<?xml version='1.0' encoding='UTF-8'?><?xml-stylesheet href="http://www.blogger.com/styles/atom.css" type="text/css"?><feed xmlns='http://www.w3.org/2005/Atom' xmlns:openSearch='http://a9.com/-/spec/opensearchrss/1.0/' xmlns:blogger='http://schemas.google.com/blogger/2008' xmlns:georss='http://www.georss.org/georss' xmlns:gd="http://schemas.google.com/g/2005" xmlns:thr='http://purl.org/syndication/thread/1.0'><id>tag:blogger.com,1999:blog-36768584</id><updated>2026-02-16T00:55:24.118-05:00</updated><category term="genome sequencing"/><category term="cancer"/><category term="biotech companies"/><category term="bioinformatics"/><category term="DNA sequencing"/><category term="biotech history"/><category term="conferences"/><category term="synthetic biology"/><category term="administration"/><category term="controversies"/><category term="evolution"/><category term="gardening"/><category term="great books"/><category term="biomarkers"/><category term="obituaries"/><category term="rare diseases"/><category term="dogs"/><category term="popular culture"/><category term="expression profiling"/><category term="metagenomics"/><category term="microarrays"/><category term="biotech buildings"/><category term="microfluidics"/><category term="programming"/><category term="space"/><category term="biotech education"/><category term="books"/><category term="immunoassays"/><category term="journals"/><category term="kinases"/><category term="proteomics"/><category term="public policy"/><category term="clinical samples"/><category term="ecology"/><category term="funny"/><category term="imaging"/><category term="patents"/><category term="structural biology"/><category term="systems biology"/><category term="array CGH"/><category term="cell sorting"/><category term="clinical trials"/><category term="comparative genomics"/><category term="gpcrs"/><category term="lupus"/><category term="media"/><category term="personalized medicine"/><category term="phosphoproteomics"/><category term="rnai"/><category term="scientific publishing"/><category term="standards"/><category term="transcription factors"/><category term="DNA-protein interactions"/><category term="GWAS"/><category term="K12 education"/><category term="RT-PCR"/><category term="android"/><category term="chemoproteomics"/><category term="dead manuscripts"/><category term="drug discovery"/><category term="drug pricing"/><category term="enzyme engineering"/><category term="etymology"/><category term="functional genomics"/><category term="genetic association studies"/><category term="history of science"/><category term="infectious disease"/><category term="microRNA"/><category term="microenvironment"/><category term="microsoft office"/><category term="museums"/><category term="pathological science"/><category term="personal genomics"/><category term="phage"/><category term="scala"/><category term="simulation"/><category term="statistics"/><category term="transgenic plants"/><category term="u"/><title type='text'>Omics! Omics!</title><subtitle type='html'>A computational biologist&#39;s personal views on new technologies &amp; publications on genomics &amp; proteomics and their impact on drug discovery</subtitle><link rel='http://schemas.google.com/g/2005#feed' type='application/atom+xml' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/feeds/posts/default'/><link rel='self' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default'/><link rel='alternate' type='text/html' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/'/><link rel='hub' href='http://pubsubhubbub.appspot.com/'/><link rel='next' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default?start-index=26&max-results=25'/><author><name>Keith Robison</name><uri>http://www.blogger.com/profile/04765318239070312590</uri><email>noreply@blogger.com</email><gd:image rel='http://schemas.google.com/g/2005#thumbnail' width='32' height='31' src='//blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_xVyJTnr62WSgPWaShtgTHw6PeTmI3OPrRnKuB6maoew9M7yjw7Irhe3LjFE2BBxukrdicyMQkjaNTL9piShDOaERcYx3ZkMsKFpde86ULRt0Khfx-eID7YHALQwyTA/s113/snip3.GIF'/></author><generator version='7.00' uri='http://www.blogger.com'>Blogger</generator><openSearch:totalResults>944</openSearch:totalResults><openSearch:startIndex>1</openSearch:startIndex><openSearch:itemsPerPage>25</openSearch:itemsPerPage><entry><id>tag:blogger.com,1999:blog-36768584.post-5401903595358314911</id><published>2026-02-08T22:05:00.000-05:00</published><updated>2026-02-08T22:05:13.756-05:00</updated><title type='text'>Pancreatic Adenocarcinoma Mutation Trajectories at Single Cell Resolution</title><content type='html'>Single cell RNA sequencing is nearly ubiquitous; single cell DNA sequencing has been much rarer. I&#39;m going to dive in a bit - but not a full review - <a href="https://www.nature.com/articles/s41588-025-02468-9">of a recent paper which described single cell DNA sequencing of pancreatic ductal adenocarcinoma</a>s. The paper applied the Mission Bio droplet-based PCR approach, which hasn&#39;t had quite the buzz of its close technological cousin 10X Genomics. And there are some interesting implications of the findings in this paper to impending developments in oncology therapeutics - including one in which I have more than academic interest.<span></span><a href="https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2026/02/pancreatic-adenocarcinoma-mutation.html#more">Read more »</a></content><link rel='replies' type='application/atom+xml' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/feeds/5401903595358314911/comments/default' title='Post Comments'/><link rel='replies' type='text/html' href='http://www.blogger.com/comment/fullpage/post/36768584/5401903595358314911' title='0 Comments'/><link rel='edit' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/5401903595358314911'/><link rel='self' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/5401903595358314911'/><link rel='alternate' type='text/html' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2026/02/pancreatic-adenocarcinoma-mutation.html' title='Pancreatic Adenocarcinoma Mutation Trajectories at Single Cell Resolution'/><author><name>Keith Robison</name><uri>http://www.blogger.com/profile/04765318239070312590</uri><email>noreply@blogger.com</email><gd:image rel='http://schemas.google.com/g/2005#thumbnail' width='32' height='31' src='//blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_xVyJTnr62WSgPWaShtgTHw6PeTmI3OPrRnKuB6maoew9M7yjw7Irhe3LjFE2BBxukrdicyMQkjaNTL9piShDOaERcYx3ZkMsKFpde86ULRt0Khfx-eID7YHALQwyTA/s113/snip3.GIF'/></author><thr:total>0</thr:total></entry><entry><id>tag:blogger.com,1999:blog-36768584.post-8767874915856929872</id><published>2026-02-02T10:28:00.005-05:00</published><updated>2026-02-02T10:28:52.509-05:00</updated><title type='text'>Non-coding DNA's Alpha Moment</title><content type='html'><span id="docs-internal-guid-be227014-7fff-a943-f37b-92206cd9ea0a"><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="font-family: Arial, sans-serif; font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-emoji: normal; font-variant-numeric: normal; font-variant-position: normal; vertical-align: baseline; white-space-collapse: preserve;">I had been meaning to read the <a href="https://www.nature.com/articles/s41586-025-10014-0">AlphaGenome paper on non-coding variant effect prediction from Google DeepMind</a> which recently showed up in Nature, but had found excuses not to dive in. Then DeciBio’s <a href="https://www.linkedin.com/posts/budel_alphagenome-article-implications-decibio-activity-7423861617357987840-FpIg?utm_source=share&amp;utm_medium=member_desktop&amp;rcm=ACoAAAAMhvIB8j25l6cK2syd0rS7dRfxfeiywzI">Stephane Budel posted on LinkedIn</a> with some incisive comments and few things spur me to action better than my sense of competition! So here&#39;s a quick, incomplete &amp; imperfect take on this giant paper.</span></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><br></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span></span></p></span><a href="https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2026/02/non-coding-dnas-alpha-moment.html#more">Read more »</a></content><link rel='replies' type='application/atom+xml' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/feeds/8767874915856929872/comments/default' title='Post Comments'/><link rel='replies' type='text/html' href='http://www.blogger.com/comment/fullpage/post/36768584/8767874915856929872' title='0 Comments'/><link rel='edit' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/8767874915856929872'/><link rel='self' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/8767874915856929872'/><link rel='alternate' type='text/html' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2026/02/non-coding-dnas-alpha-moment.html' title='Non-coding DNA's Alpha Moment'/><author><name>Keith Robison</name><uri>http://www.blogger.com/profile/04765318239070312590</uri><email>noreply@blogger.com</email><gd:image rel='http://schemas.google.com/g/2005#thumbnail' width='32' height='31' src='//blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_xVyJTnr62WSgPWaShtgTHw6PeTmI3OPrRnKuB6maoew9M7yjw7Irhe3LjFE2BBxukrdicyMQkjaNTL9piShDOaERcYx3ZkMsKFpde86ULRt0Khfx-eID7YHALQwyTA/s113/snip3.GIF'/></author><thr:total>0</thr:total></entry><entry><id>tag:blogger.com,1999:blog-36768584.post-389159471067160730</id><published>2026-01-29T12:21:00.000-05:00</published><updated>2026-01-29T12:21:11.726-05:00</updated><title type='text'>Sequencer vs. Library Prep Market Structures</title><content type='html'>Something I started pondering as I was prepping my JP Morgan items: the structure of the market for sequencing library prep is very different from that for sequencers. Perhaps this is painfully obvious to many, but I hadn&#39;t turned it over before in my mind. It also follows that the sequencer market was overweighted in who was invited to give talks at the banking conference - nearly every sequencer maker was there - Complete Genomics and Singular Genomics were the missing parties (and Singular is a bit of a quasi-sequencer company now). Note that in this piece I will not claim a complete census of companies in this space - though please feel free to note exceptions in the comments<span></span><a href="https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2026/01/sequencer-vs-library-prep-market.html#more">Read more »</a></content><link rel='replies' type='application/atom+xml' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/feeds/389159471067160730/comments/default' title='Post Comments'/><link rel='replies' type='text/html' href='http://www.blogger.com/comment/fullpage/post/36768584/389159471067160730' title='2 Comments'/><link rel='edit' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/389159471067160730'/><link rel='self' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/389159471067160730'/><link rel='alternate' type='text/html' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2026/01/sequencer-vs-library-prep-market.html' title='Sequencer vs. Library Prep Market Structures'/><author><name>Keith Robison</name><uri>http://www.blogger.com/profile/04765318239070312590</uri><email>noreply@blogger.com</email><gd:image rel='http://schemas.google.com/g/2005#thumbnail' width='32' height='31' src='//blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_xVyJTnr62WSgPWaShtgTHw6PeTmI3OPrRnKuB6maoew9M7yjw7Irhe3LjFE2BBxukrdicyMQkjaNTL9piShDOaERcYx3ZkMsKFpde86ULRt0Khfx-eID7YHALQwyTA/s113/snip3.GIF'/></author><thr:total>2</thr:total></entry><entry><id>tag:blogger.com,1999:blog-36768584.post-2664471158065616055</id><published>2026-01-28T11:01:00.001-05:00</published><updated>2026-01-28T11:01:13.433-05:00</updated><title type='text'>P2 Solo: ONT Extends Support But Not Sales</title><content type='html'>A brief update to the <a href="https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2026/01/ont-axes-p2-solo-roiling-community.html">earlier P2 Solo piece</a> - Oxford Nanopore has now announced they will extend their support for the device until 2030, but they are still ending sales this summer. So a cosmetic victory for Solo fans, but not really much gain - and certainly disappointing for anyone saving their quid for a future purchase. Solos may become very valuable, though it&#39;s hard to see ONT ever countenancing a healthy resale market.<a href="https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2026/01/p2-solo-ont-extends-support-but-not.html#more">Read more »</a></content><link rel='replies' type='application/atom+xml' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/feeds/2664471158065616055/comments/default' title='Post Comments'/><link rel='replies' type='text/html' href='http://www.blogger.com/comment/fullpage/post/36768584/2664471158065616055' title='2 Comments'/><link rel='edit' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/2664471158065616055'/><link rel='self' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/2664471158065616055'/><link rel='alternate' type='text/html' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2026/01/p2-solo-ont-extends-support-but-not.html' title='P2 Solo: ONT Extends Support But Not Sales'/><author><name>Keith Robison</name><uri>http://www.blogger.com/profile/04765318239070312590</uri><email>noreply@blogger.com</email><gd:image rel='http://schemas.google.com/g/2005#thumbnail' width='32' height='31' src='//blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_xVyJTnr62WSgPWaShtgTHw6PeTmI3OPrRnKuB6maoew9M7yjw7Irhe3LjFE2BBxukrdicyMQkjaNTL9piShDOaERcYx3ZkMsKFpde86ULRt0Khfx-eID7YHALQwyTA/s113/snip3.GIF'/></author><thr:total>2</thr:total></entry><entry><id>tag:blogger.com,1999:blog-36768584.post-5615593218260791306</id><published>2026-01-25T20:43:00.001-05:00</published><updated>2026-01-25T20:48:55.607-05:00</updated><title type='text'>ONT Axes P2 Solo, Roiling Community</title><content type='html'><div>Oxford Nanopore has a serious case of user community unrest, triggered by the announcement that the P2 Solo (aka P2s) will be phased out starting this summer. P2 Solo is the two flowcell version of PromethION which required external GPU for basecalling; P2i is the sibling with onboard GPU. P2 Solo clearly has a very passionate constituency, one which feels betrayed by its discontinuation. This ongoing episode - ONT could always change their mind and restore the P2 Solo - is a cautionary tale of the challenges of changing corporate strategy in the context of a brand which has built a near cult-like loyalty. </div><span></span><a href="https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2026/01/ont-axes-p2-solo-roiling-community.html#more">Read more »</a></content><link rel='replies' type='application/atom+xml' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/feeds/5615593218260791306/comments/default' title='Post Comments'/><link rel='replies' type='text/html' href='http://www.blogger.com/comment/fullpage/post/36768584/5615593218260791306' title='2 Comments'/><link rel='edit' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/5615593218260791306'/><link rel='self' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/5615593218260791306'/><link rel='alternate' type='text/html' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2026/01/ont-axes-p2-solo-roiling-community.html' title='ONT Axes P2 Solo, Roiling Community'/><author><name>Keith Robison</name><uri>http://www.blogger.com/profile/04765318239070312590</uri><email>noreply@blogger.com</email><gd:image rel='http://schemas.google.com/g/2005#thumbnail' width='32' height='31' src='//blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_xVyJTnr62WSgPWaShtgTHw6PeTmI3OPrRnKuB6maoew9M7yjw7Irhe3LjFE2BBxukrdicyMQkjaNTL9piShDOaERcYx3ZkMsKFpde86ULRt0Khfx-eID7YHALQwyTA/s113/snip3.GIF'/></author><media:thumbnail xmlns:media="http://search.yahoo.com/mrss/" url="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgcVqbjbA1qA5H0oOfRfmR1E7NkFo2Hj-MrdrhyphenhyphenFJQyNL78Cko8a6kd85Qs4tJhwcCroTNx_ctcKNoLPFDaOiqeBMC8lU1j_My9Lgm1ughusX33qcEYG-JCDNl4Vs6Oy6BJpm65W8bliamZmaWDhzAU1Cy7lAUtLCiQL_gersybqjV9j1Y1486MYA/s72-w400-h260-c/IMG_4940.jpg" height="72" width="72"/><thr:total>2</thr:total></entry><entry><id>tag:blogger.com,1999:blog-36768584.post-1192821632863259701</id><published>2026-01-22T09:44:00.001-05:00</published><updated>2026-01-22T09:44:16.764-05:00</updated><title type='text'>JP Morgan 2026 Roundup</title><content type='html'><div>The J.P. Morgan conference last week was mostly small tidbits of info on the sequencing front, with Element delivering the one big teaser announcement. </div><span></span><a href="https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2026/01/jp-morgan-2026-roundup.html#more">Read more »</a></content><link rel='replies' type='application/atom+xml' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/feeds/1192821632863259701/comments/default' title='Post Comments'/><link rel='replies' type='text/html' href='http://www.blogger.com/comment/fullpage/post/36768584/1192821632863259701' title='0 Comments'/><link rel='edit' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/1192821632863259701'/><link rel='self' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/1192821632863259701'/><link rel='alternate' type='text/html' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2026/01/jp-morgan-2026-roundup.html' title='JP Morgan 2026 Roundup'/><author><name>Keith Robison</name><uri>http://www.blogger.com/profile/04765318239070312590</uri><email>noreply@blogger.com</email><gd:image rel='http://schemas.google.com/g/2005#thumbnail' width='32' height='31' src='//blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_xVyJTnr62WSgPWaShtgTHw6PeTmI3OPrRnKuB6maoew9M7yjw7Irhe3LjFE2BBxukrdicyMQkjaNTL9piShDOaERcYx3ZkMsKFpde86ULRt0Khfx-eID7YHALQwyTA/s113/snip3.GIF'/></author><thr:total>0</thr:total></entry><entry><id>tag:blogger.com,1999:blog-36768584.post-3207133029428916594</id><published>2026-01-11T22:03:00.008-05:00</published><updated>2026-01-15T15:03:20.651-05:00</updated><title type='text'>JPM 2026 Schedule Through A Molecular Tools & Testing Lens</title><content type='html'>The J.P. Morgan Healthcare Conference is this week in San Francisco. As with every other one, I&#39;m tracking any news remotely from Boston. Some year I really should go to observe the sheer spectacle of it, but this isn&#39;t the year - and if I were in California now it probably would be more valuable to attend Plant &amp; Animal Genomes down in San Diego. If you do go, be sure to check out the 4 instrument autonomous laboratory Ginkgo will have running in the Marriott Marquis lobby. But here are some notes to keep track of when different companies are presenting. Public companies will make their presentations available shortly thereafter to comply with insider trading regulations. Unfortunately, several years ago J.P. Morgan ended posting presentations from private companies - these companies could choose to post their decks but I&#39;m not optimistic to see many.<span></span><a href="https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2026/01/jpm-2026-through-molecular-tools.html#more">Read more »</a></content><link rel='replies' type='application/atom+xml' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/feeds/3207133029428916594/comments/default' title='Post Comments'/><link rel='replies' type='text/html' href='http://www.blogger.com/comment/fullpage/post/36768584/3207133029428916594' title='0 Comments'/><link rel='edit' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/3207133029428916594'/><link rel='self' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/3207133029428916594'/><link rel='alternate' type='text/html' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2026/01/jpm-2026-through-molecular-tools.html' title='JPM 2026 Schedule Through A Molecular Tools & Testing Lens'/><author><name>Keith Robison</name><uri>http://www.blogger.com/profile/04765318239070312590</uri><email>noreply@blogger.com</email><gd:image rel='http://schemas.google.com/g/2005#thumbnail' width='32' height='31' src='//blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_xVyJTnr62WSgPWaShtgTHw6PeTmI3OPrRnKuB6maoew9M7yjw7Irhe3LjFE2BBxukrdicyMQkjaNTL9piShDOaERcYx3ZkMsKFpde86ULRt0Khfx-eID7YHALQwyTA/s113/snip3.GIF'/></author><thr:total>0</thr:total></entry><entry><id>tag:blogger.com,1999:blog-36768584.post-7691574874824361018</id><published>2026-01-09T12:06:00.003-05:00</published><updated>2026-01-09T18:47:37.368-05:00</updated><title type='text'>Stalking the Elusive Product Market Fit</title><content type='html'>I had a wonderful breakfast conversation back in November with Arima Genomics Founder (and now President and Chief Operating Officer) Sid Selvaraj where he brought up the topic of product market fit. I&#39;ve often kibitzed on &#39;omics companies trials and tribulations trying to achieve product market fit, but now that I&#39;m in an outward-facing product development role the concept is central to my daily work. What is it and how does one achieve it - or fail to?<span></span><a href="https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2026/01/stalking-elusive-product-market-fit.html#more">Read more »</a></content><link rel='replies' type='application/atom+xml' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/feeds/7691574874824361018/comments/default' title='Post Comments'/><link rel='replies' type='text/html' href='http://www.blogger.com/comment/fullpage/post/36768584/7691574874824361018' title='1 Comments'/><link rel='edit' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/7691574874824361018'/><link rel='self' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/7691574874824361018'/><link rel='alternate' type='text/html' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2026/01/stalking-elusive-product-market-fit.html' title='Stalking the Elusive Product Market Fit'/><author><name>Keith Robison</name><uri>http://www.blogger.com/profile/04765318239070312590</uri><email>noreply@blogger.com</email><gd:image rel='http://schemas.google.com/g/2005#thumbnail' width='32' height='31' src='//blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_xVyJTnr62WSgPWaShtgTHw6PeTmI3OPrRnKuB6maoew9M7yjw7Irhe3LjFE2BBxukrdicyMQkjaNTL9piShDOaERcYx3ZkMsKFpde86ULRt0Khfx-eID7YHALQwyTA/s113/snip3.GIF'/></author><thr:total>1</thr:total></entry><entry><id>tag:blogger.com,1999:blog-36768584.post-3757415051020343926</id><published>2026-01-07T09:37:00.002-05:00</published><updated>2026-01-07T09:37:44.277-05:00</updated><title type='text'>Scales of Instrumentation and Automation</title><content type='html'>Back in September I moved into a product role within the automation unit at Ginkgo, where we sell autonomous laboratories. I&#39;m going to end up posting a bunch on the topic, as I spend a lot of time thinking about it and this is an interesting place to expose my thinking to critique. It&#39;s also a way to solicit feedback on semi-formed ideas. I referenced autonomous laboratories in my previous post, which might have some wondering &quot;what exactly is an autonomous laboratory?&quot; So this post will lay out a description of different levels of automation (or instrumentation) so I can refer back to it in future posts - and there will certainly be further posts focused on these different scales of automation. So here I will lay out four levels of laboratory instrumentation: Bench, Walkup, Workcell and Autonomous. BTW, if you are in San Francisco next week during J.P. Morgan, there will be a small autonomous lab running in the Marriott Marquis lobby - and it can be viewed regardless of whether you are registered for the conference<span></span><a href="https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2026/01/scales-of-instrumentation-and-automation.html#more">Read more »</a></content><link rel='replies' type='application/atom+xml' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/feeds/3757415051020343926/comments/default' title='Post Comments'/><link rel='replies' type='text/html' href='http://www.blogger.com/comment/fullpage/post/36768584/3757415051020343926' title='3 Comments'/><link rel='edit' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/3757415051020343926'/><link rel='self' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/3757415051020343926'/><link rel='alternate' type='text/html' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2026/01/scales-of-instrumentation-and-automation.html' title='Scales of Instrumentation and Automation'/><author><name>Keith Robison</name><uri>http://www.blogger.com/profile/04765318239070312590</uri><email>noreply@blogger.com</email><gd:image rel='http://schemas.google.com/g/2005#thumbnail' width='32' height='31' src='//blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_xVyJTnr62WSgPWaShtgTHw6PeTmI3OPrRnKuB6maoew9M7yjw7Irhe3LjFE2BBxukrdicyMQkjaNTL9piShDOaERcYx3ZkMsKFpde86ULRt0Khfx-eID7YHALQwyTA/s113/snip3.GIF'/></author><media:thumbnail xmlns:media="http://search.yahoo.com/mrss/" url="https://blogger.googleusercontent.com/img/a/AVvXsEiEugHC7_5EttCMEGMHu5byIwzJN849QvY1QAib6vGPBjfoEVw73IQfAQ-f4nuwRrq9uiLymSmd6R3IJecTOj-CjE9C-wXn2qO0rpm5qlKfKxLY37fJovOQ6GPfYmaPLMqHnqI6aTdP980cHx76021MRYStDHwvVCesd6ppS9S_pqhW3N2WbFg4PA=s72-c" height="72" width="72"/><thr:total>3</thr:total></entry><entry><id>tag:blogger.com,1999:blog-36768584.post-3121936609687187736</id><published>2026-01-04T22:18:00.003-05:00</published><updated>2026-01-05T08:42:46.106-05:00</updated><title type='text'>Sequencing Instrument Outlook 2026</title><content type='html'><a href="https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2026/01/sequencing-instrument-outlook-2026.html#more">Read more »</a></content><link rel='replies' type='application/atom+xml' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/feeds/3121936609687187736/comments/default' title='Post Comments'/><link rel='replies' type='text/html' href='http://www.blogger.com/comment/fullpage/post/36768584/3121936609687187736' title='3 Comments'/><link rel='edit' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/3121936609687187736'/><link rel='self' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/3121936609687187736'/><link rel='alternate' type='text/html' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2026/01/sequencing-instrument-outlook-2026.html' title='Sequencing Instrument Outlook 2026'/><author><name>Keith Robison</name><uri>http://www.blogger.com/profile/04765318239070312590</uri><email>noreply@blogger.com</email><gd:image rel='http://schemas.google.com/g/2005#thumbnail' width='32' height='31' src='//blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_xVyJTnr62WSgPWaShtgTHw6PeTmI3OPrRnKuB6maoew9M7yjw7Irhe3LjFE2BBxukrdicyMQkjaNTL9piShDOaERcYx3ZkMsKFpde86ULRt0Khfx-eID7YHALQwyTA/s113/snip3.GIF'/></author><thr:total>3</thr:total></entry><entry><id>tag:blogger.com,1999:blog-36768584.post-670103842273543825</id><published>2025-12-29T21:43:00.001-05:00</published><updated>2025-12-30T11:25:08.097-05:00</updated><title type='text'>The Joy of Rediscovery</title><content type='html'>A key goal of science is to discover new information, and it is one of the great joys of science to believe you have done so. Sometimes it really does prove novel and interesting - an experience our genome explorations at Warp Drive Bio gave me often - and sometimes the joy is blunted by realizing what you thought was novel is already known. When I was a graduate student I was on an immense high having found what seemed revolutionary while trawling through Genbank, but then a few days later I uncovered a Cell paper less than a year earlier which had shown that Archea possessed a Eukaryote-like transcription initiation system. So close yet so far! But there is also a special joy in certain rediscoveries, when without trying at all a fundamental fact about the universe just reveals itself in your data. One of my New Year&#39;s resolutions is to rediscover the discipline to write frequently in this space, and so to kick that off early (and get the 2025 count to an even one quarter of a 96-well plate) I&#39;m going to review my favorite rediscovery - one that that surprisingly few (in my opinion) who should know of this result are aware of it.<span></span><a href="https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2025/12/the-joy-of-rediscovery.html#more">Read more »</a></content><link rel='replies' type='application/atom+xml' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/feeds/670103842273543825/comments/default' title='Post Comments'/><link rel='replies' type='text/html' href='http://www.blogger.com/comment/fullpage/post/36768584/670103842273543825' title='4 Comments'/><link rel='edit' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/670103842273543825'/><link rel='self' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/670103842273543825'/><link rel='alternate' type='text/html' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2025/12/the-joy-of-rediscovery.html' title='The Joy of Rediscovery'/><author><name>Keith Robison</name><uri>http://www.blogger.com/profile/04765318239070312590</uri><email>noreply@blogger.com</email><gd:image rel='http://schemas.google.com/g/2005#thumbnail' width='32' height='31' src='//blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_xVyJTnr62WSgPWaShtgTHw6PeTmI3OPrRnKuB6maoew9M7yjw7Irhe3LjFE2BBxukrdicyMQkjaNTL9piShDOaERcYx3ZkMsKFpde86ULRt0Khfx-eID7YHALQwyTA/s113/snip3.GIF'/></author><media:thumbnail xmlns:media="http://search.yahoo.com/mrss/" url="https://blogger.googleusercontent.com/img/a/AVvXsEgc55JhS3v2Rg7naH0D1mVgEz2_3caQyQifTAm9caIlbhnSjeiLomunt1062jH7A6Yg4XdDWrGjv-su9womr76cpHDQgbEIEnyQcrL4sCj6h7fTm_-0vgb_CFsGsikxlYvz6t81gr6BDRwJkoot5blJREVRMv8UIRgiC6Nuz0GrHhdEHc5En5eHnQ=s72-c" height="72" width="72"/><thr:total>4</thr:total></entry><entry><id>tag:blogger.com,1999:blog-36768584.post-6804412756982948270</id><published>2025-12-16T11:48:00.001-05:00</published><updated>2025-12-16T11:53:00.079-05:00</updated><title type='text'>UltraMarathonRT: When Your Reverse Transcription Must Go Long</title><content type='html'><span id="docs-internal-guid-06202f62-7fff-d01f-4a9c-d763379a5bae"><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="font-family: Arial, sans-serif; font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-emoji: normal; font-variant-numeric: normal; font-variant-position: normal; vertical-align: baseline; white-space-collapse: preserve;">The 1960s, 1970s and 1980s were both the early years and golden years for nucleic acid enzymology. Scientists unraveling the secrets of DNA replication and repair, RNA transcription, viral replication and other basic processes purified enzymes responsible for numerous processes. Other scientists envisioned practical applications for these enzymes and put them to work in the recombinant DNA revolution that began just over 50 years ago. Due in no small part to the great body of literature that has arisen around these pioneer enzymes, they tend to be important still today in biotechnology - sometimes retaining monopolies on a particular type of in vitro biochemistry. But there are new entrants, and today I’m going to explore a new player in the reverse transcription space, UltraMarathonRT from a small Connecticut company, RNAConnect. RNAConnect has launched two new products in the second half of this year, a kit for cDNA synthesis back in August and today a kit for generating long direct RNA reads on Oxford Nanopore platforms.</span></p><br><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="font-family: Arial, sans-serif; font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-emoji: normal; font-variant-numeric: normal; font-variant-position: normal; vertical-align: baseline; white-space-collapse: preserve;">Two reverse transcriptases have dominated the field of cDNA generation for cloning, sequencing, RT-qPCR and other applications, both arising from early research on retroviruses. Each is named for the retrovirus it was found in, Avian Myeloblastosis Virus (AMV) Reverse Transcriptase and Moloney Murine Leukemia Virus (M-MuLV, MMLV). Many of the reverse transcription kits on the market today are either formulations of one of these two retroviruses or made with versions carrying a small number of point mutations. While these enzymes have served biotechnology well, they do have shortcomings, particularly in the lack of helicase activity which can cause them to stall on templates which have formed complex and strong secondary structures.</span></p><br><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="font-family: Arial, sans-serif; font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-emoji: normal; font-variant-numeric: normal; font-variant-position: normal; vertical-align: baseline; white-space-collapse: preserve;">UltraMarathonRT is not from a eukaryotic retrovirus, but instead from a prokaryotic group II self-splicing intron. UltraMarathonRT is far more processive than the venerable eukaryotic RTs and able to reverse transcribe transcripts of 30 kilobases or longer. A key difference from another group II retron RT on the market, Induro from NEB, is that UltraMarathonRT has a temperature optimum of 30C vs 55C for Induro; higher temperatures risk more damage to template RNA. </span></p><br><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="font-family: Arial, sans-serif; font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-emoji: normal; font-variant-numeric: normal; font-variant-position: normal; vertical-align: baseline; white-space-collapse: preserve;">Template switching is a property of reverse transcriptases in which the enzyme has a 3’ terminal transferase activity which adds a predictable set of untemplated nucleotides to the 3’ end of the first strand cDNA; for UltraMarathonRT this is three As. By inclusion in the reaction of an oligo with the complementary sequence, second strand cDNA can be triggered in the same reaction. Since the template switching oligo (TSO) can have barcode and unique molecular identifier sequences as well, this makes template switching particularly valuable for sequencing applications. </span></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEhg7Tiod0aqEgU_gv1G4N2WTb7XxrewtLg9_94an1IJfOv6nquoou6q7un6sJZDCm_KCBY1L0wlnIY45tgIdZUbjmbU9XnwwhxIPdMaB-yaEmus_KX-6kOOZTD1SApgUB2M_1GEe--r_MZv0YWcq4bygOAy2ZN4nKfBUpBk8aR2MD6afF-x8c785w" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="301" data-original-width="394" height="306" src="https://blogger.googleusercontent.com/img/a/AVvXsEhg7Tiod0aqEgU_gv1G4N2WTb7XxrewtLg9_94an1IJfOv6nquoou6q7un6sJZDCm_KCBY1L0wlnIY45tgIdZUbjmbU9XnwwhxIPdMaB-yaEmus_KX-6kOOZTD1SApgUB2M_1GEe--r_MZv0YWcq4bygOAy2ZN4nKfBUpBk8aR2MD6afF-x8c785w=w400-h306" width="400"></a></div><br><br><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="font-family: Arial, sans-serif; font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-emoji: normal; font-variant-numeric: normal; font-variant-position: normal; vertical-align: baseline; white-space-collapse: preserve;">RNAConnect today launched a kit for Oxford Nanopore direct RNA sequencing which uses UltraMarathonRT. While direct RNA sequencing can work without any reverse transcription, having a first strand cDNA bound to the RNA improves performance, particularly since the helicase activity of UltraMarathonRT can unwind secondary structures which might not be unwound by the motor protein in ONT’s chemistry. RNAConnect has run comparisons of their kit to a process using Induro and shown 67% more mapped reads which are in excess of 10Kb, with this dropping to 24% for mapped reads &gt;5kb and only 11% for reads &gt;2kb. With increasing research interest in exploring long non-coding RNAs (lncRNAs) - the best known lncRNA, XIST responsible for driving X chromosome inactivation, is 17 kilobases long. The kit also has the convenience of including all required components, other than those unique to ONT.</span></p><br><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="font-family: Arial, sans-serif; font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-emoji: normal; font-variant-numeric: normal; font-variant-position: normal; vertical-align: baseline; white-space-collapse: preserve;">Higher processivity and greater ability to push through complex secondary structures - both highly desirable properties in a reverse transcriptase. As the price/performance ratio of both PacBio and ONT improve for cDNA sequencing, continued improvement of metrics for ONT direct RNA and now meso-length reads from Roche’s SBX chemistry will all enable greater surveys of RNA at longer scales. Such studies can be reasonably expected to sharpen our understanding of splicing.</span></p><br><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="font-family: Arial, sans-serif; font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-emoji: normal; font-variant-numeric: normal; font-variant-position: normal; vertical-align: baseline; white-space-collapse: preserve;">When I was an undergraduate nearly 40 years ago, we were taught that alternative splicing existed but was a rare phenomenon that only rarely deserved attention. I think we were taught about the alternative splicing that drives soluble vs membrane-bound antibodies in B cells, but probably no other examples. That view has changed radically over the last 40 years, with alternative splicing now recognized as a generator of both protein diversity and regulation.</span></p><br><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="font-family: Arial, sans-serif; font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-emoji: normal; font-variant-numeric: normal; font-variant-position: normal; vertical-align: baseline; white-space-collapse: preserve;">As a graduate student, I discovered an overlooked set of alternative exons in a Drosophila visual protein gene which my labmate Carlos Alvarez demonstrated, by clever PCR assays, that while there are theoretically 8 different splice forms possible (which would all generate valid ORFs) only three of these are detectable in flies. <a href="https://www.pnas.org/doi/10.1073/pnas.93.22.12278">Made a nice PNAS paper</a>. Nowadays we’d do that by sequencing. Cataloging such coordinated splicing would be one clear use for long read direct RNA or long read cDNA sequencing.</span></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEiNGZKrPFG3gPnewi4VtDGqw1e40GytVoLXWWdwfvIqiAAjbdlDoW3U9Z29a3X_7ajfzAT2YKMKOXZ37-e3zdohiTXpdvIpcRQDr6aSe7_HjinhFGqOZfFTOoNvTCSCdiHSv7dYerrit8teZjEhyRJN8Cbb6_4rRlEVEOsIdALW2xymSqKTWUMgpA" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="448" data-original-width="1254" height="143" src="https://blogger.googleusercontent.com/img/a/AVvXsEiNGZKrPFG3gPnewi4VtDGqw1e40GytVoLXWWdwfvIqiAAjbdlDoW3U9Z29a3X_7ajfzAT2YKMKOXZ37-e3zdohiTXpdvIpcRQDr6aSe7_HjinhFGqOZfFTOoNvTCSCdiHSv7dYerrit8teZjEhyRJN8Cbb6_4rRlEVEOsIdALW2xymSqKTWUMgpA=w400-h143" width="400"></a></div><br><div><span><br></span></div><br><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="font-family: Arial, sans-serif; font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-emoji: normal; font-variant-numeric: normal; font-variant-position: normal; vertical-align: baseline; white-space-collapse: preserve;">Another emerging class of splicing events of great interest are “poison exons” and “detained introns”. Detained introns are introns that are normally spliced out, but are systematically retained in certain contexts. If these cause the translation of a premature stop codon which leads to nonsense-mediated decay of that mRNA, then it is a poison exon. A number of labs have reported on poison exons that appear to be very carefully regulated, providing yet another opportunity for cells to regulate production of a particular gene product. Inadvertent retention of poison exons is yet another way that mutations can negatively affect mRNAs and trigger rare genetic disorders. </span></p><br><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="font-family: Arial, sans-serif; font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-emoji: normal; font-variant-numeric: normal; font-variant-position: normal; vertical-align: baseline; white-space-collapse: preserve;">Clearly for a complete survey of alternative splicing, poison exon usage, and other types of retained/detained introns it is important to have an unbiased view of a transcript, not degraded by secondary structure or biased to the 3’ end. UltraMarathonRT shows approximately 2X higher detection of retained introns than other RTs when applied to the Universal Human Reference RNA (UHRR) sample. </span></p><div><span><br></span></div><div><span id="docs-internal-guid-1ca732c3-7fff-476c-d723-673fcb9b7f9a"> <div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEgQQOwxCDmmajEaEMmpMlFIwhGxCrhYDJDJRLnwpK9MOwlB0QMMDZPmXD2V8nE9kQZmq15aBHG2H9HZ1osBm_1jWnED9yV6o4BOOm7nUfsCJ_gErTmzPWBIWMemS1ELtmDJw4fuNb2fbzDxgeIiocq96OheJpzXqNjJhuh6V1AC5YZ2cDyoaylG1Q" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="351" data-original-width="379" height="240" src="https://blogger.googleusercontent.com/img/a/AVvXsEgQQOwxCDmmajEaEMmpMlFIwhGxCrhYDJDJRLnwpK9MOwlB0QMMDZPmXD2V8nE9kQZmq15aBHG2H9HZ1osBm_1jWnED9yV6o4BOOm7nUfsCJ_gErTmzPWBIWMemS1ELtmDJw4fuNb2fbzDxgeIiocq96OheJpzXqNjJhuh6V1AC5YZ2cDyoaylG1Q" width="259"></a></div><br></span></div><br><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="font-family: Arial, sans-serif; font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-emoji: normal; font-variant-numeric: normal; font-variant-position: normal; vertical-align: baseline; white-space-collapse: preserve;">RNAConnect the company is sited in Branford CT, not far from Yale University where founder Dr. Anna Marie Pyle teaches. For this piece I spoke with Andrew Bond, previously at gene synthesis company Gen9, and Jason Underwood, ex-PacBio,</span></p><br><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="font-family: Arial, sans-serif; font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-emoji: normal; font-variant-numeric: normal; font-variant-position: normal; vertical-align: baseline; white-space-collapse: preserve;">UltraMarathonRT appears to be a useful new tool in the molecular biology toolbox, enhancing the ability to sequence long and difficult RNA templates. It shows promise for advancing the understanding of splicing as well as the medical consequences of inappropriate splicing. UltraMarathonRT citations in PubMed are currently only from Dr. Pyle’s lab; it will be interesting to see what new discoveries are made as kits with this enzyme enter widespread use in RNA sequencing laboratories.</span></p><div><span style="font-family: Arial, sans-serif; font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-emoji: normal; font-variant-numeric: normal; font-variant-position: normal; vertical-align: baseline; white-space-collapse: preserve;"><br></span></div></span><a href="https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2025/12/rnaconnect-when-your-reverse.html#more">Read more »</a></content><link rel='replies' type='application/atom+xml' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/feeds/6804412756982948270/comments/default' title='Post Comments'/><link rel='replies' type='text/html' href='http://www.blogger.com/comment/fullpage/post/36768584/6804412756982948270' title='1 Comments'/><link rel='edit' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/6804412756982948270'/><link rel='self' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/6804412756982948270'/><link rel='alternate' type='text/html' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2025/12/rnaconnect-when-your-reverse.html' title='UltraMarathonRT: When Your Reverse Transcription Must Go Long'/><author><name>Keith Robison</name><uri>http://www.blogger.com/profile/04765318239070312590</uri><email>noreply@blogger.com</email><gd:image rel='http://schemas.google.com/g/2005#thumbnail' width='32' height='31' src='//blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_xVyJTnr62WSgPWaShtgTHw6PeTmI3OPrRnKuB6maoew9M7yjw7Irhe3LjFE2BBxukrdicyMQkjaNTL9piShDOaERcYx3ZkMsKFpde86ULRt0Khfx-eID7YHALQwyTA/s113/snip3.GIF'/></author><media:thumbnail xmlns:media="http://search.yahoo.com/mrss/" url="https://blogger.googleusercontent.com/img/a/AVvXsEhg7Tiod0aqEgU_gv1G4N2WTb7XxrewtLg9_94an1IJfOv6nquoou6q7un6sJZDCm_KCBY1L0wlnIY45tgIdZUbjmbU9XnwwhxIPdMaB-yaEmus_KX-6kOOZTD1SApgUB2M_1GEe--r_MZv0YWcq4bygOAy2ZN4nKfBUpBk8aR2MD6afF-x8c785w=s72-w400-h306-c" height="72" width="72"/><thr:total>1</thr:total></entry><entry><id>tag:blogger.com,1999:blog-36768584.post-4457927077208738060</id><published>2025-12-04T10:38:00.000-05:00</published><updated>2025-12-04T10:38:20.730-05:00</updated><title type='text'>Countable Labs: New Approach to Enumerating DNA</title><content type='html'><span id="docs-internal-guid-bab528ed-7fff-38a7-3da3-2d17a576420f"><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="font-family: Arial, sans-serif; font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-emoji: normal; font-variant-numeric: normal; font-variant-position: normal; vertical-align: baseline; white-space-collapse: preserve;">Countable Labs, formerly Enumerix, was founded by serial entrepreneur Stephen Fodor, who originally stormed on the molecular tools scene with Affymetrix. I caught up with their new CEO, Giovanna Prout, at ASHG the other week and got a rundown on their new approach to counting molecules with PCR.</span></p><br><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="font-family: Arial, sans-serif; font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-emoji: normal; font-variant-numeric: normal; font-variant-position: normal; vertical-align: baseline; white-space-collapse: preserve;">Prout recently found herself out of the CEO job at Scale Biosciences after its acquisition by 10X Genomics. She says she resolved to become the best stay-at-home mother ever and her kids loved having her home - but soon urged her to find a new gig as they recognized it was what made her happiest. So she quickly landed the CEO role at Countable Labs. Formerly Enumerix, the company is yet another molecular tools company from prolific scientific entrepreneur Stephen Fodor, best known for Affymetrix.</span></p><br><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="font-family: Arial, sans-serif; font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-emoji: normal; font-variant-numeric: normal; font-variant-position: normal; vertical-align: baseline; white-space-collapse: preserve;">Countable’s standard workflow is simple. A 50 microliter reaction of sample DNA, probes, primers, PCR mastermix, and Countable’s proprietary matrix consumable are placed in a spin column. Centrifuging the columns generates a matrix, with approximately 30M individual picoliter-scale compartments capturing individual DNA molecules. After a brief (60 minute) PCR amplification in a conventional thermocycler (Countable has a list of preferred instruments), the tubes are placed in Countable’s benchtop instrument for light sheet microscopy imaging of the compartments, requiring 5 minutes of imaging per tube. There’s no dead volume - every picoliter scale chamber in the tube will be imaged. Because there are so many compartments, the system has a dynamic range of 6 logs! Countable’s instrument holds 96 tubes in the form of 24 strips of 4 tubes each. The instrument is priced at $150K with consumables adding up to $16 per sample. A full set of 96 samples can be processed in half a workday.</span></p><br><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg-LpY5G_tay7WkoWsKVmf9jt66CfwvhY2dtRF9f8KwtzYbXiZwJI_xzx0UFCuqJvVwWrNWDWCpE6AyRZIJxuztHTzox8Hz0-4volXShT0sqotTDUnXFT69AJD7LRDVorcby3ijUDYXGdI9OMH098e5LuJpiJxHKSQCFYkfHSMyD8L3VBcgFsxlkA/s934/countable-workflow.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="447" data-original-width="934" height="153" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg-LpY5G_tay7WkoWsKVmf9jt66CfwvhY2dtRF9f8KwtzYbXiZwJI_xzx0UFCuqJvVwWrNWDWCpE6AyRZIJxuztHTzox8Hz0-4volXShT0sqotTDUnXFT69AJD7LRDVorcby3ijUDYXGdI9OMH098e5LuJpiJxHKSQCFYkfHSMyD8L3VBcgFsxlkA/s320/countable-workflow.png" width="320"></a></div><br><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><br></p><br><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="font-family: Arial, sans-serif; font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-emoji: normal; font-variant-numeric: normal; font-variant-position: normal; vertical-align: baseline; white-space-collapse: preserve;">Assays can be designed using Countable’s universal multiplexing kit or conventional TaqMan hydrolysis probes can be included. The universal multiplexing kit has the advantage of enabling the use of inexpensive, fast arriving ordinary oligos which simply require a 5’ tail sequence on the forward primer to enable linking (via primer extension) the universal multiplexing codes to the user primers. Countable provides a software tool to streamline converting existing assays into universal multiplexing assays and analyze the resulting multiplex primer designs for undesirable cross-reactivity. Assays based on the universal multiplexing kit can be designed and tested in under a week</span></p><br><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="font-family: Arial, sans-serif; font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-emoji: normal; font-variant-numeric: normal; font-variant-position: normal; vertical-align: baseline; white-space-collapse: preserve;">Countable is developing a high degree of multiplexing by managing the optical system so that it is capable of distinguishing 10 different fluorescent dyes. By imaging in 9 different channels, each channel a different pairing of excitation wavelength and emission wavelength, each dye can be distinguished by the unique fingerprint of intensities in each channel. </span><span style="font-family: Arial, sans-serif; font-size: 11pt; white-space-collapse: preserve;">This yields 10 clearly separable labeling schemes. </span><span style="font-family: Arial, sans-serif; font-size: 11pt; white-space-collapse: preserve;">Theoretically 48 different labeling schemes can be distinguished in this way. </span><a href="https://www.google.com/url?q=https://cdn.prod.website-files.com/681b0fe0bc39a39f4c8f25a8/690539a6fd24517e837f1f58_CL_Poster_AMP2025_KRAS_QRcode.pdf&amp;sa=D&amp;source=docs&amp;ust=1764864846976492&amp;usg=AOvVaw0fvp4z8IFjuKe1dacRJgxJ" style="font-family: Arial, sans-serif; font-size: 11pt; white-space-collapse: preserve;">One ASHG poster</a><span style="font-family: Arial, sans-serif; font-size: 11pt; white-space-collapse: preserve;"> from Countable demonstrated 8-fold multiplexing</span></p><br><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhnbisIrY1_O0eN1hU3p285Vp8JOwvMCNCjCaF98KsQmLD2pQr5oM1xVQJGkmUW_5lpiZERDSiewGFomkZ6N8pympL0M3fbnT7JsP-0nqIQBgs1izC6m9tQPfIJPBcVeuuqezPbFonTXb-CyoLoOUHjuqgBby3LxtlZ7ihAWJdHxVHHccnN9-PoVQ/s330/countable-8%20color.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="330" data-original-width="318" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhnbisIrY1_O0eN1hU3p285Vp8JOwvMCNCjCaF98KsQmLD2pQr5oM1xVQJGkmUW_5lpiZERDSiewGFomkZ6N8pympL0M3fbnT7JsP-0nqIQBgs1izC6m9tQPfIJPBcVeuuqezPbFonTXb-CyoLoOUHjuqgBby3LxtlZ7ihAWJdHxVHHccnN9-PoVQ/s320/countable-8%20color.png" width="308"></a></div><br><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><br></p><br><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="font-family: Arial, sans-serif; font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-emoji: normal; font-variant-numeric: normal; font-variant-position: normal; vertical-align: baseline; white-space-collapse: preserve;">So what can you do with so many colors? And with 6 logs of dynamic range?</span></p><br><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="font-family: Arial, sans-serif; font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-emoji: normal; font-variant-numeric: normal; font-variant-position: normal; vertical-align: baseline; white-space-collapse: preserve;">One poster presented by ASHG focused on BRAF oncogenic mutation detection. Three clinically relevant mutations are seen at position 600 of the protein: V600E, V600K, and V600R. By first using 18 cycles of a PCR design agnostic to the status of codon 600 as a pre-amplification and then using allele-specific primers covering the four alleles (three oncogenic variants plus wildtype) and each primer a different color, Countable was able to demonstrate detection of the variants when present in a sample at a frequency of 0.08% - much better than the 1-5% achievable with qPCR and 0.1% for digital PCR. That’s also not a trivial detection limit to achieve with a sequencing assay - but at about $16 per sample the Countable assay will be far less expensive than any NGS assay unless you can batch to a very high degree. These results also leverage the high dynamic range of Countable’s assay - detecting between 400 and 700K molecules with a single assay system. </span></p><br><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="font-family: Arial, sans-serif; font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-emoji: normal; font-variant-numeric: normal; font-variant-position: normal; vertical-align: baseline; white-space-collapse: preserve;"><a href="https://www.google.com/url?q=https://cdn.prod.website-files.com/681b0fe0bc39a39f4c8f25a8/68e94aa75aa25cde545f72b1_Countable%2520Labs_Poster_Mitocondria%2520DNA%2520copy%2520number.pdf&amp;sa=D&amp;source=docs&amp;ust=1764864846977192&amp;usg=AOvVaw0safsm8OsjLiJneU6VVrog">In another poste</a>r, Countable demonstrates measuring mitochondrial genome copy number, using multiple distinguishable probes targeting the mitochondria plus an additional one to get the nuclear genome as a reference. </span></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiSUJk0eitvR_RhlcUsbchbNRLPxR007qHDPPxkVJXSVW3hbs65zZRsoZuz69LbPgDm8Kve1vaZvQHFBiZKdWyD-FxmN0uJu2kGt62y0lKegYaBbTryP4WGlpvxhI6Az7XePzrngUgNv13tVS8oV5exknXzP_yCpYF7XtLfqgQBuXzRfS3qyrXRmQ/s895/countable-lightsheet.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="448" data-original-width="895" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiSUJk0eitvR_RhlcUsbchbNRLPxR007qHDPPxkVJXSVW3hbs65zZRsoZuz69LbPgDm8Kve1vaZvQHFBiZKdWyD-FxmN0uJu2kGt62y0lKegYaBbTryP4WGlpvxhI6Az7XePzrngUgNv13tVS8oV5exknXzP_yCpYF7XtLfqgQBuXzRfS3qyrXRmQ/w400-h200/countable-lightsheet.png" width="400"></a></div><br><span style="font-family: Arial, sans-serif; font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-emoji: normal; font-variant-numeric: normal; font-variant-position: normal; vertical-align: baseline; white-space-collapse: preserve;"><br></span><p></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="font-family: Arial, sans-serif; font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-emoji: normal; font-variant-numeric: normal; font-variant-position: normal; vertical-align: baseline; white-space-collapse: preserve;"><br></span></p><br><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="font-family: Arial, sans-serif; font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-emoji: normal; font-variant-numeric: normal; font-variant-position: normal; vertical-align: baseline; white-space-collapse: preserve;">Countable is also touting that they have built the system for GMP workflows, with the built-in software providing audit trails and other required security features for 21 CFR Part II compliance. </span></p><br><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="font-family: Arial, sans-serif; font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-emoji: normal; font-variant-numeric: normal; font-variant-position: normal; vertical-align: baseline; white-space-collapse: preserve;">Another interesting feature of Countable PCR is the ability to recover samples post-amplification - a protocol is provided to extract DNA out of the matrix. So you can count from a precious sample and then potentially fully sequence it as well.</span></p><div><span style="font-family: Arial, sans-serif; font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-emoji: normal; font-variant-numeric: normal; font-variant-position: normal; vertical-align: baseline; white-space-collapse: preserve;"><br></span></div></span><a href="https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2025/12/countable-labs-new-approach-to.html#more">Read more »</a></content><link rel='replies' type='application/atom+xml' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/feeds/4457927077208738060/comments/default' title='Post Comments'/><link rel='replies' type='text/html' href='http://www.blogger.com/comment/fullpage/post/36768584/4457927077208738060' title='2 Comments'/><link rel='edit' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/4457927077208738060'/><link rel='self' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/4457927077208738060'/><link rel='alternate' type='text/html' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2025/12/countable-labs-new-approach-to.html' title='Countable Labs: New Approach to Enumerating DNA'/><author><name>Keith Robison</name><uri>http://www.blogger.com/profile/04765318239070312590</uri><email>noreply@blogger.com</email><gd:image rel='http://schemas.google.com/g/2005#thumbnail' width='32' height='31' src='//blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_xVyJTnr62WSgPWaShtgTHw6PeTmI3OPrRnKuB6maoew9M7yjw7Irhe3LjFE2BBxukrdicyMQkjaNTL9piShDOaERcYx3ZkMsKFpde86ULRt0Khfx-eID7YHALQwyTA/s113/snip3.GIF'/></author><media:thumbnail xmlns:media="http://search.yahoo.com/mrss/" url="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg-LpY5G_tay7WkoWsKVmf9jt66CfwvhY2dtRF9f8KwtzYbXiZwJI_xzx0UFCuqJvVwWrNWDWCpE6AyRZIJxuztHTzox8Hz0-4volXShT0sqotTDUnXFT69AJD7LRDVorcby3ijUDYXGdI9OMH098e5LuJpiJxHKSQCFYkfHSMyD8L3VBcgFsxlkA/s72-c/countable-workflow.png" height="72" width="72"/><thr:total>2</thr:total></entry><entry><id>tag:blogger.com,1999:blog-36768584.post-3817826255811727746</id><published>2025-11-11T22:34:00.001-05:00</published><updated>2025-11-11T22:35:49.191-05:00</updated><title type='text'>Bell Labs Wasn't Built in a Day. Or Two Years.</title><content type='html'><div>Rome is famous for persisting for centuries - and having not been built in a day. If you go there, then one of the most magnificent sites is the most famous sporting arena in the world, the Flavian Amphitheater - better known as the Coliseum. Last week there was colossal news in the biotech world that Arena Bioworks was shutting down, after only two years and $100M spent of its &quot;committed&#39; half billion in funding. What went wrong?</div><span></span><a href="https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2025/11/bell-labs-wasnt-built-in-day-or-two.html#more">Read more »</a></content><link rel='replies' type='application/atom+xml' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/feeds/3817826255811727746/comments/default' title='Post Comments'/><link rel='replies' type='text/html' href='http://www.blogger.com/comment/fullpage/post/36768584/3817826255811727746' title='7 Comments'/><link rel='edit' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/3817826255811727746'/><link rel='self' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/3817826255811727746'/><link rel='alternate' type='text/html' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2025/11/bell-labs-wasnt-built-in-day-or-two.html' title='Bell Labs Wasn't Built in a Day. Or Two Years.'/><author><name>Keith Robison</name><uri>http://www.blogger.com/profile/04765318239070312590</uri><email>noreply@blogger.com</email><gd:image rel='http://schemas.google.com/g/2005#thumbnail' width='32' height='31' src='//blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_xVyJTnr62WSgPWaShtgTHw6PeTmI3OPrRnKuB6maoew9M7yjw7Irhe3LjFE2BBxukrdicyMQkjaNTL9piShDOaERcYx3ZkMsKFpde86ULRt0Khfx-eID7YHALQwyTA/s113/snip3.GIF'/></author><thr:total>7</thr:total></entry><entry><id>tag:blogger.com,1999:blog-36768584.post-5407915272578037501</id><published>2025-11-04T23:16:00.001-05:00</published><updated>2025-11-04T23:16:05.771-05:00</updated><title type='text'>Nineteen</title><content type='html'>If I had been more atop things, I would have written this just under a week ago, on the nineteenth anniversary of my starting to write in this space. That&#39;s a milestone, and actually writing something is the way to try to push back towards some regular frequency in posting here. But the real reason for the title is something I&#39;ve mused on a small bit for many of those years: can we shave one amino acid out of the proteome?<span></span><a href="https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2025/11/nineteen.html#more">Read more »</a></content><link rel='replies' type='application/atom+xml' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/feeds/5407915272578037501/comments/default' title='Post Comments'/><link rel='replies' type='text/html' href='http://www.blogger.com/comment/fullpage/post/36768584/5407915272578037501' title='1 Comments'/><link rel='edit' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/5407915272578037501'/><link rel='self' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/5407915272578037501'/><link rel='alternate' type='text/html' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2025/11/nineteen.html' title='Nineteen'/><author><name>Keith Robison</name><uri>http://www.blogger.com/profile/04765318239070312590</uri><email>noreply@blogger.com</email><gd:image rel='http://schemas.google.com/g/2005#thumbnail' width='32' height='31' src='//blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_xVyJTnr62WSgPWaShtgTHw6PeTmI3OPrRnKuB6maoew9M7yjw7Irhe3LjFE2BBxukrdicyMQkjaNTL9piShDOaERcYx3ZkMsKFpde86ULRt0Khfx-eID7YHALQwyTA/s113/snip3.GIF'/></author><thr:total>1</thr:total></entry><entry><id>tag:blogger.com,1999:blog-36768584.post-2082358399473384773</id><published>2025-10-15T08:58:00.001-04:00</published><updated>2025-10-15T08:58:12.424-04:00</updated><title type='text'>ASHG Posters: The Agony and The Ecstasy</title><content type='html'>ASHG is a huge meeting, probably the second largest I&#39;ve ever attended after ASCO. ASBMB is similar in size perhaps, though I think a hair smaller and definitely a bigger than ESHG. And certainly multiple AGBTs in scale. And that is crashing in on me now.<a href="https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2025/10/ashg-posters-agony-and-ecstasy.html#more">Read more »</a></content><link rel='replies' type='application/atom+xml' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/feeds/2082358399473384773/comments/default' title='Post Comments'/><link rel='replies' type='text/html' href='http://www.blogger.com/comment/fullpage/post/36768584/2082358399473384773' title='4 Comments'/><link rel='edit' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/2082358399473384773'/><link rel='self' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/2082358399473384773'/><link rel='alternate' type='text/html' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2025/10/ashg-posters-agony-and-ecstasy.html' title='ASHG Posters: The Agony and The Ecstasy'/><author><name>Keith Robison</name><uri>http://www.blogger.com/profile/04765318239070312590</uri><email>noreply@blogger.com</email><gd:image rel='http://schemas.google.com/g/2005#thumbnail' width='32' height='31' src='//blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_xVyJTnr62WSgPWaShtgTHw6PeTmI3OPrRnKuB6maoew9M7yjw7Irhe3LjFE2BBxukrdicyMQkjaNTL9piShDOaERcYx3ZkMsKFpde86ULRt0Khfx-eID7YHALQwyTA/s113/snip3.GIF'/></author><thr:total>4</thr:total></entry><entry><id>tag:blogger.com,1999:blog-36768584.post-4371364991226714149</id><published>2025-10-14T09:45:00.004-04:00</published><updated>2025-10-14T12:31:04.083-04:00</updated><title type='text'>PacBio: $300 Genome Via Chemistry Update</title><content type='html'>ASHG is here in Boston, just down the street from Ginkgo&#39;s HQ. I&#39;m in a new role in Ginkgo Automation, trying to convince the NGS world that our automation platform is the bee&#39;s knees. So excellent timing. In advance of the meeting I was able to grab 30 minutes of PacBio CEO Christian Henry&#39;s time - last time I saw him he was fresh out of the legendary midnight AGBT ILMN vs. PACB doubles beer pong match. Christian gave me a heads up on some of the product news that hit the wires a bit earlier this morning. At the top of that is a new version of the core chemistry, SPRQ-Nx, which boosts yields 10-15% as well as the official launch of flowcell reuse.<a href="https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2025/10/pacbio-300-genome-via-chemistry-update.html#more">Read more »</a></content><link rel='replies' type='application/atom+xml' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/feeds/4371364991226714149/comments/default' title='Post Comments'/><link rel='replies' type='text/html' href='http://www.blogger.com/comment/fullpage/post/36768584/4371364991226714149' title='2 Comments'/><link rel='edit' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/4371364991226714149'/><link rel='self' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/4371364991226714149'/><link rel='alternate' type='text/html' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2025/10/pacbio-300-genome-via-chemistry-update.html' title='PacBio: $300 Genome Via Chemistry Update'/><author><name>Keith Robison</name><uri>http://www.blogger.com/profile/04765318239070312590</uri><email>noreply@blogger.com</email><gd:image rel='http://schemas.google.com/g/2005#thumbnail' width='32' height='31' src='//blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_xVyJTnr62WSgPWaShtgTHw6PeTmI3OPrRnKuB6maoew9M7yjw7Irhe3LjFE2BBxukrdicyMQkjaNTL9piShDOaERcYx3ZkMsKFpde86ULRt0Khfx-eID7YHALQwyTA/s113/snip3.GIF'/></author><thr:total>2</thr:total></entry><entry><id>tag:blogger.com,1999:blog-36768584.post-3619291810228604643</id><published>2025-10-09T11:47:00.000-04:00</published><updated>2025-10-09T11:47:01.891-04:00</updated><title type='text'>Ship of ThesION</title><content type='html'><a href="https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2025/10/ship-of-thesion.html#more">Read more »</a></content><link rel='replies' type='application/atom+xml' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/feeds/3619291810228604643/comments/default' title='Post Comments'/><link rel='replies' type='text/html' href='http://www.blogger.com/comment/fullpage/post/36768584/3619291810228604643' title='6 Comments'/><link rel='edit' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/3619291810228604643'/><link rel='self' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/3619291810228604643'/><link rel='alternate' type='text/html' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2025/10/ship-of-thesion.html' title='Ship of ThesION'/><author><name>Keith Robison</name><uri>http://www.blogger.com/profile/04765318239070312590</uri><email>noreply@blogger.com</email><gd:image rel='http://schemas.google.com/g/2005#thumbnail' width='32' height='31' src='//blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_xVyJTnr62WSgPWaShtgTHw6PeTmI3OPrRnKuB6maoew9M7yjw7Irhe3LjFE2BBxukrdicyMQkjaNTL9piShDOaERcYx3ZkMsKFpde86ULRt0Khfx-eID7YHALQwyTA/s113/snip3.GIF'/></author><thr:total>6</thr:total></entry><entry><id>tag:blogger.com,1999:blog-36768584.post-5120551663392933066</id><published>2025-08-07T23:01:00.003-04:00</published><updated>2025-08-07T23:01:55.381-04:00</updated><title type='text'>10X Scoops Scale</title><content type='html'><a href="https://www.genengnews.com/topics/omics/10x-genomics-scales-up-agrees-to-acquire-scale-biosciences/">News broke this afternoon </a>that microfluidics single cell genomics leader 10X Genomics has bought out split-pool single cell company Scale Biosciences for $30 million up front in cash and stock, with additional payments of undisclosed amounts if certain milestones are reached. <span></span><a href="https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2025/08/10x-scoops-scale.html#more">Read more »</a></content><link rel='replies' type='application/atom+xml' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/feeds/5120551663392933066/comments/default' title='Post Comments'/><link rel='replies' type='text/html' href='http://www.blogger.com/comment/fullpage/post/36768584/5120551663392933066' title='2 Comments'/><link rel='edit' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/5120551663392933066'/><link rel='self' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/5120551663392933066'/><link rel='alternate' type='text/html' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2025/08/10x-scoops-scale.html' title='10X Scoops Scale'/><author><name>Keith Robison</name><uri>http://www.blogger.com/profile/04765318239070312590</uri><email>noreply@blogger.com</email><gd:image rel='http://schemas.google.com/g/2005#thumbnail' width='32' height='31' src='//blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_xVyJTnr62WSgPWaShtgTHw6PeTmI3OPrRnKuB6maoew9M7yjw7Irhe3LjFE2BBxukrdicyMQkjaNTL9piShDOaERcYx3ZkMsKFpde86ULRt0Khfx-eID7YHALQwyTA/s113/snip3.GIF'/></author><thr:total>2</thr:total></entry><entry><id>tag:blogger.com,1999:blog-36768584.post-40716266695328182</id><published>2025-06-29T22:56:00.001-04:00</published><updated>2025-06-29T22:56:17.915-04:00</updated><title type='text'>Could It Have Been Found With Short Reads?</title><content type='html'><div>Initially, the ESHG program was overwhelming. With the exception of the official opening and closing sessions, every timeslot had multiple parallel sessions - and sometimes those also had competing corporate sessions. Everything would be recorded and available for playback through November. That took some pressure off &quot;did I pick the wrong session?&quot;, but also is a double-edged sword - I might be attending ESHG for half a year! So I decided that my focus would be rare diseases, and if competing sessions on rare diseases then the one that most focused on genomics technology. And that led to hearing what amounted to a refrain in the questions at the end of each long read talk: could this causative variant have been found by short reads?</div><span></span><a href="https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2025/06/could-it-have-been-found-with-short.html#more">Read more »</a></content><link rel='replies' type='application/atom+xml' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/feeds/40716266695328182/comments/default' title='Post Comments'/><link rel='replies' type='text/html' href='http://www.blogger.com/comment/fullpage/post/36768584/40716266695328182' title='2 Comments'/><link rel='edit' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/40716266695328182'/><link rel='self' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/40716266695328182'/><link rel='alternate' type='text/html' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2025/06/could-it-have-been-found-with-short.html' title='Could It Have Been Found With Short Reads?'/><author><name>Keith Robison</name><uri>http://www.blogger.com/profile/04765318239070312590</uri><email>noreply@blogger.com</email><gd:image rel='http://schemas.google.com/g/2005#thumbnail' width='32' height='31' src='//blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_xVyJTnr62WSgPWaShtgTHw6PeTmI3OPrRnKuB6maoew9M7yjw7Irhe3LjFE2BBxukrdicyMQkjaNTL9piShDOaERcYx3ZkMsKFpde86ULRt0Khfx-eID7YHALQwyTA/s113/snip3.GIF'/></author><thr:total>2</thr:total></entry><entry><id>tag:blogger.com,1999:blog-36768584.post-8523447639013057776</id><published>2025-06-26T08:13:00.001-04:00</published><updated>2025-06-26T08:13:15.775-04:00</updated><title type='text'>Food For Thought On ONT's Proteomics Push</title><content type='html'><div>This year, instead of touring London after the Nanopore confab I headed to Italy for the European Society of Human Genetics meeting. Upon hearing Lakmal Jayasinghe describe ONT&#39;s proteomics plans, I was debating what to do with my pre-LC piece on the peptide sequencing. Perhaps I could ask a restaurant owner in the shadow of the Duomo whether it would go better with risotto Milanese or perhaps as an addition to a minestrone. But with more thought, while I remain intrigued by ONT&#39;s concept, I still think many parts of what I wrote still stand up.</div><span></span><a href="https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2025/06/food-for-thought-on-onts-proteomics-push.html#more">Read more »</a></content><link rel='replies' type='application/atom+xml' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/feeds/8523447639013057776/comments/default' title='Post Comments'/><link rel='replies' type='text/html' href='http://www.blogger.com/comment/fullpage/post/36768584/8523447639013057776' title='3 Comments'/><link rel='edit' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/8523447639013057776'/><link rel='self' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/8523447639013057776'/><link rel='alternate' type='text/html' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2025/06/food-for-thought-on-onts-proteomics-push.html' title='Food For Thought On ONT's Proteomics Push'/><author><name>Keith Robison</name><uri>http://www.blogger.com/profile/04765318239070312590</uri><email>noreply@blogger.com</email><gd:image rel='http://schemas.google.com/g/2005#thumbnail' width='32' height='31' src='//blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_xVyJTnr62WSgPWaShtgTHw6PeTmI3OPrRnKuB6maoew9M7yjw7Irhe3LjFE2BBxukrdicyMQkjaNTL9piShDOaERcYx3ZkMsKFpde86ULRt0Khfx-eID7YHALQwyTA/s113/snip3.GIF'/></author><thr:total>3</thr:total></entry><entry><id>tag:blogger.com,1999:blog-36768584.post-1344929739154829766</id><published>2025-06-02T08:35:00.000-04:00</published><updated>2025-06-02T08:35:12.927-04:00</updated><title type='text'>Roche Gives SBX Updates - and a Name!</title><content type='html'>Last week I double-dipped on conferences, going from London Calling to European Society for Human Genetics (ESHG) in Milan. I have a raft of notes and ideas from these, which I&#39;ll try to spool out over the next week or two before jumping to a long list of more whimsical ideas I&#39;ve jotted down. First up are some updates on Roche&#39;s SBX sequencing technology, which has now been christened Axelios - which <a href="https://aseq.substack.com/p/axelios-roche-sbx-update">Nava Whiteford reported in his ASeq newsletter</a>.<span></span><a href="https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2025/06/roche-gives-sbx-updates-and-name.html#more">Read more »</a></content><link rel='replies' type='application/atom+xml' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/feeds/1344929739154829766/comments/default' title='Post Comments'/><link rel='replies' type='text/html' href='http://www.blogger.com/comment/fullpage/post/36768584/1344929739154829766' title='4 Comments'/><link rel='edit' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/1344929739154829766'/><link rel='self' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/1344929739154829766'/><link rel='alternate' type='text/html' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2025/06/roche-gives-sbx-updates-and-name.html' title='Roche Gives SBX Updates - and a Name!'/><author><name>Keith Robison</name><uri>http://www.blogger.com/profile/04765318239070312590</uri><email>noreply@blogger.com</email><gd:image rel='http://schemas.google.com/g/2005#thumbnail' width='32' height='31' src='//blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_xVyJTnr62WSgPWaShtgTHw6PeTmI3OPrRnKuB6maoew9M7yjw7Irhe3LjFE2BBxukrdicyMQkjaNTL9piShDOaERcYx3ZkMsKFpde86ULRt0Khfx-eID7YHALQwyTA/s113/snip3.GIF'/></author><thr:total>4</thr:total></entry><entry><id>tag:blogger.com,1999:blog-36768584.post-7700643819809715412</id><published>2025-05-21T02:46:00.001-04:00</published><updated>2025-05-21T02:46:26.022-04:00</updated><title type='text'>Oxford Nanopore Should Spin Out Protein Sequencing</title><content type='html'><div>I&#39;ve toyed with writing something on these lines for a long time but never quite pulled the trigger. But the more I think about it, the more imperative my logic feels for spinning off the nascent protein sequencing effort. I actually finally peeked at the agenda for the meeting and University of Washington&#39;s Jeff Nivala is basically closing the meeting with an update on his work in this space. </div><span></span><a href="https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2025/05/oxford-nanopore-should-spin-out-protein.html#more">Read more »</a></content><link rel='replies' type='application/atom+xml' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/feeds/7700643819809715412/comments/default' title='Post Comments'/><link rel='replies' type='text/html' href='http://www.blogger.com/comment/fullpage/post/36768584/7700643819809715412' title='3 Comments'/><link rel='edit' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/7700643819809715412'/><link rel='self' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/7700643819809715412'/><link rel='alternate' type='text/html' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2025/05/oxford-nanopore-should-spin-out-protein.html' title='Oxford Nanopore Should Spin Out Protein Sequencing'/><author><name>Keith Robison</name><uri>http://www.blogger.com/profile/04765318239070312590</uri><email>noreply@blogger.com</email><gd:image rel='http://schemas.google.com/g/2005#thumbnail' width='32' height='31' src='//blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_xVyJTnr62WSgPWaShtgTHw6PeTmI3OPrRnKuB6maoew9M7yjw7Irhe3LjFE2BBxukrdicyMQkjaNTL9piShDOaERcYx3ZkMsKFpde86ULRt0Khfx-eID7YHALQwyTA/s113/snip3.GIF'/></author><thr:total>3</thr:total></entry><entry><id>tag:blogger.com,1999:blog-36768584.post-5545314072598447553</id><published>2025-05-20T04:23:00.004-04:00</published><updated>2025-05-21T02:46:41.729-04:00</updated><title type='text'>London Calling 2025: What I'm Thinking About</title><content type='html'><div>London Calling fires up for real on Wednesday; Tuesday has the training courses I haven&#39;t signed up for. I don&#39;t have any grand predictions, but rather some thoughts of things I am trying to keep my antennae particularly tuned for. Sly tips of course are always welcome I can be DMed on Discord, LinkedIn, X, or email me at keith.e.robison at Gmail.com..</div><span></span><a href="https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2025/05/london-calling-2025-what-im-thinking.html#more">Read more »</a></content><link rel='replies' type='application/atom+xml' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/feeds/5545314072598447553/comments/default' title='Post Comments'/><link rel='replies' type='text/html' href='http://www.blogger.com/comment/fullpage/post/36768584/5545314072598447553' title='2 Comments'/><link rel='edit' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/5545314072598447553'/><link rel='self' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/5545314072598447553'/><link rel='alternate' type='text/html' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2025/05/london-calling-2025-what-im-thinking.html' title='London Calling 2025: What I'm Thinking About'/><author><name>Keith Robison</name><uri>http://www.blogger.com/profile/04765318239070312590</uri><email>noreply@blogger.com</email><gd:image rel='http://schemas.google.com/g/2005#thumbnail' width='32' height='31' src='//blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_xVyJTnr62WSgPWaShtgTHw6PeTmI3OPrRnKuB6maoew9M7yjw7Irhe3LjFE2BBxukrdicyMQkjaNTL9piShDOaERcYx3ZkMsKFpde86ULRt0Khfx-eID7YHALQwyTA/s113/snip3.GIF'/></author><thr:total>2</thr:total></entry><entry><id>tag:blogger.com,1999:blog-36768584.post-1648255560312118608</id><published>2025-05-19T18:00:00.001-04:00</published><updated>2025-05-21T02:48:06.674-04:00</updated><title type='text'>Clive Brown At ONT: A Belated Retrospective</title><content type='html'><div>on Calling is imminent, and this is a notable one: the first held without Clive Brown in an official capacity at Oxford Nanopore. I started drafting a piece on Clive&#39;s tenure at ONT as soon as Nava Whiteford first broke the rumor (soon confirmed) he was leaving - that was back in November. But first there was writer&#39;s block and then a pair of elderly relatives had health crises, only one of which resolved desirably, and then the piece got stuck in my procrastination queue. But London Calling was an absolute deadline I set for myself and here we are.</div><div><br></div><div>One contributor to my discarding early drafts was trying to set the right balance. Clive was by far the most visible leader at ONT and so to him goes much kudos but also much criticism. Of course, in many cases it was someone else who deserves the credit or the debit, or at least the story is complicated. But I was never, as the song goes, in the room where it happened, so I am sadly blind to such nuance. It&#39;s also the case that Clive of early ONT is almost certainly not Clive of late ONT, and some of the foibles I dredge up might not be repeated. But, they are part of the story.</div><div><br></div><div>It cannot be over-emphasized that under Clive&#39;s technical leadership Oxford Nanopore condensed an incredible (as in, not to be believed) concept into an incredible (as in, OMG!) working sequencing technology. ONT sequencers enable sequencing about any place on this planet (and even above this planet!) a human can go due to the compact MinION design as well as its lack of moving parts, have stunningly low capital cost and are simple enough that even middle school students can be trained to sequence. The early &quot;barely can align&quot; data quality has advanced by leaps-and-bounds so that many reads have error rates of under 1%. Data yields early in MAP were low tens of megabases; MinION flowcells now deliver a few tens of gigabases and the PromethION flowcells significantly more. I was hooked seeing a full length lambda phage of 48 kilobases in our first MinION Access Program (MAP) run; the world record ONT read length is almost 100-times that - and no other technology reliably generates high accuracy reads of even 48 kilobases.</div><div><br></div><div>Clive&#39;s team did that. He built the technical organization to make magic real. Now, it must be said that being a member of that organization came with special requirements. Some staff stayed a long time - but some did not. At the first Nanopore Community Meeting at the New York Genome Center, ONT had downplayed the idea that Clive would break any technical news - and all of us customers were madly scribbling notes and photographing slides as he blatantly violated that guidance. When it was over, one looked around to realize that ONT employees had done the same and some very much had &quot;deer in the headlines&quot; faces. Indeed, mutterances of &quot;first I&#39;ve seen of that&quot; or &quot;there goes all my timelines&quot; were heard afterwards.</div><div><br></div><div>Eventually, ONT settled on a solution to allow Clive to be minimally restrained but the company minimally exposed to his wilder extemporaneous comments. After Clive&#39;s talk (which led with a disclaimer that he might color outside the lines), Rosemary Dokos would be the voice of reason and carefully shepherd expectations into what the company was actually committing to</div><div><br></div><div>Under Clive&#39;s leadership, the MAP had some interesting aspects as well. Clive has always projected a vision of the individual biological pioneer, in many cases an amateur with no training or background, casually using ONT gear to explore the world. A parallel is often drawn, often dangerously bordering (or crossing into) fetishism, to the early days of personal computing. I know that era: my first taste of electronics was learning the color codes on resistors so I could sort them upstream of my brother and father assembling a single-board DATAC-1000 computer. But do-it-yourself can collide with amateur. When MAP rolled out the first, a thinly documented, version of MinKNOW, I started looking for what seemed obvious to me must be in the package. MinKNOW would output data in an HDF5-based <strike>POD5</strike> FAST5 format, and obviously there must be another tool to extract the reads as FASTA or FASTQ from the <strike>POD5</strike> FAST5. Right? Right? Surely????</div><div><br></div><div>No, there wasn&#39;t. If you wanted to, y&#39;know, analyze MAP data your had to dig into some very unfamiliar software guts. In my case, Perl was a dead end because the HDF5 library choked on the POD5s (by 2014 I was realizing Perl library development and maintenance was pretty much in zombie mode; around that time the PDF module in CPAN had syntax errors!). Since I wanted to learn Julia, I quickly tested if it had a working HDF5 library and wrote a simple parser. Several years later I found out it didn&#39;t work anymore for the same reason I had been reticent to open source it publicly - the implementation was tightly coupled to the POD5 implementation. Presumably the same issue befell Mick Watson&#39;s R solution and Nick Loman&#39;s Python one, though by then ONT had made FASTQ extraction a standard part of their pipeline.</div><div><br></div><div>Similarly, ONT for a long time avoided writing much in the way of documentation or having much in the way of technical support. You threw your questions to the Nanopore Community and you&#39;d often get answers. But as the Community aged, it became very hard to tell which information was still valid and which was badly obsolete. Which version of a protocol did the search find? Who knows?</div><div><br></div><div>What I said about open sourcing my extractor leads into another big tension area: openness and secrecy. I knew ONT was sensitive about internal workings and so asked if I could release my extractor, and got a not emphatic reply that suggested they wouldn&#39;t love that. Mick and Nick must not have asked, as they did open source theirs. For a long time, much of the software from ONT was only available from the Nanopore Community site, which was far less convenient to download from than GitHub or similar. Over time that went away. In general, ONT has been very open which has helped drive much innovation by the community, but now is probably enabling BGI and other Chinese competitors who are launching similar nanopore platforms. Of course, ONT in turn benefited from PacBio&#39;s great openness and particularly the long read software community that grew up around PacBio.</div><div><br></div><div>From secrecy we can slide over to an entertaining topic: Clive and ONT&#39;s penchant for combativeness which often edged into destructive corporate paranoia. In this he wasn&#39;t alone: CEO Gordon Sanghera and majordomo Spike Willcocks would also engage in this behavior; I chided Willcocks here on an egregious case that threatened to spike customer relationships. If you talk to the older ONT crowd, they have some very colorful stories to tell of then Illumina CEO Jay Flatley&#39;s behavior around them when Illumina had an investment in ONT (and yes, I&#39;d love to hear Flatley&#39;s or any other Illumina&#39;s folks take on this - as off the record as they would like). Illumina would later yank their investment in ONT and then try to sink ONT with a patent lawsuit. One can understand the bitterness after such a scorch-the-earth style of corporate battling.</div><div><br></div><div>But some of that activity, and the lawsuits with PacBio, brought out behavior in Clive that must have put the entire ONT legal team on high doses of ACE2 and proton pump inhibitors. Clive would tweet out very sharp commentary on one of ONT&#39;s legal opponents, often with insults. This would escalate a bit, until finally Clive&#39;s Twitter account would be &quot;deleted&#39;. There would be a pause for weeks or months then Clive would start tweeting innocuous stuff again - which would eventually get spicer. Rinse and repeat.</div><div><br></div><div>In a similar vein, I&#39;ll always remember the first time I met Clive face-to-face. It was at AGBT in 2013, a year after the big AGBT splash. I thought that presentation was exciting, but apparently Clive and other ONT folks were run through the wringer of criticism as purveyors of vaporware, hucksters trying to just fleece gullible investors and so forth. It had really gotten to him. We met in one of the little outside alcoves that existed at the old Marriott facility in Marco Island and he showed me a MinION - probably one revision back from what came out for MAP. And my big takeaway from that was &quot;man is that guy strung tight!&quot;. He was intense - both the great kind of someone who is passionate about their work and the less desirable intensity of someone who feels hounded. The next time I saw him, when I helped him navigate to the ONT demo that fall in Kendall Square after bumping into him on the street, he was a bit more relaxed - building towards success can do that. But still passionate - always passionate.</div><div><br></div><div>Clive&#39;s passions and ethos of the individual explorer sometimes took the company in directions that were of questionable commercial relevance. Thrilling to watch or ponder perhaps, but not much in the way of a path to profitability. For example, last year I was certainly excited at Clive saying ONT had succeeded in sequencing some of the smaller yeast chromosomes as a single fragment. But I work at a strain factory that loves to work on yeast; few are in such a situation. And yeast chromosomes are a tiny fraction of the length of even the shortest mammalian chromosome. </div><div><br></div><div>Perhaps the most egregious case of this was the &quot;Ubiqibopsy&quot; demo. Live, on stage Clive had his cheek swabbed, then some noisy bead-based sample prep, a rapid prep and by the end of the presentation ... a handful of reads. Supposedly they proved Clive is human though I don&#39;t believe any reviewer #3 got a look at the data. The device was visible later and clearly hacked together from ubiquitous lab parts - if I recall correctly there was part of a centrifuge tube, a micropipette tip and maybe one other recognizable bit. But was this the path to a real product? Given the challenges involved in getting to a data yield that might be interesting, unlikely - and little was heard of this ever again.</div><div><br></div><div>But of course nobody though the whole concept would ever work. But then again, while ONT has shown technical success it still struggles with financial success. </div><div><br></div><div>Similarly, Clive&#39;s love of the VolTRAX electrowetting technology was never returned by that tech. In one talk he presented the idea of putting the nanopores actually on the VolTRAX chip, which certainly solves the transfer problem from VolTRAX to flowcell. But the number of pores was to be tiny - so what application wanted a few hundred dollar prep to get maybe a few megabases of data? That was a question never answered - and it too disappeared from future presentations.</div><div><br></div><div>At last year&#39;s LC, Clive gave hints that he might not be at ONT by the next year - something along the line of &quot;if I&#39;m still here&quot;. There were other signs - the ElysION (formerly TurBOT) robot is the epitome of what Clive disliked, a large expensive box specialized on a single task and marketed to large faceless labs. </div><div><br></div><div>I hope Clive is enjoying his retirement. His Twitter feed shows very brief life very rarely, but mostly about non-sequencing topics. If there isn&#39;t a third act for him (he was on the team that brought Solexa&#39;s sequencing technology to life), then we all now have a name to scan for in the annual King&#39;s Honors List. Under Clive&#39;s leadership Oxford Nanopore launched a truly revolutionary platform which has delivered huge gains to genomics; we should all be very grateful for that.</div><div><br></div><div><br></div><div>[2025-05-21 fixed POD5-&gt;FAST5, as suggested by a commenter]</div><a href="https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2025/05/clive-brown-at-ont-belated-retrospective.html#more">Read more »</a></content><link rel='replies' type='application/atom+xml' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/feeds/1648255560312118608/comments/default' title='Post Comments'/><link rel='replies' type='text/html' href='http://www.blogger.com/comment/fullpage/post/36768584/1648255560312118608' title='12 Comments'/><link rel='edit' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/1648255560312118608'/><link rel='self' type='application/atom+xml' href='http://www.blogger.com/feeds/36768584/posts/default/1648255560312118608'/><link rel='alternate' type='text/html' href='https://news-technologi.netlify.app/host-http-omicsomics.blogspot.com/2025/05/clive-brown-at-ont-belated-retrospective.html' title='Clive Brown At ONT: A Belated Retrospective'/><author><name>Keith Robison</name><uri>http://www.blogger.com/profile/04765318239070312590</uri><email>noreply@blogger.com</email><gd:image rel='http://schemas.google.com/g/2005#thumbnail' width='32' height='31' src='//blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_xVyJTnr62WSgPWaShtgTHw6PeTmI3OPrRnKuB6maoew9M7yjw7Irhe3LjFE2BBxukrdicyMQkjaNTL9piShDOaERcYx3ZkMsKFpde86ULRt0Khfx-eID7YHALQwyTA/s113/snip3.GIF'/></author><thr:total>12</thr:total></entry></feed>