cegrcode.github.io/publications.html at master · CEGRcode/cegrcode.github.io · GitHub

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---
title: Publications
---

<!--Update instructions:
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<div class="publication-container d-flex flex-column">
  <h3>Publications</h3>
  <hr />

  <!--Lang et al (2023)-->
  <div class="row publication">
    <div class="col-md-1 number">
      <h6>01</h6> <!--Update-->
    </div>
    <div class="col-md-11">
      <h6>
        GenoPipe: identifying the genotype of origin within (epi)genomic datasets
      </h6>
      <small>
        Lang O, Srivastava D, Pugh BF, Lai WKM.
      </small>
      <div class="d-flex">
        <a
          class="publinks"
          href="https://pubmed.ncbi.nlm.nih.gov/37933851/"
          title="linkout to PubMed"
          > PMID <i class="fas fa-external-link-alt"></i>
        </a>
        &nbsp; &nbsp;
        <a
          class="publinks"
          href="https://doi.org/10.1093/nar/gkad950"
          title="linkout to full text"
          > PDF <i class="fas fa-file-pdf"></i>
        </a>
      </div>
    </div>
  </div>

  <!--Mittal et al (2022)-->
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    <div class="col-md-1 number">
      <h6>02</h6> <!--Update-->
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    <div class="col-md-11">
      <h6>
        An integrated SAGA and TFIID PIC assembly pathway selective for poised and induced promoters
      </h6>
      <small>
        Mittal C, Lang O, Lai WKM, Pugh BF.
      </small>
      <div class="d-flex">
        <a
          class="publinks"
          href="https://pubmed.ncbi.nlm.nih.gov/36302553/"
          title="linkout to PubMed"
          > PMID <i class="fas fa-external-link-alt"></i>
        </a>
        &nbsp; &nbsp;
        <a
          class="publinks"
          href="http://genesdev.cshlp.org/content/36/17-18/985.long"
          title="linkout to full text"
          > PDF <i class="fas fa-file-pdf"></i>
        </a>
      </div>
    </div>
  </div>

  <!--John et al (2022)-->
  <div class="row publication">
    <div class="col-md-1 number">
      <h6>03</h6> <!--Update-->
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    <div class="col-md-11">
      <h6>
        Genome-wide promoter assembly in E. coli measured at single-base
        resolution.
      </h6>
      <small>
        John J, Jabbar J, Badjatia N, Rossi MJ, Lai WKM, Pugh BF.
      </small>
      <div class="d-flex">
        <a
          class="publinks"
          href="https://pubmed.ncbi.nlm.nih.gov/35483960/"
          title="linkout to PubMed"
          > PMID <i class="fas fa-external-link-alt"></i>
        </a>
        &nbsp; &nbsp;
        <a
          class="publinks"
          href="https://genome.cshlp.org/content/32/5/878.long"
          title="linkout to full text"
          > PDF <i class="fas fa-file-pdf"></i>
        </a>
      </div>
    </div>
  </div>

  <!--Shao et al (2022)-->
  <div class="row publication">
    <div class="col-md-1 number">
      <h6>04</h6> <!--Update-->
    </div>
    <div class="col-md-11">
      <h6>
        PEGR: a flexible management platform for reproducible epigenomic and
        genomic research.
      </h6>
      <small>
        Shao D, Kellogg GD, Nematbakhsh A, Kuntala PK, Mahony S, Pugh BF,
        Lai WKM.
      </small>
      <div class="d-flex">
        <a
          class="publinks"
          href="https://pubmed.ncbi.nlm.nih.gov/35440038/"
          title="linkout to PubMed"
          > PMID <i class="fas fa-external-link-alt"></i>
        </a>
        &nbsp; &nbsp;
        <a
          class="publinks"
          href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02671-5"
          title="linkout to full text"
          > PDF <i class="fas fa-file-pdf"></i>
        </a>
      </div>
    </div>
  </div>

  <!--Sun et al (2022)-->
  <div class="row publication">
    <div class="col-md-1 number">
      <h6>05</h6> <!--Update-->
    </div>
    <div class="col-md-11">
      <h6>
        STENCIL: A web templating engine for visualizing and sharing life
        science datasets.
      </h6>
      <small>
        Sun Q, Nematbakhsh A, Kuntala PK, Kellogg G, Pugh BF, Lai WKM.
      </small>
      <div class="d-flex">
        <a
          class="publinks"
          href="https://pubmed.ncbi.nlm.nih.gov/35139076/"
          title="linkout to PubMed"
        >
          PMID <i class="fas fa-external-link-alt"></i>
        </a>
        &nbsp; &nbsp;
        <a
          class="publinks"
          href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009859"
          title="linkout to full text"
          >
          PDF <i class="fas fa-file-pdf"></i
        ></a>
      </div>
    </div>
  </div>

</div>

<!--NCBI Link Section-->
<div class="publication-container">
  <h5>
    <hr />
    Complete list of publications:
    <a
      class="NCBI"
      href="https://www.ncbi.nlm.nih.gov/sites/myncbi/benjamin.pugh.1/bibliography/40517395/public/?sort=date&direction=descending"
      target="_blank"
      >NCBI <i class="fas fa-external-link-alt"></i>
    </a>
  </h5>
</div>