Wall Street Bets Illumina Won't Acquire PacBio
The proposed PacBio-ILMN Merger remains an interesting spectator sport, with the UK's CMA looking for public input for the next round. I don't usually pay attention to stock prices, but PacBio's current state presents too juicy a situations. Just to be clear though: I do not hold any individual stock position in PacBio or Illumina (the bulk of my investing is in broad mutual funds, some of which certainly have bits of these companies).Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - August 10, 2019 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
UK CMA & ILMN/PACB: The Inconvenience of Being Earnest.
As part two of a yet-to-be-determined number of pieces on the UK's CMA preliminary analysis of the proposed Pacific Biosciences acquisition by Illumina, I'd like to briefly explore the surprising authority of this agency to plumb internal documents at the two companies.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - July 23, 2019 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
UK CMA's Write-up of PacBio Acquisition by Illumina Makes for XXX Reading; Clearly They Believe XXX and XXX
After writing my two recent pieces on the business side of the long read industry I planned, after a recent extended family vacation, to try to get back to science. Particularly after my chagrin when various correspondents pointed out a fact from each I should have found and didn't:in my ONT pieceI failed to discover that ONT has two share classes and the Woodford fund's shares cannot be used to gain control of the company and in thePacBio piecethat there is a $100M breakup fee due PacBio if for any reason the deal doesn't go thru. I'm particularly red faced on that one, as a breakup fee would play im...
Source: Omics! Omics! - July 20, 2019 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Will Regulators Scotch PacBio Acquisition?
When Illumina announced its proposed acquisition of Pacific Biosciences last fall, an immediate question arose as to whether the deal would pass antitrust review. Illumina must have been optimistic, as they originally expected the dealto close in"mid-2019". That timetable has now been rolled back to late 2019 in the face of the UK agency with jurisdiction over mergers deciding to go for a second round of review and no word yet from the U.S.'s Federal Trade Commission.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - June 30, 2019 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
ONT & The Woodford Liquidity Squeeze
There's an unfortunate chain of events that may end up causing a headache for Oxford Nanopore, and it's completely outside their control. One of the their key investors has just had his luck - or perhaps more critically his reputation -- at stock picking disintegrate. Because of some unusual choices, that has potential repercussions for ONT.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - June 17, 2019 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
ONT's Horrid Data Storage Folly
In the coverage ofONT's announcements at London Calling, I specifically left out one of Clive's Skunk Works projects. This would be a device to use nanopores to write digital information. I'll give him points for creativity, but the reason I held this for here is I truly and sincerely hatethe concept and didn't want my vitriol to distract within the other piece. But here I will let loose.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - May 29, 2019 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
The Genius of Plongle
I noted inmy roundup of Oxford Nanopore technical announcementsthat I loved the Plongle concept. This is really both a new application-specific integrated circuit (ASIC) and using it to build a 96-well sequencer. Let me expand on what there is to love.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - May 29, 2019 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
ONT's London Calling Announcements, Pass One
The annual big Clive Brown London Calling talk had a twist this year Brown introduced a set of senior lieutenants at Oxford Nanopore and then tacked on a few"and one more thing" moments at the end. If you're looking for the TL;DR version from me, it is that there were a lot of sensible but non-Earth shattering updates from the team followed by Clive updating on one prior crazy idea and throwing out two more -- one of which I love and the other I believe should be thrown out posthaste.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - May 28, 2019 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Nanopore's Long DNA Paradox
The first half day of London Calling has already delivered the usual mix of scientific excitement. The prospect of lives, particularly those of children, en masseby delivering precision oncology broadly across sub-Saharan Africa. Dizzying levels of alternative splicing in a key brain ion channel. RNA modifications in great numbers. That one was also gratifying as it was commented that even without a basecaller, modified bases can be be suggested by higher error rates around a particular motif. Around 2015 or so I no ted in the Nanopore Community post that error rates went up aroundGATC sites inE.coli, the targ...
Source: Omics! Omics! - May 22, 2019 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Care to Pore Over My Laundry List?
London Calling is this week, so get ready for lots of Oxford Nanopore in my Twitter channel and if I'm on the ball, in this space. ONT has made a number of releases and updates and there have been other developments within the nanopore ecosystem which I've failed to report. Here, in not terribly organized fashion, is a laundry list of things I'm thinking about going into the meetingRead more » (Source: Omics! Omics!)
Source: Omics! Omics! - May 20, 2019 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Mass Recoded E.coli Genome Not Tripped Up By Programmed Frameshifts
There's apaper this week in Nature announcing anE.coli genome which has had two serine codons (UCA,UCG) and one stop codon (UAG) removed from usage. It's a major work on synthetic biology and represents the largest designed sequence ever built. In contrast to Craig Venter's early effort, which moved a synthesized genome into a cellular ghost of a natural bacterium, this one replaced the nativeE.coligenome in stages --Escherichia theseusshipii would be a good name for the new strain. But is the genome quite what is advertised? Following up on a pair posts from Sandeep Chakraborty showing remainingUCA,UCG c...
Source: Omics! Omics! - May 19, 2019 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
My Career's Double Slit Experiment (or, A Funny Thing Happened on the Way to the Drydock)
WhenI announced recently that I had moved over to Ginkgo Bioworks, I was compelled to leave out an important part of that story. Indeed, by just focusing on the (still open) position of NGS Head, I could avoid the sticky subject of how exactly I ended up there. Today thepress release finallywent out and the fact that Warp Drive's genome mining business is now owned by Ginkgo is public (covered nicely by Amy Feldman in Forbes). But in the spirit of my periodic public coverage of my own journey, here is some of the rest of the story.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - May 16, 2019 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Genapsys' Base Caller: Mysterious, But Not Ideal?
WhenI wrote about Genapsys' pre-print on their sequencing system the other night, I intended that to be the last I wrote until some major news from them. But after launching that into the great Internet ether, I found myself lying awake wondering if a very simple idea had any merit. Painfully simple -- I almost didn't pursue it because it was so simple and obvious. But, it turns out it appears to have merit -- there may be an obvious route to improving the accuracy of Genapsys' basecalling on homopolymers. And that also took me into ground I've thought about before -- going back to my first yea...
Source: Omics! Omics! - May 5, 2019 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Poking at Genapsys Preprint
Genapsys is continuing down the path of pre-launch information, most recentlyreleasing a pre-print. I'm looking at this pre-print critically and unfortunately turning into a bit of Reviewer #3. Not that anything is fatal and pre-publication review is a key value to pre-prints. If I were an actual reviewer I'd be writing mostly the same things and covering more vertebrate species than they sequenced (a human exome panel was included, though most samples were bacterial) -- I'd grouse about a missing figure (which I've provided), carp about critical details not provided and beef over a public data dep...
Source: Omics! Omics! - May 1, 2019 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Want to Run An Exciting Sequencing Group? Ginkgo Is Looking for You!
I've awakened from my blogging torpor to point out a really interesting career opportunity for the types who might read this space. Ginkgo Bioworks, one of the leading synthetic biology companies in the world, is looking forsomeone to run their existing Next Generation Sequencing group. It's a chance to run an energetic high-throughput sequencing group that works on a wide range of projects. And, as you might of guessed from the fact I'm writing about it here, you'd also get to be my boss. I'm hoping many will see that as a feature and not a bug.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - April 23, 2019 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
