@RoryStewartUK Thoroughly enjoying it so far. Fascinating account of the clash between the love for what politics can be and the desperation over what it has become... Thanks for writing it!
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Pedro Ferreira
266 posts
Pedro Ferreira
@pfalef
PhD in Computational Biology @cbg_ethz
Basel, Switzerland شامل ہوئے Eylül 2018
1K فالونگ199 فالوورز
Huge thank you to everyone who is continuing to read and buy #PoliticsOnTheEdge - can’t quite believe it 🙏
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Pedro Ferreira ری ٹویٹ کیا
Excited to share one of our apex studies from our @NCIHTAN center, focused on the transition to metastasis, shedding light transition to #CRC #metastasis. Joint work with @KarunaMDPhD, led by @andrewrmoorman and @elliebenitez11. -->
nature.com/articles/s4158…
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Pedro Ferreira ری ٹویٹ کیا
Congratulations on leading this amazing project @susanavinga!
OLISSIPO Fostering Computational Biology Research@Olissipo_eu
This week all members were together in Basel, @ETH_en, for the final meeting of this amazing project. That's a wrap of these 3,5 years of training, exchanging, sharing & collaborating! Thanks to all the students, researchers and research administrators who have crossed our path!
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Pedro Ferreira ری ٹویٹ کیا
This week all members were together in Basel, @ETH_en, for the final meeting of this amazing project.
That's a wrap of these 3,5 years of training, exchanging, sharing & collaborating!
Thanks to all the students, researchers and research administrators who have crossed our path!
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Pedro Ferreira ری ٹویٹ کیا
Sigh. The level of profound confusion in the scRNA-seq analysis field keeps surprising me. I've now run into people that, in a discussion about technical artifacts of scRNA-seq, where I claimed there is no evidence for zero inflation, first insist that it does exist, and then 1/n
𝕐@nomad421
@NimwegenLab @maelouisewoods @GorinGennady @arjunrajlab The existence of ZI as a "technical artifact" is distinct from divergence from a NB or Poisson dist. This paper genomebiology.biomedcentral.com/articles/10.11… e.g. argues that zero inflation is observed for certain genes & is of Biological origin (& recommends still using a GLM with NB counts w/o ZI).
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We have made many updates to our SCICoNE results. Everything is described in this new version of our preprint: biorxiv.org/content/10.110…
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Pedro Ferreira ری ٹویٹ کیا
The choice of whether to use Seurat or Scanpy for single-cell RNA-seq analysis typically comes down to a preference of R vs. Python. But do they produce the same results? In biorxiv.org/content/10.110… w/ @Josephmrich et al. we take a close look. The results are 👀 1/🧵
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Pedro Ferreira ری ٹویٹ کیا
I see we are getting to the stage of the discussion where people are starting to defend UMAP saying it can 'reveal patterns' or 'structure' in the data. Without ever specifying what precisely these patterns/structures represent. This is not surprising because hardly anybody 1/n
Daniel MacArthur@dgmacarthur
Thoughtful, well-informed counterpoint on the use of UMAP for visualising human genetic data, following the intense debate about the All Of Us paper this week.
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Pedro Ferreira ری ٹویٹ کیا
Our latest out today in @Nature. We profiled 12 million single cells from mouse embryos spanning gastrulation to birth, defined cell type tree from zygote to birth, and unexpectedly found crazy fast changes within first hour of extrauterine life. OA PDF: rdcu.be/dyDAg
Jay Shendure@JShendure
Excited to share our lab's latest preprint, led by @CXchengxiangQIU, @bethkarenmartin & Ian Welsh of @jacksonlab. We set out to build a single cell roadmap for all of mouse prenatal development, from single cell zygote to free-living pup. Preprint: tinyurl.com/2nhe4mm9 1/n
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An interesting approach to hierarchical cell type annotation for single-cell RNA-seq using a multi-level Bayesian factorization model. #xref-ref-33-1" target="_blank" rel="nofollow noopener">biorxiv.org/content/10.110…
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Pedro Ferreira ری ٹویٹ کیا
I really dislike this race to the bottom: No need to write protocols. No need to write your own introduction section. Just copy somebody else's. Everything is too much apparently.
There are many reasons why being forced to formulate a protocol each time is helpful. 1. It 1/n
Arjun Raj@arjunrajlab
The arguments presented here against reuse of language in methods section are unconvincing. Yes, it is certainly possible to rewrite a protocol over and over again. Is that a valuable exercise in scientific writing ala Flaubert? No way. We're not writing Madame Bovary here.
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We have made many updates to our scDEF method and results. Everything is described in this new version of our preprint:
biorxiv.org/content/10.110…
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Pedro Ferreira ری ٹویٹ کیا
Delighted to present our full-length scRNA-seq study on ovarian cancer patients, in collaboration with the University Hospital Basel @labfranz ! nature.com/articles/s4146…
Can we simultaneously detect isoform-level gene expression, mutations and gene fusions in cancer cells? 1/
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Pedro Ferreira ری ٹویٹ کیا
New data arrived for #BA286 / #Pirola in #Switzerland: the variant is observed at low abundance in multiple locations through our #Wastewater surveillance of #SARSCoV2 variants.
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Pedro Ferreira ری ٹویٹ کیا
Thrilled to see our paper out today
where we use long-read whole-genome sequencing to study SNVs, structural variation and repeats in single cells
nature.com/articles/s4146…
Many thanks to everyone involved @_adameur, @Jeff_Mold, @jakmic2003, @ngisweden, @scilifelab
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Pedro Ferreira ری ٹویٹ کیا
In our detection of BA.2.86 in two wastewater samples from Laupen (BE, Switzerland) of August 5 and 6: we observed co-occurrence of these mutations on the same fragments:
– 21618: T, 21622: T, 21624: C, 21633: '---------', 21711: T, 21765: '------' (amplicon 67)
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Pedro Ferreira ری ٹویٹ کیا
The next Computational Reproducibility seminar is this Wednesday at 5 pm:
Kim Philipp Jablonski @kpj_py at @Google is going to speak about sustainable tool benchmarking and workflow development in Computational Biology.
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Join us for free at: ethz.zoom.us/j/65832714361
@SwissRN
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Pedro Ferreira ری ٹویٹ کیا
We are pleased to welcome Prof Niko Beerenwinkel of @cbg_ethz. He joins the Institute as a @royalsociety Wolfson Visiting Fellow.
He will work with @markowetzlab over the next two years to develop his research project "Single-cell copy number signatures as cancer #biomarkers".
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