Literature DB >> 29529018

Alignment of single-cell trajectories to compare cellular expression dynamics.

Ayelet Alpert1, Lindsay S Moore1, Tania Dubovik1, Shai S Shen-Orr1.   

Abstract

Single-cell RNA sequencing and high-dimensional cytometry can be used to generate detailed trajectories of dynamic biological processes such as differentiation or development. Here we present cellAlign, a quantitative framework for comparing expression dynamics within and between single-cell trajectories. By applying cellAlign to mouse and human embryonic developmental trajectories, we systematically delineate differences in the temporal regulation of gene expression programs that would otherwise be masked.

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Year:  2018        PMID： 29529018     DOI： 10.1038/nmeth.4628

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  12 in total

1.  Single-Cell Transcriptomics Reveals a Population of Dormant Neural Stem Cells that Become Activated upon Brain Injury.

Authors:  Enric Llorens-Bobadilla; Sheng Zhao; Avni Baser; Gonzalo Saiz-Castro; Klara Zwadlo; Ana Martin-Villalba
Journal:  Cell Stem Cell       Date:  2015-07-30       Impact factor: 24.633

2.  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

3.  Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells.

Authors:  Qiaolin Deng; Daniel Ramsköld; Björn Reinius; Rickard Sandberg
Journal:  Science       Date:  2014-01-10       Impact factor: 47.728

4.  Diffusion pseudotime robustly reconstructs lineage branching.

Authors:  Laleh Haghverdi; Maren Büttner; F Alexander Wolf; Florian Buettner; Fabian J Theis
Journal:  Nat Methods       Date:  2016-08-29       Impact factor: 28.547

5.  Human gene expression first occurs between the four- and eight-cell stages of preimplantation development.

Authors:  P Braude; V Bolton; S Moore
Journal:  Nature       Date:  1988-03-31       Impact factor: 49.962

6.  Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells.

Authors:  Liying Yan; Mingyu Yang; Hongshan Guo; Lu Yang; Jun Wu; Rong Li; Ping Liu; Ying Lian; Xiaoying Zheng; Jie Yan; Jin Huang; Ming Li; Xinglong Wu; Lu Wen; Kaiqin Lao; Ruiqiang Li; Jie Qiao; Fuchou Tang
Journal:  Nat Struct Mol Biol       Date:  2013-08-11       Impact factor: 15.369

7.  The ConsensusPathDB interaction database: 2013 update.

Authors:  Atanas Kamburov; Ulrich Stelzl; Hans Lehrach; Ralf Herwig
Journal:  Nucleic Acids Res       Date:  2012-11-11       Impact factor: 16.971

8.  Development and application of a modified dynamic time warping algorithm (DTW-S) to analyses of primate brain expression time series.

Authors:  Yuan Yuan; Yi-Ping Phoebe Chen; Shengyu Ni; Augix Guohua Xu; Lin Tang; Martin Vingron; Mehmet Somel; Philipp Khaitovich
Journal:  BMC Bioinformatics       Date:  2011-08-18       Impact factor: 3.169

9.  The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.

Authors:  Cole Trapnell; Davide Cacchiarelli; Jonna Grimsby; Prapti Pokharel; Shuqiang Li; Michael Morse; Niall J Lennon; Kenneth J Livak; Tarjei S Mikkelsen; John L Rinn
Journal:  Nat Biotechnol       Date:  2014-03-23       Impact factor: 54.908

10.  Single-cell RNA-seq reveals dynamic paracrine control of cellular variation.

Authors:  Alex K Shalek; Rahul Satija; Joe Shuga; John J Trombetta; Dave Gennert; Diana Lu; Peilin Chen; Rona S Gertner; Jellert T Gaublomme; Nir Yosef; Schraga Schwartz; Brian Fowler; Suzanne Weaver; Jing Wang; Xiaohui Wang; Ruihua Ding; Raktima Raychowdhury; Nir Friedman; Nir Hacohen; Hongkun Park; Andrew P May; Aviv Regev
Journal:  Nature       Date:  2014-06-11       Impact factor: 49.962
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  23 in total

1.  Sorting apples from oranges in single-cell expression comparisons.

Authors:  Fiona K Hamey; Berthold Göttgens
Journal:  Nat Methods       Date:  2018-04-27       Impact factor: 28.547

2.  Single-Cell RNA Sequencing of Human, Macaque, and Mouse Testes Uncovers Conserved and Divergent Features of Mammalian Spermatogenesis.

Authors:  Adrienne Niederriter Shami; Xianing Zheng; Sarah K Munyoki; Qianyi Ma; Gabriel L Manske; Christopher D Green; Meena Sukhwani; Kyle E Orwig; Jun Z Li; Saher Sue Hammoud
Journal:  Dev Cell       Date:  2020-06-05       Impact factor: 12.270

3.  Alignment of single-cell trajectory trees with CAPITAL.

Authors:  Reiichi Sugihara; Yuki Kato; Tomoya Mori; Yukio Kawahara
Journal:  Nat Commun       Date:  2022-10-14       Impact factor: 17.694

4.  Single-cell atlas of human liver development reveals pathways directing hepatic cell fates.

Authors:  Brandon T Wesley; Alexander D B Ross; Sarah A Teichmann; Ludovic Vallier; Daniele Muraro; Zhichao Miao; Sarah Saxton; Rute A Tomaz; Carola M Morell; Katherine Ridley; Ekaterini D Zacharis; Sandra Petrus-Reurer; Judith Kraiczy; Krishnaa T Mahbubani; Stephanie Brown; Jose Garcia-Bernardo; Clara Alsinet; Daniel Gaffney; Dave Horsfall; Olivia C Tysoe; Rachel A Botting; Emily Stephenson; Dorin-Mirel Popescu; Sonya MacParland; Gary Bader; Ian D McGilvray; Daniel Ortmann; Fotios Sampaziotis; Kourosh Saeb-Parsy; Muzlifah Haniffa; Kelly R Stevens; Matthias Zilbauer
Journal:  Nat Cell Biol       Date:  2022-09-15       Impact factor: 28.213

Review 5.  Integrative single-cell analysis.

Authors:  Tim Stuart; Rahul Satija
Journal:  Nat Rev Genet       Date:  2019-05       Impact factor: 53.242

Review 6.  Computational principles and challenges in single-cell data integration.

Authors:  Ricard Argelaguet; Anna S E Cuomo; Oliver Stegle; John C Marioni
Journal:  Nat Biotechnol       Date:  2021-05-03       Impact factor: 54.908

Review 7.  Melanoma models for the next generation of therapies.

Authors:  E Elizabeth Patton; Kristen L Mueller; David J Adams; Niroshana Anandasabapathy; Andrew E Aplin; Corine Bertolotto; Marcus Bosenberg; Craig J Ceol; Christin E Burd; Ping Chi; Meenhard Herlyn; Sheri L Holmen; Florian A Karreth; Charles K Kaufman; Shaheen Khan; Sebastian Kobold; Eleonora Leucci; Carmit Levy; David B Lombard; Amanda W Lund; Kerrie L Marie; Jean-Christophe Marine; Richard Marais; Martin McMahon; Carla Daniela Robles-Espinoza; Ze'ev A Ronai; Yardena Samuels; Maria S Soengas; Jessie Villanueva; Ashani T Weeraratna; Richard M White; Iwei Yeh; Jiyue Zhu; Leonard I Zon; Marc S Hurlbert; Glenn Merlino
Journal:  Cancer Cell       Date:  2021-02-04       Impact factor: 31.743

Review 8.  Advancing Stem Cell Research through Multimodal Single-Cell Analysis.

Authors:  Iwo Kucinski; Berthold Gottgens
Journal:  Cold Spring Harb Perspect Biol       Date:  2020-07-01       Impact factor: 9.708

9.  Current progress and potential opportunities to infer single-cell developmental trajectory and cell fate.

Authors:  Lingfei Wang; Qian Zhang; Qian Qin; Nikolaos Trasanidis; Michael Vinyard; Huidong Chen; Luca Pinello
Journal:  Curr Opin Syst Biol       Date:  2021-03-26

10.  Spearheading future omics analyses using dyngen, a multi-modal simulator of single cells.

Authors:  Robrecht Cannoodt; Wouter Saelens; Louise Deconinck; Yvan Saeys
Journal:  Nat Commun       Date:  2021-06-24       Impact factor: 14.919
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