Want to visualize & create a website for your omics data (incld CITEseq, scATACseq, #SpatialTranscriptomics)?
Try ShinyCell2!😆
Compatible with data formats Seurat Signac ArchR Scanpy
vs cellxgene WebAtlas Vitessce
github.com/the-ouyang-l...
bioRxiv 2024
www.biorxiv.org/content/10.1...
Try ShinyCell2!😆
Compatible with data formats Seurat Signac ArchR Scanpy
vs cellxgene WebAtlas Vitessce
github.com/the-ouyang-l...
bioRxiv 2024
www.biorxiv.org/content/10.1...
May 5, 2025 at 6:50 PM
Want to visualize & create a website for your omics data (incld CITEseq, scATACseq, #SpatialTranscriptomics)?
Try ShinyCell2!😆
Compatible with data formats Seurat Signac ArchR Scanpy
vs cellxgene WebAtlas Vitessce
github.com/the-ouyang-l...
bioRxiv 2024
www.biorxiv.org/content/10.1...
Try ShinyCell2!😆
Compatible with data formats Seurat Signac ArchR Scanpy
vs cellxgene WebAtlas Vitessce
github.com/the-ouyang-l...
bioRxiv 2024
www.biorxiv.org/content/10.1...
These experiments inspired our simple method for ADT denoising, dsb, which has been widely adopted and is available for R and Python github.com/niaid/dsb
GitHub - niaid/dsb: Normalize CITEseq Data
Normalize CITEseq Data. Contribute to niaid/dsb development by creating an account on GitHub.
github.com
November 27, 2024 at 8:42 PM
These experiments inspired our simple method for ADT denoising, dsb, which has been widely adopted and is available for R and Python github.com/niaid/dsb
We also want to do citeseq and sample multiplexing. No we don't have budget for test runs. LOAD THE CHIP, SHINJI, STOP CRYING.
September 20, 2025 at 5:46 AM
We also want to do citeseq and sample multiplexing. No we don't have budget for test runs. LOAD THE CHIP, SHINJI, STOP CRYING.
Deep subclustering of #SmoothMuscleCell in👤🐭 #Atherosclerosis
Human: scRNAseq n=21 + CITEseq 274 antibodies n=6
Universal surface markers of👤SMC
CD49a/ITGA1 CD146/MCAM CD29/ITGB1 EGFR
CD90/Thy1⬆️ CD142/F3⬇️ in modulated SMC
#ATVB 2024 @ahajournals.bsky.social
www.ahajournals.org/doi/10.1161/...
Human: scRNAseq n=21 + CITEseq 274 antibodies n=6
Universal surface markers of👤SMC
CD49a/ITGA1 CD146/MCAM CD29/ITGB1 EGFR
CD90/Thy1⬆️ CD142/F3⬇️ in modulated SMC
#ATVB 2024 @ahajournals.bsky.social
www.ahajournals.org/doi/10.1161/...
September 9, 2025 at 11:18 AM
Deep subclustering of #SmoothMuscleCell in👤🐭 #Atherosclerosis
Human: scRNAseq n=21 + CITEseq 274 antibodies n=6
Universal surface markers of👤SMC
CD49a/ITGA1 CD146/MCAM CD29/ITGB1 EGFR
CD90/Thy1⬆️ CD142/F3⬇️ in modulated SMC
#ATVB 2024 @ahajournals.bsky.social
www.ahajournals.org/doi/10.1161/...
Human: scRNAseq n=21 + CITEseq 274 antibodies n=6
Universal surface markers of👤SMC
CD49a/ITGA1 CD146/MCAM CD29/ITGB1 EGFR
CD90/Thy1⬆️ CD142/F3⬇️ in modulated SMC
#ATVB 2024 @ahajournals.bsky.social
www.ahajournals.org/doi/10.1161/...
Scientists have discovered two previously unknown subtypes of human basophils 🎉 The first comprehensive single-cell map 🧬 of these cells is now an open resource 🖥️ for understanding diseases like allergies 🤧
#Immunology #allergy #singlecellbiology #CITEseq
🔗 ino.to/qtQM0SI
#Immunology #allergy #singlecellbiology #CITEseq
🔗 ino.to/qtQM0SI
January 8, 2026 at 5:11 PM
Scientists have discovered two previously unknown subtypes of human basophils 🎉 The first comprehensive single-cell map 🧬 of these cells is now an open resource 🖥️ for understanding diseases like allergies 🤧
#Immunology #allergy #singlecellbiology #CITEseq
🔗 ino.to/qtQM0SI
#Immunology #allergy #singlecellbiology #CITEseq
🔗 ino.to/qtQM0SI
🧬 New paper out!
🔗 www.nature.com/articles/s41...
Frustrated by noisy CITE-seq data?
ADTNorm helps normalize it and introduces a staining index to assess antibody quality.
Great work by former postdoc Ye Zheng. Supported by @hipcproject.bsky.social
#CITEseq #SingleCell #ADTNorm
🔗 www.nature.com/articles/s41...
Frustrated by noisy CITE-seq data?
ADTNorm helps normalize it and introduces a staining index to assess antibody quality.
Great work by former postdoc Ye Zheng. Supported by @hipcproject.bsky.social
#CITEseq #SingleCell #ADTNorm
ADTnorm: robust integration of single-cell protein measurement across CITE-seq datasets - Nature Communications
Here the authors present a computational method that expands the potential of multimodal single-cell analyses by delivering an accurate, fast, and user-friendly approach for normalizing and comparing ...
www.nature.com
July 1, 2025 at 1:49 PM
🧬 New paper out!
🔗 www.nature.com/articles/s41...
Frustrated by noisy CITE-seq data?
ADTNorm helps normalize it and introduces a staining index to assess antibody quality.
Great work by former postdoc Ye Zheng. Supported by @hipcproject.bsky.social
#CITEseq #SingleCell #ADTNorm
🔗 www.nature.com/articles/s41...
Frustrated by noisy CITE-seq data?
ADTNorm helps normalize it and introduces a staining index to assess antibody quality.
Great work by former postdoc Ye Zheng. Supported by @hipcproject.bsky.social
#CITEseq #SingleCell #ADTNorm
All the data and code are available now and we have an amazing visualization tool to explore our CITEseq data! We also relate a low-dimensional gating strategy for sorting and clinical immune monitoring. apps.allenimmunology.org/aifi/resourc...
April 20, 2026 at 5:58 PM
All the data and code are available now and we have an amazing visualization tool to explore our CITEseq data! We also relate a low-dimensional gating strategy for sorting and clinical immune monitoring. apps.allenimmunology.org/aifi/resourc...
Citeseq data acquired with the ImmGenT consortium (@immgen.bsky.social) and spatial transcriptomics acquired with the @alleninstitute.org, which allowed for the visualization of transcriptional programs expressed by CD4+ Trm across distance from the TLS to the airways. Even cooler...
October 10, 2025 at 7:22 PM
Citeseq data acquired with the ImmGenT consortium (@immgen.bsky.social) and spatial transcriptomics acquired with the @alleninstitute.org, which allowed for the visualization of transcriptional programs expressed by CD4+ Trm across distance from the TLS to the airways. Even cooler...
What really happens at the onset of type 1 diabetes? The HPAP team profiled the immune system of the lymph nodes near the pancreas, the reservoir of the relevant immune cells. Read more here: www.nature.com/articles/s41...
🧪
🧪
Immune perturbations in human pancreas lymphatic tissues prior to and after type 1 diabetes onset - Nature Communications
The status of immune cells within human pancreatic lymphatic tissues during the onset and progression of type 1 diabetes (T1D) is underexplored. Here, by flow cytometry and CITEseq, the authors profil...
www.nature.com
May 23, 2025 at 1:36 PM
What really happens at the onset of type 1 diabetes? The HPAP team profiled the immune system of the lymph nodes near the pancreas, the reservoir of the relevant immune cells. Read more here: www.nature.com/articles/s41...
🧪
🧪
Our collaborators @rgottardo.bsky.social Peter Sims and Ken Stuart (and others) develop tool ADTNorm, a method of helping noisy CITE-seq data to be "normalized"
#antibody
#ImmuneSky
nature.com/articles/s41...
#CITEseq #SingleCell #ADTNorm
#antibody
#ImmuneSky
nature.com/articles/s41...
#CITEseq #SingleCell #ADTNorm
ADTnorm: robust integration of single-cell protein measurement across CITE-seq datasets - Nature Communications
Here the authors present a computational method that expands the potential of multimodal single-cell analyses by delivering an accurate, fast, and user-friendly approach for normalizing and comparing ...
nature.com
July 2, 2025 at 5:29 PM
Our collaborators @rgottardo.bsky.social Peter Sims and Ken Stuart (and others) develop tool ADTNorm, a method of helping noisy CITE-seq data to be "normalized"
#antibody
#ImmuneSky
nature.com/articles/s41...
#CITEseq #SingleCell #ADTNorm
#antibody
#ImmuneSky
nature.com/articles/s41...
#CITEseq #SingleCell #ADTNorm
Jun 2024
First data release of ImmGenT!(cbdm.connect.hms.harvard.edu/ImmgenT/Publ...). Over 30 labs to profile every mouse T cell / location / state.
In collaboration with BioLegend. The dedicated browser is developed by Dania, Niket, and Brinda. #CITEseq #TCR-V #immgen #singleCell
First data release of ImmGenT!(cbdm.connect.hms.harvard.edu/ImmgenT/Publ...). Over 30 labs to profile every mouse T cell / location / state.
In collaboration with BioLegend. The dedicated browser is developed by Dania, Niket, and Brinda. #CITEseq #TCR-V #immgen #singleCell
February 18, 2025 at 6:40 PM
Jun 2024
First data release of ImmGenT!(cbdm.connect.hms.harvard.edu/ImmgenT/Publ...). Over 30 labs to profile every mouse T cell / location / state.
In collaboration with BioLegend. The dedicated browser is developed by Dania, Niket, and Brinda. #CITEseq #TCR-V #immgen #singleCell
First data release of ImmGenT!(cbdm.connect.hms.harvard.edu/ImmgenT/Publ...). Over 30 labs to profile every mouse T cell / location / state.
In collaboration with BioLegend. The dedicated browser is developed by Dania, Niket, and Brinda. #CITEseq #TCR-V #immgen #singleCell
Excited to share my Co-First author paper describing ICI landscape of human atherosclerosis plaque &CCR7+ FSCN1+ DCs as crucial Immune-checkpoint-hub. @chiaragiannare1 @kathrynmoorelab@NYULH_DepofMed #Immunology#CyTOF #CITEseq #spatialproteomics #scRNAseq #atherosclerosis #ICIs #cancer rdcu.be/d1S6b
Immune checkpoint landscape of human atherosclerosis and influence of cardiometabolic factors
Nature Cardiovascular Research - Barcia Durán, Dayasagar, et al. map the expression of immune checkpoints in human atherosclerosis and examine the influence of lipid-lowering treatments and...
rdcu.be
February 4, 2025 at 4:15 PM
Excited to share my Co-First author paper describing ICI landscape of human atherosclerosis plaque &CCR7+ FSCN1+ DCs as crucial Immune-checkpoint-hub. @chiaragiannare1 @kathrynmoorelab@NYULH_DepofMed #Immunology#CyTOF #CITEseq #spatialproteomics #scRNAseq #atherosclerosis #ICIs #cancer rdcu.be/d1S6b
I didn't see them really assigning a subset from adults as naive with high certainty in the first place (using CITEseq or ribosomal genes among others). Without that context, it's very hard to distinguish ET from mature naive from mature early TSCM/TCM in scRNAseq.
November 9, 2025 at 3:21 PM
I didn't see them really assigning a subset from adults as naive with high certainty in the first place (using CITEseq or ribosomal genes among others). Without that context, it's very hard to distinguish ET from mature naive from mature early TSCM/TCM in scRNAseq.
Multiomic Atlas of Human Tonsil
scRNAseq
scATACseq
CITEseq
#SpatialTranscriptomics #Visium
Marginal Reticular Cells, not fibroblastic reticular cells, are high in PDGFRβ, #FibrillarCollagen, Proteoglycan core proteins & DIO2
#Immunity 2024
www.cell.com/immunity/ful...
scRNAseq
scATACseq
CITEseq
#SpatialTranscriptomics #Visium
Marginal Reticular Cells, not fibroblastic reticular cells, are high in PDGFRβ, #FibrillarCollagen, Proteoglycan core proteins & DIO2
#Immunity 2024
www.cell.com/immunity/ful...
February 1, 2024 at 12:53 PM
Multiomic Atlas of Human Tonsil
scRNAseq
scATACseq
CITEseq
#SpatialTranscriptomics #Visium
Marginal Reticular Cells, not fibroblastic reticular cells, are high in PDGFRβ, #FibrillarCollagen, Proteoglycan core proteins & DIO2
#Immunity 2024
www.cell.com/immunity/ful...
scRNAseq
scATACseq
CITEseq
#SpatialTranscriptomics #Visium
Marginal Reticular Cells, not fibroblastic reticular cells, are high in PDGFRβ, #FibrillarCollagen, Proteoglycan core proteins & DIO2
#Immunity 2024
www.cell.com/immunity/ful...
Golden et al. profile human lymphoid immune perturbations across #type1diabetes autoimmune development within pancreatic lymph nodes, mesenteric lymph nodes, and spleens from control non-diabetic autoantibody-negative, non-diabetic AAb+, and #T1D donors.🧪
#PancSky
www.nature.com/articles/s41...
#PancSky
www.nature.com/articles/s41...
Immune perturbations in human pancreas lymphatic tissues prior to and after type 1 diabetes onset - Nature Communications
The status of immune cells within human pancreatic lymphatic tissues during the onset and progression of type 1 diabetes (T1D) is underexplored. Here, by flow cytometry and CITEseq, the authors profil...
www.nature.com
June 2, 2025 at 8:10 AM
Golden et al. profile human lymphoid immune perturbations across #type1diabetes autoimmune development within pancreatic lymph nodes, mesenteric lymph nodes, and spleens from control non-diabetic autoantibody-negative, non-diabetic AAb+, and #T1D donors.🧪
#PancSky
www.nature.com/articles/s41...
#PancSky
www.nature.com/articles/s41...
Tissue-specific loss of #Tregs and rise of stem-like CD8+ T cells prior to the onset of #TypeIDiabetes may offer promising window for early intervention doi.org/10.1038/s414... @BettsLab #Diabetes #T1D #ImmunePhenotype #Autoimmunity #TranslationalScience
Immune perturbations in human pancreas lymphatic tissues prior to and after type 1 diabetes onset - Nature Communications
The status of immune cells within human pancreatic lymphatic tissues during the onset and progression of type 1 diabetes (T1D) is underexplored. Here, by flow cytometry and CITEseq, the authors profil...
doi.org
May 22, 2025 at 2:12 PM
Tissue-specific loss of #Tregs and rise of stem-like CD8+ T cells prior to the onset of #TypeIDiabetes may offer promising window for early intervention doi.org/10.1038/s414... @BettsLab #Diabetes #T1D #ImmunePhenotype #Autoimmunity #TranslationalScience
🌟The first report of GOLM1 protein-level profiling at single-cell resolution.🌟
Learn more about the Human Discovery Panel here: www.ptglab.com/products/Mul...
#Multiomics #SingleCell #BiomarkerDiscovery #CITEseq #HumanDiscoveryPanel
Learn more about the Human Discovery Panel here: www.ptglab.com/products/Mul...
#Multiomics #SingleCell #BiomarkerDiscovery #CITEseq #HumanDiscoveryPanel
June 6, 2025 at 10:37 AM
🌟The first report of GOLM1 protein-level profiling at single-cell resolution.🌟
Learn more about the Human Discovery Panel here: www.ptglab.com/products/Mul...
#Multiomics #SingleCell #BiomarkerDiscovery #CITEseq #HumanDiscoveryPanel
Learn more about the Human Discovery Panel here: www.ptglab.com/products/Mul...
#Multiomics #SingleCell #BiomarkerDiscovery #CITEseq #HumanDiscoveryPanel
(3/7) First, we followed up on our paradigm-shifting findings in @cellcellpress.bsky.social
(tinyurl.com/52u5fsfk) by diving deep into the age-unique platelet specification pathway (#megakaryopoiesis) using #CITEseq and a number of other approaches...
(tinyurl.com/52u5fsfk) by diving deep into the age-unique platelet specification pathway (#megakaryopoiesis) using #CITEseq and a number of other approaches...
December 4, 2024 at 8:19 PM
(3/7) First, we followed up on our paradigm-shifting findings in @cellcellpress.bsky.social
(tinyurl.com/52u5fsfk) by diving deep into the age-unique platelet specification pathway (#megakaryopoiesis) using #CITEseq and a number of other approaches...
(tinyurl.com/52u5fsfk) by diving deep into the age-unique platelet specification pathway (#megakaryopoiesis) using #CITEseq and a number of other approaches...
We used mass and flow cytometry, scRNAseq with TCRseq/CITEseq coupled with machine learning to dig through the mountain of data and found that our new predictor was consistent in discovery and validation cohorts and across different modalities.
November 21, 2024 at 3:32 PM
We used mass and flow cytometry, scRNAseq with TCRseq/CITEseq coupled with machine learning to dig through the mountain of data and found that our new predictor was consistent in discovery and validation cohorts and across different modalities.
Amazing new method that checks all the boxes from @mssanjavickovic and co! Automated processing of 96 samples in 2 days! ST + IF! ST + CITESEQ! I see here what the next couple years of my work looks like. https://www.biorxiv.org/content/10.1101/2020.10.14.338418v1
SM-Omics: An automated platform for high-throughput spati...
The spatial organization of cells and molecules plays a k...
www.biorxiv.org
November 14, 2024 at 7:03 AM
Amazing new method that checks all the boxes from @mssanjavickovic and co! Automated processing of 96 samples in 2 days! ST + IF! ST + CITESEQ! I see here what the next couple years of my work looks like. https://www.biorxiv.org/content/10.1101/2020.10.14.338418v1
CITEseq used to barcode cells, a.k.a. cell hashing, enables 'superloading' via efficient doublet removal. That means same doublet rate for 20k cells than 4k cells without cell hashing.
December 3, 2024 at 7:52 PM
CITEseq used to barcode cells, a.k.a. cell hashing, enables 'superloading' via efficient doublet removal. That means same doublet rate for 20k cells than 4k cells without cell hashing.
.@m_stoeckius from @nygenome kicking off the new tech session at #agta18 describing CITEseq: using antibodies with DNA barcodes to profile membrane bound proteins with single cell sequencing protocols
December 3, 2024 at 7:36 PM
.@m_stoeckius from @nygenome kicking off the new tech session at #agta18 describing CITEseq: using antibodies with DNA barcodes to profile membrane bound proteins with single cell sequencing protocols
Check out CITEseq cell hashing by @m_stoeckius if you want to get heaps more cells out of your @10xgenomics scRNAseq runs, or differentiate small cells from background noise #agta18
https://www.biorxiv.org/content/early/2017/12/21/237693
https://www.biorxiv.org/content/early/2017/12/21/237693
Cell “hashing” with barcoded antibodies enables multiplex...
Despite rapid developments in single cell sequencing tech...
www.biorxiv.org
December 3, 2024 at 7:36 PM
Check out CITEseq cell hashing by @m_stoeckius if you want to get heaps more cells out of your @10xgenomics scRNAseq runs, or differentiate small cells from background noise #agta18
https://www.biorxiv.org/content/early/2017/12/21/237693
https://www.biorxiv.org/content/early/2017/12/21/237693
People use these CITEseq antibodies without titrating them!!!
October 25, 2025 at 4:49 PM
People use these CITEseq antibodies without titrating them!!!
hopefully you will get to avoid the special data processing hell that is CITEseq (even though it’s really cool)
January 21, 2025 at 11:38 PM
hopefully you will get to avoid the special data processing hell that is CITEseq (even though it’s really cool)