Literature DB >> 28126650

Recent progress in single-cell cancer genomics.

Daphne Tsoucas1, Guo-Cheng Yuan2.   

Abstract

The advent of single-cell sequencing has been revolutionary to the field of cancer genomics. Perfectly suited to capture cancer's heterogeneous nature, single-cell analyses provide information bulk sequencing could never hope to uncover. Many mechanisms of cancer have yet to be fully understood, and single-cell approaches are showing promise in their abilities to uncover these mysteries. Here we focus on the most recent single-cell methods for cancer genomics, and how they are not only providing insights into the inner workings of cancer, but are also transforming individualized therapy and non-invasive monitoring and diagnosis.
Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

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Year:  2017        PMID: 28126650      PMCID: PMC5446798          DOI: 10.1016/j.gde.2017.01.002

Source DB:  PubMed          Journal:  Curr Opin Genet Dev        ISSN: 0959-437X            Impact factor:   5.578


  57 in total

1.  Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development.

Authors:  Sean C Bendall; Kara L Davis; El-Ad David Amir; Michelle D Tadmor; Erin F Simonds; Tiffany J Chen; Daniel K Shenfeld; Garry P Nolan; Dana Pe'er
Journal:  Cell       Date:  2014-04-24       Impact factor: 41.582

2.  Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape.

Authors:  Eugenio Marco; Robert L Karp; Guoji Guo; Paul Robson; Adam H Hart; Lorenzo Trippa; Guo-Cheng Yuan
Journal:  Proc Natl Acad Sci U S A       Date:  2014-12-15       Impact factor: 11.205

Review 3.  Computational and analytical challenges in single-cell transcriptomics.

Authors:  Oliver Stegle; Sarah A Teichmann; John C Marioni
Journal:  Nat Rev Genet       Date:  2015-01-28       Impact factor: 53.242

4.  Reproducible copy number variation patterns among single circulating tumor cells of lung cancer patients.

Authors:  Xiaohui Ni; Minglei Zhuo; Zhe Su; Jianchun Duan; Yan Gao; Zhijie Wang; Chenghang Zong; Hua Bai; Alec R Chapman; Jun Zhao; Liya Xu; Tongtong An; Qi Ma; Yuyan Wang; Meina Wu; Yu Sun; Shuhang Wang; Zhenxiang Li; Xiaodan Yang; Jun Yong; Xiao-Dong Su; Youyong Lu; Fan Bai; X Sunney Xie; Jie Wang
Journal:  Proc Natl Acad Sci U S A       Date:  2013-12-09       Impact factor: 11.205

Review 5.  The cancer stem cell hypothesis: in search of definitions, markers, and relevance.

Authors:  Michail Shipitsin; Kornelia Polyak
Journal:  Lab Invest       Date:  2008-03-31       Impact factor: 5.662

6.  Single-cell triple omics sequencing reveals genetic, epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomas.

Authors:  Yu Hou; Huahu Guo; Chen Cao; Xianlong Li; Boqiang Hu; Ping Zhu; Xinglong Wu; Lu Wen; Fuchou Tang; Yanyi Huang; Jirun Peng
Journal:  Cell Res       Date:  2016-02-23       Impact factor: 25.617

7.  RNA-Seq of single prostate CTCs implicates noncanonical Wnt signaling in antiandrogen resistance.

Authors:  David T Miyamoto; Yu Zheng; Ben S Wittner; Richard J Lee; Huili Zhu; Katherine T Broderick; Rushil Desai; Douglas B Fox; Brian W Brannigan; Julie Trautwein; Kshitij S Arora; Niyati Desai; Douglas M Dahl; Lecia V Sequist; Matthew R Smith; Ravi Kapur; Chin-Lee Wu; Toshi Shioda; Sridhar Ramaswamy; David T Ting; Mehmet Toner; Shyamala Maheswaran; Daniel A Haber
Journal:  Science       Date:  2015-09-18       Impact factor: 47.728

8.  Rapid phenotypic and genomic change in response to therapeutic pressure in prostate cancer inferred by high content analysis of single circulating tumor cells.

Authors:  Angel E Dago; Asya Stepansky; Anders Carlsson; Madelyn Luttgen; Jude Kendall; Timour Baslan; Anand Kolatkar; Michael Wigler; Kelly Bethel; Mitchell E Gross; James Hicks; Peter Kuhn
Journal:  PLoS One       Date:  2014-08-01       Impact factor: 3.240

Review 9.  Cancer genomics: one cell at a time.

Authors:  Nicholas E Navin
Journal:  Genome Biol       Date:  2014-08-30       Impact factor: 13.583

10.  De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data.

Authors:  Dominic Grün; Mauro J Muraro; Jean-Charles Boisset; Kay Wiebrands; Anna Lyubimova; Gitanjali Dharmadhikari; Maaike van den Born; Johan van Es; Erik Jansen; Hans Clevers; Eelco J P de Koning; Alexander van Oudenaarden
Journal:  Cell Stem Cell       Date:  2016-06-23       Impact factor: 24.633

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  22 in total

Review 1.  [Possibilities and limitations of molecular pathology in dermatohistology].

Authors:  V Schacht; U Lehmann; T Reineke-Plaass; F Länger; B Auber; S Morlot; H-H Kreipe
Journal:  Hautarzt       Date:  2018-07       Impact factor: 0.751

Review 2.  Next-Generation Sequencing Strategies.

Authors:  Shawn E Levy; Braden E Boone
Journal:  Cold Spring Harb Perspect Med       Date:  2019-07-01       Impact factor: 6.915

3.  Variance-adjusted Mahalanobis (VAM): a fast and accurate method for cell-specific gene set scoring.

Authors:  Hildreth Robert Frost
Journal:  Nucleic Acids Res       Date:  2020-09-18       Impact factor: 16.971

4.  Machine Learning for Nuclear Mechano-Morphometric Biomarkers in Cancer Diagnosis.

Authors:  Adityanarayanan Radhakrishnan; Karthik Damodaran; Ali C Soylemezoglu; Caroline Uhler; G V Shivashankar
Journal:  Sci Rep       Date:  2017-12-20       Impact factor: 4.379

Review 5.  Single Cell Omics of Breast Cancer: An Update on Characterization and Diagnosis.

Authors:  Shailendra Dwivedi; Purvi Purohit; Radhieka Misra; Malavika Lingeswaran; Jeewan Ram Vishnoi; Puneet Pareek; Sanjeev Misra; Praveen Sharma
Journal:  Indian J Clin Biochem       Date:  2019-01-08

6.  SECANT: a biology-guided semi-supervised method for clustering, classification, and annotation of single-cell multi-omics.

Authors:  Xinjun Wang; Zhongli Xu; Haoran Hu; Xueping Zhou; Yanfu Zhang; Robert Lafyatis; Kong Chen; Heng Huang; Ying Ding; Richard H Duerr; Wei Chen
Journal:  PNAS Nexus       Date:  2022-08-19

7.  Characterization of gene cluster heterogeneity in single-cell transcriptomic data within and across cancer types.

Authors:  Khong-Loon Tiong; Yu-Wei Lin; Chen-Hsiang Yeang
Journal:  Biol Open       Date:  2022-06-23       Impact factor: 2.643

Review 8.  Precision Oncology: The Road Ahead.

Authors:  Daniela Senft; Mark D M Leiserson; Eytan Ruppin; Ze'ev A Ronai
Journal:  Trends Mol Med       Date:  2017-09-05       Impact factor: 11.951

9.  Genetic Hallmarks and Heterogeneity of Glioblastoma in the Single-Cell Omics Era.

Authors:  Andrea Degl'Innocenti; Nicoletta di Leo; Gianni Ciofani
Journal:  Adv Ther (Weinh)       Date:  2019-12-01

Review 10.  Challenges and emerging directions in single-cell analysis.

Authors:  Guo-Cheng Yuan; Long Cai; Michael Elowitz; Tariq Enver; Guoping Fan; Guoji Guo; Rafael Irizarry; Peter Kharchenko; Junhyong Kim; Stuart Orkin; John Quackenbush; Assieh Saadatpour; Timm Schroeder; Ramesh Shivdasani; Itay Tirosh
Journal:  Genome Biol       Date:  2017-05-08       Impact factor: 13.583

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