Interact-omics is a high-throughput cytometry-based framework for cellular interaction mapping. @simonhaas.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
August 7, 2025 at 7:53 PM
Interact-omics is a high-throughput cytometry-based framework for cellular interaction mapping. @simonhaas.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
MUUMI: an R package for statistical and network-based meta-analysis for MUlti-omics data Integration www.biorxiv.org/content/10....
March 18, 2025 at 1:45 PM
MUUMI: an R package for statistical and network-based meta-analysis for MUlti-omics data Integration www.biorxiv.org/content/10....
I'm delighted to share a useful FREE web-based app portal of powerful bioinformatics tools for microbial genomes and shotgun microbiome sequences!
It's called Micromics and is built by Middle Author Bioinformatics, led by co-founder @ironark.bsky.social
omix.midauthorbio.com
It's called Micromics and is built by Middle Author Bioinformatics, led by co-founder @ironark.bsky.social
omix.midauthorbio.com
Microbial Omics
A suite of bioinformatics tools for microbial genome and metagenome analysis.
omix.midauthorbio.com
April 8, 2025 at 12:11 PM
I'm delighted to share a useful FREE web-based app portal of powerful bioinformatics tools for microbial genomes and shotgun microbiome sequences!
It's called Micromics and is built by Middle Author Bioinformatics, led by co-founder @ironark.bsky.social
omix.midauthorbio.com
It's called Micromics and is built by Middle Author Bioinformatics, led by co-founder @ironark.bsky.social
omix.midauthorbio.com
Excited to share our new preprint: “Rank-based integration identifies convergent disease mechanisms across omics” 🧬🧫🧪
Have RNA, protein or other omics from different studies/platforms and want to identify signals they consistently support?
*ORBIT* 🪐 might be useful! www.biorxiv.org/content/10.6...
Have RNA, protein or other omics from different studies/platforms and want to identify signals they consistently support?
*ORBIT* 🪐 might be useful! www.biorxiv.org/content/10.6...
October 1, 2026 at 3:09 PM
Excited to share our new preprint: “Rank-based integration identifies convergent disease mechanisms across omics” 🧬🧫🧪
Have RNA, protein or other omics from different studies/platforms and want to identify signals they consistently support?
*ORBIT* 🪐 might be useful! www.biorxiv.org/content/10.6...
Have RNA, protein or other omics from different studies/platforms and want to identify signals they consistently support?
*ORBIT* 🪐 might be useful! www.biorxiv.org/content/10.6...
More evidence that mitochondrial dysfunction is a major aftermath associated with SARS-CoV-2 infection as the impaired Mitochondria lead to an accumulation of reactive oxygen species (ROS), triggering endothelial dysfunction, and leading to the passage of harmful
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Omics-based analysis of mitochondrial dysfunction and BBB integrity in post-COVID-19 sequelae - Scientific Reports
Scientific Reports - Omics-based analysis of mitochondrial dysfunction and BBB integrity in post-COVID-19 sequelae
www.nature.com
December 28, 2024 at 5:28 PM
More evidence that mitochondrial dysfunction is a major aftermath associated with SARS-CoV-2 infection as the impaired Mitochondria lead to an accumulation of reactive oxygen species (ROS), triggering endothelial dysfunction, and leading to the passage of harmful
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Interested in spatial statistics for spatial omics data? Check out our new resource: pasta.
We show how different technologies lead to different data modalities give and overview of point-pattern and lattice-based spatial analysis. Feedback welcome!
arxiv.org/abs/2412.01561
We show how different technologies lead to different data modalities give and overview of point-pattern and lattice-based spatial analysis. Feedback welcome!
arxiv.org/abs/2412.01561
pasta: Pattern Analysis for Spatial Omics Data
Spatial omics assays allow for the molecular characterisation of cells in their spatial context. Notably, the two main technological streams, imaging-based and high-throughput sequencing-based, can gi...
arxiv.org
December 4, 2024 at 12:14 PM
Interested in spatial statistics for spatial omics data? Check out our new resource: pasta.
We show how different technologies lead to different data modalities give and overview of point-pattern and lattice-based spatial analysis. Feedback welcome!
arxiv.org/abs/2412.01561
We show how different technologies lead to different data modalities give and overview of point-pattern and lattice-based spatial analysis. Feedback welcome!
arxiv.org/abs/2412.01561
☕Li, Jiang et al present DePass, a graph-based #DeepLearning framework for integrating paired #multiomics data in spatial and single-cell contexts. A dual-enhancement approach is used to remove noise from raw omics data.
👉https://rdcu.be/kxnPQVtLvtba
www.nature.com/articles/s41...
👉https://rdcu.be/kxnPQVtLvtba
www.nature.com/articles/s41...
The dual-enhanced graph learning framework DePass allows paired data integration in single-cell and spatial multiomics - Nature Cell Biology
Li, Jiang and colleagues present DePass, a graph-based deep learning framework for integrating paired multi-omics data in spatial and single-cell contexts. A dual-enhancement approach is used to remov...
www.nature.com
September 28, 2026 at 2:46 PM
☕Li, Jiang et al present DePass, a graph-based #DeepLearning framework for integrating paired #multiomics data in spatial and single-cell contexts. A dual-enhancement approach is used to remove noise from raw omics data.
👉https://rdcu.be/kxnPQVtLvtba
www.nature.com/articles/s41...
👉https://rdcu.be/kxnPQVtLvtba
www.nature.com/articles/s41...
Study on post-COVID brain fog (76 participants):
Mitochondrial dysfunction and blood-brain barrier breakdown drive inflammation, oxidative stress, and cognitive issues.
Findings suggest a potential link to increased Alzheimer’s risk.
www.nature.com/articles/s41...
Mitochondrial dysfunction and blood-brain barrier breakdown drive inflammation, oxidative stress, and cognitive issues.
Findings suggest a potential link to increased Alzheimer’s risk.
www.nature.com/articles/s41...
Omics-based analysis of mitochondrial dysfunction and BBB integrity in post-COVID-19 sequelae - Scientific Reports
Scientific Reports - Omics-based analysis of mitochondrial dysfunction and BBB integrity in post-COVID-19 sequelae
www.nature.com
December 28, 2024 at 3:56 PM
Study on post-COVID brain fog (76 participants):
Mitochondrial dysfunction and blood-brain barrier breakdown drive inflammation, oxidative stress, and cognitive issues.
Findings suggest a potential link to increased Alzheimer’s risk.
www.nature.com/articles/s41...
Mitochondrial dysfunction and blood-brain barrier breakdown drive inflammation, oxidative stress, and cognitive issues.
Findings suggest a potential link to increased Alzheimer’s risk.
www.nature.com/articles/s41...
Update: We greatly revised our paper and renamed it “Harnessing the Potential of Spatial Statistics for Spatial Omics Data with pasta”.
We discuss the broad range of exploratory spatial statistics options for spatial Omics technologies and show relevant use cases.
arxiv.org/abs/2412.01561
We discuss the broad range of exploratory spatial statistics options for spatial Omics technologies and show relevant use cases.
arxiv.org/abs/2412.01561
Harnessing the Potential of Spatial Statistics for Spatial Omics Data with pasta
Spatial omics assays allow for the molecular characterisation of cells in their spatial context. Notably, the two main technological streams, imaging-based and high-throughput sequencing-based, can gi...
arxiv.org
June 27, 2025 at 1:28 PM
Update: We greatly revised our paper and renamed it “Harnessing the Potential of Spatial Statistics for Spatial Omics Data with pasta”.
We discuss the broad range of exploratory spatial statistics options for spatial Omics technologies and show relevant use cases.
arxiv.org/abs/2412.01561
We discuss the broad range of exploratory spatial statistics options for spatial Omics technologies and show relevant use cases.
arxiv.org/abs/2412.01561
Integration of imaging-based and sequencing-based spatial omics mapping on the same tissue section via DBiTplus www.nature.com/articles/s4...
March 8, 2026 at 2:15 PM
Integration of imaging-based and sequencing-based spatial omics mapping on the same tissue section via DBiTplus www.nature.com/articles/s4...
The second preprint presents an experiment workflow and a broadly applicable computional framework to integrate sequencing-based and imaging-based spatial omics data for the SAME tissue slide to construct a single cell spatial omics atlas.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Integration of Imaging-based and Sequencing-based Spatial Omics Mapping on the Same Tissue Section via DBiTplus
Spatially mapping the transcriptome and proteome in the same tissue section can significantly advance our understanding of heterogeneous cellular processes and connect cell type to function. Here, we ...
www.biorxiv.org
November 12, 2024 at 6:05 PM
The second preprint presents an experiment workflow and a broadly applicable computional framework to integrate sequencing-based and imaging-based spatial omics data for the SAME tissue slide to construct a single cell spatial omics atlas.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Laser-based collection of bacteria from complex communities or tissue slices for in situ microbial single-cell omics
www.cell.com/cell-genomic...
www.cell.com/cell-genomic...
January 22, 2026 at 9:32 PM
Laser-based collection of bacteria from complex communities or tissue slices for in situ microbial single-cell omics
www.cell.com/cell-genomic...
www.cell.com/cell-genomic...
Did you ever wonder what insights hide in the multiplets that are usually discarded in flow cytometry? 🫧 Find out in the first publication of my PhD, now out in Nature Methods! www.nature.com/articles/s41... (1/4)
August 7, 2025 at 8:48 PM
Did you ever wonder what insights hide in the multiplets that are usually discarded in flow cytometry? 🫧 Find out in the first publication of my PhD, now out in Nature Methods! www.nature.com/articles/s41... (1/4)
Study: Omics-based computational approaches for biomarker identification, prediction, and treatment of Long COVID
Published: Dec 9, 2025
pubmed.ncbi.nlm.nih.gov/41368891/
Published: Dec 9, 2025
pubmed.ncbi.nlm.nih.gov/41368891/
Omics-based computational approaches for biomarker identification, prediction, and treatment of Long COVID - PubMed
Long COVID, or post-acute sequelae of COVID-19 (PASC), is a major global health problem, with cumulative estimates suggesting that around 400 million people worldwide have been affected. It is characterized by persistent or new symptoms such as fatigue, cognitive impairment, and breathlessness lasti …
pubmed.ncbi.nlm.nih.gov
December 16, 2025 at 2:07 AM
Study: Omics-based computational approaches for biomarker identification, prediction, and treatment of Long COVID
Published: Dec 9, 2025
pubmed.ncbi.nlm.nih.gov/41368891/
Published: Dec 9, 2025
pubmed.ncbi.nlm.nih.gov/41368891/
DECODE: deep learning-based common deconvolution framework for various omics data www.nature.com/articles/s41... 🧬💻🧪 github.com/forceworker/...
March 4, 2026 at 9:02 PM
DECODE: deep learning-based common deconvolution framework for various omics data www.nature.com/articles/s41... 🧬💻🧪 github.com/forceworker/...
Characterizing the omics landscape based on 10,000+ datasets www.nature.com/artic...
---
#proteomics #prot-paper
---
#proteomics #prot-paper
January 26, 2025 at 9:40 AM
Characterizing the omics landscape based on 10,000+ datasets www.nature.com/artic...
---
#proteomics #prot-paper
---
#proteomics #prot-paper
Measuring biological age using omics data go.nature.com/3n0hCfZ #Review by Jarod Rutledge, Hamilton Oh & Tony Wyss-Coray #epigeneticclocks #agingclocks
Free to read here: rdcu.be/cPR6u
Free to read here: rdcu.be/cPR6u
Measuring biological age using omics data - Nature Reviews Genetics
Molecular measures of biological ageing based on high-throughput omics technologies are enabling the quantitative characterization of ageing. The authors review how epigenomic, transcriptomic, proteom...
go.nature.com
December 2, 2024 at 2:53 PM
Measuring biological age using omics data go.nature.com/3n0hCfZ #Review by Jarod Rutledge, Hamilton Oh & Tony Wyss-Coray #epigeneticclocks #agingclocks
Free to read here: rdcu.be/cPR6u
Free to read here: rdcu.be/cPR6u
Prompt-based bioinformatics: a new interface for multi-omics analysis www.nature.com/articles/s41... read free: rdcu.be/eAnf4
Vibeoinformatics... computational vibeology... 🧬🖥️🧪
Vibeoinformatics... computational vibeology... 🧬🖥️🧪
Prompt-based bioinformatics: a new interface for multi-omics analysis - Nature Reviews Genetics
Prompt-based methods, which involve the careful design of inputs to guide large language model (LLM) outputs, are beginning to reshape bioinformatic analytical workflows. The authors compare prompt-dr...
www.nature.com
August 14, 2025 at 11:51 AM
Prompt-based bioinformatics: a new interface for multi-omics analysis www.nature.com/articles/s41... read free: rdcu.be/eAnf4
Vibeoinformatics... computational vibeology... 🧬🖥️🧪
Vibeoinformatics... computational vibeology... 🧬🖥️🧪
Illumina is finally venturing into spatial www.genengnews.com/topics/omics...
Illumina Unveils Spatial Technology Days Before AGBT Meeting
Illumina announces a new NGS-based spatial technology kit and new software platform, Illumina Connected Multiomics.
www.genengnews.com
February 19, 2025 at 3:08 PM
Illumina is finally venturing into spatial www.genengnews.com/topics/omics...
This week our class had an awesome discussion on this review article discussing #transformers for #SingleCell. One of my favorite parts was discussing Figure 3 on current strategies for how to transform the counts to a format that can be used by transformer. 1/n 🧪🧬💻
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Transformers in single-cell omics: a review and new perspectives - Nature Methods
This Perspective presents a comprehensive and in-depth overview of computational models based on the deep learning architecture of transformers for single-cell omics analysis.
www.nature.com
February 13, 2025 at 12:36 AM
This week our class had an awesome discussion on this review article discussing #transformers for #SingleCell. One of my favorite parts was discussing Figure 3 on current strategies for how to transform the counts to a format that can be used by transformer. 1/n 🧪🧬💻
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Predicting complex phenotypes using multi-omics data in maize (Maddy Creach , Brandon Webster , Linsey Newton , Jon Turkus , James C Schnable , Addie Thompson , Robert VanBuren) doi.org/10.1093/plce... #PlantScience @aspbofficial
Predicting complex phenotypes using multi-omics data in maize
Integrating field gene expression, drone-based measurements, and genetic markers improves prediction of diverse, complex traits in maize.
doi.org
August 6, 2026 at 2:43 PM
Predicting complex phenotypes using multi-omics data in maize (Maddy Creach , Brandon Webster , Linsey Newton , Jon Turkus , James C Schnable , Addie Thompson , Robert VanBuren) doi.org/10.1093/plce... #PlantScience @aspbofficial
Croc-omics! 🐊 here we're looking at the bioaccumulation of contaminants and how they affect long-lived animals using omics-based ecosurveillance tools.
December 3, 2024 at 12:00 PM
Croc-omics! 🐊 here we're looking at the bioaccumulation of contaminants and how they affect long-lived animals using omics-based ecosurveillance tools.