HGP Counterfactuals, Part 3: BAC Sequencing Strategies
I introduced this seven-part series with an exploration of thevalues and challenges of counterfactual histories.  Yesterday, I looked at the"forgotten maps" which laid out the genome ready-to-sequence as a minimum tiling set of BACs, made sure that those BACs faithfully represented the genome and that this set was tied at regular intervals to the genetic markers and cytogenetic locations which were the linga franca of human geneticists.  Today, I'll look at strategies that were considered for sequencing all those BACs.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - November 12, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
HGP Counterfactuals, Part 2: The Forgotten Maps
Yesterday's post explored the concept of alternative histories, or counterfactuals and laid out why they might be a useful way to think about the value of the Human Genome Project. Â In this installment, I'll explore what I will call the forgotten maps, the critical elements of the HGP which are all too easily forgotten. Â These were both critical and expensive components of the project, so forgetting them is a mistake. Â Their prominence has faded as new technologies have come in and subsumed them, or they were mostly means to the end of a first human sequence, but understanding the project requires understanding ...
Source: Omics! Omics! - November 11, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
HGP Counterfactuals, Part 1: An Introduction
My new correspondent, Kumar Thangdu, has posed some challenging questions with regard to the Human Genome Project.  He's been good enough tocapture my initial tweet stream over at his blog, which was my initial defense.  I then followed up withmy note on my one paper in proteomics, which I received favorable feedback on  from one of my co-authors.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - November 10, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Oncology: The 10Km View
My Twitter correspondent Kumar Thangdu keeps throwing interesting but difficult questions my way, far faster than I can keep up.  Not sure I'm even particularly skilled at many of these.  But, one must try.@OmicsOmicsBlog The best thing we can do to cure cancer, might be to try not to cure cancer, but just fund basic research? accurate?— Kumar Thangudu (@datarade) November 8, 2016Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - November 9, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Homopolymers and Other Recurring Topics in Pore Taste
Some interesting comments showed up onmy piece covering Pacific Biosciences trade action launch against Oxford Nanopore. Â Alas, some silly comments showed up as well. Â Life on the Internet. Â In particular, Mohan Chennupati asked a series of questions that can be seen as more friendly to PacBio and less so to Oxford Nanopore than my analysis. Â They're all good questions and worth digging into, and you'll find some other commenters addressing them. Â I'll quote from his comments but rearrange the order a bit. Â I believe I've not changed their meaning or damaged his argument, but please check me. Â The ma...
Source: Omics! Omics! - November 3, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
PacBio's Quixotic Patent Litigation
I'm feeling very glad Iclosed out the Illumina/U. Washington litigation vs. Oxford Nanopore the other night, albeit very belatedly, as now Oxford is facing a similar set of legal actions, but this time initiated by Pacific Biosciences.  PacBio hasfiled a complaint with the U.S. International Trade Commission (ITC) alleging that Oxford is infringing on an issuedU.S. patent, 9,404,146 (aka 146 Patent).  Surely PacBio's management thought this was a good idea, but from this perspectiveRead more » (Source: Omics! Omics!)
Source: Omics! Omics! - November 2, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Tidying Loose Nanopore Patent Threads
A commenter onmy recent piece on Genia made a number of assertions with regard to nanopore patents.  A more general one was a complaint that I had covered theopening salvo of the battle from Illumina and University of Washington andOxford's formal response andfeinting to the CsgG/R9 pore, but failed to cover the campaign's termination.  It's a fair charge and I'll rectify this here.  My (rather lame) excuse is the news broke while I was on vacation in the Pacific Northwest and trying to avoid any remotely professional activities, other than readingLuke Timmerman's Lee Hood biography.  But, that do...
Source: Omics! Omics! - October 30, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
10 Years of Omicing!
Today marks a special day - it was10 years ago that I launched this endeavor. Â I'm going to take time today, and perhaps a few times in the near future, to look back on the journey. Â Ten years of blogging also happens to be around my anniversary of starting work at Millennium, which means I've been a professional in biotechnology for two decades. Â So I must be old; indeed, this summer I celebrated birthday 30 (numeric pedants might make thebase charge that I am misleading by not writing that 0x30) and about a quarter century since I launched into bioinformatics full time. Â So a bit of nostalgia seems not out of...
Source: Omics! Omics! - October 27, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Segmental Duplications and Deletions in Books of History and Life
I have long had a historical interest in the U.S. Civil War. Â In fifth grade we had an all-day field trip to theGettysburg Battlefield, which is very well preserved, and it enthralled me. Â A few years later I would hike all over the battlefield with my Boy Scout troop, which is probably even closer to experiencing a taste of what it was like to be soldier. Of course, we had good hiking boots - a proximate cause of the battle occurring there was an attempt by the Confederates to raid a shipment of shoes which had just arrived in the town. Â My great-grandfather served in the Union Army, though entirely on garrison duty. Â...
Source: Omics! Omics! - October 26, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
How Genomes Revolutionized Proteomics
Myrecent piece on the folly of moonshot projects caught the eye of a Silicon Valley blogger named Kumar Thangudu (@datarade), who gave me some nice praise. But along with that were some notes of his on other big science projects, and one he targeted was the Human Genome Project, with a sarcastic comment about the paucity of drugs coming from the HGP. Â Them's fighting words! Â So I launched a tweet stream his way outlining a number of impacts of HGP on biomedical science, and he was very nice and suggested I write more on that. I'm thinking of a number of angles on the topic, but here goes a bit of nostalgia that I...
Source: Omics! Omics! - October 25, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
How Genomes Enabled Proteomics
Myrecent piece on the folly of moonshot projects caught the eye of a Silicon Valley blogger named Kumar Thangudu (@datarade), who gave me some nice praise. But along with that were some notes of his on other big science projects, and one he targeted was the Human Genome Project, with a sarcastic comment about the paucity of drugs coming from the HGP. Â Them's fighting words! Â So I launched a tweet stream his way outlining a number of impacts of HGP on biomedical science, and he was very nice and suggested I write more on that. I'm thinking of a number of angles on the topic, but here goes a bit of nostalgia that I...
Source: Omics! Omics! - October 25, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Messaging Counts
Myrecent piece on SeqLL's reboot of the Helicos sequencing technology attracted a number of helpful comments either on blogger or via email. Â Several of which pointed out the high suitability of this box for counting applications such as expression profiling, ChIP-seq and copy number analysis. Julia Karow of GenomeWeb graciously provided me with a copy of her piece, which underscored the value of GW in having real reporters dig into a s ubject. Â Much of what she dug up concerns SeqLL's future plans and for the near term mostly confirms suspicions that the technology will mostly look like the previous Helicos box,...
Source: Omics! Omics! - October 24, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
SeqLL: Helicos van Winkle
Helicos was the first company to launch a single molecule DNA sequencing system. They never sold many systems (my estimate is fewer than 20), but some of those sites really loved their machines. One beauty of the system was a very simple sample prep: fragment your DNA, add terminal transferase and dATP and the sample was ready-to-hybridize. Â Helicos demonstrated a number of interesting applications, such as direct loading of RNA onto the system and performing capture on the flowcell. Â But with anemic demand and mounting losses, the company faded, finallyfiling for bankruptcy in November 2012. Â One true believer bought u...
Source: Omics! Omics! - October 22, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
IGenomX Launches New Linked Read Chemistry
A hot concept in the genome world is how to capture long-range information, enabling assembly through repeats, resolving haplotypes, resolving copy number variation and many other applications in which short reads from short fragments are just not sufficient. A number of approaches have been proposed and published over the years, with some hitting commercial markets and significant use.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - October 20, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Genia Publishes Polymerase-to-pore docking scheme
Back in April, Iwrote up a PNAS publication from Genia and collaborators that described the modified nucleotides they have developed for their sequencing-by-synthesis with nanopore detection sequencing scheme.  I had the opportunity to chat with George Church (who is an adviser both to my company and Genia, and a co-author on the paper) just after that and he remarked that there was a companion paper in the works describing the polymerase engineering for the system.  That paper is now out in PNAS (and Open Access) and I'll take a little walk through it.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - October 18, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
