Literature DB >> 23922233

The applications of single-cell genomics.

Michael Lovett.   

Abstract

We all start out as a single totipotent cell that is programmed to produce a multicellular organism. How do individual cells make those complex developmental switches? How do single cells within a tissue or organ differ, how do they coordinate their actions or go astray in a disease process? These are long-standing and fundamental questions in biology that are now becoming tractable because of advances in microfluidics, DNA amplification and DNA sequencing. Methods for studying single-cell transcriptomes (or at least the polyadenylated mRNA fraction of it) are by far the furthest ahead and reveal remarkable heterogeneity between morphologically identical cells. The analysis of genomic DNA variation is not far behind. The other 'omics' of single cells pose greater technological obstacles, but they are progressing and promise to yield highly integrated large data sets in the near future.

Mesh:

Year:  2013        PMID: 23922233      PMCID: PMC3782075          DOI: 10.1093/hmg/ddt377

Source DB:  PubMed          Journal:  Hum Mol Genet        ISSN: 0964-6906            Impact factor:   6.150


  39 in total

1.  Single-cell proteomic chip for profiling intracellular signaling pathways in single tumor cells.

Authors:  Qihui Shi; Lidong Qin; Wei Wei; Feng Geng; Rong Fan; Young Shik Shin; Deliang Guo; Leroy Hood; Paul S Mischel; James R Heath
Journal:  Proc Natl Acad Sci U S A       Date:  2011-12-27       Impact factor: 11.205

2.  Toward a systems biology of mouse inner ear organogenesis: gene expression pathways, patterns and network analysis.

Authors:  Samin A Sajan; Mark E Warchol; Michael Lovett
Journal:  Genetics       Date:  2007-07-29       Impact factor: 4.562

3.  Dynamic proteomics of individual cancer cells in response to a drug.

Authors:  A A Cohen; N Geva-Zatorsky; E Eden; M Frenkel-Morgenstern; I Issaeva; A Sigal; R Milo; C Cohen-Saidon; Y Liron; Z Kam; L Cohen; T Danon; N Perzov; U Alon
Journal:  Science       Date:  2008-11-20       Impact factor: 47.728

Review 4.  Structure and function of mammalian DNA methyltransferases.

Authors:  Renata Zofia Jurkowska; Tomasz Piotr Jurkowski; Albert Jeltsch
Journal:  Chembiochem       Date:  2010-11-29       Impact factor: 3.164

5.  Reverse transcriptase template switching: a SMART approach for full-length cDNA library construction.

Authors:  Y Y Zhu; E M Machleder; A Chenchik; R Li; P D Siebert
Journal:  Biotechniques       Date:  2001-04       Impact factor: 1.993

6.  Tumour evolution inferred by single-cell sequencing.

Authors:  Nicholas Navin; Jude Kendall; Jennifer Troge; Peter Andrews; Linda Rodgers; Jeanne McIndoo; Kerry Cook; Asya Stepansky; Dan Levy; Diane Esposito; Lakshmi Muthuswamy; Alex Krasnitz; W Richard McCombie; James Hicks; Michael Wigler
Journal:  Nature       Date:  2011-03-13       Impact factor: 49.962

7.  Spatially selective sampling of single cells using optically trapped fusogenic emulsion droplets: a new single-cell proteomic tool.

Authors:  Peter M P Lanigan; Karen Chan; Tanya Ninkovic; Richard H Templer; P M W French; A J de Mello; K R Willison; P J Parker; M A A Neil; Oscar Ces; D R Klug
Journal:  J R Soc Interface       Date:  2008-10-06       Impact factor: 4.118

Review 8.  Quantitative single cell and single molecule proteomics for clinical studies.

Authors:  Keith R Willison; David R Klug
Journal:  Curr Opin Biotechnol       Date:  2013-06-28       Impact factor: 9.740

9.  Highly multiplexed single-cell analysis of formalin-fixed, paraffin-embedded cancer tissue.

Authors:  Michael J Gerdes; Christopher J Sevinsky; Anup Sood; Sudeshna Adak; Musodiq O Bello; Alexander Bordwell; Ali Can; Alex Corwin; Sean Dinn; Robert J Filkins; Denise Hollman; Vidya Kamath; Sireesha Kaanumalle; Kevin Kenny; Melinda Larsen; Michael Lazare; Qing Li; Christina Lowes; Colin C McCulloch; Elizabeth McDonough; Michael C Montalto; Zhengyu Pang; Jens Rittscher; Alberto Santamaria-Pang; Brion D Sarachan; Maximilian L Seel; Antti Seppo; Kashan Shaikh; Yunxia Sui; Jingyu Zhang; Fiona Ginty
Journal:  Proc Natl Acad Sci U S A       Date:  2013-07-01       Impact factor: 11.205

Review 10.  Development and applications of single-cell transcriptome analysis.

Authors:  Fuchou Tang; Kaiqin Lao; M Azim Surani
Journal:  Nat Methods       Date:  2011-04       Impact factor: 28.547

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  12 in total

1.  Identification of a differentiation-related prognostic nomogram based on single-cell RNA sequencing in clear cell renal cell carcinoma.

Authors:  Zhi-Nan Xia; Jing-Gen Wu; Wen-Hao Yao; Yu-Yang Meng; Wen-Gang Jian; Teng-Da Wang; Wei Xue; Yi-Peng Yu; Li-Cheng Cai; Xing-Yuan Wang; Peng Zhang; Zhi-Yuan Li; Hao Zhou; Zhi-Cheng Jiang; Jia-Yu Zhou; Cheng Zhang
Journal:  Sci Rep       Date:  2022-06-29       Impact factor: 4.996

Review 2.  A new toolbox for assessing single cells.

Authors:  Konstantinos Tsioris; Alexis J Torres; Thomas B Douce; J Christopher Love
Journal:  Annu Rev Chem Biomol Eng       Date:  2014       Impact factor: 11.059

Review 3.  Computational modeling of drug response with applications to neuroscience.

Authors:  Ralf Herwig
Journal:  Dialogues Clin Neurosci       Date:  2014-12       Impact factor: 5.986

4.  ANISEED 2015: a digital framework for the comparative developmental biology of ascidians.

Authors:  Matija Brozovic; Cyril Martin; Christelle Dantec; Delphine Dauga; Mickaël Mendez; Paul Simion; Madeline Percher; Baptiste Laporte; Céline Scornavacca; Anna Di Gregorio; Shigeki Fujiwara; Mathieu Gineste; Elijah K Lowe; Jacques Piette; Claudia Racioppi; Filomena Ristoratore; Yasunori Sasakura; Naohito Takatori; Titus C Brown; Frédéric Delsuc; Emmanuel Douzery; Carmela Gissi; Alex McDougall; Hiroki Nishida; Hitoshi Sawada; Billie J Swalla; Hitoyoshi Yasuo; Patrick Lemaire
Journal:  Nucleic Acids Res       Date:  2015-09-29       Impact factor: 16.971

Review 5.  Platforms for Single-Cell Collection and Analysis.

Authors:  Lukas Valihrach; Peter Androvic; Mikael Kubista
Journal:  Int J Mol Sci       Date:  2018-03-11       Impact factor: 5.923

6.  Identification of Subtypes and a Prognostic Gene Signature in Colon Cancer Using Cell Differentiation Trajectories.

Authors:  Renshen Xiang; Jincheng Fu; Yuhang Ge; Jun Ren; Wei Song; Tao Fu
Journal:  Front Cell Dev Biol       Date:  2021-12-13

7.  A perpetual source of DNA or something really different: ethical issues in the creation of cell lines for African genomics research.

Authors:  Jantina de Vries; Akin Abayomi; James Brandful; Katherine Littler; Ebony Madden; Patricia Marshall; Odile Ouwe Missi Oukem-Boyer; Janet Seeley
Journal:  BMC Med Ethics       Date:  2014-08-07       Impact factor: 2.652

8.  Predictors of consent to cell line creation and immortalisation in a South African schizophrenia genomics study.

Authors:  Megan M Campbell; Jantina de Vries; Sibonile G Mqulwana; Michael M Mndini; Odwa A Ntola; Deborah Jonker; Megan Malan; Adele Pretorius; Zukiswa Zingela; Stephanus Van Wyk; Dan J Stein; Ezra Susser
Journal:  BMC Med Ethics       Date:  2018-07-11       Impact factor: 2.652

9.  Cell differentiation trajectory predicts patient potential immunotherapy response and prognosis in gastric cancer.

Authors:  Renshen Xiang; Yuping Rong; Yuhang Ge; Wei Song; Jun Ren; Tao Fu
Journal:  Aging (Albany NY)       Date:  2021-02-17       Impact factor: 5.682

Review 10.  New Insights From Single-Cell Sequencing Data: Synovial Fibroblasts and Synovial Macrophages in Rheumatoid Arthritis.

Authors:  Liyun Cheng; Yanyan Wang; Ruihe Wu; Tingting Ding; Hongwei Xue; Chong Gao; Xiaofeng Li; Caihong Wang
Journal:  Front Immunol       Date:  2021-07-19       Impact factor: 7.561

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