London Calling 2017: A Theme of Consolidation
London Calling 2017 came to a close last Friday. Â Any excuses of jet lag or nights running up ONT's bar tab won't hold up much longer, so time to finish this post (I really did start the night after Clive's talk!) I'm going to largely divide coverage on the dividing line of who presented: today's piece on Oxford Nanopore presentations, particularly Clive Brown's, and in the near future at least one focusing on the science users presented. Â For other summaries of the action, I've created astorify of just blog posts and similar summaries of the meeting, as there were a great number (and I am on ...
Source: Omics! Omics! - May 9, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Nanopore Workshop Notes
I attended on Wednesday theLondon Callingpre-conference workshop, an add-on for those wishing for help getting started with MinION sequencing. Â Judging from who I spoke to, many participants were utterly new to nanopore sequencing and more than a few were like me in that they had tried the platform and wanted to do better. Â My colleague has gotten some very good results recently, which has re-fired my determination to get good at that my self. Â Below are some limited notes I took that may be of general interest. Large portions of the workshop will go largely uncovered, as I focused on what was surprising or new.Read mor...
Source: Omics! Omics! - May 4, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
London Calling 2017: A Preview
Oxford Nanopore's London Calling confab runs Thursday and Friday, with a training workshop on Wednesday.  I'll be there -- who can resist a conference nearly at the Tower of London? -- and will also be testing whether my personal"field of nanopore sequencing suppression" can defeat ONT's best trainers.  Here's some preview of what I'll be particularly looking for, though being surprised will be lots of fun too. Much more fun that reading (the wrong) patents!Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - May 2, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Oxford Nanopore's Enigmatic Patent Litigation
Oxford Nanoporehas launched lawsuits in the UK and Germany against Pacific Biosciences, alleging infringement of a European patent licensed from Daniel Branton's lab at Harvard,EP1192453, which is apparently exclusively licensed to Oxford. Â When I wrote about Pacific Biosciences first lawsuit against Oxford Nanopore late last year I titled it"PacBio's Quixotic Patent Litigation", as it appeared the Oxford could easily dodge the lawsuit by abandoning the 2D sequencing technology, which Oxford is in the process of doing. Â I've swapped in"enigmatic" for this title, as I'm not even sure wh...
Source: Omics! Omics! - May 1, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Postdoc positions on context dependent cell signalling (wet and/or dry)
Why do some mutationscause cancer in some tissues and not others ? What happens to the cell signalling pathways during differentiation ? Why are some genes essential in some cell types and not others or why are some drugs more effective atkilling some cell types than others?We think that this is a great time to be asking these questions of how the genetic background or tissue of origin changes cell states. More precisely for us, how this re-wires cell signalling. It has become routine to measure changes in phosphorylation across different conditions, including different cancer types. The Sanger and others are establishing ...
Source: Evolution of Cellular Networks - April 28, 2017 Category: Cytology Tags: positions Source Type: blogs
Exercise: A Sequence Signature for Transcription-Translation Coupling in Bacteria?
A pretty common question over on Quora is something along the lines of"how do I learn bioinformatics".  Great question!  Tonight I'm going to outline a project which I think would make a good first bioinformatics project.  It is rich in content and keys off an interesting new non-computational result.  And since I've left graffiti on multiple Quora threads that I would write something like this in the immediate future, here it is!Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - April 26, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Pinniped Karyotypes & N50 Statistics
In myrecent piece on long read assembly, I laid out part of the case against the N50 statistic. Â Historically, the issues with the statistic have been around the fact it can be gamed at the expense of assembly correctness or assembly coverage. These are concerns for the typical sort of short read assemblies we've grown used to: lots of contigs and the temptation (perhaps justified) to try to go for higher N50s by more aggressive merging or by filtering out the short contigs. Â Elin Videvall over at The Molecular Ecologist has a nice ongoing series of posts illustrating the statistic and these commonplace issues:What â...
Source: Omics! Omics! - April 22, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Time to Retire HeLa?
A TV movie produced by and starring American culture mogul Oprah Winfrey is about to hit screens which dramatizes Rebecca Skloot'sThe Immortal Life of Henrietta Lacks. Â If you haven't read this remarkable book, you really should. Â It should certainly be required reading for anyone entering biomedical fields. Â That's not to claim it is perfect; one of Lacks' sons has objected to the way his family is portrayed. Â But it is a searing human story of how the most famous cell line in the world came to be. Â Even if you excuse some of the injustices done as compatible with then contemporary ethical standards, ...
Source: Omics! Omics! - April 20, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Alexandria Jumps Into Shuttle Business
A restaurant I frequented during my grad school days had a map on the wall showing Boston area transit routes from roughly the 1940s. Â Remarkably, most of those streetcar routes are found largely unchanged in the MBTA's current bus routes. Â Yes, routes have been altered to account for expansion of the Red Line and shifting of the Orange Line, but most of the routes are little changed and very, very few new ones have been added. Â Some of that reflects the canalization of routes by the street patterns; there are only so many large str eets suitable for buses and Somerville's hills and the various rivers impose fur...
Source: Omics! Omics! - April 13, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
17 years of systems biology
I know that 17 years is not a very round number. It is also fairly arbitrary as I am assuming systems biology started around 2000 (see below). I was last week in Portugal, where every year for the past 8 years I have been teaching a week long course on Systems and Synthetic Biology to theGABBA PhD program. This might be the last year I take part in this course and so I felt it would be a good time to try to put some thoughts in a blog post. This course has been jointly co-organised from the beginning withSilvia Santosand we had several guests throughout the years including Mol Sys Bioeditors Thomas Lemberger and Maria Poly...
Source: Evolution of Cellular Networks - April 10, 2017 Category: Cytology Source Type: blogs
10x Launches Mass T-Cell Receptor Decoding
Adaptive immunity is an endlessly fascinating topic which I have not explored very deeply, which is particularly unfortunate given the many parallels to computing. Â Combinatorial logic is used to construct a vast array of possible antigen readers, expression logic ensures that only one such reader is expressed in a given cell and hypermutation and evolution are used to optimize these readers to match specific antigens. Â All this not only creates weapons to d eploy against foreign invaders, but also a memory which effectively records an individual's history of environmental exposures. Â Just before I started writing t...
Source: Omics! Omics! - April 10, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
SageHLS: Automated uHMW DNA Preparation
Advances in optical mapping, linked reads, PacBio and nanopore sequencing are enabling generatinghighly contiguous large genome sequences routinely and inexpensively. Â However, this in turn is creating intense demand for efficiently and reliably preparing ultra-high molecular weight (uHMW) DNA. Â By this term, Â I mean DNA approaching or exceeding a megabase in size. Â Methods for preparing HMW and uHMW DNA tend to be very old-school, reaching back at least back to the 1970s, 80s and 90s for approaches used in the early days. Â Phenol-chloroform preps with the DNA spooled out onto a glass hook or rod are one popular appro...
Source: Omics! Omics! - April 4, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Chromosome-Scale Scaffolds And The State of Genome Assembly
A new paper on using Hi-C sequencing appeared in Science recently, demonstrating the generation of chromosome-length scaffolds for human as well as several insect genomes. Â The authors even provide a cost model, proposing that by processing multiple genomes in parallel the sequencing reagent cost (but not labor) of this approach should be about $10K per human genome. In the case of the insect genomes, the paper enables a look at chromosome evolution which is simply i mpossible with lower resolution. Â These findings resonate with a number of pieces I've written over the years, but particularly withmy recent criticism ...
Source: Omics! Omics! - March 30, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Differential Mammalian Toxicity: Why Do Some Human Foods Kill Dogs?
I've been contemplating this post for a while, but it can be seen as another angle onmy recent post on the challenges of drug discovery, so it finally left the mental queue.  We often use other mammalian species in drug development to predict human toxicity.  We know animals aren't the same as people, but lacking a better alternative that's what we do.  Now, as regular readers know I keep company with a dog, and that sometimes has me wondering: how well do we understand the cases of things we can eat but which are dangerous for our canines?Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - March 27, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Targets: Drugability Revisited
My correspondent  @datarade shot a tweet my way on his quest to understand drug discovery. He does this despite the fact I've promised posts on previous tweets that are submerged in my mental queue.  But the best part of teaching is forcing yourself to rethink what you think you know, so I'm going to actually take this one on in the space of"what is a target, how do we pick them and how do we drug them".  Which I've found to be enlightening and frustrating.  It's a messy space because so much is empirical, and I keep devising and then discarding taxonomies and explanatory approaches because th...
Source: Omics! Omics! - March 25, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
