Pablo García-Nieto, Ph.D. retweeted
I'm excited to announce that starting this week CELLxGENE Census supports categorical variables for cell metadata of the now 59M cells . Fetching data will now utilize less memory!! However in some cases the change may break existing code. Details here: chanzuckerberg.github.io/cel…
Pablo García-Nieto, Ph.D. retweeted
1/6 The @cziscience team’s preprint on how CZ #CellxGene Discover serves as a centralized hub for standardized, interoperable and openly available #SingleCell matrices is out!
Really proud of what we’re building to address the community’s needs bit.ly/40kFX2W 🧵
Pablo García-Nieto, Ph.D. retweeted
We are excited to share Geneformer, our foundation model pretrained on 30 million single cell transcriptomes to enable predictions in network biology.
Manuscript: rdcu.be/ddrx0
Model: huggingface.co/ctheodoris/Ge…
Pretraining corpus: huggingface.co/datasets/cthe…
Pablo García-Nieto, Ph.D. retweeted
I am beyond excited to share that SIMBA, a versatile single-cell graph embedding method, has been published @naturemethods nature.com/articles/s41592-0… (1/6)
Pablo García-Nieto, Ph.D. retweeted
We are excited to release Seurat v5- with new methods for multimodal, spatially resolved, and massively scalable single-cell analysis. satijalab.org/seurat
Pablo García-Nieto, Ph.D. retweeted
“Where’s my gene?”
A tweetorial 🧵on how to use #CZCellxGene to answer this question using data from multiple datasets
Pablo García-Nieto, Ph.D. retweeted
Happy to share our latest work (w/ @tagasovska, @stephenrra, @kchonyc, @jkpritch and Aviv Regev) about learning causal representations of single-cell perturbation data sets arxiv.org/pdf/2211.03553.pdf.
Pablo García-Nieto, Ph.D. retweeted
Amazing week for #DeepLearning in #spatial #singlecell biology, with 2🔥new Graph Neural Networks methods!
1.STELLAR🇺🇸 @jure: a cell type annotation & discovery atlas-type framework
2.NCEM🇪🇺 @fabian_theis: an approach to infer cellular communication patterns
Deep dive below🧵
Pablo García-Nieto, Ph.D. retweeted
2/n Here, we propose NCEM (nature.com/articles/s41587-0…) and leverage spatial proximity of cells in tissues as a prior for statistical dependency. We use graph neural networks to capture this dependency and relate this statistical phenomenon to cell communication and tissue niches.
Pablo García-Nieto, Ph.D. retweeted
Excited to present our new preprint! We sequenced 2.4 million marmoset brain cell nuclei across major neocortical and subcortical structures. Here’s what we learned.
biorxiv.org/content/10.1101/…
Pablo García-Nieto, Ph.D. retweeted
So excited our single-cell transcriptomic survey of the adult human brain is on bioRxiv! @slinnarsson @MossiAlejandro @ka_wai_rine @ErnestArenasSWE A really fun collaboration with Rebecca Hodge, Trygve Bakken, Ed Lein and others at the @AllenInstitute doi.org/10.1101/2022.10.12.5…
Pablo García-Nieto, Ph.D. retweeted
Excited to share the single-cell adult #macaque brain atlas—our contribution to a big week of #brainatlas preprints! W/ @XingfanH, @MichaelLouisPl1, @JShendure, & @SMack_Lab—we profiled 4.2M nuclei across 30 regions from females+males. Here’s what we found bit.ly/3CL0zpQ
Pablo García-Nieto, Ph.D. retweeted
Census: accurate, automated, deep, fast, and hierarchical scRNA-seq cell-type annotation biorxiv.org/content/10.1101/…
Pablo García-Nieto, Ph.D. retweeted
"We need more diversity in life experiences, perspectives and ways to do science because it is not only more inclusive, but also tests our biases and prejudices, which makes us better scientists." @daniela_oaks on why #Latinx #RepresentationMatters
#LatinxHeritageMonth
Pablo García-Nieto, Ph.D. retweeted
Single-cell biology helps researchers map biology—from development to disease—cell by cell.
#CZCellxGene empowers researchers to access and explore complex #SingleCell datasets to advance their work cellxgene.cziscience.com/lan…
Pablo García-Nieto, Ph.D. retweeted
I am happy to share with you our work which demonstrates that metastasis is not a phenomenon of cancer! #paradigm_shift #NALCN #metastasis_normal_process @CRUK_CI @RJG3062 @Cambridge_Uni @Gilbertson_Lab @NatureGenet
💥 OUT TODAY @NatureGenet
📰 The NALCN channel regulates metastasis and nonmalignant cell dissemination
🧑🏾🤝🧑🏾 @Gilbertson_Lab and team @CRUK_CI
⬇️
go.nature.com/3SLLU4i
#NALCN #metastasis_normal_process
Pablo García-Nieto, Ph.D. retweeted
“Latin America has great potential and is commonly overlooked in research; there are amazing groups worth collaborating with.”
@AleMedinaRivera's research centers on diseases like lupus + Parkinson's with a strong focus on including Mexican participants
#LatinxHeritageMonth
Pablo García-Nieto, Ph.D. retweeted
Thanks to @ChanZuckerberg for featuring our efforts to increase representation of Mexicans in genomic studies
@AlcauterSarael @ale_e_ruiz_c
@TwinsMXofficial @PJaguarLATAM
“I feel a great commitment to increase the representation of genetic and genomic data of Mexicans in biomedical studies.”
@AleMedinaRivera is creating better health outcomes by increasing diversity in her research while encouraging others to do the same
#LatinxHeritageMonth
ALT Four people smile wearing white shirts that read “twinsmx Registro Mexicano de Gemelos.”
Pablo García-Nieto, Ph.D. retweeted
Yesterday was a historic day in plant biotech: a purple tomato engineered with high antioxidants was approved by @USDA @BigPurpleTomato helps prevent cardiovascular disease and fight cancer in humans.
This approval under new regulation ushers in a new era for plant synbio!
Pablo García-Nieto, Ph.D. retweeted
Hey twitter, it's been a while. Here's a new blog post: "I don't belong in science."
olgabotvinnik.com/blog/i-don…
Curious to hear your thoughts.
#phdchat #gradschool #academia #AcademicTwitter #AcademicChatter #PhD #phdlife