Literature DB >> 22377422

Bioinformatics and systems biology.

Prahlad T Ram1, John Mendelsohn, Gordon B Mills.   

Abstract

Delivering personalized therapeutic options to cancer patients based on the genetic and molecular aberrations of the tumor offers great promise to improve the outcomes of cancer therapy. Significant progress in biotechnology has allowed the measurement of tens of thousands of "omic" data points across multiple levels (DNA, RNA protein, metabolomics) from a single tumor biopsy sample in a reasonable time frame for making clinical decisions. With this data in hand, the challenge from the bioinformatics and systems biology point of view is how does one convert data into information and knowledge that can improve the delivery of personalized therapy to the patient.
Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

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Year:  2012        PMID: 22377422      PMCID: PMC3345061          DOI: 10.1016/j.molonc.2012.01.008

Source DB:  PubMed          Journal:  Mol Oncol        ISSN: 1574-7891            Impact factor:   6.603


  70 in total

1.  Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae.

Authors:  Jan Ihmels; Ronen Levy; Naama Barkai
Journal:  Nat Biotechnol       Date:  2003-11-30       Impact factor: 54.908

2.  Building with a scaffold: emerging strategies for high- to low-level cellular modeling.

Authors:  Trey Ideker; Douglas Lauffenburger
Journal:  Trends Biotechnol       Date:  2003-06       Impact factor: 19.536

3.  Causal protein-signaling networks derived from multiparameter single-cell data.

Authors:  Karen Sachs; Omar Perez; Dana Pe'er; Douglas A Lauffenburger; Garry P Nolan
Journal:  Science       Date:  2005-04-22       Impact factor: 47.728

Review 4.  Protein networks in disease.

Authors:  Trey Ideker; Roded Sharan
Journal:  Genome Res       Date:  2008-04       Impact factor: 9.043

5.  Reverse engineering of regulatory networks in human B cells.

Authors:  Katia Basso; Adam A Margolin; Gustavo Stolovitzky; Ulf Klein; Riccardo Dalla-Favera; Andrea Califano
Journal:  Nat Genet       Date:  2005-03-20       Impact factor: 38.330

6.  Comprehensive mapping of the human kinome to epidermal growth factor receptor signaling.

Authors:  Kakajan Komurov; David Padron; Tzuling Cheng; Michael Roth; Kevin P Rosenblatt; Michael A White
Journal:  J Biol Chem       Date:  2010-04-26       Impact factor: 5.157

7.  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

8.  Network topology determines dynamics of the mammalian MAPK1,2 signaling network: bifan motif regulation of C-Raf and B-Raf isoforms by FGFR and MC1R.

Authors:  Melissa Muller; Mandri Obeyesekere; Gordon B Mills; Prahlad T Ram
Journal:  FASEB J       Date:  2008-01-02       Impact factor: 5.191

Review 9.  Cancer systems biology: a network modeling perspective.

Authors:  Pamela K Kreeger; Douglas A Lauffenburger
Journal:  Carcinogenesis       Date:  2009-10-27       Impact factor: 4.944

10.  Finding multiple target optimal intervention in disease-related molecular network.

Authors:  Kun Yang; Hongjun Bai; Qi Ouyang; Luhua Lai; Chao Tang
Journal:  Mol Syst Biol       Date:  2008-11-04       Impact factor: 11.429

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  5 in total

Review 1.  Computational systems biology approaches to anti-angiogenic cancer therapeutics.

Authors:  Stacey D Finley; Liang-Hui Chu; Aleksander S Popel
Journal:  Drug Discov Today       Date:  2014-10-05       Impact factor: 7.851

2.  Phosphoproteomics and bioinformatics analyses of spinal cord proteins in rats with morphine tolerance.

Authors:  Wen-Jinn Liaw; Cheng-Ming Tsao; Go-Shine Huang; Chin-Chen Wu; Shung-Tai Ho; Jhi-Joung Wang; Yuan-Xiang Tao; Hao-Ai Shui
Journal:  PLoS One       Date:  2014-01-02       Impact factor: 3.240

Review 3.  Application of metabolomics in drug resistant breast cancer research.

Authors:  Ayesha N Shajahan-Haq; Mehar S Cheema; Robert Clarke
Journal:  Metabolites       Date:  2015-02-16

4.  The multitude of molecular analyses in cancer: the opening of Pandora’s box.

Authors:  Hege G Russnes; Per E Lønning; Anne-Lise Børresen-Dale; Ole C Lingjærde
Journal:  Genome Biol       Date:  2014       Impact factor: 13.583

Review 5.  Systems Bioinformatics: increasing precision of computational diagnostics and therapeutics through network-based approaches.

Authors:  Anastasis Oulas; George Minadakis; Margarita Zachariou; Kleitos Sokratous; Marilena M Bourdakou; George M Spyrou
Journal:  Brief Bioinform       Date:  2019-05-21       Impact factor: 11.622

  5 in total

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