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Search · four archives
24 papers · ranked by Valyu relevance
Hongfei Li, Jiechen Wang, Qing Liu, Quan Zou + 1 more
Joint profiling technologies combining single-cell chromatin accessibility (CA) and transcriptome sequencing enable cellular heterogeneity analysis from both gene and cis-regulatory element perspectives, greatly advancing molecular biology at a cellular resolution. These techniques have been used to construct gene…
Mathini Vaikunthan, Anna C. M. Schoonen, Ioana-Teodora Lia, Jonathan Guo + 1 more
Existing targeted approaches either rely on per-gene barcoded probes and transcript tiling, which limit scalability, or forgo reverse transcription, precluding capture of highly variable transcripts. Here, we present targeted reverse transcription-linker (TRTL), a modular method that can be integrated into existing…
Saloni Bhatia, Matt A Field, Lionel Hebbard, Ulf Schmitz
Alternative splicing (AS) plays a key role in regulating gene expression, and its dysregulation is implicated in numerous human diseases, including cancer. While bulk RNA sequencing has advanced our understanding of AS, it cannot capture cellular heterogeneity or reliably reconstruct full-length isoforms, both of which…
Sherin Xirenayi, Sabrina Y. Camp, Amanda E. Garza, Yashika Rustagi + 10 more
The application of single-cell transcriptomic approaches has deepened our understanding of tumor heterogeneity, immune dynamics, and molecular programs underlying therapy response. The recent development of fixation-compatible single-cell platforms, such as 10x Genomics Flex, offers the opportunity to profile archived…
Haoxuan Luo, Ansar Hussain, Musavir Abbas, Lun Yuan + 5 more
Droplet-based single-cell RNA sequencing (scRNA-seq) has redefined biological research by resolving cellular heterogeneity with an unprecedented precision. This review synthesizes the technological evolution of the 10× Genomics Chromium platform, its Gel Bead-in-Emulsion (GEM)s technology, and end-to-end workflows…
Kayleigh Casmey, Maria Zimmermann, Yuxin Xie, Sierra A. Codeluppi-Arrowsmith + 2 more
Single-cell omics technology has advanced rapidly since its inception, offering increasing precision, resolution, and technical diversity to explore cell-specific molecular features in the human brain and neuropsychiatric disorders. While traditional bulk genomic analyses have provided valuable insights into the…
Chen, Audrey Pei-Hsuan
Representation learning on multi-omics data is challenging due to extreme dimensionality, modality heterogeneity, and cohort-specific batch effects. While pre-trained transformer backbones have shown broad generalization capabilities in biological sequence modeling, their application to multi-omics integration remains…
Anna Schwager, Eve Moutaux, Adeline Durand, Alexandra Van Keymeulen + 22 more
Single-cell multi-omics methods enable simultaneous mapping of chromatin states and transcriptomes, offering deep insights into gene regulation. Yet, the full potential of these approaches remains untapped for rare cell populations, as most methods require thousands of cells and are limited in their ability to capture…
Johannes Bues, Joern Pezoldt, Camille Lucie Lambert, Benjamin David Hale + 23 more
Single-cell technologies such as transcriptomics, microscopy, and flow cytometry have revolutionized the study of cellular identity and function. While each of these technologies is powerful on its own, their full potential lies in their integration, enabling multimodal profiling of the same cell and revealing how…
Seulkee Yang, Sudeeksha Tyagi, Christian Rosenmund, Melissa A. Herman
The rise of single-cell transcriptomics and comprehensive reference atlases promised a unifying molecular framework to classify cell identity. Yet transcriptomic identities are often interpreted outside the environmental contexts in which they arise. Here, we analyzed primary cortical cultures, which lack native tissue…
Yiyang Zhang, Bokai Zhao, Xiaoru Zhang, Zongchang Du + 2 more
Single-cell-resolution spatial transcriptomics profiles gene expression at cellular locations in native tissues, yet accurate cell-type annotation remains challenging: imaging-based platforms are constrained by targeted gene panels, whereas sequencing-based platforms often suffer from sparse molecular capture and…
Sydney B. Blattman, Nabih Maslah, Austin A. Varela, Karolis Kumpaitis + 27 more
Despite the promise of single-cell transcriptomics for understanding cell states in heterogeneous populations, widely used platforms have limited ability to link transcriptional states to somatic mutations within the same cells. Here, we introduce Genotyping in Fixed Transcriptomes (GIFT) for the simultaneous detection…
Xiaoshui Huang, Zhu, Tianlin, Yifan Zuo + 7 more
Single-cell RNA sequencing (scRNA-seq) is essential for decoding tumor heterogeneity. However, pan-cancer research still faces two key challenges: learning discriminative and efficient single-cell representations, and establishing a comprehensive evaluation benchmark. In this paper, we introduce PanFoMa, a lightweight…
Jiacheng Ding, HyunJin Kang, Amber L. Spangenberg, Yusha Liu + 3 more
RNA sequencing (RNA-seq) and the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) have become standard techniques for studying gene regulation in human populations. Single-cell (sc) “multiomic” genomic methodologies now enable researchers to dissect cellular heterogeneity while simultaneously…
Sho Iwama, Daniel Gitterman, Timothy Brendler-Spaeth, Andrew Waters + 6 more
Advances in high-throughput sequencing have associated millions of putative genetic variants with disease. However, scalable experimental methods to establish causal relationships between genetic variants and downstream transcriptional outcomes remain a major challenge. Single-cell methods that integrate genotyping…
Sydney B. Blattman, Nabih Maslah, Austin A. Varela, Karolis Kumpaitis + 27 more
Despite the promise of single-cell transcriptomics for understanding cell states in heterogeneous populations, widely used platforms have limited ability to link transcriptional states to somatic mutations within the same cells. Here, we introduce Genotyping in Fixed Transcriptomes (GIFT) for the simultaneous detection…
Alvin Sheng, Sandra E. Safo, Thierry Chekouo
Recent advances in spatial transcriptomics have enabled researchers to profile gene expression at the single-cell spatial resolution, often for multiple tissue samples in a single study. This high-dimensional molecular profile for each cell can be used to sort cells into cell types with distinct functions, or segment…
Jiabei Cheng, Jingbo Zhou, Jun Xia, Changkai Li + 3 more
Simultaneous measurement of multiple omics modalities in single cells enables researchers to gain a more comprehensive understanding of cellular states and regulatory mechanisms. However, due to high experimental costs, significant noise, and incomplete modality coverage, a variety of computational methods for modality…
Yuhang Yang, Yonggan Bu, Shengyuan Zhou, Yiming Luo + 1 more
Spatial Transcriptomics (ST) measures gene expression while preserving spatial context, but its high cost and low throughput leave public datasets small. Inferring expression directly from widely available Hematoxylin and Eosin (H&E) stained histology offers a cost-effective alternative. However, existing approaches…
Qifeng Zhou, Lei Yu, Yuzhi Guo, Yuwei Miao + 4 more
The integration of single-cell proteomic data is often hindered by the fragmented nature of targeted antibody panels. To address this limitation, we introduce scpFormer, a transformer-based foundation model designed for single-cell proteomics. Pre-trained on over 390 million cells, scpFormer replaces standard…
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The WRN helicase has recently emerged as a promising therapeutic target for microsatellite instability (MSI)-high cancers. Here, we report LXW-P1, a potent WRN degrader derived from marine bromotyrosine alkaloids. Its molecular target was identified using an AI-guided, pathway-informed perturbation transcriptomics…
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The Golgi apparatus (GA) orchestrates protein modification, trafficking, and secretion through highly dynamic remodeling, yet its proteomic complexity remains difficult to resolve in living systems. Here, we report CAT-Golgi, a genetically independent and light-controlled photocatalytic proximity labeling strategy for…
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Despite $100 billion in investment and more than 100,000 publications, nanomedicine translation fails primarily at biological validation, not at synthesis or characterization. We present the first systematic technology readiness assessment across autonomous nanomedicine components, revealing a critical finding: while…
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Quantitative analysis of small extracellular vesicles (sEVs) at single-particle resolution remains challenging due to their nanoscale dimensions and compositional heterogeneity. Existing methods often rely on specialized and costly instrumentation, limiting accessibility for many researchers and necessitates extensive…