Literature DB >> 33875884

Statistical mechanics meets single-cell biology.

Andrew E Teschendorff1,2, Andrew P Feinberg3,4,5.   

Abstract

Single-cell omics is transforming our understanding of cell biology and disease, yet the systems-level analysis and interpretation of single-cell data faces many challenges. In this Perspective, we describe the impact that fundamental concepts from statistical mechanics, notably entropy, stochastic processes and critical phenomena, are having on single-cell data analysis. We further advocate the need for more bottom-up modelling of single-cell data and to embrace a statistical mechanics analysis paradigm to help attain a deeper understanding of single-cell systems biology.

Year:  2021        PMID: 33875884     DOI: 10.1038/s41576-021-00341-z

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  161 in total

1.  Catastrophic shifts in ecosystems.

Authors:  M Scheffer; S Carpenter; J A Foley; C Folke; B Walker
Journal:  Nature       Date:  2001-10-11       Impact factor: 49.962

2.  Complex systems: Foreseeing tipping points.

Authors:  Marten Scheffer
Journal:  Nature       Date:  2010-09-23       Impact factor: 49.962

3.  Optimal protein-folding codes from spin-glass theory.

Authors:  R A Goldstein; Z A Luthey-Schulten; P G Wolynes
Journal:  Proc Natl Acad Sci U S A       Date:  1992-06-01       Impact factor: 11.205

Review 4.  Stem cells do play with dice: a statistical physics view of transcription.

Authors:  Sol Efroni; Shai Melcer; Malka Nissim-Rafinia; Eran Meshorer
Journal:  Cell Cycle       Date:  2009-01-16       Impact factor: 4.534

5.  Statistical mechanics of pluripotency.

Authors:  Ben D MacArthur; Ihor R Lemischka
Journal:  Cell       Date:  2013-08-01       Impact factor: 41.582

6.  The Human Cell Atlas: from vision to reality.

Authors:  Orit Rozenblatt-Rosen; Michael J T Stubbington; Aviv Regev; Sarah A Teichmann
Journal:  Nature       Date:  2017-10-18       Impact factor: 49.962

7.  Spin glasses and the statistical mechanics of protein folding.

Authors:  J D Bryngelson; P G Wolynes
Journal:  Proc Natl Acad Sci U S A       Date:  1987-11       Impact factor: 11.205

8.  mRNA-Seq whole-transcriptome analysis of a single cell.

Authors:  Fuchou Tang; Catalin Barbacioru; Yangzhou Wang; Ellen Nordman; Clarence Lee; Nanlan Xu; Xiaohui Wang; John Bodeau; Brian B Tuch; Asim Siddiqui; Kaiqin Lao; M Azim Surani
Journal:  Nat Methods       Date:  2009-04-06       Impact factor: 28.547

Review 9.  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

10.  The Human Cell Atlas.

Authors:  Aviv Regev; Sarah A Teichmann; Eric S Lander; Ido Amit; Christophe Benoist; Ewan Birney; Bernd Bodenmiller; Peter Campbell; Piero Carninci; Menna Clatworthy; Hans Clevers; Bart Deplancke; Ian Dunham; James Eberwine; Roland Eils; Wolfgang Enard; Andrew Farmer; Lars Fugger; Berthold Göttgens; Nir Hacohen; Muzlifah Haniffa; Martin Hemberg; Seung Kim; Paul Klenerman; Arnold Kriegstein; Ed Lein; Sten Linnarsson; Emma Lundberg; Joakim Lundeberg; Partha Majumder; John C Marioni; Miriam Merad; Musa Mhlanga; Martijn Nawijn; Mihai Netea; Garry Nolan; Dana Pe'er; Anthony Phillipakis; Chris P Ponting; Stephen Quake; Wolf Reik; Orit Rozenblatt-Rosen; Joshua Sanes; Rahul Satija; Ton N Schumacher; Alex Shalek; Ehud Shapiro; Padmanee Sharma; Jay W Shin; Oliver Stegle; Michael Stratton; Michael J T Stubbington; Fabian J Theis; Matthias Uhlen; Alexander van Oudenaarden; Allon Wagner; Fiona Watt; Jonathan Weissman; Barbara Wold; Ramnik Xavier; Nir Yosef
Journal:  Elife       Date:  2017-12-05       Impact factor: 8.140

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  16 in total

1.  Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression.

Authors:  Shaolong Cao; Jennifer R Wang; Shuangxi Ji; Peng Yang; Yaoyi Dai; Shuai Guo; Matthew D Montierth; John Paul Shen; Xiao Zhao; Jingxiao Chen; Jaewon James Lee; Paola A Guerrero; Nicholas Spetsieris; Nikolai Engedal; Sinja Taavitsainen; Kaixian Yu; Julie Livingstone; Vinayak Bhandari; Shawna M Hubert; Najat C Daw; P Andrew Futreal; Eleni Efstathiou; Bora Lim; Andrea Viale; Jianjun Zhang; Matti Nykter; Bogdan A Czerniak; Powel H Brown; Charles Swanton; Pavlos Msaouel; Anirban Maitra; Scott Kopetz; Peter Campbell; Terence P Speed; Paul C Boutros; Hongtu Zhu; Alfonso Urbanucci; Jonas Demeulemeester; Peter Van Loo; Wenyi Wang
Journal:  Nat Biotechnol       Date:  2022-06-13       Impact factor: 54.908

2.  Systematic identification of cell-fate regulatory programs using a single-cell atlas of mouse development.

Authors:  Lijiang Fei; Haide Chen; Lifeng Ma; Weigao E; Renying Wang; Xing Fang; Ziming Zhou; Huiyu Sun; Jingjing Wang; Mengmeng Jiang; Xinru Wang; Chengxuan Yu; Yuqing Mei; Danmei Jia; Tingyue Zhang; Xiaoping Han; Guoji Guo
Journal:  Nat Genet       Date:  2022-07-11       Impact factor: 41.307

Review 3.  Reconstructing data-driven governing equations for cell phenotypic transitions: integration of data science and systems biology.

Authors:  Jianhua Xing
Journal:  Phys Biol       Date:  2022-09-09       Impact factor: 2.959

4.  Detecting critical transition signals from single-cell transcriptomes to infer lineage-determining transcription factors.

Authors:  Xinan H Yang; Andrew Goldstein; Yuxi Sun; Zhezhen Wang; Megan Wei; Ivan P Moskowitz; John M Cunningham
Journal:  Nucleic Acids Res       Date:  2022-09-09       Impact factor: 19.160

5.  Forest Fire Clustering for single-cell sequencing combines iterative label propagation with parallelized Monte Carlo simulations.

Authors:  Zhanlin Chen; Jeremy Goldwasser; Philip Tuckman; Jason Liu; Jing Zhang; Mark Gerstein
Journal:  Nat Commun       Date:  2022-06-20       Impact factor: 17.694

6.  Computational approaches for direct cell reprogramming: from the bulk omics era to the single cell era.

Authors:  Andy Tran; Pengyi Yang; Jean Y H Yang; John Ormerod
Journal:  Brief Funct Genomics       Date:  2022-07-27       Impact factor: 4.840

Review 7.  How a cell decides its own fate: a single-cell view of molecular mechanisms and dynamics of cell-type specification.

Authors:  Maria Mircea; Stefan Semrau
Journal:  Biochem Soc Trans       Date:  2021-12-17       Impact factor: 5.407

8.  Reverse engineering of a mechanistic model of gene expression using metastability and temporal dynamics.

Authors:  Elias Ventre
Journal:  In Silico Biol       Date:  2021

9.  Simplifying the Process of Going From Cells to Tissues Using Statistical Mechanics.

Authors:  Jagir R Hussan; Mark L Trew; Peter J Hunter
Journal:  Front Physiol       Date:  2022-03-25       Impact factor: 4.566

10.  Tipping the Balance: A Criticality Perspective.

Authors:  Indrani Bose
Journal:  Entropy (Basel)       Date:  2022-03-14       Impact factor: 2.524

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