Bioinformatics approaches to single-cell analysis in developmental biology

Dicle Yalcin, Zeynep M. Hakguder, Hasan H Otu

Research output: Contribution to journalReview article

9 Citations (Scopus)

Abstract

Individual cells within the same population show various degrees of heterogeneity, which may be better handled with single-cell analysis to address biological and clinical questions. Single-cell analysis is especially important in developmental biology as subtle spatial and temporal differences in cells have significant associations with cell fate decisions during differentiation and with the description of a particular state of a cell exhibiting an aberrant phenotype. Biotechnological advances, especially in the area of microfluidics, have led to a robust, massively parallel and multi-dimensional capturing, sorting, and lysis of single-cells and amplification of related macromolecules, which have enabled the use of imaging and omics techniques on single cells. There have been improvements in computational single-cell image analysis in developmental biology regarding feature extraction, segmentation, image enhancement and machine learning, handling limitations of optical resolution to gain new perspectives from the raw microscopy images. Omics approaches, such as transcriptomics, genomics and epigenomics, targeting gene and small RNA expression, single nucleotide and structural variations and methylation and histone modifications, rely heavily on high-throughput sequencing technologies. Although there are well-established bioinformatics methods for analysis of sequence data, there are limited bioinformatics approaches which address experimental design, sample size considerations, amplification bias, normalization, differential expression, coverage, clustering and classification issues, specifically applied at the single-cell level. In this review, we summarize biological and technological advancements, discuss challenges faced in the aforementioned data acquisition and analysis issues and present future prospects for application of single-cell analyses to developmental biology.

Original languageEnglish (US)
Pages (from-to)182-192
Number of pages11
JournalMolecular Human Reproduction
Volume22
Issue number3
DOIs
StatePublished - Dec 1 2015

Fingerprint

Single-Cell Analysis
Developmental Biology
Computational Biology
Histone Code
Image Enhancement
Microfluidics
Gene Targeting
Genomics
Epigenomics
Sample Size
Methylation
Sequence Analysis
Cluster Analysis
Microscopy
Research Design
Nucleotides
RNA
Technology
Phenotype

Keywords

  • Clustering
  • Differential expression
  • Missing data
  • Normalization
  • Single-cell bioinformatics

ASJC Scopus subject areas

  • Reproductive Medicine
  • Embryology
  • Molecular Biology
  • Genetics
  • Obstetrics and Gynecology
  • Developmental Biology
  • Cell Biology

Cite this

Bioinformatics approaches to single-cell analysis in developmental biology. / Yalcin, Dicle; Hakguder, Zeynep M.; Otu, Hasan H.

In: Molecular Human Reproduction, Vol. 22, No. 3, 01.12.2015, p. 182-192.

Research output: Contribution to journalReview article

Yalcin, Dicle ; Hakguder, Zeynep M. ; Otu, Hasan H. / Bioinformatics approaches to single-cell analysis in developmental biology. In: Molecular Human Reproduction. 2015 ; Vol. 22, No. 3. pp. 182-192.
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