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    <title>Paul W. Hook</title>
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    <description>Recent content on Paul W. Hook</description>
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      <title>Scraping bioRxiv</title>
      <link>/blog/2018/04/10/2018-02-27-scraping-biorxiv-getting-started/</link>
      <pubDate>Tue, 10 Apr 2018 00:00:00 +0000</pubDate>
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      <description>This post is the first of a series focusing on tracking preprints on bioRxiv. The motivation behind this and a more detailed explanantion can be found here.
Scraping in R When I began to approach preprint tracking, the mysterious world of &amp;ldquo;HTML scraping&amp;rdquo; seemed like something that would help. Simply, scraping allows you to extract information from the underlying HTML (Hypertext Markup Language) documents that make up websites.
HTML scraping seemed like a good idea for preprint tracking because: A) It doesn&amp;rsquo;t seem like there are simple/easy ways to access a bioRxiv database that holds such information (especially for someone with limited experience in this like me) and B) Whether or not the paper is published in a peer-reviewed journal is displayed clearly on each preprint&amp;rsquo;s page (see below on the webpage in red).</description>
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      <title>Keeping track of preprints</title>
      <link>/blog/2018/04/04/2018-02-25-scraping-biorxiv-part-1/</link>
      <pubDate>Wed, 04 Apr 2018 00:00:00 +0000</pubDate>
      <guid>/blog/2018/04/04/2018-02-25-scraping-biorxiv-part-1/</guid>
      <description>Premise For my first set of blog posts, I have decided to start a series about preprints. Awhile ago, an interesting question was brought up by Shannon Ellis in her wonderful blog post &amp;ldquo;Let there be preprint citations!&amp;quot; (emphasis is mine):
Problem #2: Preprints often become peer-reviewed research. How will we keep track?
Solution #2a (if this occurs during while the manuscript is being drafted): It is up to the author(s) to ensure that their manuscript is as up to date as possible upon submission for publication.</description>
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      <title>My first blog post!</title>
      <link>/blog/2018/04/02/2018-02-20-my-first-blog-post/</link>
      <pubDate>Mon, 02 Apr 2018 00:00:00 +0000</pubDate>
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      <description>Hello! If you haven&amp;rsquo;t been able to tell by the website already, my name is Paul Hook.
I am a fourth year Ph.D. student in the Human Genetics program in the McKusick-Nathans Institute of Genetic Medicine at the Johns Hopkins University School of Medicine. I am in Dr. Andy McCallion&amp;rsquo;s lab.
You can learn a little more about me here, so I won&amp;rsquo;t go on and on in the inaugural blog post.</description>
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      <title>about</title>
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      <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
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      <description>Hello! My name is Paul Hook. I am a Postdoctoral Fellow in Dr. Winston Timp&amp;rsquo;s lab in the Department of Biomedical Engineering at Johns Hopkins University. I received my PhD from the Human Genetics program in the McKusick-Nathans Institute of Genetic Medicine at the Johns Hopkins University School of Medicine. I did my thesis work in Dr. Andy McCallion&amp;rsquo;s lab. There I focused on trying to elucidate the genetics that underlie Parkinson disease and schizophrenia.</description>
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      <title>analyses/data</title>
      <link>/project/</link>
      <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
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      <description>T2T chrY GitHub: https://github.com/arangrhie/T2T-HG002Y
This GitHub repo contains all the code from Rhie, 2023.
I contributed to this work through the analysis of a variety of epigenetics datasets including CpG 5-methylcytosine measured with whole genome bisulfite sequencing (WGBS), enzymatic methyl-seq (EM-seq), PacBio, and ONT, as well as nanoNOMe GpC 5-methylcytosine data. Documentation for the analysis of this data can be found within the main GitHub repo here.
T2T epigenetics GitHub: https://github.</description>
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      <title>contact</title>
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      <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
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      <description> Email me: phook2 [at] jhmi.edu I&amp;rsquo;m on Twitter/X: @pwhook Find my code and analyses on Github Check me out on Google Scholar </description>
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      <title>CV</title>
      <link>/cv/</link>
      <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
      <guid>/cv/</guid>
      <description> </description>
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      <title>FAQ</title>
      <link>/faq/</link>
      <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
      <guid>/faq/</guid>
      <description>Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas. Vestibulum tortor quam, feugiat vitae, ultricies eget, tempor sit amet, ante. Donec eu libero sit amet quam egestas semper. Aenean ultricies mi vitae est. Mauris placerat eleifend leo.
1. WHAT TO DO IF I HAVE STILL NOT RECEIVED THE ORDER? Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas. Vestibulum tortor quam, feugiat vitae, ultricies eget, tempor sit amet, ante.</description>
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      <title>papers</title>
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      <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
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      <description>Postdoc 2024 Lin, K.N., Volkel, K., Cao, C., Hook, P.W., Polak, R.E., Clark, A.S., San Miguel, A., Timp, W., Tuck, J.M., Velev, O.D., et al. (2024). A primordial DNA store and compute engine. Nat. Nanotechnol., 1–11. https://doi.org/10.1038/s41565-024-01771-6
Volkel, K.D., Hook, P.W., Keung, A., Timp, W., and Tuck, J.M. (2024). Nanopore Decoding with Speed and Versatility for Data Storage. bioRxiv, 2024.06.18.599582. https://doi.org/10.1101/2024.06.18.599582
Guerrero Zuniga, A., Aikin, T.J., McKenney, C., Lendner, Y.</description>
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