Literature DB >> 27571553

Diffusion pseudotime robustly reconstructs lineage branching.

Laleh Haghverdi1,2, Maren Büttner1, F Alexander Wolf1, Florian Buettner1,3, Fabian J Theis1,2.   

Abstract

The temporal order of differentiating cells is intrinsically encoded in their single-cell expression profiles. We describe an efficient way to robustly estimate this order according to diffusion pseudotime (DPT), which measures transitions between cells using diffusion-like random walks. Our DPT software implementations make it possible to reconstruct the developmental progression of cells and identify transient or metastable states, branching decisions and differentiation endpoints.

Mesh：

Year:  2016        PMID： 27571553     DOI： 10.1038/nmeth.3971

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


  19 in total

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Authors:  Paul M Magwene; Paul Lizardi; Junhyong Kim
Journal:  Bioinformatics       Date:  2003-05-01       Impact factor: 6.937

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.  Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells.

Authors:  Allon M Klein; Linas Mazutis; Ilke Akartuna; Naren Tallapragada; Adrian Veres; Victor Li; Leonid Peshkin; David A Weitz; Marc W Kirschner
Journal:  Cell       Date:  2015-05-21       Impact factor: 41.582

4.  Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.

Authors:  Evan Z Macosko; Anindita Basu; Rahul Satija; James Nemesh; Karthik Shekhar; Melissa Goldman; Itay Tirosh; Allison R Bialas; Nolan Kamitaki; Emily M Martersteck; John J Trombetta; David A Weitz; Joshua R Sanes; Alex K Shalek; Aviv Regev; Steven A McCarroll
Journal:  Cell       Date:  2015-05-21       Impact factor: 41.582

5.  Diffusion maps for high-dimensional single-cell analysis of differentiation data.

Authors:  Laleh Haghverdi; Florian Buettner; Fabian J Theis
Journal:  Bioinformatics       Date:  2015-05-21       Impact factor: 6.937

6.  destiny: diffusion maps for large-scale single-cell data in R.

Authors:  Philipp Angerer; Laleh Haghverdi; Maren Büttner; Fabian J Theis; Carsten Marr; Florian Buettner
Journal:  Bioinformatics       Date:  2015-12-14       Impact factor: 6.937

7.  Geometric diffusions as a tool for harmonic analysis and structure definition of data: diffusion maps.

Authors:  R R Coifman; S Lafon; A B Lee; M Maggioni; B Nadler; F Warner; S W Zucker
Journal:  Proc Natl Acad Sci U S A       Date:  2005-05-17       Impact factor: 12.779

8.  Decoding the regulatory network of early blood development from single-cell gene expression measurements.

Authors:  Victoria Moignard; Steven Woodhouse; Laleh Haghverdi; Andrew J Lilly; Yosuke Tanaka; Adam C Wilkinson; Florian Buettner; Iain C Macaulay; Wajid Jawaid; Evangelia Diamanti; Shin-Ichi Nishikawa; Nir Piterman; Valerie Kouskoff; Fabian J Theis; Jasmin Fisher; Berthold Göttgens
Journal:  Nat Biotechnol       Date:  2015-02-09       Impact factor: 54.908

9.  MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data.

Authors:  Greg Finak; Andrew McDavid; Masanao Yajima; Jingyuan Deng; Vivian Gersuk; Alex K Shalek; Chloe K Slichter; Hannah W Miller; M Juliana McElrath; Martin Prlic; Peter S Linsley; Raphael Gottardo
Journal:  Genome Biol       Date:  2015-12-10       Impact factor: 13.583

10.  Wishbone identifies bifurcating developmental trajectories from single-cell data.

Authors:  Manu Setty; Michelle D Tadmor; Shlomit Reich-Zeliger; Omer Angel; Tomer Meir Salame; Pooja Kathail; Kristy Choi; Sean Bendall; Nir Friedman; Dana Pe'er
Journal:  Nat Biotechnol       Date:  2016-05-02       Impact factor: 54.908
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  330 in total

1.  Single-Cell RNA-Seq Mapping of Human Thymopoiesis Reveals Lineage Specification Trajectories and a Commitment Spectrum in T Cell Development.

Authors:  Justin Le; Jeong Eun Park; Vi Luan Ha; Annie Luong; Sergio Branciamore; Andrei S Rodin; Grigoriy Gogoshin; Fan Li; Yong-Hwee Eddie Loh; Virginia Camacho; Sweta B Patel; Robert S Welner; Chintan Parekh
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2.  Prioritizing network communities.

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3.  Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis.

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4.  Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation.

Authors:  Jason D Buenrostro; M Ryan Corces; Caleb A Lareau; Beijing Wu; Alicia N Schep; Martin J Aryee; Ravindra Majeti; Howard Y Chang; William J Greenleaf
Journal:  Cell       Date:  2018-04-26       Impact factor: 41.582

Review 5.  Advances in Transcriptomics: Investigating Cardiovascular Disease at Unprecedented Resolution.

Authors:  Robert C Wirka; Milos Pjanic; Thomas Quertermous
Journal:  Circ Res       Date:  2018-04-27       Impact factor: 17.367

Review 6.  Cellular and molecular basis of liver regeneration.

Authors:  Sushant Bangru; Auinash Kalsotra
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Review 7.  Revolutionizing immunology with single-cell RNA sequencing.

Authors:  Haide Chen; Fang Ye; Guoji Guo
Journal:  Cell Mol Immunol       Date:  2019-02-22       Impact factor: 11.530

8.  Modelling acute myeloid leukaemia in a continuum of differentiation states.

Authors:  H Cho; K Ayers; L DePills; Y-H Kuo; J Park; A Radunskaya; R Rockne
Journal:  Lett Biomath       Date:  2018-06-18

Review 9.  Revolutionizing Cancer Immunology: The Power of Next-Generation Sequencing Technologies.

Authors:  Meromit Singer; Ana C Anderson
Journal:  Cancer Immunol Res       Date:  2019-02       Impact factor: 11.151

10.  Aldh1b1 expression defines progenitor cells in the adult pancreas and is required for Kras-induced pancreatic cancer.

Authors:  Ekaterina Mameishvili; Ioannis Serafimidis; Sara Iwaszkiewicz; Mathias Lesche; Susanne Reinhardt; Nora Bölicke; Maren Büttner; Dimitris Stellas; Adriana Papadimitropoulou; Matthias Szabolcs; Konstantinos Anastassiadis; Andreas Dahl; Fabian Theis; Argiris Efstratiadis; Anthony Gavalas
Journal:  Proc Natl Acad Sci U S A       Date:  2019-09-23       Impact factor: 11.205
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