Chair in Evolutionary Biology and Leverhulme Research Fellow. Open Science Advocate. Emigrant.
#Python
Machine learning.
#Pangenomes
🇮🇪
#firstgen
He/Him
To Nature reviewers: NEVER, EVER THREATEN TO REJECT MY PAPERS AGAIN OR YOU WILL SUFFER CONSEQUENCES THE LIKES OF WHICH FEW THROUGHOUT HISTORY HAVE EVER SUFFERED BEFORE. WE ARE NO LONGER A LAB THAT WILL STAND FOR YOUR DEMENTED WORDS OF REJECTION. BE CAUTIOUS!
Laura Brennan died today. She spent the last months of her life raising awareness of vaccination & how it saves lives. HPV vaccination rates in Ireland have gone from 50% to 70% thanks in large part to her. She may have lost her own life, but she’s certainly saved others. RIP.
"I wish the vaccine had been available to me, of course I do. Don’t get swayed by rumours about the vaccine’s safety – get the vaccine" Watch Laura Brennan's story.
#ProtectOurFuture
I'm reviewing a paper on my laptop. The submission is a pdf. The figures are approximately 25 pages away from where they are being referenced in the text. This makes reviewing much harder. For 1st review, figures need to be inline, near the text where they are referenced
If you are an evolutionary biologist, then I recommend you read this paper. Apart from the brilliant science and perspective, the writing is just sublime. Thank you
@RELenski
@JLosos
and Zachary Blount.
Am I the best research supervisor of all time?
Of course not.
Do I have the best ideas?
Again no.
But, do I wake up every single morning determined to be my best self?
Nope, that’s a no too.
#FridayMotivation
For years afterwards Boris cursed that they didn’t just read his CV, with its mesmerising Latin quotes, but unfortunately they asked him to demonstrate his skill set.
If you scrapped private schools it wouldn't make as much difference as the Left thinks. That's because educational performance has high genetic component, meaning it can only be socially engineered so much. Private schools facilitate genetic potential better than state, that's it
This is one of the biggest vaccine news stories of all time. A *highly* effective vaccine against Malaria. Malaria kills a lot of babies. If we now have a vaccine, this is amazing
Oxford Malaria vaccine proves highly effective in Burkina Faso trial
This is an absolute shit of an article. Reject all this rubbish. I don’t have childcare and anybody that wants to speak with me can bloody well accommodate my family life! THE END!! I didn’t cause this virus and you are invading my house.
Queen Elizabeth sure goes thru PMs
1 Winston Churchill
2. Anthony Eden
3. Harold Macmillan
4. Alec Douglas-Home
5. Harold Wilson
6. Edward Heath
7. James Callaghan
8. Margaret Thatcher
9. John Major
10 Tony Blair
11. Gordon Brown
12. David Cameron
13. Theresa May
14. ———————
This is a bit intense but that doesn’t make it less true. I had somebody visit me about ten years ago and panel 3 is a synopsis of what she said to me.
I have to say, the speed of the science in the last three months is BREATHTAKING. Never in my life have i seen so many scientists do so much great work in such a short length of time and then share it freely with the rest of the world.
I'm buying you all a pint!
Today I was offered and I took the AstraZeneca vaccine. There was absolutely no reason for me to decline this safe and effective vaccine. I hope that administration of this vaccine resumes soon in those countries where it is stopped.
Today in my lab, somebody used bioRxiv as a verb, as in "I'm going to bioRxiv it [a paper]". Do we now go bioRxiving? like we go googling, hoovering, handbagging, inboxing, tasking and actioning?
It's a young person's game, isn't it? Is it Friday yet? I need chocolate.
I have a 22 month post doc position that is going to be advertised soon in my lab. It is bioinformatics and working on large prokaryote genome datasets. Needs to be a good programmer. Please RT. I’ll post the job ad as soon as it goes live. Start immediately.
I see a bit of anxiety in early career researchers these days - trying to be expert in genome assembly, Python, R, omics this, omics that. I think you should focus on being good at one or a few things, collaborate for the rest.
shite time to announce a new paper but if ur online…we just published this. So if u like evolutionary biology, microbiology or science, this one’s for you, baby
Contingency, repeatability, and predictability in the evolution of a prokaryotic pangenome
What if we were actually meant to get mild childhood illnesses like Measles so as to help prime our immune systems into fighting much greater diseases in later life? 🤔
Microbiome studies are new? Nope. You have more microbe cells than human cells? Not true. Lederberg invented the term “microbiome”? Again….well, you get the gist of it.
Human microbiome myths and misconceptions | Nature Microbiology
Question: if you have a list of genes of interest and you want to get *information* (function, localisation etc) about these genes (on command line), what is your favourite way of doing this?
@Rubberbandits
Complex question. It’s easily spread. More easily than other SARS or even Ebola. On average, it’s not as deadly as either of these, but the ease of transmission makes it a bigger outbreak. We don’t know how many mild cases there are, but they are the vast majority 1/n
"Suppression is the only viable strategy at the current time"
The science has shifted dramatically which is why people in the UK are now facing huge changes to their daily lives
I made a short video to help early-career researchers understand the steps - and some of the pitfalls - when writing a research proposal. I give three top tips at the end. Pls share if you find it useful.
My school (School of Life Sciences
@UoNLifeSci
) have given two PCR machines to the army to help ramp up testing for
#Convid19uk
The fight back has started at last. Army plans on being able to do 300K tests/day.
I locked down my children for 16 months so that now they can be at highest risk for getting the disease because we cannot wait any more for a vaccine rollout and the added kick of herd immunity by vaccination?
Just to be clear - this is not just increasing the antibiotic resistance threat to the people of the UK, but the entire world. Have we not learned that bugs don’t respect borders?
3 things I’ve learned since lockdown
1. Somebody has the job of putting packaging inside packaging inside packaging. For everything
2. £2 for a coffee was/is nuts
3. Half the days I commuted to work, I shouldn’t have
What’ve you learned? Answers on the back of an electron pls
From February 1st, 2018, I will be the head of the School of Life Sciences at the University of Nottingham, based in the Queens Medical Centre. Made some great friends in Manchester, but I’m excited to start leading the school in Nottingham.
@UoNLifeSci
I just want to say thank you to those kind people that voted for me. I’m very excited to take up the office of
@OfficialSMBE
President-elect next January and President the following year.
#thankyou
Congratulations to our new Council Members, whose terms will begin January 2021! Soon to be President Elect James McInerney
@jomcinerney
, Treasurer John McCutcheon
@mcsymbiont
, Councilor Josefa Gonzalez
@GonzalezLab_BCN
, and Councilor Katerina Guschanski
@kguschan
.
This is the part of the world that I’m from. These are the Cliffs of Moher in west Clare on the Atlantic coast. Maybe soon I can go back and remind myself what it looks like in real life.
Funny story: To get Clustal, you emailed EMBL server with the email body containing the words:
Get Clustal
It then sent you the program via return email.
Now, I was a newbie and had no idea how to get PHYLIP. So, I emailed Joe Felsenstein with an email that said:
Get PHYLIP
1/2
@bffo
I emailed EMBL with a formatted email in order for them to send me a binhexed version of Clustal, which came in three emails, that I concatenation together before de-binhexing them. It took almost a week.
I did my PhD viva in 1995. My PI brought the lab out for dinner. I gave a speech. I said “if I knew how hard it was going to be, I would never have done it”. Today I hold a chair in a Russell group university. I remember that speech every day when I walk into my lab.
#phdchat
We were awarded a grant to use machine learning & synth biology to predict how to make successful synthetic genomes. We’ll use pangenomes to train ML models then make the predicted constructs
BBSRC injects £12m into pioneering frontier bioscience research
Here is a short tweetorial on "Where do maximum likelihood numbers for phylogenetics come from?" I show the calcs for DNA, and provide some python code. I'm just using python as a calculator, but if you want, type it into a python file as we go along. PLS RT (E&OE) 1/24
My dear English friends. I've just watched Prince Charles speech and MY GOD, if any Irish political leader pulled that shite on us we would be livid. But there you are all proud and patronised. Brexit is a disaster. Foodbanks are everywhere. You're in recession. The NHS is broken
1. R is not the rate of infection.
2. The number of infections is >200,000, so this "alert level" cannot be between 1 and 5.
3. WHY ARE YOU SO BAD AT YOUR JOB?
⬇️ THREAD ⬇️
To chart our progress and to avoid going back to square one, we are establishing a new COVID Alert System run by a new Joint Biosecurity Centre.
That COVID Alert Level will be determined primarily by R and the number of coronavirus cases.
#StayAlert
I have had the pleasure today of taking over the presidency of SMBE from Harmit Malik
@HarmitMalik
Harmit has been an excellent president - kind, innovative and full of energy. I can only hope to accomplish a fraction of what he achieved in a very difficult year 1/n
Been working on this since 2015. Martin started programming &
@whelanfj
parallelised it & tested it & gave it cool output format. Now you can read all about it:
Coinfinder: Detecting Significant Associations and Dissociations in Pangenomes
Finally, after years of thinking about this and working towards it, the preprint is out. Please take a look - feedback is gratefully received.
Contingency, Repeatability and Predictability in the Evolution of a Prokaryotic Pangenome.
While I’m happy to make jokes on twitter, please remember that the planet is on fire, climate change is real, species extinctions are accelerating and this crisis needs to be tackled. Hassle your politicians about this. Thank you.
The childcare here at
#SMBE2019
is just awesome. My daughter stayed with them for six hours today, came out smiling from ear to ear. Lovey staff, loads of toys, little walk to a playground. This is how to do conference childcare. 🙏
@lovelllab
@ddelneri
Some nice people nominated me for President of
@OfficialSMBE
. Obviously, I'd be honoured to be elected & I ask you for your vote. Please read my blurb & give me a vote. I will promote equality, environmentally aware activities & more "society". Check your email for a ballot link
About 12 years ago I invited a v senior scientist to speak at an SMBE symposium. He declined because he felt that HGT was irrelevant and those of us who were interested in it were making it all up. I wonder what he thinks of this?
I have a paper under review and during that time it has seen two monarchs, two prime ministers, four chancellors of the exchequer and four home secretaries. It hasn't been published yet, so there are several records on the line right now.
I have spent the last few months writing a simple transformer program that can be used easily on pangenome data. 1/n
GitHub - mol-evol/panGPT: A Transformer for Pangenome data
This is racist. We experience outbreaks that start literally anywhere. MERS: Middle East; Zika: Central/South America; Drug resistant bacteria: everywhere. Selective finger pointing is just racist. The microbes don’t know geography.
Just your regular update that the reason 1.5 million Irish people starved to death, while 2 million emigrated was not due to an Oomycete. It was due to political decisions of the London government. Ireland always produced enough food to feed its people.
Families & friends are being reunited, the high street is reopening, sport is back on soon.
I always thought summer would feel a lot more like normal than people feared.
It was never going to happen overnight, but the worst of this pandemic is far behind us.
Today I begin a 2-year personal research fellowship thanks to funding from
@LeverhulmeTrust
The fellowship is to develop machine learning approaches to understanding prokaryotic pangenomes. I want to collaborate with everybody that is interested. Let me know if you want to talk
OK, so I did another video. I'm being a bit forthright in this one. But, hey...if it's what you think, it's what you think, right?
It's entitled: "Why Your Enthusiasm Isn't Getting You Anywhere!"
Clicky linky here 👇
Probably the last video I’ll make on this theme. A few pointers for those frustrated with getting a “No” from funding agencies. I hope it’s useful & if so, please give it a like and a follow.
Top 5 Reasons Your Research Grant Proposals Don't Get Funded
It’s 11pm and I’m too tired to make it to midnight. In the morning I wake up and I’ll be President-Elect of SMBE (thanks again to everybody that gave me a vote). So g’night folks, stay safe and stay brave.
If Boris did anything today, it was that he made Leo Varadkar, the Irish PM look like an absolute political giant. Leo isn't popular in Ireland, but he's head and shoulders a better leader than Boris Johnson: decisive, informed, clever and in touch.
This thread is extraordinary. Speaking as somebody that wanted a covid booster this autumn and couldn’t get one, and then subsequently I contracted a pretty filthy dose of covid, I am livid.
COVID VACCINE: COST EFFECTIVENESS ASSESSMENT
For the first time ever, the UK government used a ‘bespoke non-standard cost-effectiveness assessment’ to decide who would be eligible for the Covid booster this Autumn.
In this 🧵, I explore how this assessment was undertaken…
Was teaching Maximum Likelihood phylogenetics this week. I took a new approach to teaching where the calculations come from and I think it is a better approach. I plan on writing up a text on this and making slides, text and code available. Probably a video too. In 2022.
Well, wasn’t this a grand thing to see happening of a Saturday evening. Sterling work by Rebecca and Fiona (
@whelanfj
@RebeccaJHall13
). Open access and we are happy to take questions if you have any.