PhD in Computational Biology @cbg_ethz
Basel, Switzerland
Joined September 2018
- Tweets265
- Following1K
- Followers198
- Likes2.4K
Pedro Ferreira retweeted
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/s41586-0…
Congratulations on leading this amazing project @susanavinga!
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!
Pedro Ferreira retweeted
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!
Pedro Ferreira retweeted
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
The existence of ZI as a "technical artifact" is distinct from divergence from a NB or Poisson dist. This paper genomebiology.biomedcentral.… 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).
We have made many updates to our SCICoNE results. Everything is described in this new version of our preprint: biorxiv.org/content/10.1101/…
Pedro Ferreira retweeted
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/10.1101/… w/ @Josephmrich et al. we take a close look. The results are 👀 1/🧵
Pedro Ferreira retweeted
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
Pedro Ferreira retweeted
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
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
Pedro Ferreira retweeted
An interesting approach to hierarchical cell type annotation for single-cell RNA-seq using a multi-level Bayesian factorization model. biorxiv.org/content/10.1101/…
Pedro Ferreira retweeted
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
We have made many updates to our scDEF method and results. Everything is described in this new version of our preprint:
biorxiv.org/content/10.1101/…
Pedro Ferreira retweeted
Delighted to present our full-length scRNA-seq study on ovarian cancer patients, in collaboration with the University Hospital Basel @labfranz ! nature.com/articles/s41467-0…
Can we simultaneously detect isoform-level gene expression, mutations and gene fusions in cancer cells? 1/
Pedro Ferreira retweeted
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.
Pedro Ferreira retweeted
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/s41467-0…
Many thanks to everyone involved @_adameur, @Jeff_Mold, @jakmic2003, @ngisweden, @scilifelab
Pedro Ferreira retweeted
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)
Pedro Ferreira retweeted
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.
--
Join us for free at: ethz.zoom.us/j/65832714361
@SwissRN
Pedro Ferreira retweeted
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".
ALT Niko Beerenwinkel, Professor of Computational Biology at ETH Zurich, joins the Institute as a Royal Society Wolfson Visiting Fellow. Prof Beerenwinkel will work with the Markowetz Group over the next two years to develop his research project "Single-cell copy number signatures as cancer biomarkers".
Pedro Ferreira retweeted
NOW OUT @ScienceMagazine 🧬🐾🤓
“The evolution of two transmissible cancers in Tasmanian devils”
A 🧵 on our deep DNA sequencing dive into the startling genetic history of contagious tumours (1/n)
👇
doi.org/10.1126/science.abq6…
Pedro Ferreira retweeted
We are thrilled to have @ArthurDondi from @ETH Zürich, as a part of our webinar on May 10! Arthur will discuss how #PacBio HiFi sequencing can be used to help detect cancer-related RNA dysregulation.
Register today: bit.ly/3KsV5nA
#HiFisequencing
