Template-Based and Template-Free Approaches in Cellular Cryo-Electron Tomography Structural Pattern Mining

Xindi Wu; Xiangrui Zeng; Zhenxi Zhu; Xin Gao; Min Xu

doi:10.15586/computationalbiology.2019.ch11

Template-Based and Template-Free Approaches in Cellular Cryo-Electron Tomography Structural Pattern Mining

Xindi Wu, Xiangrui Zeng, Zhenxi Zhu, Xin Gao, Min Xu

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Abstract

Cryo-electron tomography (Cryo-ET) has made possible the observation of cellular organelles and macromolecular complexes at nanometer resolution in native conformations. Without disrupting the cell, Cryo-ET directly visualizes both known and unknown structures in situ and reveals their spatial and organizational relationships. Consequently, structural pattern mining (a.k.a. visual proteomics) needs to be performed to detect, identify and recover different sub-cellular components and their spatial organization in a systematic fashion for further biomedical analysis and interpretation. This chapter presents three major Cryo-ET structural pattern mining approaches to give an overview of traditional methods and recent advances in Cryo-ET data analysis. Template-based, supervised deep learning-based and template-free approaches are introduced in detail. Examples of recent biological and medical applications and future perspectives are provided.

Original language	English (US)
Title of host publication	Computational Biology
Publisher	Codon Publications
Pages	175-186
Number of pages	12
ISBN (Print)	9780994438195
DOIs	https://doi.org/10.15586/computationalbiology.2019.ch11
State	Published - Dec 10 2019

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10.15586/computationalbiology.2019.ch11

https://repository.kaust.edu.sa/bitstream/10754/670270/1/226-Book%20Chapter-1337-1-10-20200220.pdf

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title = "Template-Based and Template-Free Approaches in Cellular Cryo-Electron Tomography Structural Pattern Mining",

abstract = "Cryo-electron tomography (Cryo-ET) has made possible the observation of cellular organelles and macromolecular complexes at nanometer resolution in native conformations. Without disrupting the cell, Cryo-ET directly visualizes both known and unknown structures in situ and reveals their spatial and organizational relationships. Consequently, structural pattern mining (a.k.a. visual proteomics) needs to be performed to detect, identify and recover different sub-cellular components and their spatial organization in a systematic fashion for further biomedical analysis and interpretation. This chapter presents three major Cryo-ET structural pattern mining approaches to give an overview of traditional methods and recent advances in Cryo-ET data analysis. Template-based, supervised deep learning-based and template-free approaches are introduced in detail. Examples of recent biological and medical applications and future perspectives are provided.",

author = "Xindi Wu and Xiangrui Zeng and Zhenxi Zhu and Xin Gao and Min Xu",

note = "KAUST Repository Item: Exported on 2021-07-27 Acknowledged KAUST grant number(s): BAS/1/1624, FCC/1/1976-18, FCC/1/1976-23, FCC/1/1976-25, FCC/1/1976-26 Acknowledgements: This work was supported in part by U.S. National Institutes of Health (NIH) grant P41 GM103712. XZ was supported by a fellowship from Carnegie Mellon University{\textquoteright}s Center for Machine Learning and Health. XG acknowledges the support by the King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) under Award No. BAS/1/1624, FCC/1/1976-18, FCC/1/1976-23, FCC/1/1976-25, and FCC/1/1976-26.",

year = "2019",

month = dec,

day = "10",

doi = "10.15586/computationalbiology.2019.ch11",

language = "English (US)",

isbn = "9780994438195",

pages = "175--186",

booktitle = "Computational Biology",

publisher = "Codon Publications",

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TY - CHAP

T1 - Template-Based and Template-Free Approaches in Cellular Cryo-Electron Tomography Structural Pattern Mining

AU - Wu, Xindi

AU - Zeng, Xiangrui

AU - Zhu, Zhenxi

AU - Gao, Xin

AU - Xu, Min

N1 - KAUST Repository Item: Exported on 2021-07-27 Acknowledged KAUST grant number(s): BAS/1/1624, FCC/1/1976-18, FCC/1/1976-23, FCC/1/1976-25, FCC/1/1976-26 Acknowledgements: This work was supported in part by U.S. National Institutes of Health (NIH) grant P41 GM103712. XZ was supported by a fellowship from Carnegie Mellon University’s Center for Machine Learning and Health. XG acknowledges the support by the King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) under Award No. BAS/1/1624, FCC/1/1976-18, FCC/1/1976-23, FCC/1/1976-25, and FCC/1/1976-26.

PY - 2019/12/10

Y1 - 2019/12/10

N2 - Cryo-electron tomography (Cryo-ET) has made possible the observation of cellular organelles and macromolecular complexes at nanometer resolution in native conformations. Without disrupting the cell, Cryo-ET directly visualizes both known and unknown structures in situ and reveals their spatial and organizational relationships. Consequently, structural pattern mining (a.k.a. visual proteomics) needs to be performed to detect, identify and recover different sub-cellular components and their spatial organization in a systematic fashion for further biomedical analysis and interpretation. This chapter presents three major Cryo-ET structural pattern mining approaches to give an overview of traditional methods and recent advances in Cryo-ET data analysis. Template-based, supervised deep learning-based and template-free approaches are introduced in detail. Examples of recent biological and medical applications and future perspectives are provided.

AB - Cryo-electron tomography (Cryo-ET) has made possible the observation of cellular organelles and macromolecular complexes at nanometer resolution in native conformations. Without disrupting the cell, Cryo-ET directly visualizes both known and unknown structures in situ and reveals their spatial and organizational relationships. Consequently, structural pattern mining (a.k.a. visual proteomics) needs to be performed to detect, identify and recover different sub-cellular components and their spatial organization in a systematic fashion for further biomedical analysis and interpretation. This chapter presents three major Cryo-ET structural pattern mining approaches to give an overview of traditional methods and recent advances in Cryo-ET data analysis. Template-based, supervised deep learning-based and template-free approaches are introduced in detail. Examples of recent biological and medical applications and future perspectives are provided.

UR - http://hdl.handle.net/10754/670270

UR - https://exonpublications.com/index.php/exon/article/view/226

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SN - 9780994438195

SP - 175

EP - 186

BT - Computational Biology

PB - Codon Publications

ER -

Template-Based and Template-Free Approaches in Cellular Cryo-Electron Tomography Structural Pattern Mining

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