idk who this @pathogenomenick guy is but he seems like a big deal 
Here early to get a seat for Nick's inaugural lecture at @unibirmingham @IMIBirmingham. The Dome theatre is living up to its name.
Over to head of @LES_UniBham, Prof. Laura Green who introduces @pathogenomenick to a packed out theatre. Note: Any errors and omissions are his.
"I normally write my talks the day before, but I wanted to talk this one seriously, so I wrote it on the weekend."
After making chair in 2017, @pathogenomenick has finally got around to his inaugural lecture.
After making chair in 2017, @pathogenomenick has finally got around to his inaugural lecture.
Hidden in the presentation are some unicorns
You can spot the first one here
@pathogenomenick's first computer obsession was an Amstrad, referenced often in his homework. "I like to type programs on my computer: and I still do that, so that's good."
Interviewed on camera often as a child ("a bit weird"), even a young Nick was thinking about how computers could be used for "serious stuff" like databases (for estate agents)
Developed the Zeus bulletin board system
...but things were ruined by this man "who really annoyed me at the time" because he killed the Amiga and bulletin boards
At Barts, he met his partner Hannah and also got involved with the beginning of microbial genomics. At this time, the ideas behind the human genome project were rest tested on smaller bacterial genomes.
Huge sequencing centres like Sanger used to dump their reads as they were generated on FTP, but not look at them. People really wanted to see what was going on, so @pathogenomenick wrote "a rather lame genome browser, but people loved it"
Not necessarily seeing the utility of this sort of genomic tools at the time, he became a doctor instead, only to find you couldn't really change the NHS from the inside. The experience summed by a photo: a result of a lot of long nights
Nick took an opportunity to move to @unibirmingham and after a serendipitous improvement in sequencing technology, got into genomic epidemiology for investigating bacterial outbreaks. Showed in 2010 military patients brought Acinetobacter and spread it to civilian patients in QE
This was a eureka moment, demonstrating the power of genomics in outbreaks.
The German O104:H4 outbreak was first accidentally tracked to cucumbers in a patient's house, leading to whole crops of cucumbers being destroyed on false inference
Getting distracted at a conference, the idea of crowd-sourcing analysis of public data drove a consortium from around the world to assemble the E coli genomes from this 2011 outbreak. "Ideal for me: pissing around on social media and doing science"
Jumping to 2014. We need infrastructure! Placing the ability to generate and analysis sequences in the hands of users, Nick has been integral to both @MRCClimb and @microbesNG
fifty pounds a genome if you're wondering @microbesNG
Onto long reads with @nanopore. "It's like going from the PC to the iPhone". "That's a cool idea and there's no way it's going to work... and for a little bit of time in 2014 we were worried that it didn't"
But it does. And this technology has enabled almost all the work from the lab since.
"somehow you got it working, which is amazing"
Shout out to @Scalene, whose just been awarded a UKRI fellowship, who spearheaded a lot of the work on using the nanopore to investigate bacterial outbreaks like Salmonella in Heartlands in 2014/2015
So we can confirm cases with nanopore but what about using it to influence response. Reading an article about how sequenced genomes don't tie up with the number of confirmed Ebola cases, an idea to use the nanopore to fill the gap was born
And this fell to @Scalene, who put together the first lab in a suitcase. With a bunch of kit and enough room for some clean clothes. As the bioinformatician, Nick decided that Josh should go into the field.
At the same time, @igoodfel had the same idea. This is what transporting a bunch of ion torrents to the field looks like. Between the two groups, sharing their data, they could actually see there was transmission between countries
Lots of diversity in RNA viruses and Ebola evolves at around two mutations a month. Sequenced genomes means you can cluster cases and see whether strains are related: which means you can track movement for real time genomic epidemiology
And the nanopore helped give rapid time to answer
Found that survivors were really important. Survivors could transmit Ebola through sexual transmission or breastfeeding. Genomics linked these cases
This stunning visual from @evogytis makes an appearance
Now onto the Zibra project. Semi inspired by Top Gear and a tight deadline to get started, they got a bus, drove around, did some sequencing, job done. "It wasn't that easy, it was actually a bit of a nightmare"
"We had lots of problems... our bus caught fire... it was hot and sweaty, which is the reality of doing field work"
Problems with sequencing in the field but @Scalene worked it out after they got back, and they did find out what was going on with Zika. The main takeaway was pathogen surveillance didn't catch this!
...and it's not just exotic diseases. There are plenty of outbreaks and sadly many are vaccine-preventable
building a toolkit for pathogen surveillance and deployable field genomic epidemiology is the goal of @NetworkArtic
annoyed once again by Bill Gates
Concluding: pathogens don't respect borders!
Now for some nostalgia: @pathogenomenick's wishlist for 1995
Doesn't care at all about golf
and doesn't work for a company that no longer exists
Welcome Professor Loman
A debrief from @RobinMay9. Nick is integral to the @IMIBirmingham family. Some nice comments: "the closest we have to a genomics rockstar without the drug habit", "an amazing researcher but I wished he answered his email", "I wasn't sure he existed outside of Twitter"
I've not seen @pathogenomenick this happy since the seafood at EBAME last year
