Literature DB >> 23352243

From systems to structure: bridging networks and mechanism.

James S Fraser1, John D Gross, Nevan J Krogan.   

Abstract

There is a wide gap between the generation of large-scale biological data sets and more-detailed, structural and mechanistic studies. However, recent studies that explicitly combine data from systems and structural biological approaches are having a profound effect on our ability to predict how mutations and small molecules affect atomic-level mechanisms, disrupt systems-level networks, and ultimately lead to changes in organismal fitness. In fact, we argue that a shared framework for analysis of nonadditive genetic and thermodynamic responses to perturbations will accelerate the integration of reductionist and global approaches. A stronger bridge between these two areas will allow for a deeper and more-complete understanding of complex biological phenomenon and ultimately provide needed breakthroughs in biomedical research.
Copyright © 2013 Elsevier Inc. All rights reserved.

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Year:  2013        PMID: 23352243      PMCID: PMC3558917          DOI: 10.1016/j.molcel.2013.01.003

Source DB:  PubMed          Journal:  Mol Cell        ISSN: 1097-2765            Impact factor:   17.970


  104 in total

1.  Structure-based assembly of protein complexes in yeast.

Authors:  Patrick Aloy; Bettina Böttcher; Hugo Ceulemans; Christina Leutwein; Christian Mellwig; Susanne Fischer; Anne-Claude Gavin; Peer Bork; Giulio Superti-Furga; Luis Serrano; Robert B Russell
Journal:  Science       Date:  2004-03-26       Impact factor: 47.728

2.  Crystal structure of an ancient protein: evolution by conformational epistasis.

Authors:  Eric A Ortlund; Jamie T Bridgham; Matthew R Redinbo; Joseph W Thornton
Journal:  Science       Date:  2007-08-16       Impact factor: 47.728

3.  Selected reaction monitoring mass spectrometry reveals the dynamics of signaling through the GRB2 adaptor.

Authors:  Nicolas Bisson; D Andrew James; Gordana Ivosev; Stephen A Tate; Ron Bonner; Lorne Taylor; Tony Pawson
Journal:  Nat Biotechnol       Date:  2011-06-26       Impact factor: 54.908

4.  Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae.

Authors:  Mohan Babu; James Vlasblom; Shuye Pu; Xinghua Guo; Chris Graham; Björn D M Bean; Helen E Burston; Franco J Vizeacoumar; Jamie Snider; Sadhna Phanse; Vincent Fong; Yuen Yi C Tam; Michael Davey; Olha Hnatshak; Navgeet Bajaj; Shamanta Chandran; Thanuja Punna; Constantine Christopolous; Victoria Wong; Analyn Yu; Gouqing Zhong; Joyce Li; Igor Stagljar; Elizabeth Conibear; Shoshana J Wodak; Andrew Emili; Jack F Greenblatt
Journal:  Nature       Date:  2012-09-02       Impact factor: 49.962

5.  Hot spots for allosteric regulation on protein surfaces.

Authors:  Kimberly A Reynolds; Richard N McLaughlin; Rama Ranganathan
Journal:  Cell       Date:  2011-12-23       Impact factor: 41.582

6.  BRCA2 function in DNA binding and recombination from a BRCA2-DSS1-ssDNA structure.

Authors:  Haijuan Yang; Philip D Jeffrey; Julie Miller; Elspeth Kinnucan; Yutong Sun; Nicolas H Thoma; Ning Zheng; Phang-Lang Chen; Wen-Hwa Lee; Nikola P Pavletich
Journal:  Science       Date:  2002-09-13       Impact factor: 47.728

7.  The spatial architecture of protein function and adaptation.

Authors:  Richard N McLaughlin; Frank J Poelwijk; Arjun Raman; Walraj S Gosal; Rama Ranganathan
Journal:  Nature       Date:  2012-10-07       Impact factor: 49.962

8.  Sequential application of anticancer drugs enhances cell death by rewiring apoptotic signaling networks.

Authors:  Michael J Lee; Albert S Ye; Alexandra K Gardino; Anne Margriet Heijink; Peter K Sorger; Gavin MacBeath; Michael B Yaffe
Journal:  Cell       Date:  2012-05-11       Impact factor: 41.582

9.  ModBase, a database of annotated comparative protein structure models, and associated resources.

Authors:  Ursula Pieper; Benjamin M Webb; David T Barkan; Dina Schneidman-Duhovny; Avner Schlessinger; Hannes Braberg; Zheng Yang; Elaine C Meng; Eric F Pettersen; Conrad C Huang; Ruchira S Datta; Parthasarathy Sampathkumar; Mallur S Madhusudhan; Kimmen Sjölander; Thomas E Ferrin; Stephen K Burley; Andrej Sali
Journal:  Nucleic Acids Res       Date:  2010-11-19       Impact factor: 16.971

10.  High-throughput, quantitative analyses of genetic interactions in E. coli.

Authors:  Athanasios Typas; Robert J Nichols; Deborah A Siegele; Michael Shales; Sean R Collins; Bentley Lim; Hannes Braberg; Natsuko Yamamoto; Rikiya Takeuchi; Barry L Wanner; Hirotada Mori; Jonathan S Weissman; Nevan J Krogan; Carol A Gross
Journal:  Nat Methods       Date:  2008-09       Impact factor: 28.547

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  17 in total

Review 1.  Systems Biology for Smart Crops and Agricultural Innovation: Filling the Gaps between Genotype and Phenotype for Complex Traits Linked with Robust Agricultural Productivity and Sustainability.

Authors:  Anil Kumar; Rajesh Kumar Pathak; Sanjay Mohan Gupta; Vikram Singh Gaur; Dinesh Pandey
Journal:  OMICS       Date:  2015-10

2.  Systematic exploration of ubiquitin sequence, E1 activation efficiency, and experimental fitness in yeast.

Authors:  Benjamin P Roscoe; Daniel N A Bolon
Journal:  J Mol Biol       Date:  2014-05-24       Impact factor: 5.469

Review 3.  Modeling thrombin generation: plasma composition based approach.

Authors:  Kathleen E Brummel-Ziedins; Stephen J Everse; Kenneth G Mann; Thomas Orfeo
Journal:  J Thromb Thrombolysis       Date:  2014-01       Impact factor: 2.300

Review 4.  Comparing protein folding in vitro and in vivo: foldability meets the fitness challenge.

Authors:  Karan S Hingorani; Lila M Gierasch
Journal:  Curr Opin Struct Biol       Date:  2014-01-14       Impact factor: 6.809

Review 5.  Genotype to phenotype via network analysis.

Authors:  Hannah Carter; Matan Hofree; Trey Ideker
Journal:  Curr Opin Genet Dev       Date:  2013-11-14       Impact factor: 5.578

Review 6.  High-resolution network biology: connecting sequence with function.

Authors:  Colm J Ryan; Peter Cimermančič; Zachary A Szpiech; Andrej Sali; Ryan D Hernandez; Nevan J Krogan
Journal:  Nat Rev Genet       Date:  2013-11-07       Impact factor: 53.242

Review 7.  Design principles of regulatory networks: searching for the molecular algorithms of the cell.

Authors:  Wendell A Lim; Connie M Lee; Chao Tang
Journal:  Mol Cell       Date:  2013-01-24       Impact factor: 17.970

8.  DEEPN as an Approach for Batch Processing of Yeast 2-Hybrid Interactions.

Authors:  Natasha Pashkova; Tabitha A Peterson; Venkatramanan Krishnamani; Patrick Breheny; Mark Stamnes; Robert C Piper
Journal:  Cell Rep       Date:  2016-09-27       Impact factor: 9.423

Review 9.  Structural bioinformatics of the interactome.

Authors:  Donald Petrey; Barry Honig
Journal:  Annu Rev Biophys       Date:  2014       Impact factor: 12.981

Review 10.  Protein production from the structural genomics perspective: achievements and future needs.

Authors:  Steven C Almo; Scott J Garforth; Brandan S Hillerich; James D Love; Ronald D Seidel; Stephen K Burley
Journal:  Curr Opin Struct Biol       Date:  2013-05-01       Impact factor: 6.809

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