ReviewFrontiers in oncology2014
Current challenges in the bioinformatics of single cell genomics.
Review in Frontiers in oncology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- SC-framework: A robust and FAIR semi-interactive environment for single-cell resolution datasets.iScience · 2026Article
- Single-Thallus Genomics of Ejectosporus trisporus, an Unculturable Stonefly Gut Fungal Symbiont.Environmental microbiology · 2026Article
- SVCROWS: a user-defined tool for interpreting significant structural variants in heterogeneous datasets.Nucleic acids research · 2026Article
- A Tailing Method of Quality Control on MALBAC-Based Whole-Genome Amplification Products.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Pannexins in the vasculature.American journal of physiology. Heart and circulatory physiology · 2025Review
- Pannexin channels in the kidney.American journal of physiology. Renal physiology · 2025Review
- IndepthPathway: an integrated tool for in-depth pathway enrichment analysis based on single-cell sequencing data.Bioinformatics (Oxford, England) · 2023Article
- Reciprocal recombination genomic signatures in the symbiotic arbuscular mycorrhizal fungi Rhizophagus irregularis.PloS one · 2022Article
- An Optimised Protocol Harnessing Laser Capture Microdissection for Transcriptomic Analysis on Matched Primary and Metastatic Colorectal Tumours.Scientific reports · 2020Article
- Assessing the reliability of gene expression measurements in very-low-numbers of human monocyte-derived macrophages.Scientific reports · 2019Article
- Revealing tumor heterogeneity of breast cancer by utilizing the linkage between somatic and germline mutations.Briefings in bioinformatics · 2019Article
- A low cost and input tailing method of quality control on multiple annealing, and looping-based amplification cycles-based whole-genome amplification products.Journal of clinical laboratory analysis · 2019Article
- Innovative strategies for annotating the "relationSNP" between variants and molecular phenotypes.BioData mining · 2019Review
- Computational enhancement of single-cell sequences for inferring tumor evolution.Bioinformatics (Oxford, England) · 2018Article
- Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms.Scientific reports · 2018Article
- Single-Cell Genomic Analysis in Plants.Genes · 2018Review
- A Retrospective Review of Microbiological Methods Applied in Studies Following the Deepwater Horizon Oil Spill.Frontiers in microbiology · 2018Review
- Single-cell SNP analyses and interpretations based on RNA-Seq data for colon cancer research.Scientific reports · 2016Article
- Clonal genotype and population structure inference from single-cell tumor sequencing.Nature methods · 2016Article
- Estrogen receptor alpha gene amplification in breast cancer: 25 years of debate.World journal of clinical oncology · 2016Review
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Single cell genomics is a rapidly growing field with many new techniques emerging in the past few years. However, few bioinformatics tools specific for single cell genomics analysis are available. Single cell DNA/RNA sequencing data usually have low genome coverage and high amplification bias, which makes bioinformatics analysis challenging. Many current bioinformatics tools developed for bulk cell sequencing do not work well with single cell sequencing data. Here, we summarize current challenges in the bioinformatics analysis of single cell genomic DNA sequencing and single cell transcriptomes. These challenges include calling copy number variations, identifying mutated genes in tumor samples, reconstructing cell lineages, recovering low abundant transcripts, and improving the accuracy of quantitative analysis of transcripts. Development in single cell genomics bioinformatics analysis will promote the application of this technology to basic biology and medical research.
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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.