Literature DB >> 24766803

Siri of the cell: what biology could learn from the iPhone.

Anne-Ruxandra Carvunis1, Trey Ideker2.   

Abstract

Modern genomics is very efficient at mapping genes and gene networks, but how to transform these maps into predictive models of the cell remains unclear. Recent progress in computer science, embodied by intelligent agents such as Siri, inspires an approach for moving from networks to multiscale models able to predict a range of cellular phenotypes and answer biological questions.
Copyright © 2014 Elsevier Inc. All rights reserved.

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Year:  2014        PMID： 24766803      PMCID： PMC4154484          DOI： 10.1016/j.cell.2014.03.009

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


  11 in total

1.  Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

Authors:  M Ashburner; C A Ball; J A Blake; D Botstein; H Butler; J M Cherry; A P Davis; K Dolinski; S S Dwight; J T Eppig; M A Harris; D P Hill; L Issel-Tarver; A Kasarskis; S Lewis; J C Matese; J E Richardson; M Ringwald; G M Rubin; G Sherlock
Journal:  Nat Genet       Date:  2000-05       Impact factor: 38.330

Review 2.  Network biology: understanding the cell's functional organization.

Authors:  Albert-László Barabási; Zoltán N Oltvai
Journal:  Nat Rev Genet       Date:  2004-02       Impact factor: 53.242

3.  Allosteric proteins and cellular control systems.

Authors:  J MONOD; J P CHANGEUX; F JACOB
Journal:  J Mol Biol       Date:  1963-04       Impact factor: 5.469

4.  Enzyme associations in T4 phage DNA precursor synthesis.

Authors:  G P Reddy; A Singh; M E Stafford; C K Mathews
Journal:  Proc Natl Acad Sci U S A       Date:  1977-08       Impact factor: 11.205

5.  Question answering systems in biology and medicine--the time is now.

Authors:  Jonathan D Wren
Journal:  Bioinformatics       Date:  2011-06-14       Impact factor: 6.937

6.  Ontology engineering.

Authors:  Gil Alterovitz; Michael Xiang; David P Hill; Jane Lomax; Jonathan Liu; Michael Cherkassky; Jonathan Dreyfuss; Chris Mungall; Midori A Harris; Mary E Dolan; Judith A Blake; Marco F Ramoni
Journal:  Nat Biotechnol       Date:  2010-02       Impact factor: 54.908

Review 7.  The cell-bag of enzymes or network of channels?

Authors:  C K Mathews
Journal:  J Bacteriol       Date:  1993-10       Impact factor: 3.490

Review 8.  A decade of systems biology.

Authors:  Han-Yu Chuang; Matan Hofree; Trey Ideker
Journal:  Annu Rev Cell Dev Biol       Date:  2010       Impact factor: 13.827

9.  A gene ontology inferred from molecular networks.

Authors:  Janusz Dutkowski; Michael Kramer; Michal A Surma; Rama Balakrishnan; J Michael Cherry; Nevan J Krogan; Trey Ideker
Journal:  Nat Biotechnol       Date:  2013-01       Impact factor: 54.908

10.  The automation of science.

Authors:  Ross D King; Jem Rowland; Stephen G Oliver; Michael Young; Wayne Aubrey; Emma Byrne; Maria Liakata; Magdalena Markham; Pinar Pir; Larisa N Soldatova; Andrew Sparkes; Kenneth E Whelan; Amanda Clare
Journal:  Science       Date:  2009-04-03       Impact factor: 47.728
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  16 in total

1.  Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities.

Authors:  Marinka Zitnik; Francis Nguyen; Bo Wang; Jure Leskovec; Anna Goldenberg; Michael M Hoffman
Journal:  Inf Fusion       Date:  2018-09-21       Impact factor: 12.975

Review 2.  From analog to digital models of gene regulation.

Authors:  Brian Munsky; Gregor Neuert
Journal:  Phys Biol       Date:  2015-06-18       Impact factor: 2.583

3.  A user's guide to the Arabidopsis T-DNA insertion mutant collections.

Authors:  Ronan C O'Malley; Cesar C Barragan; Joseph R Ecker
Journal:  Methods Mol Biol       Date:  2015

4.  Half dozen of one, six billion of the other: What can small- and large-scale molecular systems biology learn from one another?

Authors:  Ian A Mellis; Arjun Raj
Journal:  Genome Res       Date:  2015-10       Impact factor: 9.043

5.  Context Specificity in Causal Signaling Networks Revealed by Phosphoprotein Profiling.

Authors:  Steven M Hill; Nicole K Nesser; Katie Johnson-Camacho; Mara Jeffress; Aimee Johnson; Chris Boniface; Simon E F Spencer; Yiling Lu; Laura M Heiser; Yancey Lawrence; Nupur T Pande; James E Korkola; Joe W Gray; Gordon B Mills; Sach Mukherjee; Paul T Spellman
Journal:  Cell Syst       Date:  2016-12-22       Impact factor: 10.304

6.  From word models to executable models of signaling networks using automated assembly.

Authors:  Benjamin M Gyori; John A Bachman; Kartik Subramanian; Jeremy L Muhlich; Lucian Galescu; Peter K Sorger
Journal:  Mol Syst Biol       Date:  2017-11-24       Impact factor: 11.429

7.  Inferring gene ontologies from pairwise similarity data.

Authors:  Michael Kramer; Janusz Dutkowski; Michael Yu; Vineet Bafna; Trey Ideker
Journal:  Bioinformatics       Date:  2014-06-15       Impact factor: 6.937

Review 8.  Discoveries and advances in plant and animal genomics.

Authors:  Rudi Appels; Johan Nystrom; Hollie Webster; Gabriel Keeble-Gagnere
Journal:  Funct Integr Genomics       Date:  2015-03-13       Impact factor: 3.410

9.  Translation of Genotype to Phenotype by a Hierarchy of Cell Subsystems.

Authors:  Michael Ku Yu; Michael Kramer; Janusz Dutkowski; Rohith Srivas; Katherine Licon; Jason Kreisberg; Cherie T Ng; Nevan Krogan; Roded Sharan; Trey Ideker
Journal:  Cell Syst       Date:  2016-02-24       Impact factor: 10.304

10.  Predicting multicellular function through multi-layer tissue networks.

Authors:  Marinka Zitnik; Jure Leskovec
Journal:  Bioinformatics       Date:  2017-07-15       Impact factor: 6.937
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