@matiasmfalco

Postdoctoral researcher at #ONCOSYS in @helsinkiuni | #MSCA postdoc fellow | It will be fun they said...Let's complicate things a bit and work with scRNAseq

Joined September 2020
  • Tweets65
  • Following153
  • Followers91
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Great interdisciplinary effort to track down cancer resistant phenotypes. Glad to be part of the team!!
Anna Vähärautio@AnnaVaharautio9 Feb 2024
How do #cancer cells with resistant fates differ from the sensitive, already before the treatment? To answer this, we developed ReSisTrace, a cellular time-travel method that uses the similarity of sister cells to trace back pre-existing resistance. nature.com/articles/s41467-0…
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Lior Pachter@lpachter23 Aug 2023
A 🧵 on why Seurat and Scanpy's log fold change calculations are discordant. 1/ (based on the Supplementary Notes from biorxiv.org/content/10.1101/…).
Lior Pachter@lpachter22 Aug 2023
Replying to @slavov_n
The LFC implementation of both is incorrect, for different reasons. The arithmetic is in the Supplementary Notes of biorxiv.org/content/10.1101/… I can write a short thread explaining their shortcomings tomorrow (one of the programs is in a sense more wrong than the other!)
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IMO this must be done in all comp bio papers. Without annotations, many model explanations in comp bio papers are very hard to follow. When explaining many inputs in the likelihood or many regularisation terms - you need to label what they mean. Easier to read -> more citations.
alex peysakhovich
@alex_peys18 Aug 2023
really love when authors do things like explain equations in-line with colors etc... just makes papers so much easier to read.
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Simona Cristea
@simocristea20 Jun 2023
Twitter messed up my previous thread, but this is too important to let it slide: Here are (again) my summary & thoughts on early detection & an amazing work Deep learning model trained on 9 million patient records in Denmark & US finds people at risk for pancreatic cancer 🧵🧵
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Nice work by the @WennerbergLab: A platform for efficient establishment and drug-response profiling of high-grade serous #ovariancancer @wojtsen @AnnaVaharautio organoids cell.com/developmental-cell/…

A platform for efficient establishment and drug-response profiling of high-grade serous ovarian...

Establishment of robust high-grade serous ovarian cancer (HGSC) organoid cultures has proven difficult. Senkowski et al. present a protocol for long-term culture of HGSC organoids from cryopreserved...

cell.com
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Fabian Theis
@fabian_theis8 May 2023
So excited to see our compositional perturbation autoencoder (CPA) paper out @MolSystBiol! This generative DL model leverages single cell perturbation (drug, CRISPR etc) studies to predict cellular response. Great collab w @MetaAI! github.com/theislab/cpa embopress.org/doi/full/10.15…
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Karen Ahlnäs@KarenAhl_4 May 2023
The rowing season has started for #ONCOSYS! Despite the icy morning we had beautiful sunshine in the evening!
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Hello #ScienceTwitter! 🔬 We are PostdoCaRe! The European Network for Postdocs in #cancerresearch! Founded by #Postdocs for Postdocs as a platform for scientific and personal exchange. Follow us on our LinkedIn page and join our Slack channel 😁 Please RT.
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Now it’s time for another delicatessen, “arròs al forn”. This food is prepared in a flat, wide and low-height clay stewpot, a traditional casserole inherited form our muslim settlers in the past. The rice is cooked in the oven.
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Rahul Satija@satijalab8 Mar 2023
We've been working on Seurat v5 for two years and are excited to share it with you soon! In a webinar w/@10xGenomics and @ScienceMagazine on 3/29, I'll introduce new methods to analyze spatial/multimodal datasets that scale to tens of millions of cells: view6.workcast.net/register?…
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Treutlein lab@TreutleinLab4 Feb 2023
Save the date! Single Cell Genomics 2023 #SCG2023 takes place Oct. 9-11 2023 in the beautiful mountain town Engelberg in Switzerland! 10th year anniversary of this unique experience. @IdoAmitLab, @slinnarsson, @AlexandervanOu1, @MarioniLab, @sandberglab, Aviv Regev, Amos Tanay
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antisense.@razoralign12 Feb 2023
CellOracle: Dissecting cell identity via network inference and in silico gene perturbation nature.com/articles/s41586-0…
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Vince Buffalo@vsbuffalo31 Jan 2023
If you are annoyed by connecting and reconnecting Jupyter sessions running on a remote server via SSH tunneling, you might enjoy this command-line tool I made to make this easier: github.com/vsbuffalo/remote_… #compbio
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Fabian Theis
@fabian_theis25 Jan 2023
Interest @naturemethods paper by Qing Nie lab @UCI_CMCF that allows to learn cell–cell communication from spatial transcriptomics data based on optimal transport. nature.com/articles/s41592-0…
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Valentina Boeva
@val_boeva19 Jan 2023
Happy to share our recent work on the discovery of shared transcriptional states across cancer patients from single-cell RNA sequencing data biorxiv.org/content/10.1101/… by @JoYatesResearch @flobarkmann @cbg_ethz and the team. #CancerResearch 1/n

CanSig: discovery of shared transcriptional states across cancer patients from single-cell RNA...

Multiple cancer types have been shown to exhibit heterogeneity in the transcriptional states of malignant cells across patients and within the same tumor. The intra-tumor transcriptional heterogene...

biorxiv.org
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Promising technique for improving detection of cfDNA.
Albert Vilella@AlbertVilella16 Jan 2023
An intravenous DNA-binding priming agent protects cell-free DNA and improves the sensitivity of liquid biopsies biorxiv.org/content/10.1101/…
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Postdocs_eternos@PostdocsE10 Jan 2023
Pedimos que l@s investigador@s que tengan el #certificadoi3 no tengan que obtener también el #R3 como comentaron en el webinario #RyC2022.Nos hacéis perder el tiempo con tantas evaluaciones y burocracia @AgEInves @UniversidadGob.Nos ayudáis con un RT?#ciencia #España #precariedad
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I write my books with vim. Why tough? While there are many good reasons to use Vim for book writing, one stands out: I don't know how to exit Vim.
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Interested in deconvolution of bulk RNA-seq data? Check out our new preprint, "Performance of computational algorithms to deconvolve heterogeneous bulk tumor tissue depends on experimental factors" biorxiv.org/content/10.1101/… 1/

Performance of computational algorithms to deconvolve heterogeneous bulk tumor tissue depends on...

Background Single-cell gene expression profiling provides unique opportunities to understand tumor heterogeneity and the tumor microenvironment. Because of cost and feasibility, profiling bulk tumors...

biorxiv.org
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Bone is the most frequent site for #metastasis for many cancers, notably for #tumours originating in the breast and the prostate go.nature.com/3jW7mlU #BoneMetastases
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