ArticleNucleic acids research2018
CellAtlasSearch: a scalable search engine for single cells.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Single-cell signatures identify microenvironment factors in tumors associated with patient outcomes.Cell reports methods · 2024Article
- A combined experimental-computational approach uncovers a role for the Golgi matrix protein Giantin in breast cancer progression.PLoS computational biology · 2023Article
- Matching queried single-cell open-chromatin profiles to large pools of single-cell transcriptomes and epigenomes for reference supported analysis.Genome research · 2023Article
- Computational Approaches and Challenges in Spatial Transcriptomics.Genomics, proteomics & bioinformatics · 2023Review
- Improved downstream functional analysis of single-cell RNA-sequence data using DGAN.Scientific reports · 2023Article
- scMTD: a statistical multidimensional imputation method for single-cell RNA-seq data leveraging transcriptome dynamic information.Cell & bioscience · 2022Article
- GenomicSuperSignature facilitates interpretation of RNA-seq experiments through robust, efficient comparison to public databases.Nature communications · 2022Article
- Toward a unified information framework for cell atlas assembly.National science review · 2022Article
- Fast searches of large collections of single-cell data using scfind.Nature methods · 2021Article
- Erratum: Iyer, A., et al. Integrative Analysis and Machine Learning Based Characterization of Single Circulating Tumor Cells.Journal of clinical medicine · 2021Article
- Automatic cell type identification methods for single-cell RNA sequencing.Computational and structural biotechnology journal · 2021Review
- Using DenseFly algorithm for cell searching on massive scRNA-seq datasets.BMC genomics · 2020Article
- Human Cell Atlas and cell-type authentication for regenerative medicine.Experimental & molecular medicine · 2020Review
- Searching large-scale scRNA-seq databases via unbiased cell embedding with Cell BLAST.Nature communications · 2020Article
- Eleven grand challenges in single-cell data science.Genome biology · 2020Review
- Using transfer learning from prior reference knowledge to improve the clustering of single-cell RNA-Seq data.Scientific reports · 2019Article
- Next-generation computational tools for interrogating cancer immunity.Nature reviews. Genetics · 2019Review
- Challenges in unsupervised clustering of single-cell RNA-seq data.Nature reviews. Genetics · 2019Review
- CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA sequencing.Genome biology · 2019Article
- Discovery of rare cells from voluminous single cell expression data.Nature communications · 2018Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Owing to the advent of high throughput single cell transcriptomics, past few years have seen exponential growth in production of gene expression data. Recently efforts have been made by various research groups to homogenize and store single cell expression from a large number of studies. The true value of this ever increasing data deluge can be unlocked by making it searchable. To this end, we propose CellAtlasSearch, a novel search architecture for high dimensional expression data, which is massively parallel as well as light-weight, thus infinitely scalable. In CellAtlasSearch, we use a Graphical Processing Unit (GPU) friendly version of Locality Sensitive Hashing (LSH) for unmatched speedup in data processing and query. Currently, CellAtlasSearch features over 300 000 reference expression profiles including both bulk and single-cell data. It enables the user query individual single cell transcriptomes and finds matching samples from the database along with necessary meta information. CellAtlasSearch aims to assist researchers and clinicians in characterizing unannotated single cells. It also facilitates noise free, low dimensional representation of single-cell expression profiles by projecting them on a wide variety of reference samples. The web-server is accessible at: http://www.cellatlassearch.com.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.