Personalized_Medicine_A_New_Medical_and_Social_Challenge

(Barré) #1

Lee DS, Park J, Kay KA, Christakis NA, Oltvai ZN, Barabsi AL (2008) The implications of human
metabolic network topology for disease comorbidity. Proc Natl Acad Sci 105(29):9880–9885.
doi:10.1073/pnas.0802208105
Li S, Armstrong C, Bertin N et al (2004) A map of the interactome network of the metazoan
c. elegans. Science 303(5657):540–543. doi:10.1126/science.1091403
Linghu B, Snitkin E, Hu Z, Xia Y, DeLisi C (2009) Genome-wide prioritization of disease genes
and identification of disease-disease associations from an integrated human functional linkage
network. Genome Biol 10(9):R91. doi:10.1186/gb-2009-10-9-r91
Lu LJ, Xia Y, Paccanaro A, Yu H, Gerstein M (2005) Assessing the limits of genomic data
integration for predicting protein networks. Genome Res 15(7):945–953. doi:10.1101/gr.
3610305
Luo F, Yang Y, Zhong J, Gao H, Khan L, Thompson D, Zhou J (2007) Constructing gene
co-expression networks and predicting functions of unknown genes by random matrix theory.
BMC Bioinform 8(1):299. doi:10.1186/1471-2105-8-299
Ma X, Chen T, Sun F (2013) Integrative approaches for predicting protein function and prioritizing
genes for complex phenotypes using protein interaction networks. Brief Bioinform. doi:10.
1093/bib/bbt041
Mani R, StOnge RP, Hartman JL, Giaever G, Roth FP (2008) Defining genetic interaction. Proc
Natl Acad Sci 105(9):3461–3466. doi:10.1073/pnas.0712255105
Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y (2008) RNA-seq: an assessment of
technical reproducibility and comparison with gene expression arrays. Genome Res
18:1509–1517
Mccarthy MI, Abecasis GR, Cardon LR, Goldstein DB, Little J, Ioannidis JPA, Hirschhorn JN
(2008) Genome-wide association studies for complex traits: consensus, uncertainty and chal-
lenges. Nat Rev Genet 9(5):356–369. doi:10.1038/nrg2344
Milenkovic ́T, Pržulj N (2008) Uncovering Biological Network Function via Graphlet Degree
Signatures. Cancer Inform 6:00. doi:10.4137/CIN.S680
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying
mammalian transcriptomes by RNA-seq. Nat Meth 5(7):621–628. doi:10.1038/nmeth.1226
Napolitano F, Zhao Y, Moreira VM, Tagliaferri R, Kere J, D’Amato M, Greco D (2013) Drug
repositioning: a machine-learning approach through data integration. J Cheminform 5:30
Nariai N, Kolaczyk ED, Kasif S (2007) Probabilistic protein function prediction from heteroge-
neous genome-wide data. PLoS One 2(3):e337. doi:10.1371/journal.pone. 0000337
Natarajan N, Dhillon IS (2014) Inductive matrix completion for predicting gene-disease associa-
tions. Bioinformatics 30(12):i60–i68. doi:10.1093/bioinformatics/btu269
Nelson S, Schopen M, Savage A, Schulman J, Arluk N (2004) The mesh translation maintenance
system: structure, interface design, and implementation. In: Proceedings of the 11th World
Congress on Medical Informatics, IOS Press, pp 67–69
Newman M (2010) Networks: an introduction. Oxford University Press, Inc., New York
Ooi SL, Shoemaker DD, Boeke JD (2003) DNA helicase gene interaction network defined using
synthetic lethality analyzed by microarray. Nat Genet 35(3):277–286
Osborne J, Flatow J, Holko M, Lin S, Kibbe W, Zhu L, Danila M, Feng G, Chisholm R (2009)
Annotating the human genome with disease ontology. BMC Genomics 10(Suppl 1):S6. doi:10.
1186/1471-2164-10-S1-S6
Parkinson H, Sarkans U, Shojatalab M, Abeygunawardena N, Contrino S, Coulson R, Farne A,
Garcia Lara G, Holloway E, Kapushesky M, Lilja P, Mukherjee G, Oezcimen A, Rayner T,
Rocca-Serra P, Sharma A, Sansone S, Brazma A (2005) ArrayExpress – a public repository for
microarray gene expression data at the ebi. Nucleic Acids Res 33(Suppl 1):D553–D555.
doi:10.1093/nar/gki056
Prieto C, Risueo A, Fontanillo C, De Las Rivas J (2008) Human gene coexpression landscape:
confident network derived from tissue transcriptomic profiles. PLoS One 3(12), e3911. doi:10.
1371/journal.pone.0003911


Computational Methods for Integration of Biological Data 175

Free download pdf