Ruminant metabolic systems biology: Reconstruction and integration of transcriptome dynamics underlying functional responses of tissues to nutrition and physiological state

Gene Regulation and Systems Biology

Volumn 2012, Issue 6, 2012, Pages 109-125

  Bionaz, Massimo ^a   Loor, Juan J ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

Bioinformatics; Bovine; Dairy cow; Dynamic impact approach; Lactation; Microarray

Indexed keywords

AMINO ACID; CARBOHYDRATE; FATTY ACID; LIPID; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR; TRANSCRIPTOME;

ADIPOSE TISSUE; AMINO ACID METABOLISM; ANALYTIC METHOD; BIOINFORMATICS; BIRTH; BREAST; CARBOHYDRATE METABOLISM; DAIRY CATTLE; DYNAMIC IMPACT APPROACH; ENERGY BALANCE; ENERGY CONSUMPTION; FATTY ACID METABOLISM; GENE EXPRESSION; GENETIC DATABASE; GLUCONEOGENESIS; GLYCOLYSIS; HIGH THROUGHPUT SCREENING; LACTATION; LIPID METABOLISM; LIPID STORAGE; LIVER METABOLISM; MAMMAL; METABOLIC REGULATION; MILK PRODUCTION; MOLECULAR BIOLOGY; MOLECULAR DYNAMICS; MOLECULAR GENETICS; NONHUMAN; NUTRITION; OXIDATIVE PHOSPHORYLATION; PERINATAL PERIOD; PHYSIOLOGY; PREGNANCY; PUERPERIUM; REVIEW; RUMINANT STOMACH; SYSTEMS BIOLOGY; TISSUE METABOLISM; TRANSCRIPTOMICS;

ANIMALIA; BOVINAE; MAMMALIA;

EID: 84863744233     PISSN: None     EISSN: 11776250     Source Type: Journal    
DOI: 10.4137/GRSB.S9852     Document Type: Review

References (26)

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8. Loor JJ, Bionaz M, Invernizzi G. Systems biology and animal nutrition: insights from the dairy cow during growth and the lactation cycle. In: te Pas MFW, Woelders H, Bannink A, editors. Systems Biology and Livestock Science. Wiley-Blackwell; 2011:215-46.
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12. Huang da W, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. Jan 2009;37(1):1-13.
13. Bionaz M, Periasamy K, Rodriguez-Zas SL, Hurley WL, Loor JJ. A novel dynamic impact approach (DIA) for functional analysis of time-course omics studies: validation using the bovine mammary transcriptome. PloS One. 2012;7(3):e32455.
14. von Bertalanffy L. General system theory: a new approach to unity of science.
15. Problems of general system theory. Human Biol. 1951;23(4): 302-12.
16. Cornish-Bowden A. Making systems biology work in the 21st century. Genome Biol. 2005;6(4):317.
17. Cornish-Bowden A, Cardenas ML. Systems biology may work when we learn to understand the parts in terms of the whole. Biochem Soc Trans. Jun 2005;33(Pt 3):516-9.
18. Mo ML, Palsson BO. Understanding human metabolic physiology: a genome-to-systems approach. Trends Biotechnol. Jan 2009;27(1):37-44.
19. Dobrin R, Zhu J, Molony C, et al. Multi-tissue coexpression networks reveal unexpected subnetworks associated with disease. Genome Biol. 2009;10(5):R55.
20. Barendse W, Reverter A, Bunch RJ, Harrison BE, Barris W, Thomas MB. A validated whole-genome association study of efficient food conversion in cattle. Genetics. Jul 2007;176(3):1893-905.
21. Loor JJ, Bionaz M, Invernizzi G. Systems biology and animal nutrition: insights from the dairy cow during growth and the lactation cycle. In: te Pas MFW, Woelders H, Bannink A, editors. Systems Biology and Livestock Science. Wiley-Blackwell; 2011:215-46.
22. Loor JJ. Genomics of metabolic adaptations in the peripartal cow. Animal. 2010;4:1110-39.
23. Bruggeman FJ, Westerhoff HV. The nature of systems biology. Trends Microbiol. Jan 2007;15(1):45-50.
24. Luscombe NM, Greenbaum D, Gerstein M. What is bioinformatics? A proposed definition and overview of the field. Methods Inf Med. 2001; 40(4):346-58.
25. Huang da W, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. Jan 2009;37(1):1-13.
26. Bionaz M, Periasamy K, Rodriguez-Zas SL, Hurley WL, Loor JJ. A novel dynamic impact approach (DIA) for functional analysis of time-course omics studies: validation using the bovine mammary transcriptome. PloS One. 2012;7(3):e32455.