From Single Cell to A Story: How Single-Cell Sequencing & AI Are Revolutionizing Biology

From Single Cell to A Story: How Single-Cell Sequencing & AI Are Revolutionizing Biology

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Single-cell RNA sequencing (scRNA-seq) is a technique that facilitates the characterization of transcriptomes on a per-cell basis within a heterogeneous cell population. This approach contrasts with conventional bulk RNA sequencing, which offers an averaged gene expression profile across all cells. By enabling high-resolution interrogation of cellular heterogeneity, scRNA-seq workflows incorporate dimensionality reduction techniques to transform complex gene expression data into lower-dimensional representations. This facilitates downstream unsupervised clustering analyses, where algorithms like K-means clustering in tandem with community detection methods such as Louvain or Leiden, enable the identification of distinct cell populations or clusters. Characterization of the gene expression signatures associated with these cellular clusters grants insights into cellular function, disease mechanisms, and developmental trajectories.

Single-cell analysis is revolutionizing biological research by offering insights into cellular functions, heterogeneity, and interactions. Recent advancements in the single cell field have integrated multi-omics data, enhanced spatial resolution, and leveraged artificial intelligence (AI).

In this blog, we delve into a series of insightful articles from Bridge Informatics that showcase the transformative impact of single-cell sequencing technologies and analysis. These articles illustrate how advancements, such as the use of AI and large language models (LLMs) in single-cell annotation, are revolutionizing our understanding of cellular heterogeneity. We will highlight the applications of single cell technologies in various fields, such cancer and immunology research, where they aid in identifying unique tumor cell populations and in deciphering complex immune responses, respectively. This comprehensive overview will demonstrate the significant strides made in these areas and the future potential of single-cell analysis.

Advancements in Single Cell Sequencing Technologies

One of the most significant advancements in single-cell analysis is the integration of multi-omic data. Traditional single arm approaches, such as transcriptomics or proteomics, provide valuable insights but often miss the bigger picture. scPerturb, which is a harmonized single cell perturbation data collected from 44 publicly available studies, is an extensive resource that addresses this limitation by offering a comprehensive platform for analyzing and integrating single-cell perturbation data across multiple omics layers, including transcriptomics, proteomics, and epigenomics​ (Bridge Informatics)​. This integrated approach provides a holistic view of cellular responses, enabling researchers to uncover key regulatory mechanisms and identify potential therapeutic targets more efficiently.

Single cell multi-omic data analysis goes beyond combining data. It reveals how cellular processes work together. This holistic perspective is crucial for understanding complex biological systems and diseases, which paves the way for more targeted and effective treatments. Spatial multi-omics is another transformative approach in single-cell analysis, which combines spatial information with molecular data to provide a detailed map of cellular functions within tissues. The Slide-Tags methodology exemplifies this advancement by utilizing spatial barcode oligonucleotides to label cellular nuclei in tissue sections​ (Bridge Informatics)​. This technique allows for high-resolution spatial analysis, enabling researchers to study gene expression, receptor-ligand interactions, and chromatin accessibility with unprecedented detail. High-resolution spatial multi-omics is particularly valuable for studying complex tissues and organs, where cellular context and interactions play crucial roles. By providing spatially resolved data at the single-cell level, Slide-Tags enhances our understanding of tissue architecture and cellular heterogeneity, offering novel insights into disease mechanisms and potential therapeutic strategies.

In addition to slide-tags, we also discussed Light-Seq , which is a technique utilizing multiplexed spatial indexing of intact biological samples via light-directed DNA barcoding in fixed cells and tissues followed by sequencing. Light-seq  has been used to accelerate the discovery of rare retinal biomarkers by providing rapid and efficient sequencing capabilities​ (Bridge Informatics)​. The ability to quickly identify rare biomarkers with Light-Seq can significantly speed up the research and development process, leading to faster diagnosis and treatment of diseases. This acceleration is particularly valuable in fields like ophthalmology, where early detection of biomarkers can prevent vision loss and improve patient outcomes.

Optimization of reference transcriptomes to enable accurate detection of novel cell types

A key item in single cell sequencing analysis that is often overlooked is the utilization of optimized reference transcriptomes. In scRNA-seq data, certain genes are often excluded from analysis primarily by three main factors: poorly annotated 3′ gene ends, issues with incorporating reads from introns, and gene overlap causing read loss. We discussed in our blog on the Pool et al. (2023) publication, that the issue of missed gene expression can be resolved by optimizing the reference transcriptome for scRNA-seq through recovering reads from between genes (intergenic reads), using a new method that maps both pre-mRNA and mature mRNA (hybrid pre-mRNA mapping strategy), and resolving areas where genes overlap. Optimized reference transcriptomes shed light on previously undetected cell types and gene expression patterns, thereby, providing a more detailed and accurate understanding of cellular diversity​ (Bridge Informatics)​. These improvements enable researchers to uncover new insights into cellular functions and interactions, enhancing our ability to study complex biological systems.

When applied to real data from mouse and human tissues, this optimized reference transcriptome approach significantly improves the identification of different cell types and the genes associated with them. This suggests that researchers should optimize their reference transcriptomes for scRNA-seq analysis, and that re-analyzing previously published data sets with this approach may reveal new information.

Statistical Testing During Single-Cell Clustering

There are several challenges associated with scRNA-seq clustering. First, scRNA-seq data is inherently noisy due to the low amount of RNA captured from each cell. This noise can lead to inaccurate clustering, where cells from distinct populations are grouped together or conversely, cells from the same population are scattered across different clusters. Second, the choice of clustering algorithm and its parameters can significantly impact the clustering outcome. Different algorithms make different assumptions about the underlying structure of the data, and there is no single “best” algorithm for all scRNA-seq datasets.

Accurate clustering of scRNA-seq data is essential for several reasons. First, it allows researchers to identify and characterize novel cell types that may be present in a sample. These novel cell types may play important roles in development, regeneration, or disease progression. Second, accurate clustering can help to elucidate the functional roles of different cell types. By examining the genes that are differentially expressed between clusters, researchers can gain insights into the cellular processes that are unique to each population. Third, accurate clustering can be used to track the differentiation trajectory of cells from one state to another. This information is valuable for understanding development and lineage relationships between cell types

In our blog on sc-SHC (single-cell statistical hypothesis clustering), we highlighted how sc-SHC offers a robust framework for statistical testing during single-cell clustering, ensuring that clustering results are statistically significant and biologically relevant​ (Bridge Informatics)​. By providing a statistical foundation for clustering, sc-SHC ensures that researchers can confidently identify and study distinct cellular populations. This accuracy is crucial for understanding cellular heterogeneity and its implications in health and disease, enabling more precise and informative single-cell studies. This accuracy is crucial for understanding cellular heterogeneity and its implications in health and disease, enabling more precise and informative single-cell studies.

Use of AI in Single Cell Analysis and Annotation

The integration of AI into single-cell analysis has opened new avenues for data analysis and interpretation. scGPT, the first AI LLM for scRNA-seq, represents a pioneering effort in this direction​ (Bridge Informatics)​. By leveraging advanced AI algorithms, scGPT improves the accuracy and efficiency of cell-type identification and gene expression analysis. This model handles complex datasets and generates meaningful insights, making scRNA-seq analysis more precise and scalable.

Building on the success of scGPT, GPT-4 further automates and refines cell type annotation in scRNA-seq experiments​(Bridge Informatics)​. By enhancing the precision and speed of cell-type classification, GPT-4 makes the annotation process more scalable. These AI-driven advancements facilitate more accurate and comprehensive single-cell studies, demonstrating the transformative potential of AI in biological research.

In addition to scGPT, a new generative AI model has been introduced to improve sample and cell level representations in scRNA-seq data analysis​. This model enhances the accuracy and depth of scRNA-seq data interpretation, thereby providing researchers with more detailed insights into cellular functions and interactions. The application of generative AI to scRNA-seq analysis allows for a more nuanced and detailed understanding of cellular processes, making it easier to identify subtle differences and interactions. This capability is crucial for studying complex biological systems and developing targeted therapies, highlighting the importance of AI-driven advancements in single-cell research.


The field of single-cell analysis is experiencing a period of rapid innovation, driven by advancements in multi-omic data integration, spatial resolution, and artificial intelligence. Tools like scPerturb, Slide-Tags, and scGPT are transforming the way researchers analyze and interpret single-cell data, providing unprecedented insights into cellular functions and interactions. These innovations are not only enhancing our understanding of basic biology but also paving the way for new therapeutic strategies and medical breakthroughs. As single-cell technologies continue to evolve, they hold the promise of unlocking new frontiers in biological research and medicine.

For a deeper dive into these advancements, check out the articles from Bridge Informatics:

Outsourcing Bioinformatics Analysis: How Bridge Informatics (BI) Can Help

At Bridge Informatics, we are passionate about empowering life science companies with the latest and most advanced technologies, including large language models (LLM) inspired tools, such as GPTs, to ensure they stay at the forefront of their fields. BI’s data scientists prioritize studying, understanding, and reporting on the latest developments so we can advise our clients confidently. Our bioinformaticians are trained bench biologists, so they understand the biological questions driving your computational analysis.

From pipeline development and software engineering to deploying your existing bioinformatic tools, BI can help you on every step of your research journey. As experts across data types from leading sequencing platforms, we can help you tackle the challenging computational tasks of storing, analyzing and interpreting genomic and transcriptomic data. Click here to schedule a free introductory call with a member of our team.

Haider M. Hassan, Data Scientist, Bridge Informatics

Haider is one of our premier data scientists. He provides bioinformatic services to clients, including high throughput sequencing, data pre-processing, analysis, and custom pipeline development. Drawing on his rich experience with a variety of high-throughput sequencing technologies, Haider analyzes transcriptional (spatial and single-cell), epigenetic, and genetic landscapes.

Before joining Bridge Informatics, Haider was a Postdoctoral Associate at the London Regional Cancer Centre in Ontario, Canada. During his postdoc, he investigated the epigenetics of late-onset liver cancer using murine and human models. Haider holds a Ph.D. in biochemistry from Western University, where he studied the molecular mechanisms behind oncogenesis. Haider still lives in Ontario and enjoys spending his spare time visiting local parks. If you’re interested in reaching out, please email [email protected] or [email protected]

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