Literature DB >> 29552672

Single-cell systems biology: probing the basic unit of information flow.

Simona Patange1,2, Michelle Girvan2,3, Daniel R Larson1.   

Abstract

Gene expression varies across cells in a population or a tissue. This heterogeneity has come into sharp focus in recent years through developments in new imaging and sequencing technologies. However, our ability to measure variation has outpaced our ability to interpret it. Much of the variability may arise from random effects occurring in the processes of gene expression (transcription, RNA processing and decay, translation). The molecular basis of these effects is largely unknown. Likewise, a functional role of this variability in growth, differentiation and disease has only been elucidated in a few cases. In this review, we highlight recent experimental and theoretical advances for measuring and analyzing stochastic variation.

Entities:  

Year:  2017        PMID: 29552672      PMCID: PMC5851483          DOI: 10.1016/j.coisb.2017.11.011

Source DB:  PubMed          Journal:  Curr Opin Syst Biol        ISSN: 2452-3100


  76 in total

1.  Real-time observation of transcription initiation and elongation on an endogenous yeast gene.

Authors:  Daniel R Larson; Daniel Zenklusen; Bin Wu; Jeffrey A Chao; Robert H Singer
Journal:  Science       Date:  2011-04-22       Impact factor: 47.728

2.  Stochastic models of transcription: from single molecules to single cells.

Authors:  Alvaro Sanchez; Sandeep Choubey; Jane Kondev
Journal:  Methods       Date:  2013-04-01       Impact factor: 3.608

3.  Fluctuation Analysis: Dissecting Transcriptional Kinetics with Signal Theory.

Authors:  A Coulon; D R Larson
Journal:  Methods Enzymol       Date:  2016-04-12       Impact factor: 1.600

4.  High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization.

Authors:  Jeffrey R Moffitt; Junjie Hao; Guiping Wang; Kok Hao Chen; Hazen P Babcock; Xiaowei Zhuang
Journal:  Proc Natl Acad Sci U S A       Date:  2016-09-13       Impact factor: 11.205

5.  Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues.

Authors:  Je Hyuk Lee; Evan R Daugharthy; Jonathan Scheiman; Reza Kalhor; Thomas C Ferrante; Richard Terry; Brian M Turczyk; Joyce L Yang; Ho Suk Lee; John Aach; Kun Zhang; George M Church
Journal:  Nat Protoc       Date:  2015-02-12       Impact factor: 13.491

6.  Enhancer Control of Transcriptional Bursting.

Authors:  Takashi Fukaya; Bomyi Lim; Michael Levine
Journal:  Cell       Date:  2016-06-09       Impact factor: 41.582

Review 7.  RNA-Seq: a revolutionary tool for transcriptomics.

Authors:  Zhong Wang; Mark Gerstein; Michael Snyder
Journal:  Nat Rev Genet       Date:  2009-01       Impact factor: 53.242

Review 8.  Variation is function: Are single cell differences functionally important?: Testing the hypothesis that single cell variation is required for aggregate function.

Authors:  Hannah Dueck; James Eberwine; Junhyong Kim
Journal:  Bioessays       Date:  2015-12-02       Impact factor: 4.345

9.  A pathway-centric view of spatial proximity in the 3D nucleome across cell lines.

Authors:  Hiren Karathia; Carl Kingsford; Michelle Girvan; Sridhar Hannenhalli
Journal:  Sci Rep       Date:  2016-12-15       Impact factor: 4.379

10.  Single-cell differences in matrix gene expression do not predict matrix deposition.

Authors:  Allison J Cote; Claire M McLeod; Megan J Farrell; Patrick D McClanahan; Margaret C Dunagin; Arjun Raj; Robert L Mauck
Journal:  Nat Commun       Date:  2016-03-03       Impact factor: 14.919

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  7 in total

Review 1.  Quantifying information of intracellular signaling: progress with machine learning.

Authors:  Ying Tang; Alexander Hoffmann
Journal:  Rep Prog Phys       Date:  2022-07-12

2.  Nuclear Localization of Huntingtin mRNA Is Specific to Cells of Neuronal Origin.

Authors:  Marie-Cécile Didiot; Chantal M Ferguson; Socheata Ly; Andrew H Coles; Abigail O Smith; Alicia A Bicknell; Lauren M Hall; Ellen Sapp; Dimas Echeverria; Athma A Pai; Marian DiFiglia; Melissa J Moore; Lawrence J Hayward; Neil Aronin; Anastasia Khvorova
Journal:  Cell Rep       Date:  2018-09-04       Impact factor: 9.423

3.  Single-Cell RNA Sequencing of In Vitro Expanded Chondrocytes: MSC-Like Cells With No Evidence of Distinct Subsets.

Authors:  Tommy A Karlsen; Arvind Y M Sundaram; Jan E Brinchmann
Journal:  Cartilage       Date:  2019-05-09       Impact factor: 3.117

Review 4.  Spatial-omics: Novel approaches to probe cell heterogeneity and extracellular matrix biology.

Authors:  Grace C Bingham; Fred Lee; Alexandra Naba; Thomas H Barker
Journal:  Matrix Biol       Date:  2020-05-19       Impact factor: 10.447

Review 5.  Monitoring the spatio-temporal organization and dynamics of the genome.

Authors:  Haitham A Shaban; Andrew Seeber
Journal:  Nucleic Acids Res       Date:  2020-04-17       Impact factor: 16.971

6.  The variome concept: focus on CNVariome.

Authors:  Ivan Y Iourov; Svetlana G Vorsanova; Yuri B Yurov
Journal:  Mol Cytogenet       Date:  2019-12-19       Impact factor: 2.009

Review 7.  mRNA Metabolism in Cardiac Development and Disease: Life After Transcription.

Authors:  Chen Gao; Yibin Wang
Journal:  Physiol Rev       Date:  2019-11-21       Impact factor: 37.312

  7 in total

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