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<!DOCTYPE html>
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<meta content="4DNucleome Hackathon" name="description">
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<title>4D Nucleome Hackathon</title>
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<h1 style="font-size:50px">4D Nucleome Hackathon</h1>
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<p style="font-size:18px", align="justify">
<a href="#Description">Description</a> • 
<a href="#Event Details">Event Details</a> • 
<a href="#Project 1">Project 1</a> • 
<a href="#Project 2">Project 2</a> • 
<a href="#Project 3">Project 3</a> • 
<a href="#Project 4">Project 4</a> • 
<a href="#Project 5">Project 5</a>
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<a name="#Description"><div class="jumbotron"><a></a>
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<h2 style="font-size:26px"><b>Description</b></h2>
<p style="font-size:20px", align="justify"> Do you love innovation and challenge? Do you like problem solving in collaborative environments? Do you want to learn new technical skills outside of your current projects? Most importantly, do you want to make tools that will improve the field of genomics and make it more accessible to the public?
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<p style="font-size:20px", align="justify"> If so, the department of Genome Sciences proudly invites you to participate in our second annual Hackathon! The Hackathon will span 5 days, from Monday September 18th through Friday September 22nd. All GS trainees and faculty (graduate, post-doctoral, and staff) are invited to participate. There will be four teams led by your amazing colleagues, where each team will build a deliverable by the end of the five days. This is an opportunity to build something cool, learn from colleagues outside of your lab, and have fun!
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<p style="font-size:20px", align="justify"> If you’re interested, please read the project details below and fill out the interest form: <br>
<a href="https://forms.gle/eDxhcwNoa34wwkSm8" target="_blank" class="aaastandout">https://forms.gle/eDxhcwNoa34wwkSm8</a></p>
<p style="font-size:20px", align="justify"> If you have any questions about the event, please contact Sayeh Gorjifard <sgorji [ a t ] uw.edu></p>
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<a name="#Event Details"><div class="jumbotron"><a></a>
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<h2 style="font-size:26px"><b>Event Details</b></h2>
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<b>Location</b>: University of Washington, Seattle <br>
<b>Dates</b>: March 18-21, 2024 <br>
<b>Times</b>: 9 am - 5 pm <br>
<b>Food</b>: Breakfast, Lunch, Dinner and Snacks provided daily. <br>
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<h2 style="font-size:26px"><b>Project 1</b></h2>
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<b>Leading lab</b>: Noble Lab <br>
<b>Stakeholders</b>: Anupama Jha (anupamaj [ a t ] uw.edu) and Gang Li (gangliuw [ a t ] uw.edu) <br>
<b>Hackathon project title</b>: Integrating single-cell Hi-C and single-cell RNA sequencing data <br>
<b>Desired deliverable</b>: Benchmarking results comparing multiple existing software tools for integrating scHiC and scRNA data. <br>
<b>Expected coding experience level</b>: Intermediate-Advanced. <br>
<b>Abstract</b>: Recently, Liu et al. developed HiRES, a multi-omics sequencing approach to simultaneously profile 3D chromatin contacts and gene expression in single cells. The HiRES assay thus directly links chromatin conformation and gene expression profiles within single cells. Previous studies that aimed to investigate the interplay between chromatin interactions and transcriptomic profiles necessarily generated unpaired single-cell RNA-sequencing and chromatin conformation data. For the hackathon, we will use the newly available HiRES data to benchmark existing software tools developed for matching cells across modalities. In particular, we evaluate GLUE, LS-MMDMA (<a href="https://academic.oup.com/bioinformatics/article/39/7/btad420/7221538" target="_blank" class="aaastandout">Meng 2023</a>), Pomona (<a href="https://pubmed.ncbi.nlm.nih.gov/34398192/" target="_blank" class="aaastandout">Cao 2021</a>), SCOT (<a href="https://pubmed.ncbi.nlm.nih.gov/35050714/" target="_blank" class="aaastandout">Demetci 2022</a>), Synmatch (<a href="https://academic.oup.com/bioinformatics/article/38/Supplement_2/ii148/6702005?login=false" target="_blank" class="aaastandout">Hristov 2022</a>), and CMOT (<a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-02989-8" target="_blank" class="aaastandout">Alatkar 2023</a>). In addition, we will consider four different techniques for representing the scHi-C contact matrices, including the contact decay profile, the HiCRep (<a href="https://academic.oup.com/bioinformatics/article/37/18/2996/6133255?login=false" target="_blank" class="aaastandout">Lin 2021</a>) similarity score, a latent Dirichlet allocation model (<a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008173" target="_blank" class="aaastandout">Kim 2020</a>), and the scGAD method (<a href="https://academic.oup.com/bioinformatics/article/38/14/3642/6598798" target="_blank" class="aaastandout">Shen 2022</a>). Our results will compare and contrast the performance of these tools and Hi-C representation techniques in the context of integration with scRNA-seq data. For the hackathon, we will use co-assay data to validate integration of scRNA-seq and scHi-C. <br>
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