Comput Biol 4(7):e1000112. https://doi.
org/10.1371/journal.pcbi.1000112
- Movahedi S, Van de Peer Y, Vandepoele K
Comparative network analysis reveals that tis-
sue specificity and gene function are important
factors influencing the mode of expression evo-
lution in Arabidopsis and rice. Plant Physiol
156(3):1316–1330. https://doi.org/10.
1104/pp.111.177865
- Oliver S (2000) Guilt-by-association goes
global. Nature 403(6770):601–603.https://
doi.org/10.1038/35001165
- Barabasi AL, Gulbahce N, Loscalzo J (2011)
Network medicine: a network-based approach
to human disease. Nat Rev Genet 12
(1):56–68. https://doi.org/10.1038/
nrg2918
- Schwikowski B, Uetz P, Fields S (2000) A net-
work of protein-protein interactions in yeast.
Nat Biotechnol 18(12):1257–1261.https://
doi.org/10.1038/82360
- Macropol K, Can T, Singh AK (2009) RRW:
repeated random walks on genome-scale pro-
tein networks for local cluster discovery. BMC
bioinformatics 10:283. https://doi.org/10.
1186/1471-2105-10-283
- Li Y, Patra JC (2010) Genome-wide inferring
gene-phenotype relationship by walking on the
heterogeneous network. Bioinformatics 26
(9):1219–1224. https://doi.org/10.1093/
bioinformatics/btq108
- Kohler S, Bauer S, Horn D, Robinson PN
(2008) Walking the interactome for prioritiza-
tion of candidate disease genes. Am J Hum
Genet 82(4):949–958. https://doi.org/10.
1016/j.ajhg.2008.02.013
- Jiang R, Gan M, He P (2011) Constructing a
gene semantic similarity network for the infer-
ence of disease genes. BMC Syst Biol 5(Suppl
2):S2.https://doi.org/10.1186/1752-0509-
5-S2-S2
- Chen X, Liu MX, Yan GY (2012) Drug-target
interaction prediction by random walk on the
heterogeneous network. Mol BioSyst 8
(7):1970–1978. https://doi.org/10.1039/
c2mb00002d
- Shi H, Xu J, Zhang G, Xu L, Li C, Wang L,
Zhao Z, Jiang W, Guo Z, Li X (2013) Walking
the interactome to identify human miRNA-
disease associations through the functional
link between miRNA targets and disease
genes. BMC Syst Biol 7:101. https://doi.
org/10.1186/1752-0509-7-101
- Huang T, Liu C-L, Li L-L, Cai M-H, Chen
W-Z, Y-F X, O’Reilly PF, Cai L, He L (2016) A
new method for identifying causal genes of
schizophrenia and anti-tuberculosis drug-
induced hepatotoxicity. Sci Rep 6:32571.
https://doi.org/10.1038/srep32571
- Chen L, Yang J, Xing Z, Yuan F, Shu Y,
Zhang Y, Kong X, Huang T, Li H, Cai Y-D
(2017) An integrated method for the identifi-
cation of novel genes related to oral cancer.
PLoS One 12(4):e0175185
- Chen L, Chu C, Kong X, Huang G, Huang T,
Cai YD (2015) A hybrid computational
method for the discovery of novel
reproduction-related genes. PLoS One 10(3):
e0117090.https://doi.org/10.1371/journal.
pone.0117090
- Lee I, Blom UM, Wang PI, Shim JE, Marcotte
EM (2011) Prioritizing candidate disease
genes by network-based boosting of genome-
wide association data. Genome Res 21
(7):1109–1121.https://doi.org/10.1101/gr.
118992.110
- Managbanag JR, Witten TM, Bonchev D, Fox
LA, Tsuchiya M, Kennedy BK, Kaeberlein M
(2008) Shortest-path network analysis is a use-
ful approach toward identifying genetic deter-
minants of longevity. PLoS One 3(11):e3802.
https://doi.org/10.1371/journal.pone.
0003802
- Zhang J, Jiang M, Yuan F, Feng KY, Cai YD,
Xu X, Chen L (2013) Identification of
age-related macular degeneration related
genes by applying shortest path algorithm in
protein-protein interaction network. Biomed
Res Int 2013:523415
- Li B-Q, You J, Chen L, Zhang J, Zhang N, Li
H-P, Huang T, Kong X-Y, Cai Y-D (2013)
Identification of lung-cancer-related genes
with the shortest path approach in a protein-
protein interaction network. Biomed Res Int
2013:267375. https://doi.org/10.1155/
2013/267375
- Jiang M, Chen Y, Zhang Y, Chen L, Zhang N,
Huang T, Cai Y-D, Kong X (2013) Identifica-
tion of hepatocellular carcinoma related genes
with k-th shortest paths in a protein–protein
interaction network. Mol BioSyst 9
(11):2720–2728
- Dijkstra EW (1959) A note on two problems in
connexion with graphs. Numer Math
1:269–271
- Chartrand G, Oellermann OR (1992) Applied
and algorithmic graph theory. Mcgraw-Hill
College, Pennsylvania NY
- Cormen TH, Leiserson CE, R RL, Stein C
(2001) Introduction to algorithms, second
edn. MIT press and Mcgraw-Hill, Cambridge
MA
- Hart PENN, Raphael B (1968) A formal basis
for the heuristic determination of minimum
The Reconstruction and Analysis of Gene Regulatory Networks 153
