Daniel MacArthur @dgmacarthur Twitter profile

Last Seen Profiles

@bad_texter

@_gee36

@eiieminaj

@JeffKCollins

@dotdump

@akinkartal1

@___Mthembu

@Zervas_

@ZSpavital

@duckyboat

@drewfanacc

@baitomist

@blank0429

@_MorrTex

@CrosenderWay

@TheGigiSweets

@billdownes1

@baseballcrank

@MoSportsHall

@yatoken0916

@Tichooune

@aylulmadrid

@Carnomiuart

@BkPradh98332766

@amuknet

@umiemuts

@ahad_en

@Mikatzy

@aka_mkhewa

@pmarshwx

@clem_burke

@9_A_FORCE945

@p8899q

@JoePierreIII

@graphific

@dr_folviv

Daniel MacArthur

@dgmacarthur

3 years

The FBI is going after the founder of Sci-Hub, for the appalling crime of making publicly funded research freely available.

Alexandra Elbakyan

@ringo_ring

3 years

received a few minutes ago to my GMail. at first I thought it was a spam and was about to delete the email, but it turned out to be about FBI requesting my data from Apple

240

3K

14K

116

6K

14K

Daniel MacArthur

@dgmacarthur

2 years

Chris Goodnow is a world-renowned immunologist. Before catching COVID in May, he was also an avid cyclist and surfer, the director of a major medical research institute, and my boss. And then, like many other COVID patients, the virus hit his heart.

Three myths about COVID-19 — and the biggest challenge that lies ahead

With four decades of research on antibodies under my belt, I always felt like I had a pretty good handle on COVID-19. But when I caught the virus in May, my hubris quickly turned into humility,...

www.abc.net.au

67

1K

2K

Daniel MacArthur

@dgmacarthur

2 years

I shouldn’t have to say this, but calibrating COVID measures with the goal of keeping health systems *right* at the brink of collapse - but never over that line! - is not sustainable. It’s a recipe for healthcare workforce burnout + massive long-term disability. Stop it.

28

443

2K

Daniel MacArthur

@dgmacarthur

6 years

Having a rough day? In 1988 a Russian technician missed a single hyphen in his code, transmitted it without checking, and thus instantly and irreversibly bricked a 6,200 kg spacecraft en route to Mars. So. You’re doing OK.

23

832

2K

Daniel MacArthur

@dgmacarthur

2 years

23

230

2K

Daniel MacArthur

@dgmacarthur

7 years

I will never stop being astonished by this plot. (via @Noahpinion )

107

1K

Daniel MacArthur

@dgmacarthur

4 years

It's live! After years of work and more than 16 months in peer review, the gnomAD package is now up at Nature. We have seven papers in total, exploring different scientific aspects of this collection of more than 140,000 exomes and genomes:

42

470

1K

Daniel MacArthur

@dgmacarthur

4 years

After seven amazing years in Boston, I am both sad and excited to (finally) be able to officially announce that I'll be returning to my native Australia in 2020 to start a new adventure!

95

68

1K

Daniel MacArthur

@dgmacarthur

6 years

“Working to benefit humanity is a priority,” says the company extracting 40% profit margins while blocking rare disease families from accessing publicly funded research. GFY.

Elsevier

@ElsevierConnect

6 years

We're hiring for a new position at Elsevier: Global Head of Diversity & Inclusion. Working to benefit humankind is a priority at Elsevier and we know that diverse minds are key to creating better solutions. Apply now:

15

32

48

9

306

926

Daniel MacArthur

@dgmacarthur

2 years

The majority of senior academics still don’t understand how fast this is coming. This isn’t about trainees pursuing industry when academia doesn’t work out. Many of the best trainees are looking at academic life and deciding, quite sensibly, that there are better options.

Colin Zamecnik, PhD

@ColinZamecnik

2 years

I am witnessing - and a part of - a seismic shift in attitude from late stage postdocs considering leaving academia. A short🧵 Biotech funding bubble or not - the exodus of mid-career faculty is going to have a bigger impact than it seems on the upcoming talent pool 1/5

33

122

727

38

160

956

Daniel MacArthur

@dgmacarthur

3 years

*ﾟ　･ﾟ* ･｡ *･｡ *.｡｡･ °*. Those clever methods you made for your study matter so much less than your sample size ﾟ*. ｡｡･｡･ﾟ｡°*. ｡*･｡

18

122

924

Daniel MacArthur

@dgmacarthur

2 years

This has been the most surreal phase of the pandemic in Australia - mass infections, widespread absences, burned-out workforces, catastrophic load in hospitals, and total silence from the people who should be in charge.

40

324

912

Daniel MacArthur

@dgmacarthur

11 months

Amazing. Someone in Ohio is shitting out a *staggering* amount of COVID from a chronic GI infection, making up almost the entirety of the detectable virus in local wastewater.

Marc Johnson

@SolidEvidence

11 months

Ohio cryptic lineage update. We’ve made no progress identifying the individual, but we have learned a few things. 1/

192

2K

9K

13

194

883

Daniel MacArthur

@dgmacarthur

1 year

Yep. We’re witnessing the slow death of hypothesis-driven science, and (contrary to reports) this is mostly positive. It doesn’t mean ignoring biology; it means letting the data tell you what’s interesting, then designing experiments to validate and explore new patterns.

Shyam Prabhakar Lab

@shyam_lab

1 year

Very true. As a genomics researcher, I’ve had many people tell me that real biology starts with a hypothesis. Starting with big data is a no-no, a fishing expedition. The success of gwas over candidate-gene studies hasn’t changed their views. But younger people are more open …

9

20

136

78

119

811

Daniel MacArthur

@dgmacarthur

6 years

Five years on, it's disappointing that the data visualization community never fully recognized the benefits of 3D stacked scatter pie columns:

48

234

804

Daniel MacArthur

@dgmacarthur

2 years

So here's my advice on a career mindset for young academics: forget the serial model, and go parallel. Figure out what you're good at, and what you enjoy. Determine the full range of careers consistent with these parameters, and investigate all of them.

20

234

785

Daniel MacArthur

@dgmacarthur

5 years

So here's the preprint for the gnomAD flagship paper, which describes our work over the last three years generating and QCing this resource, and figuring out how to use it to understand human variation and gene function: (thread)

12

344

666

Daniel MacArthur

@dgmacarthur

2 years

Would the last academic in human genomics please remember to turn out the lights as they leave?

29

65

650

Daniel MacArthur

@dgmacarthur

4 years

Tackling COVID-19 effectively requires: - sacrificing some individual liberty and privacy - robust public health systems for testing and tracing - public trust in scientific guidance - clear messaging from government Seriously, this virus is like America's kryptonite.

12

196

628

Daniel MacArthur

@dgmacarthur

5 years

I'm delighted to announce the release of a brand new gnomAD dataset, v3, our first whole-genome call set natively aligned to GRCh38, containing 71,702 whole genomes: . #ASHG19

Laurent Francioli

@LFranciol

5 years

Thrilled to announce the release of gnomAD v3, a catalogue of 700M genetics variants based on WGS from 71k samples! It is our first release mapped to GRCh38 and represents a massive leap in analysis power for all non-coding analysis using gnomAD.

8

171

301

12

281

638

Daniel MacArthur

@dgmacarthur

7 years

Q: How can you tell if someone is using deep learning in genomics? A: Oh, don't worry. They'll tell you.

13

188

623

Daniel MacArthur

@dgmacarthur

6 years

That Gmail predictive text thing is impressively good, but I'm disappointed that it hasn't yet learned to just preface all of my emails with "Really sorry for the delayed reply."

7

69

618

Daniel MacArthur

@dgmacarthur

2 years

Heart complications are a common and serious side effect of COVID infection. There's a huge spike of new cardiac diagnoses made within 3 months of COVID infections, resulting in increased risk of death and long-term side effects.

33

247

612

Daniel MacArthur

@dgmacarthur

5 years

Scientists: seriously, don’t fabricate your results. (1) It’s morally wrong; (2) it hurts science; (3) @MicrobiomDigest is going to catch you in like 5 minutes. Just don’t.

Elisabeth Bik

@MicrobiomDigest

5 years

From a paper published in @nature yesterday by @HarvardMed scientists. I just reported it to the EiC, with shaking hands and pounding heart because scary to see that this passed #peerreview and editorial screening in such a high impact journal.

216

1K

3K

8

122

591

Daniel MacArthur

@dgmacarthur

4 years

As academic institutions around the globe come under increasing financial pressure, here’s a thought: we need to stop feeding the 40% profit margins of Elsevier executives, and spend that money on research instead.

[email protected]

@tomstafford

4 years

Answer: UK higher education institutions spent close to £1,000,000,000 with these ten publishers 2010-2019

4

55

70

12

147

443

Daniel MacArthur

@dgmacarthur

5 years

My lab subscribes to the Rule Of Threes, which says that you should be able to communicate the core messages of your poster: - in 3 minutes - at a distance of 3 meters - after both you and your discussant have consumed 3 beers …but a wide variety of formats achieve these goals.

Tony Merriman

@TonyMerriman2

5 years

@dgmacarthur We are overthinking posters. The title is important to draw in the casual poster cruiser. After that then just provide the scientific information in any fashion you please

0

2

18

7

90

430

Daniel MacArthur

@dgmacarthur

4 years

To all the conference organizers currently making the brave (and expensive) decision to cancel, reschedule, or go remote: it’s the right call, and we appreciate it. Thanks.

7

69

421

Daniel MacArthur

@dgmacarthur

5 years

The authors of the non-heterosexual behavior GWAS have sent a letter to the company offering that terrible “How gay are you?” genetic test, asking them to take it down. Let’s hope they listen.

7

157

409

Daniel MacArthur

@dgmacarthur

2 years

COVID won't be forever. But it hasn't gone away yet, and pretending it has is leading to millions of people suffering illness and permanent disability, as well as breeding the variants that will lead to the next wave, and the next. We need to break this cycle.

10

116

412

Daniel MacArthur

@dgmacarthur

3 years

Dear press offices: if you’re writing something on cool new genomics work, don’t illustrate it with an image of someone pointing at an artifact in the read-out of a long obsolete technology.

Karolinska Institutet

@karolinskainst

3 years

Over 1,200 with rare diseases received a diagnosis thanks to the integration of large-scale genomics into Stockholm's healthcare system, constituting a major leap forward in the emerging field of #precisionmedicine . Results out in @GenomeMedicine .

2

38

84

27

34

404

Daniel MacArthur

@dgmacarthur

2 years

We’ve just been awarded AU$10M from the Medical Research Future Fund to support the development of OurDNA, a new program to increase the inclusion of under-represented communities in genomic research. Here's why I'm excited about this work. 🧵

23

60

399

Daniel MacArthur

@dgmacarthur

2 years

In addition to being fit, Chris was 4x vaccinated. But while vaccines provide strong protection against acute disease and death, they seem to provide little or no protection against long COVID and other long-term virus-induced symptoms.

34

92

392

Daniel MacArthur

@dgmacarthur

5 years

One of the weakness of the gnomAD data set is that we've focused entirely on small variants (SNVs and indels). UNTIL NOW. I'm excited to announce a new chapter in the project: gnomAD-SV, a systematic investigation of structural variants. Preprint here:

An open resource of structural variation for medical and population genetics

Structural variants (SVs) rearrange the linear and three-dimensional organization of the genome, which can have profound consequences in evolution, diversity, and disease. As national biobanks, human...

www.biorxiv.org

5

179

385

Daniel MacArthur

@dgmacarthur

8 years

For those who missed it: we just posted variant frequencies from 126,216 exomes and 15,136 genomes at Enjoy! #ASHG16

12

353

375

Daniel MacArthur

@dgmacarthur

2 years

New policy: if you ask me to join a video call on Microsoft Teams I'll take it without complaint. But you're now dead to me, and I will spend the rest of my life secretly working towards your personal and professional downfall.

24

25

366

Daniel MacArthur

@dgmacarthur

7 years

The long-awaited gnomAD VCF is here - sites + frequencies for 123,136 exomes and 15,496 genomes:

9

335

360

Daniel MacArthur

@dgmacarthur

5 years

The bioRxiv team has done far, far more for science than most scientists will ever do. Huge congratulations to @cshperspectives and his crew - transforming biology one preprint at a time.

Richard Sever

@cshperspectives

5 years

Excited to announce something very meta – a paper on bioRxiv about bioRxiv! 1/n

7

135

314

3

67

340

Daniel MacArthur

@dgmacarthur

2 years

And they hit healthy people too. Chris was insanely fit. But as he notes in his article, 2.3% of professional athletes with COVID suffer heart problems severe enough to restrict them from training and competitive play:

Prevalence of Clinical and Subclinical Myocarditis in Competitive Athletes With Recent SARS-CoV-2...

This cohort study assesses the prevalence of myocarditis in athletes with COVID-19 and compares screening strategies for safe return to play.

jamanetwork.com

5

94

341

Daniel MacArthur

@dgmacarthur

7 years

Strong, unambiguous message from @eric_lander to the @broadinstitute community. The EO is morally wrong, and damages science + the nation.

5

212

324

Daniel MacArthur

@dgmacarthur

5 years

Beautiful story about two of the most remarkable humans I have ever had the privilege of meeting - and their urgent fight against a rare and horrible genetic disease:

One Couple’s Tireless Crusade to Stop a Genetic Killer

When Sonia Vallabh lost her mother to a rare disease, she and her husband, Eric Minikel, set out to find a cure.

www.wired.com

5

140

325

Daniel MacArthur

@dgmacarthur

2 years

That means getting boosted, wearing a fitted N95/P2 mask to protect yourself and others, isolating and RAT-testing if you have symptoms, and avoiding crowded indoor places. And, as Chris says, it means working on new transmission-blocking vaccines.

Three myths about COVID-19 — and the biggest challenge that lies ahead

With four decades of research on antibodies under my belt, I always felt like I had a pretty good handle on COVID-19. But when I caught the virus in May, my hubris quickly turned into humility,...

www.abc.net.au

12

67

327

Daniel MacArthur

@dgmacarthur

2 years

This excellent thread captures something I've seen so many times when mentoring young academics through career choices: the sense of guilt and failure that often comes with deciding to leave academia. Academia is *built* to reinforce this sense. It's hard to fight it.

Ashley Ruba, PhD

@ashleyruba_phd

2 years

I've thought about how to write this tweet for a few weeks now. But I don't have anything clever so here it is: I'm leaving academia. 1/

133

229

5K

7

106

321

Daniel MacArthur

@dgmacarthur

2 years

Excellent post from @EricTopol . This resonated strongly - the fact that boosters against an outdated strain work so well against omicron is amazing. We got *so lucky*. But this makes our vaccination failures (anti-vaxxers, global inequity) feel worse.

5

66

306

Daniel MacArthur

@dgmacarthur

6 years

"our code is on github and our preprint is up on bioRxiv" - things I love hearing during #ASHG18 talks. Instant credibility boost.

8

49

306

Daniel MacArthur

@dgmacarthur

4 years

UK geneticists: as a fellow Brit, my condolences. And a reminder that I’m launching a new centre for population genomics in Australia next May. If you’re interested in doing large-scale human genomics in a slightly better physical and political climate, message me and let’s chat.

11

56

306

Daniel MacArthur

@dgmacarthur

6 years

Our paper just out in Nature Methods describes work led by @lh3lh3 to create a powerful new resource for validating variant-calling methods (thread):

5

166

303

Daniel MacArthur

@dgmacarthur

2 years

Australia and many other countries continue to persist in a bubble of denial. But with each new variant wave we are seeing another surge of preventable long-term disease triggered by this virus. This won't stop until we stop it.

3

59

303

Daniel MacArthur

@dgmacarthur

4 years

The field of psychology has a new logo.

Wolfgang Viechtbauer

@wviechtb

4 years

@ianhussey

9

141

692

5

50

296

Daniel MacArthur

@dgmacarthur

5 years

My PhD mentor and personal hero, Kathryn North, was just awarded one of Australia’s highest honors for her service to genomic medicine. Incredibly well-deserved recognition both of her work and the importance of the field! 🏅🏅🏅

Australia Day 2019:

When Professor Kathryn North started in genetics, DNA was sequenced a gene at a time. It could take years for a child with a genetic condition to receive the right diagnosis.

www.smh.com.au

6

45

294

Daniel MacArthur

@dgmacarthur

7 years

Thanks to my brilliant lab and amazing collaborators for making this work possible!

ASHG

@GeneticsSociety

7 years

Congrats to @dgmacarthur , recipient of ASHG's first-ever Early Career Award! #ExAC #gnomAD #genomics @broadinstitute

20

62

200

24

35

286

Daniel MacArthur

@dgmacarthur

8 years

I'm delighted to announce the (open access) publication of the ExAC paper in Nature:

Analysis of protein-coding genetic variation in 60,706 humans

Nature - As part of the Exome Aggregation Consortium (ExAC) project, Daniel MacArthur and colleagues report on the generation and analysis of high-quality exome sequencing data from 60,706...

www.nature.com

18

224

280

Daniel MacArthur

@dgmacarthur

5 years

As @my_helix and other consumer genomics companies embraced diet genetics bullshit, @23andMe has generally stuck to solid science. Until now. This is disappointing to see.

23andMe Will Add Weight-Loss Advice to Its DNA-Testing Services

Consumer DNA-testing giant 23andMe Inc. plans to add new wellness offerings it hopes will help its customers shed a few pounds, but some genetics experts say the jury is still out on the science...

www.bloomberg.com

27

133

278

Daniel MacArthur

@dgmacarthur

4 years

End of an era: on Monday night this week we officially retired the old ExAC browser, after more than 5 years of continuous operation and over 13.5 million page views. (thread)

7

63

278

Daniel MacArthur

@dgmacarthur

3 years

Like gnomAD, but with deep phenotype data, thanks to over 280,000 exomes from @uk_biobank . An absolutely transformative resource - and more to come!

Matthew Solomonson

@mattsolomonson

3 years

Super excited to release , a web application for browsing association results for 3,700 phenotypes across 281,850 individuals from the UK Biobank. The site features plots, tables, and controls for exploring billions of associations.

7

231

601

3

61

255

Daniel MacArthur

@dgmacarthur

6 years

Excited to announce the beta release of a new version of the gnomAD browser, thanks to heroic work by @mattsolomonson . We’re looking for test users to check their favorite genes and give us feedback on the new features - check it out:

18

182

247

Daniel MacArthur

@dgmacarthur

6 months

Massive new @gnomad_project release (v4) spanning exome/genome data from *over 800,000 individuals*. Huge congratulations to the entire gnomAD production team for their incredible work getting this over the line! A total game-changer for rare variant interpretation.

Genome Aggregation Database

@gnomad_project

6 months

The #gnomAD team is proud to announce the release of gnomAD v4! The v4 dataset includes 730,947 exomes & 76,215 genomes, which is ~5x larger than the v2 & v3 releases combined, & includes nearly 120K indivs of non-European genetic ancestry #ASHG23 (1/11)

7

275

735

2

72

252

Daniel MacArthur

@dgmacarthur

8 years

I just rolled my eyes so hard I may have torn all of my optic muscles.

Lab Spend

@LabSpend

8 years

Microsoft will 'solve' cancer within 10 years by 'reprogramming' diseased cells @Dereklowe

3

0

5

32

111

246

Daniel MacArthur

@dgmacarthur

3 years

One of the great frustrations of gnomAD: literally thousands of people with clinically actionable genetic variants, almost all of them likely unaware of their risk, and with no path for return of results. I now design all our genomic studies to allow return of secondary findings.

Cristen Willer, PhD

@cristenw

3 years

Are you a researcher working with humans or their samples? Did you ever find something in the lab that you wanted to tell the research participant? Or find something *you* would want to be told if you were the study participant?

3

10

83

9

40

248

Daniel MacArthur

@dgmacarthur

4 years

It now seems clear that the actions that governments and individuals take over the next few weeks will save, or cost, tens to hundreds of thousands of lives, and every day matters. This is an excellent summary:

4

164

245

Daniel MacArthur

@dgmacarthur

5 years

Massive congratulations to @beryl_bbc for successfully defending her thesis today! An amazing presentation to cap off a stellar PhD. I’m incredibly fortunate to have had her as my first grad student. 🍾🍾🍾

18

11

246

Daniel MacArthur

@dgmacarthur

5 years

Oh no, dude. Finding out you having a 15% inferred risk of disease, vs a 12% population risk, is not "saving your life".

Matt Hancock

@MattHancock

5 years

ICYMI: The power of genomics to save lives is extraordinary - and this week it may have saved my life. My piece in @TimesRedBox on genome sequencing & the need to get the ethics right:

14

16

22

17

62

240

Daniel MacArthur

@dgmacarthur

7 years

Preprint describing disastrous statistical flaws in a recent @NatureGenet paper reporting new autism genes:

11

239

Daniel MacArthur

@dgmacarthur

7 years

Latest from Ioannidis et al is a must-read for any scientist. How can we innovate, while ensuring robust results?

6

214

239

Daniel MacArthur

@dgmacarthur

7 years

Massive thanks to my lab, my mentors, and my collaborators for the opportunities that led to this award. #ASHG17

13

15

240

Daniel MacArthur

@dgmacarthur

6 years

This whole piece on deep learning in genomics is worth reading, but I especially appreciated this point. Exquisite sensitivity to confounding => need for ever more careful study design.

6

112

235

Daniel MacArthur

@dgmacarthur

4 years

The Biogen cluster is a cautionary tale for anyone still considering conferences/large meetings over the coming weeks. At this point we all have enough information. Organizers: cancel/reschedule/go remote, or any transmissions are on you.

How the Biogen leadership conference in Boston spread the coronavirus - The Boston Globe

Amid ominous signs after a routine conference, a frightening realization slowly dawned: The virus was on the loose.

www.bostonglobe.com

6

139

229

Daniel MacArthur

@dgmacarthur

8 years

Prediction: my grandchildren will be embryo-screened, germline-edited. Won't "change what it means to be human". It'll be like vaccination.

34

141

219

Daniel MacArthur

@dgmacarthur

4 years

@ASlavitt @carlzimmer It is horrifying how comprehensively this virus plays to America's weaknesses.

Daniel MacArthur

@dgmacarthur

4 years

Tackling COVID-19 effectively requires: - sacrificing some individual liberty and privacy - robust public health systems for testing and tracing - public trust in scientific guidance - clear messaging from government Seriously, this virus is like America's kryptonite.

12

196

628

9

62

225

Daniel MacArthur

@dgmacarthur

3 years

This is absolutely appalling, and totally incompatible with the way science is being done in 2021. The majority of cutting-edge science is now shared through preprints. @arc_gov_au you need to revert this policy and make amends to those affected.

ARC Tracker

@ARC_Tracker

3 years

The @arc_gov_au has ruled *dozens* of fellowship grants ineligible because the applications cited "preprints". Not just in the applicants' publication list, but *anywhere* in the app. Not just those co-authored by the applicant, but *any* "preprint".

21

105

249

5

49

225

Daniel MacArthur

@dgmacarthur

9 years

From an email I just sent to a reporter asking about how to evaluate potential human genetics stories: http://t.co/EsmIEnDN8D

18

213

221

Daniel MacArthur

@dgmacarthur

4 years

Remarkable, horrifying visualization of how easily coronavirus spread across the globe:

2

131

216

Daniel MacArthur

@dgmacarthur

2 years

Finally, a massive thank you to Chris, who played a huge role in bringing me back to Australia and supporting the development of my new team, and who steered the @GarvanInstitute successfully through COVID. Fingers crossed for a full recovery!

9

18

221

Daniel MacArthur

@dgmacarthur

6 years

Well, wow. @illumina to purchase long-read sequencing technology company @PacBio for $1.2B:

Illumina to Acquire Pacific Biosciences for Approximately $1.2 Billion, Broadening Access to...

Illumina, Inc. (NASDAQ: ILMN) and Pacific Biosciences (NASDAQ:PACB) today announced they have signed an agreement for Illumina to acquire Pacific Bios

www.businesswire.com

7

190

221

Daniel MacArthur

@dgmacarthur

5 years

Important session at @broadinstitute this morning - a discussion of the need for greater diversity in human genetics, led by @genetisaur . She leads off with a pretty astonishing statistic: Europeans are 80% of samples in genetic studies, vs 16% of the global population.

10

122

224

Daniel MacArthur

@dgmacarthur

6 years

Remember FOXP2, the "gene for language" that was recently positively selected in humans? Turns out it wasn't: Lovely work by @egatkinson and colleagues.

6

136

215

Daniel MacArthur

@dgmacarthur

8 years

We’ve released the code so you can reproduce all the figures in the ExAC paper. Here’s how to do it:

Reproduce all the figures!: a user’s guide to ExAC, part 2

As we were organizing analyses for the ExAC flagship paper, we were inspired by Titus Brown’s manifesto on reproducibility. As with most collaborative papers, we had a core team of analysts, each r…

macarthurlab.org

12

126

215

Daniel MacArthur

@dgmacarthur

4 years

As Australia begins to emerge from lockdown, I'm launching a search for several key staff for our new Centre for Population Genomics, which will now be launching at the beginning of July with physical sites in Sydney and Melbourne. Please RT!

5

261

214

Daniel MacArthur

@dgmacarthur

3 months

tl;dr 1. don't use UMAP for genetic ancestry 2. be careful with ancestry labels; they matter 3. All Of Us is one of the most thoughtfully inclusive programs in the history of human genetics, and will have enormous impact on reducing inequity in genomic medicine

4

28

215

Daniel MacArthur

@dgmacarthur

4 years

Whenever I start getting too pessimistic about the US, I think about the incredible feat @BroadGenomics has managed to pull off in massive-scale COVID testing. It's exactly the kind of relentless innovation the country needs. Plus @HeidiRehm is a badass.

Heidi Rehm

@HeidiRehm

4 years

@dgmacarthur @BroadGenomics The team has not slept much lately. Even I joined them to work an overnight shift 4 pm to 4 am last night to help accession the >60,000 samples we got yesterday!

8

13

187

1

23

213

Daniel MacArthur

@dgmacarthur

7 years

Super cool preprint from Lander and Regev labs - using scRNA-seq to reconstruct developmental landscapes:

5

132

208

Daniel MacArthur

@dgmacarthur

13 years

If Google wants us to trust it with our online lives it needs to do a lot better than this: http://t.co/eJ6O36g (via @neilfws )

43

878

201

Daniel MacArthur

@dgmacarthur

5 years

We've just added multinucleotide variant annotations to the gnomAD browser - so you can now see when a variant has another in-phase variant in the same codon that affects its interpretation. Example:

7

87

206

Daniel MacArthur

@dgmacarthur

5 years

Roses are red Violets are blue Please stop using gnomAD as a control group for association studies Unless you have a really firm grasp of the associated statistical challenges #AcademicValentine

Sek Kathiresan MD

@skathire

5 years

Genetic analysis to make discovery claim 👇🏽 seems suspect 😳 Variant PADI3 in Central Centrifugal Cicatricial Alopecia | NEJM

3

19

48

6

40

205

Daniel MacArthur

@dgmacarthur

3 months

I definitely accept partial responsibility here - this approach leans on methods we used in the 2020 gnomAD paper - but endorse the concerns raised by @jkpritch , @Graham_Coop , @ewanbirney and others. UMAP isn't the right approach for showing genetic ancestry.

Jonathan Pritchard

@jkpritch

3 months

It's a pity that All of Us used UMAP to visualize ancestry variation in their new marker paper, out today in Nature. The UMAP algorithm, by design, exaggerates the distinctiveness of the most frequent ancestries, a message that can be misinterpreted by the public.

29

327

1K

8

28

206

Daniel MacArthur

@dgmacarthur

3 years

Has anyone ever done a proper model of the price difference for institutions between Teams vs Slack/Zoom/GSuite, accounting for the productivity and morale loss incurred by Teams being fucking awful? Asking for a friend.

13

17

207

Daniel MacArthur

@dgmacarthur

5 years

A more interesting but less visible trend is the (perfectly sensible) shift in attitudes of genomics trainees towards industry jobs being as or more appealing/prestigious as academic roles. The longer-term effects of this will be far more profound than PI departures.

Yaniv Erlich 💔

@erlichya

5 years

Here is a partial list of academic PIs in genomics/bioinfo who left (or LoA) their position to join the industry in the last ~2 years: @cdbustamante @jgschraiber @KMS_Meltzy @gabecasis @markmccarthyoxf @joe_pickrell @srikosuri @adamauton @Piwdb @erlichya

23

69

248

12

53

203

Daniel MacArthur

@dgmacarthur

5 years

Many of you will know the remarkable story of Eric and Sonia, and their battle to cure the disease that killed Sonia's mother (and will kill Sonia, if they don't stop it). If you don't know the story, read it here: And now, they need your help.

One Couple’s Tireless Crusade to Stop a Genetic Killer

When Sonia Vallabh lost her mother to a rare disease, she and her husband, Eric Minikel, set out to find a cure.

www.wired.com

3

150

204

Daniel MacArthur

@dgmacarthur

4 years

Look, I’ve been on Twitter for a decade, so I knew that effective virus containment would be followed by an outbreak of dumb “your numbers were wrong lol owned libs” takes. But somehow - despite all my mental preparation - they’re even stupider than I imagined.

10

37

201

Daniel MacArthur

@dgmacarthur

5 years

Don’t do this. Anyone who makes a substantive scientific contribution to a paper should be an author.

Lorena Pantano

@lopantano

5 years

life in a core: you made an analysis that leads to a cell report paper, participated in the review process, and you end up in the acknowledgment section just because they had to pay for the service. #bioinformatics . work is paid with authorship or money, is that right?

43

187

8

52

202

Daniel MacArthur

@dgmacarthur

3 years

Tufekci and other outsiders systematically out-performed the public health establishment over the last year to a degree that should embarrass us all out of arguments from authority. And yet, hey, here we are again.

13

40

195

Daniel MacArthur

@dgmacarthur

4 years

I'll be directing a new centre for population genomics as a partnership between the Garvan Institute of Medical Research in Sydney and the Murdoch Children's Research Institute in Melbourne, bridging two world-class research institutes in the two largest cities in the country.

8

22

195

Daniel MacArthur

@dgmacarthur

9 years

My tweet advice for new PIs: 1. Don't be an asshole; 2. Don't work with assholes; 3. Politely say no a lot; 4. Don't. Write. Book. Chapters.

30

128

194

Daniel MacArthur

@dgmacarthur

4 years

Still can’t quite believe the speed with which Eric and Sonia have gone from deciding on a research program to having a drug in the pipeline. A drug which, if successful, will save Sonia’s life. Testament to the power of hard work and intense focus:

Eric Vallabh Minikel

@cureffi

4 years

Immensely proud to see today, for the first time, a drug candidate for prion disease — ION716 targeting PRNP — officially listed in @ionispharma 's pipeline:

17

60

373

1

52

193

Daniel MacArthur

@dgmacarthur

4 years

Timely public health message writ large over inner-west Sydney this afternoon:

2

66

188

Daniel MacArthur

@dgmacarthur

6 years

If you believe that people have a right to access their own genetic info, but also that this info should not be used to calculate insurance premiums, then the inevitable logical outcome is some form of socialized healthcare.

Paul Appelbaum

@appelbap

6 years

This thread points to an issue that we discussed in JAMA a couple of years ago: the threat that spread of personal genetic information has for insurance underwriting decisions, and the likely pressure to come for insurer access

2

11

26

10

72

188

Daniel MacArthur

@dgmacarthur

5 years

. @JShendure calls for a Manhattan Project to understand the function of all human genes, including genome-wide perturbation studies, systematically engineering variants, predictive modeling, and doubling down on model organisms #genomics2020

12

84

189

Daniel MacArthur

@dgmacarthur

5 years

I expect (and hope) to see many more institutions sensibly follow UC’s example and unsubscribe from Elsevier’s price-gouging model. So, want to make sure your science is read widely? (1) post it as a preprint; (2) talk about it on Twitter; (3) don’t publish in Elsevier journals.

6

57

189

Daniel MacArthur

@dgmacarthur

29 days

This is so cool - a remarkably frequent mutation in a non-protein-coding RNA gene, which causes around one in every 200 currently undiagnosed cases of developmental delay around the world (including 8 Australian families so far!). A couple of thoughts (1/3)

Nicky Whiffin

@nickywhiffin

29 days

Would you believe me if I told you that a single variant in a non-coding RNA explains ~0.5% of all undiagnosed individuals with neurodevelopmental disorders (NDD) in @GenomicsEngland ??? I didn’t initially either, but here is the story of RNU4-2 🧵1/9

15

213

640

4

50

188

Daniel MacArthur

@dgmacarthur

5 years

I’ll say it again: Gattaca. Dude with a deadly heart condition fakes and lies his way into a mission-critical role on a space shuttle, selfishly endangering his crew-mates. Audience inexplicably cheers him on.

Paul Mackie

@paulmac708

5 years

Most overrated film of all time - what's the first one you think of?

2K

64

324

25

27

178