Literature DB >> 21044756

Integrative systems biology for data-driven knowledge discovery.

Casey S Greene1, Olga G Troyanskaya.   

Abstract

Integrative systems biology is an approach that brings together diverse high-throughput experiments and databases to gain new insights into biological processes or systems at molecular through physiological levels. These approaches rely on diverse high-throughput experimental techniques that generate heterogeneous data by assaying varying aspects of complex biological processes. Computational approaches are necessary to provide an integrative view of these experimental results and enable data-driven knowledge discovery. Hypotheses generated from these approaches can direct definitive molecular experiments in a cost-effective manner. By using integrative systems biology approaches, we can leverage existing biological knowledge and large-scale data to improve our understanding of as yet unknown components of a system of interest and how its malfunction leads to disease. 2010 Published by Elsevier Inc.

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Year:  2010        PMID: 21044756      PMCID: PMC4734377          DOI: 10.1016/j.semnephrol.2010.07.002

Source DB:  PubMed          Journal:  Semin Nephrol        ISSN: 0270-9295            Impact factor:   5.299


  70 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.  BIND: the Biomolecular Interaction Network Database.

Authors:  Gary D Bader; Doron Betel; Christopher W V Hogue
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

3.  Integrating high-throughput and computational data elucidates bacterial networks.

Authors:  Markus W Covert; Eric M Knight; Jennifer L Reed; Markus J Herrgard; Bernhard O Palsson
Journal:  Nature       Date:  2004-05-06       Impact factor: 49.962

4.  Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.

Authors:  Aravind Subramanian; Pablo Tamayo; Vamsi K Mootha; Sayan Mukherjee; Benjamin L Ebert; Michael A Gillette; Amanda Paulovich; Scott L Pomeroy; Todd R Golub; Eric S Lander; Jill P Mesirov
Journal:  Proc Natl Acad Sci U S A       Date:  2005-09-30       Impact factor: 11.205

5.  Direct analysis of protein complexes using mass spectrometry.

Authors:  A J Link; J Eng; D M Schieltz; E Carmack; G J Mize; D R Morris; B M Garvik; J R Yates
Journal:  Nat Biotechnol       Date:  1999-07       Impact factor: 54.908

6.  Human Zwint-1 specifies localization of Zeste White 10 to kinetochores and is essential for mitotic checkpoint signaling.

Authors:  Hongmei Wang; Xiaoyu Hu; Xia Ding; Zhen Dou; Zhihong Yang; Andrew W Shaw; Maikun Teng; Don W Cleveland; Michael L Goldberg; Liwen Niu; Xuebiao Yao
Journal:  J Biol Chem       Date:  2004-10-13       Impact factor: 5.157

Review 7.  RNA-Seq: a revolutionary tool for transcriptomics.

Authors:  Zhong Wang; Mark Gerstein; Michael Snyder
Journal:  Nat Rev Genet       Date:  2009-01       Impact factor: 53.242

Review 8.  The nature of systems biology.

Authors:  Frank J Bruggeman; Hans V Westerhoff
Journal:  Trends Microbiol       Date:  2006-11-20       Impact factor: 17.079

9.  Genome-wide genotyping in amyotrophic lateral sclerosis and neurologically normal controls: first stage analysis and public release of data.

Authors:  Jennifer C Schymick; Sonja W Scholz; Hon-Chung Fung; Angela Britton; Sampath Arepalli; J Raphael Gibbs; Federica Lombardo; Mar Matarin; Dalia Kasperaviciute; Dena G Hernandez; Cynthia Crews; Lucie Bruijn; Jeffrey Rothstein; Gabriele Mora; Gabriella Restagno; Adriano Chiò; Andrew Singleton; John Hardy; Bryan J Traynor
Journal:  Lancet Neurol       Date:  2007-04       Impact factor: 44.182

10.  Designing genome-wide association studies: sample size, power, imputation, and the choice of genotyping chip.

Authors:  Chris C A Spencer; Zhan Su; Peter Donnelly; Jonathan Marchini
Journal:  PLoS Genet       Date:  2009-05-15       Impact factor: 5.917

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  6 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.  Integrative biology of renal disease: toward a holistic understanding of the kidney's function and failure.

Authors:  Matthias Kretzler; Clemens D Cohen
Journal:  Semin Nephrol       Date:  2010-09       Impact factor: 5.299

Review 3.  Functional adaptations of the transcriptome to mastitis-causing pathogens: the mammary gland and beyond.

Authors:  Juan J Loor; Kasey M Moyes; Massimo Bionaz
Journal:  J Mammary Gland Biol Neoplasia       Date:  2011-10-04       Impact factor: 2.673

4.  The need for mouse models in osteoporosis genetics research.

Authors:  Cheryl L Ackert-Bicknell; Matthew A Hibbs
Journal:  Bonekey Rep       Date:  2012-06-13

Review 5.  Defining nephrotic syndrome from an integrative genomics perspective.

Authors:  Matthew G Sampson; Jeffrey B Hodgin; Matthias Kretzler
Journal:  Pediatr Nephrol       Date:  2014-06-03       Impact factor: 3.714

6.  Abasy Atlas v2.2: The most comprehensive and up-to-date inventory of meta-curated, historical, bacterial regulatory networks, their completeness and system-level characterization.

Authors:  Juan M Escorcia-Rodríguez; Andreas Tauch; Julio A Freyre-González
Journal:  Comput Struct Biotechnol J       Date:  2020-05-16       Impact factor: 7.271

  6 in total

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