Literature DB >> 19690627

Bioinformatic primer for clinical and translational science.

Randolph S Faustino1, Anca Chiriac, Andre Terzic.   

Abstract

The advent of high-throughput technologies has accelerated generation and expansion of genomic, transcriptomic, and proteomic data. Acquisition of high-dimensional datasets requires archival systems that permit efficiency of storage and retrieval, and so, multiple electronic repositories have been initiated and maintained to meet this demand. Bioinformatic science has evolved, from these intricate bodies of dynamically updated information and the tools to manage them, as a necessity to harness and decipher the inherent complexity of high-volume data. Large datasets are associated with a variable degree of stochastic noise that contributes to the balance of an ordered, multistable state with the capacity to evolve in response to stimulus, thus exhibiting a hallmark feature of biological criticality. In this context, the network theory has become an invaluable tool to map relationships that integrate discrete elements that collectively direct global function within a particular -omic category, and indeed, the prioritized focus on the functional whole of the genomic, transcriptomic, or proteomic strata over single molecules is a primary tenet of systems biology analyses. This new biology perspective allows inspection and prediction of disease conditions, not limited to a monogenic challenge, but as a combination of individualized molecular permutations acting in concert to effect a phenotypic outcome. Bioinformatic integration of multidimensional data within and between biological layers thus harbors the potential to identify unique biological signatures, providing an enabling platform for advances in clinical and translational science.

Entities:  

Keywords:  bioinformatics; data analysis; information integration

Mesh:

Year:  2008        PMID: 19690627      PMCID: PMC2727724          DOI: 10.1111/j.1752-8062.2008.00038.x

Source DB:  PubMed          Journal:  Clin Transl Sci        ISSN: 1752-8054            Impact factor:   4.689


  43 in total

Review 1.  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

2.  Control of stochasticity in eukaryotic gene expression.

Authors:  Jonathan M Raser; Erin K O'Shea
Journal:  Science       Date:  2004-05-27       Impact factor: 47.728

3.  Systems biology and new technologies enable predictive and preventative medicine.

Authors:  Leroy Hood; James R Heath; Michael E Phelps; Biaoyang Lin
Journal:  Science       Date:  2004-10-22       Impact factor: 47.728

4.  Identification of a common gene expression signature in dilated cardiomyopathy across independent microarray studies.

Authors:  Andreas S Barth; Ruprecht Kuner; Andreas Buness; Markus Ruschhaupt; Sylvia Merk; Ludwig Zwermann; Stefan Kääb; Eckart Kreuzer; Gerhard Steinbeck; Ulrich Mansmann; Annemarie Poustka; Michael Nabauer; Holger Sültmann
Journal:  J Am Coll Cardiol       Date:  2006-09-27       Impact factor: 24.094

5.  Cell-specific expression and pathway analyses reveal alterations in trauma-related human T cell and monocyte pathways.

Authors:  Krzysztof Laudanski; Carol Miller-Graziano; Wenzhong Xiao; Michael N Mindrinos; Daniel R Richards; Asit De; Lyle L Moldawer; Ronald V Maier; Paul Bankey; Henry V Baker; Bernard H Brownstein; J Perren Cobb; Steve E Calvano; Ronald W Davis; Ronald G Tompkins
Journal:  Proc Natl Acad Sci U S A       Date:  2006-10-10       Impact factor: 11.205

6.  Identification of a gene expression profile that differentiates between ischemic and nonischemic cardiomyopathy.

Authors:  Michelle M Kittleson; Shui Q Ye; Rafael A Irizarry; Khalid M Minhas; Gina Edness; John V Conte; Giovanni Parmigiani; Leslie W Miller; Yingjie Chen; Jennifer L Hall; Joe G N Garcia; Joshua M Hare
Journal:  Circulation       Date:  2004-11-22       Impact factor: 29.690

7.  Herrick's 1910 case report of sickle cell anemia. The rest of the story.

Authors:  T L Savitt; M F Goldberg
Journal:  JAMA       Date:  1989-01-13       Impact factor: 56.272

8.  Multiple abnormal beta-hexosaminidase alpha chain mRNAs in a compound-heterozygous Ashkenazi Jewish patient with Tay-Sachs disease.

Authors:  K Ohno; K Suzuki
Journal:  J Biol Chem       Date:  1988-12-05       Impact factor: 5.157

Review 9.  Predicting disease using genomics.

Authors:  John Bell
Journal:  Nature       Date:  2004-05-27       Impact factor: 49.962

10.  Noise minimization in eukaryotic gene expression.

Authors:  Hunter B Fraser; Aaron E Hirsh; Guri Giaever; Jochen Kumm; Michael B Eisen
Journal:  PLoS Biol       Date:  2004-04-27       Impact factor: 8.029

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  6 in total

1.  Applying knowledge-anchored hypothesis discovery methods to advance clinical and translational research: the OAMiner project.

Authors:  Philip R O Payne; Rebecca D Jackson; Thomas M Best; Tara B Borlawsky; Albert M Lai; Stephen James; Metin N Gurcan
Journal:  J Am Med Inform Assoc       Date:  2012-05-30       Impact factor: 4.497

2.  Decoded calreticulin-deficient embryonic stem cell transcriptome resolves latent cardiophenotype.

Authors:  Randolph S Faustino; Anca Chiriac; Nicolas J Niederlander; Timothy J Nelson; Atta Behfar; Prasanna K Mishra; Slobodan Macura; Marek Michalak; Andre Terzic; Carmen Perez-Terzic
Journal:  Stem Cells       Date:  2010-07       Impact factor: 6.277

3.  Cardiogenic induction of pluripotent stem cells streamlined through a conserved SDF-1/VEGF/BMP2 integrated network.

Authors:  Anca Chiriac; Timothy J Nelson; Randolph S Faustino; Atta Behfar; Andre Terzic
Journal:  PLoS One       Date:  2010-04-01       Impact factor: 3.240

4.  Multi-dimensional discovery of biomarker and phenotype complexes.

Authors:  Philip R O Payne; Kun Huang; Kristin Keen-Circle; Abhisek Kundu; Jie Zhang; Tara B Borlawsky
Journal:  BMC Bioinformatics       Date:  2010-10-28       Impact factor: 3.169

5.  Developmental enhancement of adenylate kinase-AMPK metabolic signaling axis supports stem cell cardiac differentiation.

Authors:  Petras P Dzeja; Susan Chung; Randolph S Faustino; Atta Behfar; Andre Terzic
Journal:  PLoS One       Date:  2011-04-27       Impact factor: 3.240

6.  Systems biology surveillance decrypts pathological transcriptome remodeling.

Authors:  Randolph S Faustino; Saranya P Wyles; Jody Groenendyk; Marek Michalak; Andre Terzic; Carmen Perez-Terzic
Journal:  BMC Syst Biol       Date:  2015-07-17
  6 in total

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