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update website for fall 2023
- fix typo on index.html - add reunion flyer to navbar and its own page - add links to resources.html - add favicon - update positions descriptions with detail
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‎_data/navigation.yml‎

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link: /resources.html
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- name: Positions
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link: /positions.html
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- name: Reunion!
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link: /reunion.html

‎_includes/header.html‎

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@@ -28,5 +28,6 @@ <h1><a class="blog-header-logo" href="/">Pugh Lab</a></h1>
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/>
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</div>
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</div>
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<link rel="icon" type="image/x-icon" href="favicon.ico">
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</header>
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</div>

‎favicon.ico‎

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‎index.html‎

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@@ -17,8 +17,8 @@ <h5>YEP</h5>
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<h6>Yeast Epigenome Project</h6>
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<p class="card-text">
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Comprehensive look at the yeast epigenome through the use of ultra
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high resolution ChIP-exo. Summary of the work is published inNature in
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2021.
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high resolution ChIP-exo. Summary of the work is published in Nature
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(Rossi et al, 2021).
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</p>
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<a href="/resources#YEP"
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>Read more <i class="fas fa-external-link-alt"></i

‎positions.html‎

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state-of-the-art research in molecular biology and computational biology,
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with emphasis in eukaryotic gene regulation, transcription, epigenetics,
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epigenomics, tumor diagnostics, and high-throughput computer-aided analytic
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workflows. We are looking for undergraduates, graduate students,
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workflows.
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</p>
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<p>
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<b>We are looking for undergraduates, graduate students,
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technicians, and postdocs who are excited and motivated to push the
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frontiers of gene regulation research. Please inquire with Dr. Pugh
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frontiers of gene regulation research. Please inquire with Dr. Pugh.</b>
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</p>
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<br />
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<h4>Graduate Students</h4>
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<p>
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We are recruiting graduate students with wet-bench and computational backgrounds from the following graduate fields:
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</p>
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<ul>
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<li>Genetics, Genomics, and Development (GGD)</li>
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<li>Biochemistry, Molecular, and Cell Biology (BMCB)</li>
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<li>Computational Biology (CB)</li>
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</ul>
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<h4>Undergraduate Students</h4>
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<p>
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We have worked with undergraduates from a variety of backgrounds ranging
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from design to computer science to molecular biology. The projects have
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included UX design and application building for our tool development.
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</p>
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<h4>Job postings</h4>
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<!--ul>
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<li>

‎publications.html‎

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title: Publications
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---
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<div class="container">
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<div class="d-flex flex-column publication-container">
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<!-- Section -->
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<!--Update instructions:
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Delete oldest publication
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For each publication separated by 01-05 comments, increment the h6 label
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Copy-paste one of the other publications and append it to the top
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Update the copied entry:
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- update the paper comment name
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- rename the h6 header to "01"
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- update the paper title
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- update the author list with year
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- update the PMID link
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- update the PDF/DOI/Full-text link
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-->
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<div class="publication-container d-flex flex-column">
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<div>
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<h3>Publications</h3>
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<hr />
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<!--Mittal et al (2022)-->
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<div class="row publication">
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<div class="col-md-1 number">
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<h6>01</h6>
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<h6>01</h6> <!--Update-->
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</div>
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<div class="col-md-11">
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<h6>
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<small>
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Mittal C, Lang O, Lai WKM, Pugh BF.
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</small>
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<!-- <hr /> -->
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<div class="d-flex">
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<a
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class="publinks"
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href="https://pubmed.ncbi.nlm.nih.gov/36302553/"
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title="linkout to PubMed"
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>
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PMID <i class="fas fa-external-link-alt"></i>
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> PMID <i class="fas fa-external-link-alt"></i>
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</a>
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&nbsp; &nbsp;
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<a
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class="publinks"
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href="http://genesdev.cshlp.org/content/36/17-18/985.long"
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title="linkout to full text"
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>
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PDF <i class="fas fa-file-pdf"></i
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></a>
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> PDF <i class="fas fa-file-pdf"></i>
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</a>
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</div>
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</div>
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</div>
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<!--John et al (2022)-->
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<div class="row publication">
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<div class="col-md-1 number">
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<h6>02</h6>
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<h6>02</h6> <!--Update-->
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</div>
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<h6>
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class="publinks"
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href="https://pubmed.ncbi.nlm.nih.gov/35483960/"
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title="linkout to PubMed"
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>
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PMID <i class="fas fa-external-link-alt"></i
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></a>
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> PMID <i class="fas fa-external-link-alt"></i>
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</a>
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&nbsp; &nbsp;
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<a
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href="https://genome.cshlp.org/content/32/5/878.long"
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title="linkout to full text"
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>
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PDF <i class="fas fa-file-pdf"></i
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></a>
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> PDF <i class="fas fa-file-pdf"></i>
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</a>
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</div>
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</div>
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</div>
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<!--Shao et al (2022)-->
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<div class="row publication">
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<h6>03</h6>
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<h6>03</h6> <!--Update-->
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</div>
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<h6>
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Shao D, Kellogg GD, Nematbakhsh A, Kuntala PK, Mahony S, Pugh BF,
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Lai WKM.
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</small>
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<!-- <hr /> -->
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<div class="d-flex">
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<a
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class="publinks"
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href="https://pubmed.ncbi.nlm.nih.gov/35440038/"
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title="linkout to PubMed"
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>
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PMID <i class="fas fa-external-link-alt"></i
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></a>
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> PMID <i class="fas fa-external-link-alt"></i>
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</a>
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&nbsp; &nbsp;
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href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02671-5"
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title="linkout to full text"
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>
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PDF <i class="fas fa-file-pdf"></i
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></a>
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> PDF <i class="fas fa-file-pdf"></i>
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</a>
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</div>
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</div>
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</div>
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<h6>04</h6>
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<h6>04</h6> <!--Update-->
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</div>
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<small>
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Sun Q, Nematbakhsh A, Kuntala PK, Kellogg G, Pugh BF, Lai WKM.
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</small>
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<a
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class="publinks"
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href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009859"
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title="linkout to full text"
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>
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>
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></a>
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</div>
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<h6>05</h6> <!--Update-->
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<h6>
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Zhao T, Vvedenskaya IO, Lai WK, Basu S, Pugh BF, Nickels BE, Kaplan
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CD.
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</small>
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>
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PMID <i class="fas fa-external-link-alt"></i
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></a>
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> PMID <i class="fas fa-external-link-alt"></i>
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</a>
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&nbsp; &nbsp;
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> PDF <i class="fas fa-file-pdf"></i>
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</a>
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{% for publication in site.data.publications.publications %}
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{% assign namefive = publicaiton.name[5] %}
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{% assign authorfive = publicaiton.author[5] %}
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<h6>{{ publication.name}}</h6>
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<small>
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{{ publication.author }}
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</small>
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<hr>
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<div class="d-flex">
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<a class="publinks" href="{{ publication.url }}" title="project website" ><i class="fas fa-external-link-alt"></i></a>
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<a class="publinks" href="https://doi.org/10.1101/2020.06.08.140046" title="pubmed link"><i class="fas fa-file-pdf"></i></a>
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</div>
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{% endfor %}
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</div-->
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{% for publication in site.data.publications.publications %}
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<h6>{{ publication.name1 }}</h6>
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{% endfor %}
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{% for publication in site.data.publications.publications %}
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<small>
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{{ publication.author1 }}
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{% endfor %}
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<hr>
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<div class="d-flex">
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<a class="publinks" href="{{ publication.url1 }}" title="project website" ><i class="fas fa-external-link-alt"></i></a>
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<a class="publinks" href="https://doi.org/10.1101/2020.06.08.140046" title="pubmed link"><i class="fas fa-file-pdf"></i></a>
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</div>
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</div-->
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<!--ul>
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{% for publication in site.data.publications.publications %}
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<li>{{ publication.name }}</li>
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{% endfor %}
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</ul-->
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<h4>Latest</h4>
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Authors
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<a class="publinks" href="#" title="project website" ><i class="fas fa-external-link-alt"></i></a>
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<a class="publinks" href="#" title="pubmed link"><i class="fas fa-file-pdf"></i></a>
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<a class="publinks" href="#" title="pubmed link"><i class="fas fa-file-pdf"></i></a>
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</div>
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-->
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Complete list of publications :
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<!--NCBI Link Section-->
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<div class="publication-container">
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<h5>
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<hr />
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Complete list of publications:
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<a
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class="NCBI"
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target="_blank"
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>NCBI <i class="fas fa-external-link-alt"></i
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‎resources.html‎

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<img class="resources-icon" src="assets/images/resource-yep.svg" />
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</div>
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<div class="publication" id="YEP">
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Gene regulation is central for life to function in a wide range of
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<!-- image grid or slideshow of screenshots -->
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</div>
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</div>
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<strong>
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Check out our data at <a href="https://www.yeastepigenome.org">www.yeastepigenome.org <i class="fas fa-external-link-alt"></i></a>
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</strong>
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<img class="resources-icon" src="assets/images/resources-PCRP.svg" />
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<div class="publication" id="PCRP">
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Knowledge of where proteins bind along a genome informs us of how
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<strong>
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Check out our data at <a href="http://www.pcrpvalidation.org/">www.pcrpvalidation.org <i class="fas fa-external-link-alt"></i></a>
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</strong>
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Genomic projects are slowed by a general lack of end-to-end
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