mechanisms underlying thermal adaptation of Escherichia coli.</a></span> <span class="pub-venue"><strong>Genome Biology and Evolution</strong> 2025 Sep 30;17(10):evaf171.</span></li>
<li><span class="pub-authors">Kundu BB; Krishnan J; Szubin R; <strong>Patel A</strong>; Palsson BO; Zielinski DC; Ajo-Franklin CM.</span> <span class="pub-title"><a class="pub-link" href="https://doi.org/10.1016/j.cell.2025.03.016" target="_blank" rel="noopener noreferrer">Extracellular respiration is a latent energy metabolism in Escherichia coli.</a></span> <span class="pub-venue"><strong>Cell</strong> 188(11), 2907–2924.e23.</span></li>
<li><span class="pub-authors">Catoiu EA; Krishnan J; Li G; Lou XA; Rychel K; Yuan Y; Bajpe H; <strong>Patel A</strong>; Choe D; Shin J; Burrows J; Phaneuf PV; Zielinski DC; Palsson BO.</span> <span class="pub-title"><a class="pub-link" href="https://doi.org/10.1093/nar/gkae1009" target="_blank" rel="noopener noreferrer">iModulonDB 2.0: dynamic tools to facilitate knowledge-mining and user-enabled analyses of curated transcriptomic datasets.</a></span> <span class="pub-venue"><strong>Nucleic Acids Research</strong> 53(D1), D99–D106.</span></li>
<li><span class="pub-authors">Beulig F; Bafna-Rührer J; Jensen PE; Kim SH; <strong>Patel A</strong>; Kandasamy V; Steffen CS; Decker K; Zielinski DC; Yang L; Ozdemir E; Sudarsan S; Palsson BO.</span> <span class="pub-title"><a class="pub-link" href="https://doi.org/10.1128/msystems.00323-25" target="_blank" rel="noopener noreferrer">Trade-off between resistance and persistence in high cell density Escherichia coli cultures.</a></span> <span class="pub-venue"><strong>mSystems</strong> 10(7), e0032325.</span></li>
</ol>
<h3 class="pub-year" id="pub-2024">2024</h3>
<ol class="pub-list">
<li><span class="pub-authors"><strong>Patel A</strong>; McGrosso D; Hefner Y; Campeau A; Sastry AV; Maurya S; Rychel K; Gonzalez DJ; Palsson BO.</span> <span class="pub-title"><a class="pub-link" href="https://doi.org/10.1038/s41467-024-49231-y" target="_blank" rel="noopener noreferrer">Proteome allocation is linked to transcriptional regulation through a modularized transcriptome.</a></span> <span class="pub-venue"><strong>Nature Communications</strong> 15(1), 5234.</span></li>
<li><span class="pub-authors">Dalldorf C; Rychel K; Szubin R; Hefner Y; <strong>Patel A</strong>; Zielinski DC; Palsson BO.</span> <span class="pub-title"><a class="pub-link" href="https://doi.org/10.1128/msystems.00305-24" target="_blank" rel="noopener noreferrer">The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions.</a></span> <span class="pub-venue"><strong>mSystems</strong> 9(7), e00305-24.</span></li>
</ol>
<h3 class="pub-year" id="pub-2023">2023</h3>
<ol class="pub-list">
<li><span class="pub-authors">Rychel K; Tan J; <strong>Patel A</strong>; Lamoureux C; Hefner Y; Szubin R; Johnsen J; Mohamed ETT; Phaneuf PV; Anand A; Olson CA; Park JH; Sastry AV; Yang L; Feist AM; Palsson BO.</span> <span class="pub-title"><a class="pub-link" href="https://doi.org/10.1016/j.celrep.2023.113105" target="_blank" rel="noopener noreferrer">Laboratory evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance.</a></span> <span class="pub-venue"><strong>Cell Reports</strong> 42(9):113105.</span></li>
<li><span class="pub-authors">Goel N; Srivastav S; <strong>Patel A</strong>; Shirsath A; Panda TR; Patra M; Feist AM; Anand A.</span> <span class="pub-title"><a class="pub-link" href="https://doi.org/10.1128/spectrum.02225-23" target="_blank" rel="noopener noreferrer">TCA cycle tailoring facilitates optimal growth of proton-pumping NADH dehydrogenase-dependent Escherichia coli.</a></span> <span class="pub-venue"><strong>Microbiology Spectrum</strong> 11(6), e02225-23.</span></li>
</ol>
<h3 class="pub-year" id="pub-2022">2022</h3>
<ol class="pub-list">
<li><span class="pub-authors">Anand A; <strong>Patel A</strong>; Chen K; Olson CA; Phaneuf PV; Lamoureux C; Hefner Y; Szubin R; Feist AM; Palsson BO.</span> <span class="pub-title"><a class="pub-link" href="https://doi.org/10.1038/s41467-022-30877-5" target="_blank" rel="noopener noreferrer">Laboratory evolution of synthetic electron transport system variants reveals a larger metabolic respiratory system and its plasticity.</a></span> <span class="pub-venue"><strong>Nature Communications</strong> 13(1), 3682.</span></li>
</ol>
<h3 class="pub-year" id="pub-2021">2021</h3>
<ol class="pub-list">
<li><span class="pub-authors">Anand A; Olson CA; Sastry AV; <strong>Patel A</strong>; Szubin R; Yang L; Feist AM; Palsson BO.</span> <span class="pub-title"><a class="pub-link" href="https://doi.org/10.1016/j.celrep.2021.108961" target="_blank" rel="noopener noreferrer">Restoration of fitness lost due to dysregulation of the pyruvate dehydrogenase complex is triggered by ribosomal binding site modifications.</a></span> <span class="pub-venue"><strong>Cell Reports</strong> 35(1), 108961.</span></li>
</ol>
<h3 class="pub-year" id="pub-2020">2020</h3>
<ol class="pub-list">
<li><span class="pub-authors">Zielinski DC; <strong>Patel A</strong>; Palsson BO.</span> <span class="pub-title"><a class="pub-link" href="https://doi.org/10.3390/microorganisms8122050" target="_blank" rel="noopener noreferrer">The expanding computational toolbox for engineering microbial phenotypes at the genome scale.</a></span> <span class="pub-venue"><strong>Microorganisms</strong> 8(12), 2050.</span></li>
</ol>
<h3 class="pub-year" id="pub-2018">2018</h3>
<ol class="pub-list">
<li><span class="pub-authors">Imbach K; <strong>Patel A</strong>; Levine AD.</span> <span class="pub-title"><a class="pub-link" href="https://doi.org/10.18609/cgti.2018.030" target="_blank" rel="noopener noreferrer">Ethical considerations in the translation of CAR-T cell therapies.</a></span> <span class="pub-venue"><strong>Immuno-oncology Insights</strong></span></li>
</ol>
</div>
</div>
</section>
<section id="cv" class="section">
<div class="container">
<h2>CV</h2>
<div class="cv-grid">
<div>
<h3>Education</h3>
<ul class="bullets">
<li><strong>PhD, Bioengineering</strong> — University of California, San Diego (Nov 2025) — GPA: 3.833</li>
<li><strong>BS, Biomedical Engineering</strong> — Georgia Institute of Technology (May 2019), minor in Engineering and Business — GPA: 4.0</li>
</ul>
<h3>Focus areas</h3>
<ul class="bullets">
<li>Genome-scale metabolic and expression (ME) modeling (COBRAme, DynamicME, StressME)</li>
<li>Stress-integrated ME-models (AcidifyME, FoldME) for pH and temperature response</li>
<li>Constraint-based modeling workflows (FBA/ME), resource allocation, condition-specific modeling</li>
<li>Multi-omics integration and interpretable ML for regulatory structure discovery</li>
<li>Software engineering for reproducible modeling pipelines (Python, Docker, GitHub)</li>
</ul>
</div>
<div>
<h3>Experience (condensed)</h3>
<ul class="bullets">
<li><strong>Postdoctoral Scholar — San Diego State University, Computational Biotechnology Research Group</strong> (2026–present)<br/>
ME-models for plant rhizosphere bacteria under pH and temperature stress; bioenergy applications; DOE/NSF proposals.</li>
<li><strong>Scientific Consultant — independent contractor</strong> (2026–present)<br/>
Computational systems biology consulting for academic research groups.</li>
<li><strong>Graduate Student Researcher — UC San Diego, Systems Biology Research Group (Palsson Lab)</strong> (2019–2025)<br/>
Genome-scale modeling + multi-omics analytics; tool development and collaborations across projects.</li>
</ul>
<h3>Selected highlights</h3>
<ul class="bullets">
<li>14 peer-reviewed publications, including first-author papers in <em>Nature Communications</em> and <em>iScience</em></li>
<li>Invited flash talk and first-author poster, Center for Bioenergy Innovation 2026 Annual Science Meeting; first-author poster, GLBRC 2026</li>
<li>Invited lectures at Tata Institute of Fundamental Research, Mumbai (2025, 2026) and San Diego State University (2026)</li>
<li>Hosted and organized the pre-conference COBRA methods workshop, COBRA 2024</li>
<li>Patent WO2018045287 — Solid Particulate Measuring Devices, Systems and Methods</li>
</ul>
<h3>Download</h3>
<p><a class="btn" href="assets/Arjun_Patel_CV.pdf" target="_blank" rel="noopener noreferrer">Download full CV (PDF)</a></p>
<p class="muted">The on-page CV is intentionally condensed for readability; the PDF contains the full academic CV.</p>
</div>
</div>
</div>
</section>
<section id="contact" class="section alt">
<div class="container">
<h2>Contact</h2>
<div class="contact-grid">
<div class="card">
<h3>Email</h3>
<p><a href="mailto:arjun.patel1296@gmail.com">arjun.patel1296@gmail.com</a></p>
<p class="muted">Best for project inquiries, contracting, and collaboration.</p>
</div>
<div class="card">
<h3>Links</h3>
<ul class="bullets">
<li><a href="https://www.linkedin.com/in/arjunpatel96" target="_blank" rel="noopener noreferrer">LinkedIn <span aria-hidden="true">↗</span></a></li>
<li><a href="https://github.com/arjunpatel96" target="_blank" rel="noopener noreferrer">GitHub <span aria-hidden="true">↗</span></a></li>
<li><a href="https://scholar.google.com/citations?user=5Ym5JKAAAAAJ&hl=en" target="_blank" rel="noopener noreferrer">Google Scholar <span aria-hidden="true">↗</span></a></li>
<li><a href="https://www.cobrame.org" target="_blank" rel="noopener noreferrer">COBRAme.org <span aria-hidden="true">↗</span></a></li>
</ul>
</div>
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<p class="footer muted">© 2026 Arjun Patel, PhD. Built with GitHub Pages.</p>
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