Igor Dolgalev

Assistant Professor @NYUGSOM_PMED @nyugrossman

see also:

[Igor Dolgalev @bioigor]

@arjunrajlab Cell Cell Atlas

[Igor Dolgalev @bioigor]

@joinshiftX Shift

[Sasha Gusev @SashaGusevPosts]

Monthly median Received to Accepted time (days) at Nature Genetics

[Yusuf Roohani @yusufroohani]

scBaseCamp was built by directly mining all publicly accessible 10X Genomics scRNAseq data from the Sequence Read Archive (SRA)

With over 230M cells drawn from 21 species, 72 tissues, scBaseCamp is significantly larger and more diverse than existing single-cell data repositories

[Igor Dolgalev @bioigor]

@ItaiYanai But they didn't add checkboxes to all sorts of applications to confirm that internet/iPhone were not used in preparing this submission

[Igor Dolgalev @bioigor]

DeepCellTypes pre-print: https://t.co/8vD471yKbR
Code and vignettes: https://t.co/DxvsD2dXk2

[Igor Dolgalev @bioigor]

Thank you @xuefei_w (@davidvanvalen lab) for a great presentation of DeepCellTypes at our NYU Single-Cell Club. DeepCellTypes is a spatial proteomics phenotyping method with the ability to generalize across diverse datasets with varying marker panels.

[Nature Methods @naturemethods]

The wait is over!! We are thrilled to announce that we have chosen Spatial Proteomics as 2024’s Method of the Year! 🥳

For more on Spatial Proteomics and a road map to this special issue, please see this month’s Editorial or read on in this thread.

https://t.co/phXooJzJda

[Simon Duerr @simonduerr]

This is great! @NIAIDNews have launched a collection of public domain illustrations (currently 550 individual icons) https://t.co/qYzIsbr0TH

[Igor Dolgalev @bioigor]

TCAT pre-print: https://t.co/nnPQ9zIGDL
Code and vignettes: https://t.co/TsmmW7Sdvv

[Igor Dolgalev @bioigor]

Thank you @DKotliar (@soumya_boston lab) for a great presentation of CellAnnoTator (*CAT) and T-CellAnnoTator (TCAT) at our NYU Single-Cell Club. TCAT annotates scRNA-Seq T-cell subsets with predefined gene expression programs compiled from a range of reference datasets.

[Christoph Bock Lab @ CeMM & MedUni Vienna @BockLab]

🗨️ WANNA TALK TO YOUR CELLS? Try out CellWhisperer – our new multimodal AI that turns single-cell RNA-seq analysis into a conversation. No coding needed, just chat in plain English. Short walkthrough below. Web app & bioRxiv preprint linked in the thread. Let's dive in! (1/9)

[Luciano Martelotto 🛠🧬💻🇦🇺 @LGMartelotto]

Here we go…repurposing spatial imaging techs to achieve ultra-low to ultra-high, multiplexing, nuclei, cells, single (RNA or Protein), multimodal (RNA and Protein), super cheap! NO SEQUENCING!

@10xGenomics @nanostringtech @AkoyaBio @bruker

[Constantin Ahlmann-Eltze (@const-ae.bsky.social) @const_ae]

There's a lot of excitement about foundation models and their ability to learn biology 🧬💻

But current tools for perturbation prediction perform worse than simple linear models! We need more careful benchmarking to make progress.

https://t.co/lTJM7ghk2r

[Igor Dolgalev @bioigor]

@OmicsOmicsBlog Their shares are at a multi-year low. The management may want to signal that the company is currently undervalued.

[Stathis Megas @St_Megas]

Are you missing cells and cell types in your single-cell multiome experiments @10xGenomics? Check out EmptyDropsMultiome @MarioniLab

[Seeking Alpha Market Currents @MarketCurrents]

$ILMN - Illumina buys Fluent Biosciences to accelerate single-cell analysis https://t.co/MUcjskfvrp

[Ankur Sharma @asharmaiisc]

Systematic comparison of sequencing-based spatial transcriptomic methods in @naturemethods

In summary:
“- Stereo-seq, Slide-tag, Visium shows the better capture efficiency with raw sequencing depth
- Slide-seq V2, Visium (probe), DynaSpatial gives the better capture efficiency with normalized sequencing depth.”

https://t.co/bhpzVnoNpX

[Igor Dolgalev @bioigor]

CellChat v2 pre-print: https://t.co/NkeKUatB9R
Code and vignettes: https://t.co/wlGahIRkj6

[Igor Dolgalev @bioigor]

Thank you @suoqin_jin for a great presentation of CellChat at our NYU Single-Cell Club. CellChat v2 expands the underlying CellChatDB database, extends the inference of cell-cell communication to spatially-resolved datasets, and adds an interactive browser for output exploration.