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James McInerney Profile
James McInerney

@jomcinerney

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Chair in Evolutionary Biology and Leverhulme Research Fellow. Open Science Advocate. Emigrant. #Python Machine learning. #Pangenomes 🇮🇪 #firstgen He/Him

Nottingham, England
Joined March 2009
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@jomcinerney
James McInerney
3 years
Stunning summary of the last year of living with covid.
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@jomcinerney
James McInerney
1 year
Being an academic mostly involves saying “it will all calm down next week and I’ll get some proper work done”.
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@jomcinerney
James McInerney
4 years
Wow. Did not know this.
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@jomcinerney
James McInerney
7 years
Sorry I don't know who made this, but this be funny.
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@jomcinerney
James McInerney
6 years
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!
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@jomcinerney
James McInerney
3 years
Little bit of a laugh.
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@jomcinerney
James McInerney
5 years
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.
@HSELive
HSE Ireland
5 years
"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
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@jomcinerney
James McInerney
3 years
Fabulous front page. The man is the president of Ireland. The lady is Denise Chaila, singer and rapper from Limerick.
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@jomcinerney
James McInerney
1 year
Did I have amazing success in 2022? No. But did I get up every morning and go out and do my very, very best to improve myself? Again No.
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@jomcinerney
James McInerney
2 years
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
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@jomcinerney
James McInerney
1 year
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.
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@jomcinerney
James McInerney
5 years
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
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@jomcinerney
James McInerney
6 years
Scientific fields ranked: 10. You 9. Cannot 8. Rank 7. Them 6. They 5. Are 4. All 3. Equally 2. Important 1. Evolutionary biology
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@jomcinerney
James McInerney
3 years
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.
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@jomcinerney
James McInerney
2 years
This is how to deal with the arrant nonsense from this ambassador. Well done David McCullagh
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@jomcinerney
James McInerney
5 years
Me, a professor with 32 years of experience studying genetics, proclaim this quoted tweet to be 100% nonsense.
@CharlotteCGill
Charlotte Gill
5 years
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
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@jomcinerney
James McInerney
3 years
Listen to every word of this. It’s time to take stock.
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@jomcinerney
James McInerney
3 years
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
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@jomcinerney
James McInerney
4 years
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.
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@jomcinerney
James McInerney
3 years
If you are finding this lockdown to be difficult, maybe this poem can be some help. This is Irish poet, John O’Donohoe. This is the time to be slow.
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@jomcinerney
James McInerney
5 years
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. ———————
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@jomcinerney
James McInerney
4 years
Apparently somebody said “your Ma makes phylogenetic trees using parsimony”
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@jomcinerney
James McInerney
3 years
Mike Tyson called it right.
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@jomcinerney
James McInerney
4 years
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.
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@jomcinerney
James McInerney
4 years
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!
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@jomcinerney
James McInerney
3 years
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.
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@jomcinerney
James McInerney
4 years
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.
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@jomcinerney
James McInerney
1 year
@NoContextBrits Oh look, the neighbours got a new car.
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@jomcinerney
James McInerney
3 years
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.
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James McInerney
2 years
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.
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@jomcinerney
James McInerney
4 months
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
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@jomcinerney
James McInerney
4 years
What’s the best method for building a phylogenetic tree? Wrong answers only.
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@jomcinerney
James McInerney
5 years
Anti-vaccine nut invents vaccination concept.
@Jimcorrsays
Jim Corr
5 years
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? 🤔
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@jomcinerney
James McInerney
10 months
Ecologist turns up at a medical conference.
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@jomcinerney
James McInerney
8 months
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
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@jomcinerney
James McInerney
2 years
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?
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James McInerney
4 years
@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
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James McInerney
4 years
I feel nothing but RAGE with this headline. The science has NOT shifted. We have been saying the same thing for weeks and weeks. RAGE!
@BBCNews
BBC News (UK)
4 years
"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
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@jomcinerney
James McInerney
1 year
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.
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@jomcinerney
James McInerney
5 years
Who else out there is “Sanger sequencing with radioactive nucleotides” years old?
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@jomcinerney
James McInerney
4 years
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.
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@jomcinerney
James McInerney
3 years
Amazing photo from @WildAtlanticBae These are the three sisters in Kerry.
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@jomcinerney
James McInerney
3 years
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?
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@jomcinerney
James McInerney
3 years
Mike Ryan takes no hostages. Speaking about the new U.K. strategy.
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@jomcinerney
James McInerney
2 years
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?
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@jomcinerney
James McInerney
4 years
FLATTEN THE CURVE!!
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@jomcinerney
James McInerney
4 years
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
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@jomcinerney
James McInerney
4 years
All my life I have struggled for a way of saying this. I love this tweet.
@PeterBrannen1
Peter🌲Brannen
4 years
You: This one untested supplement will restore balance to my body Your body:
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@jomcinerney
James McInerney
8 years
Guess who has a h-index of 333 and is cited 2,414,149 times. She is the most cited of all time!!
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@jomcinerney
James McInerney
6 years
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
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@jomcinerney
James McInerney
4 years
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
@OfficialSMBE
OfficialSMBE
4 years
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 .
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@jomcinerney
James McInerney
3 years
On this week 11 years ago, this classic bit of tv happened. Happy Friday folks.
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@jomcinerney
James McInerney
3 years
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.
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@jomcinerney
James McInerney
4 years
Well said Emanuelle Charpentier.
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@jomcinerney
James McInerney
2 years
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
@jomcinerney
James McInerney
2 years
@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.
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@jomcinerney
James McInerney
1 year
I think this paper is awesome. I highly recommend it. Machine learning enables prediction of metabolic system evolution in bacteria
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@jomcinerney
James McInerney
3 years
I know I post this on this day every year. Doesn’t make it any less funny.
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@jomcinerney
James McInerney
4 years
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
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@jomcinerney
James McInerney
5 years
Yes. DNA is actually made of unicorns.
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@jomcinerney
James McInerney
6 months
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
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@jomcinerney
James McInerney
2 years
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
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James McInerney
1 year
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
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@jomcinerney
James McInerney
4 years
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?
@BorisJohnson
Boris Johnson
4 years
⬇️ 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
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James McInerney
2 years
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
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@jomcinerney
James McInerney
4 years
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
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@jomcinerney
James McInerney
2 years
By return email a few hours later, I received this text from Joe: That Not Way Get PHYLIP I remember it in mortification to this day.
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@jomcinerney
James McInerney
4 years
I HATE when they leave aeroplane flying to the expert pilots. I’d much prefer if they gave us all a go.
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@jomcinerney
James McInerney
7 years
I love this letter from Pauling to Crick. Polite but firm. "A man giving a seminar..."
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@jomcinerney
James McInerney
6 years
We are looking for fellows!! Come to Nottingham. Do your best research, and there are permanent jobs at the end. Please RT.
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@jomcinerney
James McInerney
1 year
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.
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James McInerney
4 years
This diagram explains everything we are talking about.
@procellaria11
Louise Blight
4 years
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James McInerney
3 years
I got the AstraZeneca vaccine on Monday and I had no adverse reaction to it. Nothing at all. Not even a sore arm. I think it’s important to say this.
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@jomcinerney
James McInerney
5 years
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.
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@jomcinerney
James McInerney
5 years
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
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@jomcinerney
James McInerney
4 years
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
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James McInerney
4 years
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?
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James McInerney
2 years
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.
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James McInerney
2 months
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
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James McInerney
4 years
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.
@Nigel_Farage
Nigel Farage
4 years
It really is about time we all said it. China caused this nightmare. Period.
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James McInerney
3 years
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.
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James McInerney
4 years
Here’s a tweet that will age like milk in the sun.
@ProfKarolSikora
Professor Karol Sikora
4 years
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.
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James McInerney
4 years
Cumulative daily cases of #COVID19 in the UK. Nothing to worry about. It’s only exponential. #sarcasm
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@jomcinerney
James McInerney
6 years
On the left is how I approached the first half of my PhD. On the right is how I approached the second half.
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@jomcinerney
James McInerney
11 months
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
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James McInerney
1 year
This is great. Also: Lecture notes going to be rewritten. Base editing: Revolutionary therapy clears girl's incurable cancer - BBC News
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James McInerney
11 months
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 👇
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James McInerney
7 months
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
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James McInerney
6 years
First day in my new school. Start as you mean to go on, they say. I’m opening a brand new staff common area this morning. That’s a good start. 🤓
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James McInerney
4 years
This might be the most stunning, complex and thought-provoking cover of the New Yorker I have ever seen.
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James McInerney
3 years
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.
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James McInerney
4 years
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.
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James McInerney
6 months
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.
@_CatintheHat
Cat in the Hat 🐈‍⬛ 🎩 🇬🇧
6 months
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…
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James McInerney
2 years
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.
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James McInerney
3 years
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.
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James McInerney
10 years
Dr. Khan, of Sierra Leone, was invited to spend the summer at Harvard, but he stayed to fight Ebola. He died at 39. http://t.co/lcSdPIPEbf
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James McInerney
4 years
10 years ago today and it just gets better every time I see it.
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James McInerney
4 years
Finally it’s out. Coinfinder: detecting significant associations and dissociations in pangenomes. Microbial Genomics DOI 10.1099/mgen.0.000338
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James McInerney
4 years
Everybody should watch this video.
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James McInerney
5 years
#TenYearChallenge 2008 versus 2018
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