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Anup Malani @anup_malani
, 3 tweets, 1 min read Read on Twitter
Just posted a revision of my paper with @sarahcobey & Frank Wen on the effects of flu vaccine on evolution of seasonal flu. biorxiv.org/content/early/…
Main points: 1/ Vaccination *on ave* slows antigenic drift of flu, so it has dynamic benefits not previously thought.
2/ Evolutionary effects raise social benefit of vaccination, thereby lowering its private benefit. This increases the severity of the collective action problem, making vaccination policy more important.
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So so so so excited to share this!
This preprint summarizes my journey of trying to engineer the brain parasite Toxoplasma gondii to deliver therapeutic proteins into neurons, together with @OdedRechavi and @SheinerLab 1/n biorxiv.org/content/early/… #bioRxiv
You probably heard of Toxoplasma because of the way it cycles between cats and their prey. However, Toxoplasma also infects people. 2/n
Toxoplasmosis can be dangerous in people with weakened immune systems, but in most people infections are asymptomatic, and aren’t even noticed. In fact, it is estimated that a third of the human population are chronically infected with Toxoplasma. 3/n
Read 15 tweets
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#Golgi2018 @FEBSnews Meeting. Looking forward to sharing my notebook on another day of great talks!

Micrograph: Judith Klumperman.
First talk of the day: Mukund Thattai: Algorithmic biosynthesis of glycans in Golgi compartments

@veeslerlab and @coronalexington would dig this talk.
Cryo-EM structure of Coronavirus spike protein with glycan shield.

From Lexi @coronalexington and colleagues @UWBiochemistry.
Read 87 tweets
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A thread about this Nature advice column about how female scientists can combat gender bias - To be clear, I'm incredibly grateful to the women in this piece. The advice is clear-eyed & I definitely got some ideas. But I am also really tired of being told this is MY problem 1/n
to solve. Let's start here: Ladies, you need to somehow address the problem that you are SIGNIFICANTLY under-represented as editors, reviewers, & last authors. nature.com/articles/d4158…. Here's the preprint they're talking about - biorxiv.org/content/early/… 2/n
Here's another thing we #ladyscientists are supposed to solve from that paper - manuscripts with female last authors were significantly less likely to be accepted (50% versus 58%) when the reviewing panel was all-male.
Read 20 tweets
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Latest lab pre-print: Excited to share yet another strange beast from our zoo - Emergent hunting mechanics of Lacrymaria olor - an incredible ciliate. biorxiv.org/content/early/… Phenomenal work by Scott Coyle scottmcoyle.com - postdoc in lab leading this effort.
This is a team effort, led by amazing postdoc Scott Coyle; who started as a biochemist - but morphed into a system biologist. Congrats to all co-authors including Scott, Ellie Fluam, Hongquan Li and @deepak_me90 To appreciate this story, start with movies: youtube.com/playlist?list=…
The question we ask here is - how is complex morphological behavior encoded in active systems in this incredible hunting ciliate? We find that multiple antagonistic active systems (contractile proteins and ciliary dynamics) work together to encode complex behavior of single cells
Read 13 tweets
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SuperFreq: Integrated mutation detection and clonal tracking in cancer biorxiv.org/content/early/…

If you want to use: github.com/ChristofferFle…
I've developed and used this the last 4+ years, and now finally out! 🎉

Let me make a thread (or tree?) from here.
What is superFreq?
It analyses cancer exomes, especially geared for multiple matched cancer samples.
- calls somatic SNVs
- calls CNAs
- calls clones and phylogeny

as well as quality of life:
- annotates variants (effect, dbSNP, ExAC, COSMIC)
- lots of plots: results and QC
Why should you use it?
Not because it beats some other method in precision/recall on simulated data, but because it's been developed to answer questions from ours and others data. So focus has been on:
- robust to noise
- working without matched normal
- lots of QC
Read 10 tweets
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Genetic differences between human populations: more than meets the eye (link thread):
Indonesian Bajau divers have recently evolved 50% larger spleens for storing reserve of oxygenated blood needed in long dives dropbox.com/s/w5t351hboh14…
Greenlandic Inuit show genetic signatures of diet and climate adaptation science.sciencemag.org/content/349/62…
Read 44 tweets

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