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<!DOCTYPE html>
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    <title>The Carter Lab - Computational Cancer Genomics</title>
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<body>
    <header class="site-header">
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                <h1 class="site-title">The Carter Lab</h1>
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    <nav class="main-nav">
        <a href="#home">Home</a>
        <a href="#research">Research</a>
        <a href="#people">People</a>
        <a href="#software">Software</a>
        <a href="#publications">Publications</a>
        <a href="#contact">Contact</a>
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    <main class="container">
        <section id="home" class="intro">
            <h2 class="section-title">Computational Cancer Genomics</h2>
            <p>Welcome to the Carter Lab! We are located in the School of Medicine of <a href="https://ucsd.edu/">UC San Diego</a>.</p>
        </section>

        <section id="news" class="news-section">
            <h2 class="section-title">Latest News</h2>
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                <a href="latest_news/archive.html" class="view-all-button">View All News →</a>
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        <section id="research" class="research-section">
            <h1>Research Areas</h1>
            <hr>

            <div class="research-area">
                <div class="research-content">
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                        <img src="assets/images/research_immune_trait.png" alt="Genetic determinants research" />
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                        <h3>Genetic determinants of anti-tumor immunity</h3>
                        <p>Genetic variation in immune genes creates inter-individual differences in immune traits. We are investigating the implications of these differences for cancer risk, progression and response to therapy. By jointly analyzing matched tumor and normal genomic data, we have found that individual immune genotypes can influence the evolution of tumor genomes, shape the tumor immune microenvironment and modify response to immunotherapy treatment. These studies will ultimately guide development of precision immunotherapies.</p>
                    </div>
                </div>
            </div>

            <div class="research-area">
                <h3>Predicting the effects of genetic variants on biological systems</h3>
                <p>Experimental assays to probe genetic variants at the single cell level provide new opportunities to model the effects of variants on biological processes and cellular activities. We are developing new experimental and computational approaches to investigate the context-specific consequences of genetic variation for biological systems to better understand their implications for human health.</p>
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            <div class="research-area">
                <div class="research-content reverse">
                    <div class="research-text">
                        <h3>Uncovering interactions between the inherited genome and tumor development</h3>
                        <p>Cancer develops on an individual's unique genetic background. While some inherited mutations are known to predispose individuals to developing tumors, little is known about the effects of such inherited genetic variation on the evolution of the tumor genome. We are working to uncover new regions of the genome that influence the probability that certain mutations will occur during tumor development. We previously described multiple loci that influence mutation rates of known cancer genes and the site at which a tumor will occur.</p>
                    </div>
                    <div class="research-image">
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                        <img src="assets/images/research_germline_interaction.png" alt="Inherited genome interactions" />
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                </div>
            </div>

            <div class="research-area">
                <div class="research-content">
                    <div class="research-image">
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                        <img src="assets/images/research_cancer_drivers.png" alt="Cancer drivers research" />
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                    <div class="research-text">
                        <h3>Discriminating cancer drivers from passengers</h3>
                        <p>Each cancer genome is characterized by tens-to-thousands of DNA mutations, but only a minority of those mutations is expected to drive tumor development and progression. The vast majority of mutations are so called passenger mutations that are carried along in the genomes of proliferating tumor cells. Discriminating drivers from passengers remains an important challenge in cancer 'omics research. We are developing new strategies to improve identification of drivers by studying mutations in the context of protein interaction networks.</p>
                    </div>
                </div>
            </div>
        </section>

        <section id="people" class="people-section">
            <h1>People</h1>
            <p>Members of the Carter lab, past and present.</p>
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            <h2>Current Members</h2>
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            <h2>Alumni</h2>
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            <div id="alumni-grid" class="people-grid"></div>
        </section>

        <section id="software" class="software-section">
            <h1>Software</h1>
            <p>Tools we have created including those we are actively working on.</p>
            <hr>

            <div class="software-grid">
                <div class="software-card">
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                    <img src="assets/images/software/bento.png" alt="Bento" class="software-logo" />
                    <h3>Bento</h3>
                    <p>A Python toolkit for subcellular analysis of spatial transcriptomics data</p>
                    <div class="software-links">
                        <a href="https://bento-tools.readthedocs.io/en/latest/">Docs</a> |
                        <a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-024-03217-7">Paper</a> |
                        <a href="http://github.com/ckmah/bento-tools">GitHub</a>
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                </div>

                <div class="software-card">
                    <!-- TODO: Upload image to assets/images/software/grievous.png -->
                    <img src="assets/images/software/grievous.png" alt="GRIEVOUS" class="software-logo" />
                    <h3>GRIEVOUS</h3>
                    <p>Generalized Realignment of Innocuous and Essential Variants Otherwise Utilized as Skewed</p>
                    <div class="software-links">
                        <a href="https://github.com/jvtalwar/GRIEVOUS/wiki">Docs</a> |
                        <a href="https://academic.oup.com/bioinformatics/article/40/8/btae489/7723992?login=true">Paper</a> |
                        <a href="https://github.com/jvtalwar/GRIEVOUS">GitHub</a>
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                </div>

                <div class="software-card">
                    <!-- TODO: Upload image to assets/images/software/eugene.png -->
                    <img src="assets/images/software/eugene.png" alt="EUGENe" class="software-logo" />
                    <h3>EUGENe</h3>
                    <p>Elucidating the Utility of Genomic Elements with Neural Nets</p>
                    <div class="software-links">
                        <a href="https://eugene-tools.readthedocs.io/en/latest/?badge=latest">Docs</a> |
                        <a href="https://www.nature.com/articles/s43588-023-00544-w">Paper</a> |
                        <a href="https://github.com/cartercompbio/EUGENe">GitHub</a>
                    </div>
                </div>

                <div class="software-card">
                    <!-- TODO: Upload image to assets/images/software/genvarloader.png -->
                    <img src="assets/images/software/genvarloader.png" alt="GenVarLoader" class="software-logo" />
                    <h3>GenVarLoader</h3>
                    <p>Pipeline for efficient genomic data processing</p>
                    <div class="software-links">
                        <a href="https://genvarloader.readthedocs.io/en/latest/">Docs</a> |
                        <a href="https://github.com/mcvickerlab/GenVarLoader">GitHub</a>
                    </div>
                </div>
            </div>
        </section>

        <section id="publications" class="publications-section">
            <h1>Selected Publications</h1>
            <div id="publications-list"></div>
        </section>

        <section id="contact" class="contact-section">
            <h1>Contact</h1>
            <div class="contact-info">
                <p>✉️ <a href="mailto:hkcarter@ucsd.edu">hkcarter@ucsd.edu</a></p>
                <p>📞 <a href="tel:8588224706">858 822 4706</a></p>
                <p>📍 BRFII Room 3A18, 9500 Gilman Dr., La Jolla, CA 92093-0688</p>
                <p><a href="https://www.google.com/maps/place/Biomedical+Research+Facility+II/@32.8744664,-117.2371338,17z/data=!3m1!4b1!4m5!3m4!1s0x80dc06cf83785c07:0xef0daf822e4bf0d4!8m2!3d32.8744663!4d-117.2349198?hl=en-US" target="_blank">View on Google Maps</a></p>
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        <p>&copy; 2025 The Carter Lab, UC San Diego. All rights reserved.</p>
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