Insights That Power the Future of Science — Sharing Knowledge, Driving Discovery

A Story Told by Data

Once upon a time, a brave team was given a very dangerous mission: to bring down two giant castles that had stood for a long, long time. The team was made up of many small squads — T cells, B cells, Myeloid cells, and more — each with a special role. They

Gemcitabine efficacy across tumor types: A pan-cancer study of 50 cancer cell lines

Gemcitabine (2′,2′-difluorodeoxycytidine) is a nucleoside analog widely used in the treatment of various solid tumors, including pancreatic, non-small cell lung, breast, and bladder cancers. Although its primary mechanism involves inhibition of DNA synthesis leading to S-phase arrest and apoptosis, variability in drug response across different cancer types remains

A Synergistic Future: Integrating AI and Human Expertise for Robust Cell Annotation

The world of single-cell genomics is buzzing with excitement, and for good reason. A new wave of powerful AI tools, including foundation models like Geneformer and scGPT, promises to automate one of the most laborious steps in scRNA-seq analysis: cell type annotation. What once took experts weeks of painstaking manual

When to use Application vs Scripts in scRNA-seq analysis

Single-cell RNA sequencing (scRNA-seq) has become a cornerstone of modern biology, offering unprecedented resolution into cellular diversity, states, and functions. With this power comes complexity: analyzing scRNA-seq data involves multiple steps, from quality control and normalization to clustering, visualization, and differential expression analysis. Each step can be approached through two

Unveiling clonotype diversity and repertoire overlap in diseased PBMCs through OmnibusX analysis

Introduction Understanding the dynamics of T-cell receptor (TCR) and B-cell receptor (BCR) clonotypes is essential for advancing our knowledge of immune system functionality and its role in health and disease. Single-cell RNA sequencing (scRNAseq) combined with TCR/BCR sequencing provides a robust framework for analyzing clonotype diversity and repertoire structure

Cell Type Prediction: A Review of Current Approaches and Emerging Challenges

Introduction Recent advances in single-cell RNA sequencing (scRNAseq) technologies have revolutionized the study of cellular heterogeneity, characteristics, and activity in various environments. Yet accurate, reproducible, harmonized, consistent, and automated cell type annotation remains a significant challenge. In this blog post, we will explore some of the major approaches of automated

Uncovering Alzheimer’s Chromatin Accessibility: scATAC-seq Data Re-analysis with OmnibusX

Introduction Unlocking the molecular mechanisms of Alzheimer's disease involves exploring both genetic and epigenetic factors that contribute to cellular dysfunction. Single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) is a powerful technique that provides insights into chromatin accessibility at the single-cell level, shedding light on gene regulation and

Dive with Visium HD: Uncover Spatial Cell Communication at Single-Cell Clarity

In the ever-changing world of biological research, understanding how cells communicate within their spatial context is crucial. The 10X Visium HD technology has become a game-changer, allowing scientists to study cell interactions with amazing detail and clarity. In this post, we explore the capabilities of the Visium HD dataset to

Define novel cell subtype using single-cell datasets

Uncovering hidden treasures in cellular diversity The advent of single-cell technologies has revolutionized our understanding of biological complexity, providing a lens through which we can discern the fine details of cellular heterogeneity. This transformative approach enables researchers to characterize cell types and discover new subtypes that have remained elusive with