Literature DB >> 29570991

Opportunities and Challenges in Building a Spatiotemporal Multi-scale Model of the Human Pancreatic β Cell.

Jitin Singla1, Kyle M McClary2, Kate L White3, Frank Alber4, Andrej Sali5, Raymond C Stevens6.   

Abstract

The construction of a predictive model of an entire eukaryotic cell that describes its dynamic structure from atomic to cellular scales is a grand challenge at the intersection of biology, chemistry, physics, and computer science. Having such a model will open new dimensions in biological research and accelerate healthcare advancements. Developing the necessary experimental and modeling methods presents abundant opportunities for a community effort to realize this goal. Here, we present a vision for creation of a spatiotemporal multi-scale model of the pancreatic β-cell, a relevant target for understanding and modulating the pathogenesis of diabetes.
Copyright © 2018 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  Whole-cell modeling; convergent bioscience; data-driven modeling; diabetes; integrative modeling; modeling of dynamics; multi-scale modeling; pancreatic β–cells; structure modeling

Mesh:

Substances:

Year:  2018        PMID: 29570991      PMCID: PMC6014618          DOI: 10.1016/j.cell.2018.03.014

Source DB:  PubMed          Journal:  Cell        ISSN: 0092-8674            Impact factor:   41.582


  85 in total

1.  E-CELL: software environment for whole-cell simulation.

Authors:  M Tomita; K Hashimoto; K Takahashi; T S Shimizu; Y Matsuzaki; F Miyoshi; K Saito; S Tanida; K Yugi; J C Venter; C A Hutchison
Journal:  Bioinformatics       Date:  1999-01       Impact factor: 6.937

Review 2.  Integrated, multi-scale, spatial-temporal cell biology--A next step in the post genomic era.

Authors:  Rick Horwitz
Journal:  Methods       Date:  2015-09-07       Impact factor: 3.608

3.  Reversal of diabetes with insulin-producing cells derived in vitro from human pluripotent stem cells.

Authors:  Alireza Rezania; Jennifer E Bruin; Payal Arora; Allison Rubin; Irina Batushansky; Ali Asadi; Shannon O'Dwyer; Nina Quiskamp; Majid Mojibian; Tobias Albrecht; Yu Hsuan Carol Yang; James D Johnson; Timothy J Kieffer
Journal:  Nat Biotechnol       Date:  2014-09-11       Impact factor: 54.908

4.  PDB-Dev: a Prototype System for Depositing Integrative/Hybrid Structural Models.

Authors:  Stephen K Burley; Genji Kurisu; John L Markley; Haruki Nakamura; Sameer Velankar; Helen M Berman; Andrej Sali; Torsten Schwede; Jill Trewhella
Journal:  Structure       Date:  2017-09-05       Impact factor: 5.006

5.  Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm.

Authors:  Sean R McGuffee; Adrian H Elcock
Journal:  PLoS Comput Biol       Date:  2010-03-05       Impact factor: 4.475

Review 6.  Uncertainty in integrative structural modeling.

Authors:  Dina Schneidman-Duhovny; Riccardo Pellarin; Andrej Sali
Journal:  Curr Opin Struct Biol       Date:  2014-08-28       Impact factor: 6.809

7.  D²P²: database of disordered protein predictions.

Authors:  Matt E Oates; Pedro Romero; Takashi Ishida; Mohamed Ghalwash; Marcin J Mizianty; Bin Xue; Zsuzsanna Dosztányi; Vladimir N Uversky; Zoran Obradovic; Lukasz Kurgan; A Keith Dunker; Julian Gough
Journal:  Nucleic Acids Res       Date:  2012-11-29       Impact factor: 16.971

8.  Quantitative proteomics of rat and human pancreatic beta cells.

Authors:  B Brackeva; G Kramer; J P C Vissers; G A Martens
Journal:  Data Brief       Date:  2015-03-10

9.  Accelerated discovery via a whole-cell model.

Authors:  Jayodita C Sanghvi; Sergi Regot; Silvia Carrasco; Jonathan R Karr; Miriam V Gutschow; Benjamin Bolival; Markus W Covert
Journal:  Nat Methods       Date:  2013-11-03       Impact factor: 28.547

10.  A comprehensive lipidomic screen of pancreatic β-cells using mass spectroscopy defines novel features of glucose-stimulated turnover of neutral lipids, sphingolipids and plasmalogens.

Authors:  Gemma L Pearson; Natalie Mellett; Kwan Yi Chu; Ebru Boslem; Peter J Meikle; Trevor J Biden
Journal:  Mol Metab       Date:  2016-04-13       Impact factor: 7.422

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  22 in total

Review 1.  From Atoms to Cells: Using Mesoscale Landscapes to Construct Visual Narratives.

Authors:  David S Goodsell; Margaret A Franzen; Tim Herman
Journal:  J Mol Biol       Date:  2018-06-07       Impact factor: 5.469

Review 2.  Principles for Integrative Structural Biology Studies.

Authors:  Michael P Rout; Andrej Sali
Journal:  Cell       Date:  2019-05-30       Impact factor: 41.582

Review 3.  Whole-Cell Models and Simulations in Molecular Detail.

Authors:  Michael Feig; Yuji Sugita
Journal:  Annu Rev Cell Dev Biol       Date:  2019-07-12       Impact factor: 13.827

4.  The European Research Network on Signal Transduction (ERNEST): Toward a Multidimensional Holistic Understanding of G Protein-Coupled Receptor Signaling.

Authors:  Martha E Sommer; Jana Selent; Jens Carlsson; Chris De Graaf; David E Gloriam; Gyorgy M Keseru; Mickey Kosloff; Stefan Mordalski; Aurelien Rizk; Mette M Rosenkilde; Eddy Sotelo; Johanna K S Tiemann; Andrew Tobin; Nina Vardjan; Maria Waldhoer; Peter Kolb
Journal:  ACS Pharmacol Transl Sci       Date:  2020-03-31

5.  Genetic interaction mapping informs integrative structure determination of protein complexes.

Authors:  Hannes Braberg; Ignacia Echeverria; Stefan Bohn; Peter Cimermancic; Anthony Shiver; Richard Alexander; Jiewei Xu; Michael Shales; Raghuvar Dronamraju; Shuangying Jiang; Gajendradhar Dwivedi; Derek Bogdanoff; Kaitlin K Chaung; Ruth Hüttenhain; Shuyi Wang; David Mavor; Riccardo Pellarin; Dina Schneidman; Joel S Bader; James S Fraser; John Morris; James E Haber; Brian D Strahl; Carol A Gross; Junbiao Dai; Jef D Boeke; Andrej Sali; Nevan J Krogan
Journal:  Science       Date:  2020-12-11       Impact factor: 47.728

6.  Building Structural Models of a Whole Mycoplasma Cell.

Authors:  Martina Maritan; Ludovic Autin; Jonathan Karr; Markus W Covert; Arthur J Olson; David S Goodsell
Journal:  J Mol Biol       Date:  2021-11-10       Impact factor: 5.469

7.  Bayesian metamodeling of complex biological systems across varying representations.

Authors:  Barak Raveh; Liping Sun; Kate L White; Tanmoy Sanyal; Jeremy Tempkin; Dongqing Zheng; Kala Bharath; Jitin Singla; Chenxi Wang; Jihui Zhao; Angdi Li; Nicholas A Graham; Carl Kesselman; Raymond C Stevens; Andrej Sali
Journal:  Proc Natl Acad Sci U S A       Date:  2021-08-31       Impact factor: 11.205

Review 8.  Art and Science of the Cellular Mesoscale.

Authors:  David S Goodsell; Arthur J Olson; Stefano Forli
Journal:  Trends Biochem Sci       Date:  2020-03-21       Impact factor: 13.807

Review 9.  From integrative structural biology to cell biology.

Authors:  Andrej Sali
Journal:  J Biol Chem       Date:  2021-05-03       Impact factor: 5.157

Review 10.  Mapping the multiscale structure of biological systems.

Authors:  Leah V Schaffer; Trey Ideker
Journal:  Cell Syst       Date:  2021-06-16       Impact factor: 11.091

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