{"id":4579,"date":"2019-03-18T10:43:34","date_gmt":"2019-03-18T10:43:34","guid":{"rendered":"https:\/\/www.blopig.com\/blog\/?p=4579"},"modified":"2019-03-18T11:15:28","modified_gmt":"2019-03-18T11:15:28","slug":"a-blog-post-about-a-blog","status":"publish","type":"post","link":"https:\/\/www.blopig.com\/blog\/2019\/03\/a-blog-post-about-a-blog\/","title":{"rendered":"A blog post about a blog"},"content":{"rendered":"\n<p>I thought I would make this blog post very meta by referring to another blog, written by Lior Pachter, which I think has something for many of us in it: <a href=\"http:\/\/liorpachter.wordpress.com\">http:\/\/liorpachter.wordpress.com<\/a>  (networks people, there\u2019s a pretty scathing take-down of a quite well cited 2013 paper as one of the last posts &#8211; there seem to be a couple of posts labelled  \u201cnetwork nonsense\u201d!)<br><\/p>\n\n\n\n<p>In particular I refer you to the list, that Lior Pachter has curated, which includes all variations of *-seq. You&#8217;ll see that practically all sequencing protocols take on this nomenclature of  catchy descriptor + seq. <br><\/p>\n\n\n\n<figure class=\"wp-block-embed is-type-link is-provider-bits-of-dna\"><div class=\"wp-block-embed__wrapper\">\n<blockquote class=\"wp-embedded-content\" data-secret=\"jXiVQYxTOI\"><a href=\"https:\/\/liorpachter.wordpress.com\/seq\/\">*Seq<\/a><\/blockquote><iframe loading=\"lazy\" class=\"wp-embedded-content\" sandbox=\"allow-scripts\" security=\"restricted\" style=\"position: absolute; clip: rect(1px, 1px, 1px, 1px);\" title=\"&#8220;*Seq&#8221; &#8212; Bits of DNA\" src=\"https:\/\/liorpachter.wordpress.com\/seq\/embed\/#?secret=MigszBht6m#?secret=jXiVQYxTOI\" data-secret=\"jXiVQYxTOI\" width=\"600\" height=\"338\" frameborder=\"0\" marginwidth=\"0\" marginheight=\"0\" scrolling=\"no\"><\/iframe>\n<\/div><\/figure>\n\n\n\n<p>You will have heard mention of Ig-seq in talks by antibody people (with all Ig-seq experiments being curated in OAS by Alex). Ig-seq comes under the &#8220;Phenotyping&#8221; section of Lior&#8217;s list. <\/p>\n\n\n\n<p><\/p>\n\n\n\n<!--more-->\n\n\n\n<p>There\u2019s also a few quirky theoretical applications of sequencing, for example a 2012 paper attempting to use sequencing for WIMP (<a href=\"https:\/\/en.wikipedia.org\/wiki\/Weakly_interacting_massive_particles\">https:\/\/en.wikipedia.org\/wiki\/Weakly_interacting_massive_particles<\/a>) detection (which doesn\u2019t seem to have taken off but it\u2019s nice to see that the word has spread). There\u2019s also BOINC-seq (Barcoding of Individual Neuronal Connections), which would use sequencing to reconstruct the neural connectome as an alternative to labour-intensive EM reconstruction (image segmentation algorithms have won out on this one, though). <br><\/p>\n\n\n\n<p>These technologies either do underlie or could underlie a lot of our work &#8211; be this expression data for networks people (sequencing technologies which rely on differential chromatin or methylation states (e.g. FAIRE-seq and TAB-seq, respectively)), data on translation for the protein folders (Ribo-seq), or good old Ig-seq for antibody people such as myself. <\/p>\n\n\n\n<p>I\u2019m afraid small molecule and crystallography people are somewhat excluded from this sequencing party, but in any case I think it&#8217;s a cool blog!<\/p>\n\n\n\n<p>All best wishes<\/p>\n\n\n\n<p>Eve<br><\/p>\n","protected":false},"excerpt":{"rendered":"<p>I thought I would make this blog post very meta by referring to another blog, written by Lior Pachter, which I think has something for many of us in it: http:\/\/liorpachter.wordpress.com (networks people, there\u2019s a pretty scathing take-down of a quite well cited 2013 paper as one of the last posts &#8211; there seem to [&hellip;]<\/p>\n","protected":false},"author":58,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"nf_dc_page":"","wikipediapreview_detectlinks":true,"_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"ngg_post_thumbnail":0,"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[30,31],"tags":[217,216],"ppma_author":[540],"class_list":["post-4579","post","type-post","status-publish","format-standard","hentry","category-links","category-notes","tag-computational-biology","tag-sequencing"],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"authors":[{"term_id":540,"user_id":58,"is_guest":0,"slug":"eve","display_name":"Eve Richardson","avatar_url":"https:\/\/secure.gravatar.com\/avatar\/9891300fda41850fb2fc859ef2ee18aae341c49e520511adc5684413cc356ff7?s=96&d=mm&r=g","0":null,"1":"","2":"","3":"","4":"","5":"","6":"","7":"","8":""}],"_links":{"self":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/4579","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/users\/58"}],"replies":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/comments?post=4579"}],"version-history":[{"count":4,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/4579\/revisions"}],"predecessor-version":[{"id":4583,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/4579\/revisions\/4583"}],"wp:attachment":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/media?parent=4579"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/categories?post=4579"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/tags?post=4579"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/ppma_author?post=4579"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}