Nick Loman
@pathogenomenick
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Professor of Microbial Genomics and Bioinformatics @unibirmingham , @MRCClimb , Sr. Genomics Adviser @UKHSA , CSO @microbesNG
Birmingham, UK
Joined October 2009
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Academics, don't forget to submit all your papers this week so they can sit on someone else's desk until January!!
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Serious question. Where can you go "without access to emails" as claimed in some out of office replies. I want to go there.
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Very pleased to say that as of 5 minutes ago I'm now a Professor of Microbial Genomics and Bioinformatics
@unibirmingham
!
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Bioinformatics is just writing the same script over and over again because you forgot where you put it last time you wrote it.
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Considering organising a virtual conference on genomic epidemiology of COVID-19 - over Hangouts or some such. Interested in attending? Presenting?
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I think this is a terrific updated summary of current state of knowledge on the science of the new variant from
@JamesTGallagher
:
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If the storm is rubbish where you are, tune into this instead:
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The only disturbing thing about these Fauci emails is that he tried to reply to them all.
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Alternatively let's use these remarkable times to admit that the journal peer review system is inefficient, unmanageable and unsustainable for academics
I am getting really frustrated by the number of scientists declining to peer-review manuscripts at the moment. Please step up and help us academic editors out. We don't have time either, especially to chase after 10s of names to get reviewers. Support the system.
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Confirming that all mistakes in nucleic acid molecular biology can be traced to use of the Nanodrop
Hold up.
The accidental low dose in the AstraZeneca trial was because Oxford insisted that NANODROP was more accurate than qPCR?!
Ahahahahahahahahahahahaha
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PNAS .. how far you done fall
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Excited to announce 'COG-UK' after 10 days of rapid setup: the government have today announced £20M for distributed (12 centre) real-time sequencing for COVID-19 inc
@IMIBirmingham
, feeding data into
@MRCClimb
using
@NetworkArtic
sequencing protocols.
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Journals have sensibly removed paywalls for COVID-19 manuscripts. I'd quite like to see the popular press do the same for COVID-19 articles (at least, the useful, sensible ones) how about it
@washingtonpost
@thetimes
@nytimes
?
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Have been offline because busy getting married - at last. Thought some of you might like to see the cake.
@tattooedbakers
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Open science is ... downloading your own stuff off the Internet because you can't find where it is on your server.
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If there’s one thing that this pandemic has made clear it is that NO ONE understands immunology (especially me)
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Unpopular opinion (?) but most university staff are not key workers by any reasonable definition. The idea is to keep people at home to reduce the numbers of cases and also to reduce the numbers in school dramatically to reduce opportunities for transmission.
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Hydroxychloroquine and azithromycin as a treatment of COVID-19: results of an openlabel non-randomized clinical trial
- small n but intriguing:
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I am constitutionally unable to write a talk until the day before I give it. Is this a recognised disorder?
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Charles Darwin did about 4h/day
There are way easier places to work, but nobody ever changed the world on 40 hours a week
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Bioinformatics is ... spending 5 minutes deciding if it's quicker to hand type:
for barcode in "NB01 NB02 NB03 NB04 NB05 NB06 NB07 NB08 NB09 NB10 NB11 NB12 NB13 NB14 NB15 NB16"
or write a Python script. Then spending 2 weeks writing a Nextflow pipeline.
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Life is much more manageable/less guilt-ridden if you recognise that procrastination is just your brain working asynchronously on a problem.
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Gosh feels very weird to be on other side after months of urging caution on mutation stories. Most mutations we never even see because they stop the virus functioning, most of the rest are very boring. Very occasionally some look extremely interesting. This is one of those times.
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Nice article in FT by
@clivecookson
focusing on
@nextstrain
with great quotes from
@firefoxx66
has little quote from me:
“We could certainly have mutations that change the character of the virus,” he added, “though we have not yet seen this happening.”
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This whole "COVID-19 was circulating in late 2019" thing is getting me properly riled up. One very badly reported study on one sample does not change anything.
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Imagine a world where everyone just stood three feet back from the baggage carousel.
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If I was in charge (and providing sufficient vaccine available): shut as much as possible down during Jan-Feb, pay everyone to stay home, vaccinate everyone with massive scale logistics. Why not?
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@aphillippy
"I'm sure it took a lot of hard work ;)". I can feel the sarcasm dripping from the page!
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We've just bought a hamster to get us through the long weeks ahead. Although looks like barely a full meal to me.
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Rules for my daughter from her mum, but we could all use them too in 2019.
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Recent Ebola cases in Guinea linked to transmission following latent infection of between 5-7 years since original 2014-2016 Makona strain outbreak, rather than new virus spillover. Nice to see coordinated reports from separate groups on Virological
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It’s harder to think of a more insane idea than the Olympics right now
BREAKING: Japanese government declares state of emergency in Tokyo due to coronavirus, just 2 weeks before the Olympics
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Anyone else noticed there’s basically just too much to do?
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My hot take: to succeed in academia requires on average somewhere between 0 and 168 hours per week of work.
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Rule 8: Believe in yourself
Rule 11: Don't go chasing Waterfalls
Rule 12: Please stick to the rivers and the lakes that you're used to
Rule 13: Dreams are hopeless aspirations
Rule 14: No .... scrubs ....
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Fascinating look at mutational hotspots in spike associated with human and animal passage from Robert Garry, these are clearly the areas that can get "tuned up"
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My guilty bioinformatics pleasure is using Geneious- it really is very good for messing around with viral genome sequences.
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I’ve been moderately sceptical that a fourth (third) wave was likely this summer even based on the transmission advantage of delta, mainly given the massive progress on vaccination in UK, but the data’s the data and we now need to plan accordingly.
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Easiest way to get someone to move onto another project is to ask them to write up their current one.
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Our primer on shotgun metagenomics now out! Hopefully useful to those dipping toes into field
@NatureBiotech
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It's been hard for me to conceptualise this because we've been head down working on COVID so hard past 2 years but the fun bits of being an academic have been absolutely annihilated by the combination of enforced home working and lack of travel.
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Calling microbiologists! Would you be interested in attending a
@mrcclimb
workshop around use of machine learning and GPU accelerated applications in microbial genomics or other omics? Particular focus on implementation. If so, give me a reply and state in person (UK) or virtual!
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Guy that admits to not knowing about viral genomics continues to commentate on genomics despite high profile error in past few days. No, it doesn't seem to mutate rather fast.
Evidence emerging that the new
#coronavirus
🦠 seems to mutate rather fast. Authors say “Close monitoring of the virus’s mutation, evolution, and adaptation is needed”. In a family of 6 infected people, 2 ‘nonsynonymous’ mutations occurred during human-to-human transmission.🤔
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How about using the extra 140 characters for useful disclaimers?
---
Tweets can be misinterpreted. Be warned this tweet may contain irony, sarcasm, or other devices intended to misdirect the reader. If this tweet provokes a strong emotional reaction, think before replying.
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On a train. Lots of people are coughing. No one is wearing a mask (except me). We've learnt nothing particularly.
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It's not been an easy ride by any means, but very proud of what
@CovidGenomicsUK
have achieved in a short timescale: article in
@LancetMicrobe
today describes the distributed and diverse sequencing and analysis model we chose for genomics of SARS-CoV-2:
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Genuine thrill for the first pint at staff house bar for over a year
@IMIBirmingham
@unibirmingham
with
@alanmcn1
@WvSchaik
@MikeyJ
@scalene
and - yay, finally! - new starter
@nwheeler443
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NOT THIS AGAIN
A series of DNA tests has confirmed that NYC subway Is a germaphobe's worst nightmare. Researchers identified 15,152 types of life forms, ranging from rodents and insects to the bacteria that cause the bubonic plague
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Based on this analysis, do we conclude the CDC haven't heard of Primer3? Or have a license for Geneious. It actually boggles the mind.
The CDC-provided COVID-19 primers have potential issues with hairpins and dimerization, writes
@tomeraltman
.
In his new blog post, he designs better candidate primers to help develop better diagnostic kits.
Please RT.
#COVID19
#COVID_19
#Coronavirus
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Delighted to announce
@wellcometrust
funded our 3y Technology Development Grant
@unibirmingham
to develop novel ultra-long extraction&library methods: (slightly tenuously) titled: "A New Durable Read EXtension method for very, very long reads" with
@mattloose
@uninottingham
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It's incredibly hard to effectively nuance the potential impact of P.1 (detected in Manaus, Brazil) and B1.351 (detected in South Africa) on the vaccine for a media friendly soundbite (and I think I did a rubbish job on BBC News tonight on the clip they used). 1/n
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"He noticed that when he ate potato starch, he was able to increase the amount of a microbe called bifidobacterium"
"I saw a bloom (of it), and sure enough, my sleep that night was amazing."
Well, I'm convinced
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"Never get high on your own supply". Biggy, was, of course talking about the importance of maintaining independent testing and training sets in machine learning.
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Siri, design me a controlled experiment for mask wearing
UK Parliament right now - has mask wearing become a political act? Stark difference between both sides of the House
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Very excited to be one of
@unibirmingham
's new Alan Turing Fellows working
@turinginst
- aim to form collaborations at their London base to help drive 'big data microbiology' apps focused on pandemic preparation and AMR.
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Wow, huge announcement from
@cziscience
at
#GrandChallenges
: 128 x $1m grants to place sequencers and hire staff in 23 countries to do clinical metagenomics!
@edyong209
has the scoop here:
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Free coffee
The big idea: what single change to university practice would have the most positive and far-reaching consequences? Eight academics and thinkers give us their views
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Just accept that your job is writing emails for the rest of your life and relax.
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Nearly a week with this puppy and I can feel my microbione getting stronger, more vigorous, more diverse, I feel invincible now resistant to all gut pathogens
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Desperate scrabbling for scientific credit in a pandemic is not becoming scientists. Team game, bigger things at stake.
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Author list
Which major section of a scientific paper do you find the most difficult to write?
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If I had to sum up 90% of practicing bioinformatics I think it would take the form of a deep sigh.
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Anyone else when they are stuck on writing like to print it off, take it out to the garden with a pen and a drink, then just ignore it and check their phone instead?
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"Roberts acknowledges that her team still needs to rule out contamination."
Ideally before the poster gets reported in Science?
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This is the easily the worst bit of the job as a bioinformatician.
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Struggling to find much positive in this month, but at least can we at least all agree pathogen genomics is the best genomics now?
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The team have been working on this for a while! Excited to announce complete Nanopore+Illumina hybrid genomes as a service from £250 a strain.
Do you use whole genome sequencing? Do you get too many contigs? You need to try our Enhanced Genome Service, combining short and long reads
#EGS
Visit us at Stand 16
#Microbio18
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Was just talking coronavirus genomics,
@CovidGenomicsUK
and whether there's more than one strain of SARS-CoV-2 (hint: there isn't) on
@BBCRadio4
@BBCr4today
(scroll to 8:35am!).
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What's the word for the sense of paralysis that stops you doing anything else when a long-running bioinformatics job is running?
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That
#bioinformaticsshame
where you start a job with tr/cut/awk and finish it off in Excel
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Which will you miss the most?
Gas
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Petrol
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Food
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Reproducible with horrible code is basically academic badge of honour
Influential model judged reproducible — although software engineers called its code 'horrible' and 'a buggy mess'.
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Methods: "We performed BLAST searches at the NCBI. However, the searches were performed during the government shutdown, potentially invalidating the results."
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Oh OK, this actually happened.
The Great British Germ Hunt. Sunday - 7pm - Channel 4.
I'll be live tweeting the end of my serious scientific career.
@arwynedwards
@scalene
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Epi modelling equations on BBC news the other night: my dream is to see a detailed explanation of the SAM format.
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Bit fed up of takes telling us things will be back to normal in variably: spring, summer, autumn 2021. In truth we haven't got a clue. Plan accordingly!
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'WHO advises all countries to increase the sequencing of SARS-CoV-2 viruses where possible and sharing the sequence data internationally.'
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Sneak preview of our DNA extraction, sample prep and QC chapter by
@Scalene
and I from the upcoming "Nanopore Sequencing: An Introduction" book edited by Deamer and Branton. Hope it's of use to folk at
#nanoporeconf
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Disappointed to hear about the death of bioinformatics so am now rebranding myself as filecopyist
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Considering writing my COVID memoirs (everyone’s doing it) but just checked my notes and it’s just a load of partially completed todo lists.
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"Once again, it seems to be modelling not data driving decisions." says Steve Baker of the CRG - presumably unaware that modelling is required to predict events that have not yet happened, and are themselves produced from data.
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"Panic and hysteria are not appropriate. This is a disease that is in the cases and their close contacts. It’s not a hidden enemy lurking behind bushes. Get organized, get educated, and get working."
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Today my first time sitting on a
@wellcometrust
Expert Review Group grant panel. Eye-opening experience, very tough decisions to make, many people expend much effort to ensure fairness. Feel like everyone writing grants should get the opportunity to see how panels work.
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Look everyone I know that virtual conferences are not as appealing as real ones but please submit some Genome Informatics 2020 abstracts right now as we don’t have many at all, deadline a week Tuesday
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Brexit customs delay shit is real and intensely frustrating for biomedical research. I realise small beer compared to everything else going on but don't let anyone gaslight you into saying it's not a thing.
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This is too awesome. Direct 16S sequencing with modification detection on
@nanopore
congrats
@MitenJain
@AkesonUCSC
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Asked to comment on "how worried should people be about mutations re vaccines" on BBC News. Tricky line to walk. Basically the vaccines are going to be brilliant, but there's going to be some variation in their performance, and some of that variation will be down to mutations.
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