KJWON_LAB

Computational Biology Lab at BRIC, University of Copenhagen

[Bo Wang @BoWang87]

🔬Can whole-slide Hematoxylin and eosin (H&E) stained histology images predict gene expression profiles in single-cell spatial omics? #spatial #SingleCell

Introduce our latest paper, BLEEP (Bi-modaL Embedding for Expression Prediction): a state-of-the-art tool predicting spatial gene expression profiles purely from histology images.

👉 Paper: https://t.co/YZjfKRBao5
👉 Code: https://t.co/rG31TXrx8U

Compared to alternatives, it offers superior correlation & captures the variance of original expression profiles more effectively.

Understanding molecular mechanisms behind tissue architecture is key to unraveling disease pathways & formulating effective treatments. Yet, gene expression profiling is often a costly, lengthy process.

BLEEP is a game-changing bi-modal embedding framework. It uses a contrastive learning approach to create a low-dimensional joint embedding space from paired image & expression profiles at micrometer resolution. This space serves as a reference for predicting expression in unknown image patches from whole-slide H&E stained histology images.

Benchmarked on a human liver tissue dataset from the 10x Visium platform, BLEEP outperforms ST-Net & His2Gene in terms of gene expression correlation & variance.

All the credits go to the amazing PHD student Ronald (@RonaldXie1 ), who is co-supervised by @garybader1 and myself. @pmcc_ai @VectorInst @UofT_TCAIREM @DonnellyCentre @UHN

[Tune H. Pers @tunepers]

Dinner & goodbye. The social side of science is what makes the difference. #singlecellCPH23 🌿

Vanessa Hall, Jeff Moffit, @adameykolab⁩ ⁦@KharchenkoLab⁩ ⁦@KhodosevichLab⁩ ⁦⁦@KrishnaswamyLab⁩ ⁦@ravnskjaer_lab⁩ ⁦@AUGCsoup⁩ ⁦@KjwonL⁩

[Josh Brickman @josh_brickman]

Nice safari into hundreds(instead of thousands) of cells to infer inductive interactions!
Great work by @JunilKim_caleb and @MichaelaRothova who interrogated these critters in @KjwonL
Shout out to collaborators: @IdoAmitLab @SiyeonRhee @rajangogna_ .

https://t.co/DIr420GhI1

[KJWON_LAB @KjwonL]

@RongFan8 @JunilKim_caleb @juhyunk_ @josh_brickman @IdoAmitLab @SiyeonRhee @rajangogna_ Thanks.

[KJWON_LAB @KjwonL]

Gene expression changes due to cell-contact with neighbors @pnas. Neighboring cell type prediction from #scRNAseq.
Works by @JunilKim_caleb and Michaela. Collaboration with @josh_brickman, Rajan, and @IdoAmitLab. Thanks to @lundbeckfonden.
https://t.co/7KFQlD6Q0x

[Jason H. Moore, PhD @moorejh]

CFP: The Symposium on Artificial Intelligence for Learning Health Systems (SAIL) is a new annual conference on AI for clinical medicine. SAIL will be held in Puerto Rico on May 9-12, 2023. https://t.co/CXxjqvg8FH #bioinformatics #artificialintelligence

[KJWON_LAB @KjwonL]

Gene regulatory network reconstruction from scRNAseq: Greatly reduced false positives using multivariate transfer entropy. Great work by Guangzheng and @JunilKim_caleb. Collaboration with @kedar_natarajan
https://t.co/bWVU2N2Vec

[KJWON_LAB @KjwonL]

@Tech_Networks highlighted our works for spatial biology.
https://t.co/zFkd2QKVGX

[ryan lister @ry_lister]

In our new study we chart human prefrontal cortex gene regulatory dynamics from gestation to adulthood at single-cell resolution (RNA + ATAC) @CellCellPress https://t.co/jqTWLOZEIu

[Denis Wirtz @deniswirtz]

We updated our database and now list 385 postdoc fellowship opportunities (w/ description, deadline, amount, eligibility, etc).

Getting one means a lot more freedom to do the work you want to do.

[Jason H. Moore, PhD @moorejh]

We have an open search for a collaborative biostatistician to join our faculty at @CedarsSinai! Please RT! https://t.co/AcrtJi0ZAT #biostatistics #statstwitter #epitwitter #datascience

[KJWON_LAB @KjwonL]

This time, tissue territory detection. Next version is coming.

[KJWON_LAB @KjwonL]

It is great to see an algorithmic development (TENET) leads to finding a new factor important for autophagy. Great work by @JunilKim_caleb in collaboration with Sunghee Baek and Dongha Kim.

[Junil Kim @JunilKim_caleb]

Systemic approaches using single cell transcriptome reveal that C/EBPγ regulates autophagy under amino acid starved condition https://t.co/3xZctBGrta

[KJWON_LAB @KjwonL]

scRNAseq analysis revealed the role for Shank3 neural stem cells and the association with autism. Collaboration with Jongphil Kim.
https://t.co/5YC7P9zQvJ

[Mori @Morteza_C_H]

We (@KjwonL & @WennerbergLab )designed a tool for identifying and grouping effective drugs based on their response in multiparameter high-throughput and high-content screenings
#cancer #AML #MDS #chemotherapy #immunotherapy
https://t.co/qHcH5eg6Za @eLife

[Gray Camp @GrayCampLab]

Space-time analytics in digital human organoids! Stellar work from talents @WahlePhilipp @brangiov @HarmelChristoph @zhisong_he + team! Collab with @lucaspelkmans @TreutleinLab. Thanks @OrganoidAtlas @cziscience @humancellatlas @ETH_BSSE @IOB_ch #organoids https://t.co/DxqNpmCLJ7

[KJWON_LAB @KjwonL]

A new type of analyzing spatial transcriptomics data.

[Hyobin Kim @HyobinKim4]

Excited to announce our latest work in the @KjwonL Lab! We study cell contact-dependent gene expression using the transcriptome of spatial beads composed of multiple cell types.

https://t.co/9tyWSxLA9Z

#SpatialTranscriptomics #SlideSeq #CellContact #CellCellInteractions

[Rong Fan @RongFan8]

What an exciting week for CUT&Tag!!! After we published spatial-CUT&Tag in Science last week, Prof. Xiaowei Zhang lab demonstrated combining CUT&Tag and MERFISH to image, for example, 127 target H3K4me3 loci or 139 H3K27ac loci in mouse brain. Very cool!

https://t.co/BWddFt1Kdb

[Wennerberg Lab @WennerbergLab]

We’re excited to have this approach by @Morteza31846588 & @EllaKarjalainen published. A great collaboration with @KjwonL @HelinLab and the Grønbæk lab @UCPH_BRIC

[KJWON_LAB @KjwonL]

Spatial biology meeting organized by Oxford Global. Vesalius by
@pcnmartin
and
@HyobinKim4
will be introduced.
https://t.co/C110m2q5PN