From a45848925d277da2ebc516eb4a8ad5ccb7d39f2e Mon Sep 17 00:00:00 2001 From: Zechen Chong Date: Sun, 12 Jul 2026 16:06:59 -0400 Subject: [PATCH 1/2] On branch research-page-redesign modified: _data/navigation.yml modified: _sass/custom.scss modified: about.md modified: index.html --- _data/navigation.yml | 2 + _sass/custom.scss | 174 +++++++++++++++++++++++++++++++++++++++++++ about.md | 80 +++++--------------- index.html | 83 ++++----------------- 4 files changed, 212 insertions(+), 127 deletions(-) diff --git a/_data/navigation.yml b/_data/navigation.yml index 21875a5..9781d9c 100644 --- a/_data/navigation.yml +++ b/_data/navigation.yml @@ -1,6 +1,8 @@ header: - title: "Home" url: "/" + - title: "Research" + url: "/research/" - title: "News" url: "/news/" - title: "Team" diff --git a/_sass/custom.scss b/_sass/custom.scss index d108b2a..db8388d 100644 --- a/_sass/custom.scss +++ b/_sass/custom.scss @@ -257,4 +257,178 @@ font-size: 1.25rem; } +.publication-item, +.news-item, +.software-card { + margin-bottom: 2rem; +} + +.publication-authors, +.publication-title, +.publication-journal, +.news-title { + font-size: 1.15rem; +} + +.software-card { + padding: 1.5rem; + border: 1px solid rgba(0, 0, 0, 0.12); + border-radius: 0.5rem; +} + +.news-image { + display: block; + width: 100%; + max-width: 30rem; + height: auto; + margin-top: 0.75rem; +} + +.album-item img { + width: 100%; + max-width: 42rem; + height: auto; + border-radius: 0.5rem; +} + +.album-item figcaption { + margin-top: 0.5rem; + font-weight: 700; +} + +.lab-logo { + display: block; + width: 50%; + max-width: 32rem; + height: auto; + margin: 0 auto; +} + +.lab-timeline, +.contact-map-frame { + width: 100%; + border: 0; +} + +.lab-timeline { + height: 650px; +} + +.contact-map-frame { + min-height: 28rem; +} + +.alumni-list li { + margin-bottom: 0.5rem; +} + +@media (max-width: 600px) { + .main { + padding: 1rem; + } + + .lab-logo { + width: 80%; + max-width: 24rem; + } +} + +/* Simple academic homepage */ +.lab-intro { + display: grid; + grid-template-columns: minmax(0, 1fr) 16rem; + align-items: center; + gap: 4rem; + max-width: 68rem; + margin: 2rem auto 4rem; + padding: 2rem; +} +.lab-intro h1 { + margin: 0 0 0.4rem; + color: #134e5e; + font-size: 3rem; + line-height: 1.1; +} + +.lab-actions { + display: flex; + flex-wrap: wrap; + gap: 1.5rem; + margin-top: 1.5rem; +} + +.lab-intro__tagline { + margin: 0 0 1.5rem; + color: #327b88; + font-size: 1.35rem; +} + +.lab-intro__text > p:not(.lab-intro__tagline) { + font-size: 1.08rem; + line-height: 1.75; +} + +.lab-intro__logo { + width: 100%; + height: auto; +} + +.simple-section { + max-width: 64rem; + margin: 0 auto; + padding: 0 2rem 3rem; +} + +.simple-section h2 { + color: #134e5e; + font-size: 2rem; +} + +.simple-section--bordered { + padding-top: 2.5rem; + border-top: 1px solid #d6e2e4; +} + +.interest-list { + display: grid; + grid-template-columns: repeat(3, minmax(0, 1fr)); + gap: 2rem; + margin: 2rem 0; +} + +.interest-list article { + padding-top: 1rem; + border-top: 3px solid #59a5ad; +} + +.interest-list h3 { + margin-top: 0; + color: #205d69; + font-size: 1.15rem; +} + +.simple-link { + color: #147d8a; + font-weight: 700; + text-decoration: none; +} + +.simple-link:hover { + text-decoration: underline; +} + +@media (max-width: 760px) { + .lab-intro { + grid-template-columns: 1fr; + gap: 2rem; + } + + .lab-intro__logo { + max-width: 13rem; + } + + .interest-list { + grid-template-columns: 1fr; + } +} diff --git a/about.md b/about.md index 6a7019d..b6f9343 100644 --- a/about.md +++ b/about.md @@ -1,74 +1,34 @@ --- -layout: article -titles: - # @start locale config - en : &EN About - en-GB : *EN - en-US : *EN - en-CA : *EN - en-AU : *EN - zh-Hans : &ZH_HANS 关于 - zh : *ZH_HANS - zh-CN : *ZH_HANS - zh-SG : *ZH_HANS - zh-Hant : &ZH_HANT 關於 - zh-TW : *ZH_HANT - zh-HK : *ZH_HANT - ko : &KO 소개 - ko-KR : *KO - fr : &FR À propos - fr-BE : *FR - fr-CA : *FR - fr-CH : *FR - fr-FR : *FR - fr-LU : *FR - # @end locale config -key: page-about +layout: page +title: Research +description: Research interests of the Chong Lab at the University of Virginia. +permalink: /research/ --- -![TeXt Theme](https://raw.githubusercontent.com/kitian616/jekyll-TeXt-theme/master/screenshots/TeXt-home.jpg) +# Research -TeXt is a super customizable Jekyll theme for personal site, team site, blog, project, documentation, etc. Similar to iOS 11 style, it has large and prominent titles, round buttons and cards. +Our lab develops computational methods for analyzing large-scale genomic data and applies these methods to fundamental questions in genome biology and human disease. -```javascript -(() => console.log('Hello, World!'))(); -``` +## Algorithm development for emerging sequencing data -## Features +The scale and complexity of modern genomic data demand computational methods that are more sensitive, efficient, and precise. Long-read platforms such as PacBio HiFi and Oxford Nanopore generate reads spanning thousands of base pairs, creating powerful opportunities for haplotype resolution, genome assembly, and the study of complex genomic regions. -- Responsive -- Semantic HTML -- Skins -- Highlight Theme -- Internationalization -- Search -- Table of contents -- Authors -- Additional styles (alert, tag, image, icon, button, grid, etc) -- Extensions (audios, videos, slides, demos) -- Markdown enhancements ([MathJax](https://www.mathjax.org/), [mermaid](https://mermaidjs.github.io/), [chartjs](http://www.chartjs.org/)) -- Sharing ([AddToAny](https://www.addtoany.com/), [AddThis](https://www.addthis.com/)) -- Comments ([Disqus](https://disqus.com/), [Gitalk](https://gitalk.github.io/), [Valine](https://valine.js.org/en/)) -- Pageview ([LeanCloud](https://leancloud.cn/)) -- Analytics ([Google Analytics](https://analytics.google.com/analytics/web/)) -- RSS ([jekyll-feed](https://github.com/jekyll/jekyll-feed)) +Our lab develops algorithms that address platform-specific errors and analytical challenges while unlocking the full value of these data. We also design methods for emerging technologies, including pangenomics, single-cell sequencing, strand-seq, and other multi-omic platforms. -## Skins +## Functions and mechanisms of genomic rearrangements -TeXt has 6 built-in skins, you can also set up your own skin. +Structural variants and other genomic rearrangements play a central role in shaping genetic diversity within and between species. Yet their functions, origins, and biological consequences remain incompletely understood. -| `default` | `dark` | `forest` | -| --- | --- | --- | -| ![Default](https://raw.githubusercontent.com/kitian616/jekyll-TeXt-theme/master/screenshots/skins_default.jpg) | ![Dark](https://raw.githubusercontent.com/kitian616/jekyll-TeXt-theme/master/screenshots/skins_dark.jpg) | ![Forest](https://raw.githubusercontent.com/kitian616/jekyll-TeXt-theme/master/screenshots/skins_forest.jpg) | +We investigate these complex events through computational, integrative, and hypothesis-driven approaches. Our work explores structural variation, chromothripsis, and other large-scale rearrangements to reveal how genomes change and how those changes affect phenotype. -| `ocean` | `chocolate` | `orange` | -| --- | --- | --- | -| ![Ocean](https://raw.githubusercontent.com/kitian616/jekyll-TeXt-theme/master/screenshots/skins_ocean.jpg) | ![Chocolate](https://raw.githubusercontent.com/kitian616/jekyll-TeXt-theme/master/screenshots/skins_chocolate.jpg) | ![Orange](https://raw.githubusercontent.com/kitian616/jekyll-TeXt-theme/master/screenshots/skins_orange.jpg) | +## Disease genomics -### Highlight Theme +Disease often emerges from a complex interplay of genetic, epigenetic, and environmental factors. We study this interface by identifying disease-associated variants and integrating genomic, transcriptomic, epigenomic, and clinical data. -TeXt use [Tomorrow](https://github.com/chriskempson/tomorrow-theme) as the highlight theme. +Through pan-disease, pan-cancer, and multi-omic analyses, we aim to deepen understanding of genotype-to-phenotype relationships and contribute to improved diagnosis, prognosis, and therapeutic strategies. -| `tomorrow` | `tomorrow-night` | `tomorrow-night-eighties` | `tomorrow-night-blue` | `tomorrow-night-bright` | -| --- | --- | --- | --- | --- | -| ![Tomorrow](https://raw.githubusercontent.com/kitian616/jekyll-TeXt-theme/master/screenshots/highlight_tomorrow.png) | ![Tomorrow Night](https://raw.githubusercontent.com/kitian616/jekyll-TeXt-theme/master/screenshots/highlight_tomorrow-night.png) | ![Tomorrow Night Eighties](https://raw.githubusercontent.com/kitian616/jekyll-TeXt-theme/master/screenshots/highlight_tomorrow-night-eighties.png) | ![Tomorrow Night Blue](https://raw.githubusercontent.com/kitian616/jekyll-TeXt-theme/master/screenshots/highlight_tomorrow-night-blue.png) | ![Tomorrow Night Bright](https://raw.githubusercontent.com/kitian616/jekyll-TeXt-theme/master/screenshots/highlight_tomorrow-night-bright.png) | +## Collaborations + +Complex questions in genomics are best addressed through collaboration. We work with investigators across the University of Virginia and with national and international partners. These collaborations bring together expertise in computation, biology, and medicine and expand our ability to translate new methods into meaningful discoveries. + +[Contact us to discuss a collaboration →]({{ '/contact/' | relative_url }}) diff --git a/index.html b/index.html index 2300252..587a10f 100644 --- a/index.html +++ b/index.html @@ -1,71 +1,20 @@ --- layout: home -# title: Chong lab at UVA -# articles: -# excerpt_type: html +title: Chong Lab +description: Computational genomics research at the University of Virginia. --- -
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About the lab 

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- We are a computational genomics research group in the Department of Genome Sciences at the University of Virginia School of Medicine. Our research focuses on developing innovative computational methods and bioinformatics tools to advance genomic discovery. We are particularly interested in leveraging cutting-edge sequencing technologies, including next-generation sequencing, long-read sequencing (PacBio HiFi and Oxford Nanopore), and emerging multi-omics platforms to better understand human genome variation and its role in health and disease. -

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Vision of the lab

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- The rapid evolution of sequencing and biotechnology is transforming biology at an unprecedented pace. Our lab is dedicated to leveraging these breakthroughs to extract meaningful insights from both healthy and diseased genomes. By combining innovation in bioinformatics with state-of-the-art sequencing platforms, our ultimate goal is to advance precision medicine and improve human health. -

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Algorithm development for new sequencing data

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- While numerous tools exist for next-generation sequencing, the sheer volume and complexity of modern data demand new, more sensitive, and more efficient computational methods. Third-generation sequencing platforms such as PacBio and Oxford Nanopore provide long reads spanning thousands of base pairs, offering tremendous potential for haplotype resolution and genome assembly. However, these platforms are also characterized by high error rates, presenting significant analytical challenges. Our research develops novel algorithms to overcome these barriers and unlock the full value of TGS data. In addition, we address data generated by emerging biotechnologies—including 10X Genomics, strand-seq, and advanced single-cell sequencing—designing solutions tailored to these rapidly evolving data types. -

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Functions and mechanisms of genomic rearrangements

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- Structural variations (genomic rearrangements) play a central role in shaping genetic diversity within and between species. Yet their functions and underlying mechanisms remain incompletely understood. Our group investigates these complex variations through integrative and hypothesis-driven approaches, exploring phenomena such as chromothripsis and other large-scale rearrangements to shed light on their biological consequences. -

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Disease genomics

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- A disease represents a disruption of normal phenotype, often resulting from a complex interplay of genetic, epigenetic, and environmental factors. Our lab explores fundamental questions at this interface, including the identification of disease-causing variants, integrative pan-disease and pan-cancer genomics, and multi-omic data analysis. Through these efforts, we aim to deepen understanding of the genotype-to-phenotype relationship and contribute to improved diagnosis, prognosis, and therapeutic strategies. -

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Collaborations

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- In the past few years, we have established extensive collaborations across the UAB community and with partners nationwide. We envision to expand the fruitful collaborations at UVA. These collaborations strengthen our ability to tackle challenging problems at the intersection of computational biology, genomics, and medicine. -

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Lab Timeline

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Making sense of biology using bioinformatics

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Computational genomics at the University of Virginia

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We are a research group in the Department of Genome Sciences at the University of Virginia School of Medicine.

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We develop computational methods for long-read sequencing, structural variation, genome assembly, and disease genomics to better understand human genome variation and its role in health and disease.

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From df0b482144490e8c998e337051146c7ba82724ab Mon Sep 17 00:00:00 2001 From: Zechen Chong Date: Sun, 12 Jul 2026 16:21:08 -0400 Subject: [PATCH 2/2] Apply UVA-inspired website redesign --- _includes/footer.html | 54 ++---- _includes/head/custom.html | 12 ++ _includes/header.html | 53 +++--- _sass/custom.scss | 327 +++++++++++++++++++++++++++++++++++++ about.md | 2 - index.html | 4 +- 6 files changed, 377 insertions(+), 75 deletions(-) diff --git a/_includes/footer.html b/_includes/footer.html index 2dfd9f9..12d6a98 100644 --- a/_includes/footer.html +++ b/_includes/footer.html @@ -1,48 +1,14 @@ - -