Stephanie Hicks
@stephaniehicks.bsky.social
Associate Professor of Biostatistics and Biomedical Engineering at Johns Hopkins. stephaniehicks.com
New paper out in @genomeresearch.bsky.social on using contrastive self-supervised learning for spatial domain detection with multi-omics data! Huge congratulations to Jianing Yao and coauthors Jinglun Yu, Brian Caffo Stephanie Page & @martinowk.bsky.social! 🧬 🖥️ 🧪
doi.org/10.1101/gr.2...
doi.org/10.1101/gr.2...
May 21, 2025 at 1:14 PM
New paper out in @genomeresearch.bsky.social on using contrastive self-supervised learning for spatial domain detection with multi-omics data! Huge congratulations to Jianing Yao and coauthors Jinglun Yu, Brian Caffo Stephanie Page & @martinowk.bsky.social! 🧬 🖥️ 🧪
doi.org/10.1101/gr.2...
doi.org/10.1101/gr.2...
Rafa has come out swinging this morning 😂
April 11, 2025 at 1:26 PM
Rafa has come out swinging this morning 😂
Always excited to have @rafalab.bsky.social visit Hopkins! He’s talk about statistical challenges in single single and spatial omics. 🧪🧬🖥️
April 11, 2025 at 1:13 PM
Always excited to have @rafalab.bsky.social visit Hopkins! He’s talk about statistical challenges in single single and spatial omics. 🧪🧬🖥️
So this weekend I won the veggie category at @jhubiostat.bsky.social annual Chili Cookoff! Huge congratulations to @statsprofo.bsky.social — winner of the meat category! We have the privilege of wearing these hats for the next year 😂 🌶️ #stats 🧪🧬💻
PS thank you @lizstuart.bsky.social for hosting! 🌸
PS thank you @lizstuart.bsky.social for hosting! 🌸
March 31, 2025 at 1:06 AM
So this weekend I won the veggie category at @jhubiostat.bsky.social annual Chili Cookoff! Huge congratulations to @statsprofo.bsky.social — winner of the meat category! We have the privilege of wearing these hats for the next year 😂 🌶️ #stats 🧪🧬💻
PS thank you @lizstuart.bsky.social for hosting! 🌸
PS thank you @lizstuart.bsky.social for hosting! 🌸
Very excited to be here too. Btw, I saw someone walking around with their @genomeresearch.bsky.social tshirt! 🙃 #AGBT25 #AGBTGM
February 23, 2025 at 10:23 PM
Very excited to be here too. Btw, I saw someone walking around with their @genomeresearch.bsky.social tshirt! 🙃 #AGBT25 #AGBTGM
It became clear in the discussion that investing energy in more biologically meaningful ways to embed the data (compared to existing approaches) is likely where comp biologists can have a huge impact with these models. 2/n
February 13, 2025 at 12:36 AM
It became clear in the discussion that investing energy in more biologically meaningful ways to embed the data (compared to existing approaches) is likely where comp biologists can have a huge impact with these models. 2/n
Spent the day at the Maryland Science Center & a German Christmas along the Baltimore waterfront today! 🎄🧬🖥️🧪
December 22, 2024 at 12:20 AM
Spent the day at the Maryland Science Center & a German Christmas along the Baltimore waterfront today! 🎄🧬🖥️🧪
Using simulated data, we show how spatialMNN can identify spatial domains across N=64 tissue sections with less than 5Gb memory (RAM) in under 10 mins! 🔥
December 5, 2024 at 4:31 PM
Using simulated data, we show how spatialMNN can identify spatial domains across N=64 tissue sections with less than 5Gb memory (RAM) in under 10 mins! 🔥
Using mouse Alzheimer's Disease tissue sections profiling genes and proteins on STARmap PLUS, we found spatialMNN is able to find disease-related niches (unsupervised clusters using gene expression) where the Abeta protein accumulates (dark blue dots)
December 5, 2024 at 4:31 PM
Using mouse Alzheimer's Disease tissue sections profiling genes and proteins on STARmap PLUS, we found spatialMNN is able to find disease-related niches (unsupervised clusters using gene expression) where the Abeta protein accumulates (dark blue dots)
It's designed for barcode- or imaged-based spatial technologies and we compare the performance (accuracy, memory, and speed) of spatialMNN to other existing spatial clustering algorithms and find it's fast, memory-efficient, and accurate! 💃
December 5, 2024 at 4:31 PM
It's designed for barcode- or imaged-based spatial technologies and we compare the performance (accuracy, memory, and speed) of spatialMNN to other existing spatial clustering algorithms and find it's fast, memory-efficient, and accurate! 💃
Excited to share a new algorithm that we have been working on over the last year.
💡 idea is to extend mutual nearest neighbors for
#spatial data. We call it spatial mutual nearest neighbors (spatialMNN) 😄
Thank you @haowen-zhou.bsky.social @pratibha-panwar.bsky.social who led this work! 👏 🧬🖥️🧪
💡 idea is to extend mutual nearest neighbors for
#spatial data. We call it spatial mutual nearest neighbors (spatialMNN) 😄
Thank you @haowen-zhou.bsky.social @pratibha-panwar.bsky.social who led this work! 👏 🧬🖥️🧪
December 5, 2024 at 4:31 PM
Excited to share a new algorithm that we have been working on over the last year.
💡 idea is to extend mutual nearest neighbors for
#spatial data. We call it spatial mutual nearest neighbors (spatialMNN) 😄
Thank you @haowen-zhou.bsky.social @pratibha-panwar.bsky.social who led this work! 👏 🧬🖥️🧪
💡 idea is to extend mutual nearest neighbors for
#spatial data. We call it spatial mutual nearest neighbors (spatialMNN) 😄
Thank you @haowen-zhou.bsky.social @pratibha-panwar.bsky.social who led this work! 👏 🧬🖥️🧪
Using simulated data, we show how spatialMNN can identify spatial domains across N=64 tissue sections with less than 5Gb memory (RAM) in under 10 mins! 🔥
December 5, 2024 at 4:25 PM
Using simulated data, we show how spatialMNN can identify spatial domains across N=64 tissue sections with less than 5Gb memory (RAM) in under 10 mins! 🔥
Using mouse Alzheimer's Disease tissue sections profiling genes and proteins on STARmap PLUS, we found spatialMNN is able to find disease-related niches (unsupervised clusters using gene expression) where the Abeta protein accumulates (dark blue dots)
December 5, 2024 at 4:25 PM
Using mouse Alzheimer's Disease tissue sections profiling genes and proteins on STARmap PLUS, we found spatialMNN is able to find disease-related niches (unsupervised clusters using gene expression) where the Abeta protein accumulates (dark blue dots)
It's designed for barcode- or imaged-based spatial technologies and we compare the performance (accuracy, memory, and speed) of spatialMNN to other existing spatial clustering algorithms and find it's fast, memory-efficient, and accurate! 💃
December 5, 2024 at 4:25 PM
It's designed for barcode- or imaged-based spatial technologies and we compare the performance (accuracy, memory, and speed) of spatialMNN to other existing spatial clustering algorithms and find it's fast, memory-efficient, and accurate! 💃
Excited to have Francis Collin’s visiting @johnshopkins.bsky.social today! Packed house.
December 4, 2024 at 7:10 PM
Excited to have Francis Collin’s visiting @johnshopkins.bsky.social today! Packed house.
November 29, 2024 at 2:03 AM
Wearing the new (and most importantly warm) @jhubiostat.bsky.social swag!
November 21, 2024 at 3:47 PM
Wearing the new (and most importantly warm) @jhubiostat.bsky.social swag!
Thank you #biodata24! I really enjoyed all the scientific talks and can’t wait for the next one #biodata26! 3yo approves 😃
November 18, 2024 at 11:10 PM
Thank you #biodata24! I really enjoyed all the scientific talks and can’t wait for the next one #biodata26! 3yo approves 😃
I am watching outside my @jhubiostat.bsky.social’s office a building being built literally from the ground up over the next few years.
Stay tuned die updates and the demise of my office view! 😅
Stay tuned die updates and the demise of my office view! 😅
November 18, 2024 at 5:28 PM
I am watching outside my @jhubiostat.bsky.social’s office a building being built literally from the ground up over the next few years.
Stay tuned die updates and the demise of my office view! 😅
Stay tuned die updates and the demise of my office view! 😅
Fantastic poster from @kinnaryshah.bsky.social tonight at #biodata24! She developed the spoon package to correct for the mean variance relationship in #spatial transcriptomics data
#ProudPI #stats 🖥️🧬🧪🧠📈
Preprint: www.biorxiv.org/content/10.1...
Software: www.bioconductor.org/packages/spoon
#ProudPI #stats 🖥️🧬🧪🧠📈
Preprint: www.biorxiv.org/content/10.1...
Software: www.bioconductor.org/packages/spoon
November 16, 2024 at 3:12 AM
Fantastic poster from @kinnaryshah.bsky.social tonight at #biodata24! She developed the spoon package to correct for the mean variance relationship in #spatial transcriptomics data
#ProudPI #stats 🖥️🧬🧪🧠📈
Preprint: www.biorxiv.org/content/10.1...
Software: www.bioconductor.org/packages/spoon
#ProudPI #stats 🖥️🧬🧪🧠📈
Preprint: www.biorxiv.org/content/10.1...
Software: www.bioconductor.org/packages/spoon
Congratulations to @findycang.bsky.social from @jhubiostat.bsky.social who did an amazing job presenting her work at #biodata24 tonight! Preprint coming soon. ☺️
#ProudPI #stats #spatial #omics #transferlearning 🧪🧬🖥️🧠📈
#ProudPI #stats #spatial #omics #transferlearning 🧪🧬🖥️🧠📈
November 15, 2024 at 4:07 AM
Congratulations to @findycang.bsky.social from @jhubiostat.bsky.social who did an amazing job presenting her work at #biodata24 tonight! Preprint coming soon. ☺️
#ProudPI #stats #spatial #omics #transferlearning 🧪🧬🖥️🧠📈
#ProudPI #stats #spatial #omics #transferlearning 🧪🧬🖥️🧠📈
Today we celebrated some highs and lows in the group, but overall it was a science win! 🧪 💻 🧬
Bonus: I appreciated hanging out with @boyiguo.bsky.social Michael Totty this afternoon. ☺️
#psychscisky #neuroskyence #StatsSky #rstats
Bonus: I appreciated hanging out with @boyiguo.bsky.social Michael Totty this afternoon. ☺️
#psychscisky #neuroskyence #StatsSky #rstats
May 24, 2024 at 1:43 AM
Today we celebrated some highs and lows in the group, but overall it was a science win! 🧪 💻 🧬
Bonus: I appreciated hanging out with @boyiguo.bsky.social Michael Totty this afternoon. ☺️
#psychscisky #neuroskyence #StatsSky #rstats
Bonus: I appreciated hanging out with @boyiguo.bsky.social Michael Totty this afternoon. ☺️
#psychscisky #neuroskyence #StatsSky #rstats
Very excited to be attending #STATGEN2024! 🧬 🧪 👩🔬 💻
Presentations from me + @kasperdhansen.bsky.social's groups @jhubiostat. We've got loads of methods for #spatial #transcriptomics along w/ prediction of #genotypes and #cellcycle and super cool #longread #RNAseq!
🔗 sph.pitt.edu/statgen-2024...
Presentations from me + @kasperdhansen.bsky.social's groups @jhubiostat. We've got loads of methods for #spatial #transcriptomics along w/ prediction of #genotypes and #cellcycle and super cool #longread #RNAseq!
🔗 sph.pitt.edu/statgen-2024...
May 1, 2024 at 1:58 PM
Very excited to be attending #STATGEN2024! 🧬 🧪 👩🔬 💻
Presentations from me + @kasperdhansen.bsky.social's groups @jhubiostat. We've got loads of methods for #spatial #transcriptomics along w/ prediction of #genotypes and #cellcycle and super cool #longread #RNAseq!
🔗 sph.pitt.edu/statgen-2024...
Presentations from me + @kasperdhansen.bsky.social's groups @jhubiostat. We've got loads of methods for #spatial #transcriptomics along w/ prediction of #genotypes and #cellcycle and super cool #longread #RNAseq!
🔗 sph.pitt.edu/statgen-2024...
Little bayou and crawfish holes along a walking trail in north Louisiana
March 25, 2024 at 1:01 AM
Little bayou and crawfish holes along a walking trail in north Louisiana