Literature DB >> 20061351

Toward the dynamic interactome: it's about time.

Teresa M Przytycka1, Mona Singh, Donna K Slonim.   

Abstract

Dynamic molecular interactions play a central role in regulating the functioning of cells and organisms. The availability of experimentally determined large-scale cellular networks, along with other high-throughput experimental data sets that provide snapshots of biological systems at different times and conditions, is increasingly helpful in elucidating interaction dynamics. Here we review the beginnings of a new subfield within computational biology, one focused on the global inference and analysis of the dynamic interactome. This burgeoning research area, which entails a shift from static to dynamic network analysis, promises to be a major step forward in our ability to model and reason about cellular function and behavior.

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Year:  2010        PMID: 20061351      PMCID: PMC2810115          DOI: 10.1093/bib/bbp057

Source DB:  PubMed          Journal:  Brief Bioinform        ISSN: 1467-5463            Impact factor:   11.622


  166 in total

1.  KEGG: kyoto encyclopedia of genes and genomes.

Authors:  M Kanehisa; S Goto
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  Inferring subnetworks from perturbed expression profiles.

Authors:  D Pe'er; A Regev; G Elidan; N Friedman
Journal:  Bioinformatics       Date:  2001       Impact factor: 6.937

3.  Network component analysis: reconstruction of regulatory signals in biological systems.

Authors:  James C Liao; Riccardo Boscolo; Young-Lyeol Yang; Linh My Tran; Chiara Sabatti; Vwani P Roychowdhury
Journal:  Proc Natl Acad Sci U S A       Date:  2003-12-12       Impact factor: 11.205

4.  An integrative genomics approach to infer causal associations between gene expression and disease.

Authors:  Eric E Schadt; John Lamb; Xia Yang; Jun Zhu; Steve Edwards; Debraj Guhathakurta; Solveig K Sieberts; Stephanie Monks; Marc Reitman; Chunsheng Zhang; Pek Yee Lum; Amy Leonardson; Rolf Thieringer; Joseph M Metzger; Liming Yang; John Castle; Haoyuan Zhu; Shera F Kash; Thomas A Drake; Alan Sachs; Aldons J Lusis
Journal:  Nat Genet       Date:  2005-06-19       Impact factor: 38.330

5.  Subspace differential coexpression analysis: problem definition and a general approach.

Authors:  Gang Fang; Rui Kuang; Gaurav Pandey; Michael Steinbach; Chad L Myers; Vipin Kumar
Journal:  Pac Symp Biocomput       Date:  2010

6.  A novel genetic system to detect protein-protein interactions.

Authors:  S Fields; O Song
Journal:  Nature       Date:  1989-07-20       Impact factor: 49.962

7.  KELLER: estimating time-varying interactions between genes.

Authors:  Le Song; Mladen Kolar; Eric P Xing
Journal:  Bioinformatics       Date:  2009-06-15       Impact factor: 6.937

8.  Genome-wide mapping of in vivo protein-DNA interactions.

Authors:  David S Johnson; Ali Mortazavi; Richard M Myers; Barbara Wold
Journal:  Science       Date:  2007-05-31       Impact factor: 47.728

9.  Boolean network simulations for life scientists.

Authors:  István Albert; Juilee Thakar; Song Li; Ranran Zhang; Réka Albert
Journal:  Source Code Biol Med       Date:  2008-11-14

10.  Learning a prior on regulatory potential from eQTL data.

Authors:  Su-In Lee; Aimée M Dudley; David Drubin; Pamela A Silver; Nevan J Krogan; Dana Pe'er; Daphne Koller
Journal:  PLoS Genet       Date:  2009-01-30       Impact factor: 5.917

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  80 in total

1.  Topological analysis and interactive visualization of biological networks and protein structures.

Authors:  Nadezhda T Doncheva; Yassen Assenov; Francisco S Domingues; Mario Albrecht
Journal:  Nat Protoc       Date:  2012-03-15       Impact factor: 13.491

2.  Integrating heterogeneous gene expression data for gene regulatory network modelling.

Authors:  Alina Sîrbu; Heather J Ruskin; Martin Crane
Journal:  Theory Biosci       Date:  2011-09-24       Impact factor: 1.919

3.  Categorizing biases in high-confidence high-throughput protein-protein interaction data sets.

Authors:  Xueping Yu; Joseph Ivanic; Vesna Memisević; Anders Wallqvist; Jaques Reifman
Journal:  Mol Cell Proteomics       Date:  2011-08-29       Impact factor: 5.911

Review 4.  Systems biology for molecular life sciences and its impact in biomedicine.

Authors:  Miguel Ángel Medina
Journal:  Cell Mol Life Sci       Date:  2012-08-19       Impact factor: 9.261

Review 5.  Spatiotemporal positioning of multipotent modules in diverse biological networks.

Authors:  Yinying Chen; Zhong Wang; Yongyan Wang
Journal:  Cell Mol Life Sci       Date:  2014-01-11       Impact factor: 9.261

Review 6.  On the role of electrostatics in protein-protein interactions.

Authors:  Zhe Zhang; Shawn Witham; Emil Alexov
Journal:  Phys Biol       Date:  2011-05-13       Impact factor: 2.583

7.  Dynamic Protein Interactions of the Polycomb Repressive Complex 2 during Differentiation of Pluripotent Cells.

Authors:  Giorgio Oliviero; Gerard L Brien; Ariane Waston; Gundula Streubel; Emilia Jerman; Darrell Andrews; Benjamin Doyle; Nayla Munawar; Kieran Wynne; John Crean; Adrian P Bracken; Gerard Cagney
Journal:  Mol Cell Proteomics       Date:  2016-09-15       Impact factor: 5.911

8.  Comparing signaling networks between normal and transformed hepatocytes using discrete logical models.

Authors:  Julio Saez-Rodriguez; Leonidas G Alexopoulos; Mingsheng Zhang; Melody K Morris; Douglas A Lauffenburger; Peter K Sorger
Journal:  Cancer Res       Date:  2011-07-08       Impact factor: 12.701

Review 9.  Beyond modules and hubs: the potential of gene coexpression networks for investigating molecular mechanisms of complex brain disorders.

Authors:  C Gaiteri; Y Ding; B French; G C Tseng; E Sibille
Journal:  Genes Brain Behav       Date:  2013-12-10       Impact factor: 3.449

10.  Cross-platform microarray data normalisation for regulatory network inference.

Authors:  Alina Sîrbu; Heather J Ruskin; Martin Crane
Journal:  PLoS One       Date:  2010-11-12       Impact factor: 3.240

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