Biomedical Engineering Reference
In-Depth Information
Shafer , J. and K. Strimmer ( 2005b ). ' A shrinkage approach to inferring large scale
gene association networks.'
Stat. Appl. Genet. Mol. Biol.
,
4
: Article 32 .
Shwe , M. and G. Cooper ( 1991 ). ' An empirical analysis of likelihood-weighting simu-
lation on a large, multiply connected medical belief network'.
Comput. Biomed.
Res.
,
24
(5): 453-75 .
Smyth , Gordon K. ( 2004 ) ' Linear models and empirical Bayes methods for assessing
differential expression in microarray experiments'.
Stat. Appl. Genet. Mol. Biol
.,
3
(1), Article 3. DOI: 10.2202/1544-6115.1027.
Smyth , G.K. and T.P. Speed ( 2003 ). ' Normalization of cDNA microarray data '.
Methods
,
31
, 265-73 .
Spellman , P.T. , G. Sherlock , M. Q. Zhang , V. R. Iyer , K. Anders , M. B. Eisen , P. O.
Brown , D. Botstein and B. Futcher ( 1998 ). ' Comprehensive identifi cation of
cell cycle-regulated genes of the yeast
Saccharomyces cerevisiae
by microarray
hybridization '.
Mol. Biol. Cell
.,
9
(12): 3273-97 .
Subramanian , A. , P. Tamayo , V.K. Mootha , S. Mukherjee , B.L. Ebert , M.A. Gillette ,
A. Paulovich , S.L. Pomeroy , T.R. Golub , E.S. Lander and J.P. Mesirov ( 2005 ).
'Gene set enrichment analysis: a knowledge-based approach for interpreting
genome-wide expression profi les'.
Proc. Natl. Acad. Sci. U.S.A.
,
102
(43): 15545-
50 . doi:10.1073/pnas.0506580102
Tamayo , P. , D. Slonim , J. Mesirov , Q. Zhu , S. Kitareewan , E. Dmitrovsky , E.S.
Lander and T.R. Golub ( 1999 ). ' Interpreting patterns of gene expression with
self-organizing maps: methods and application to hematopoietic differentia-
tion '.
Proc. Natl. Acad. Sci. U.S.A.
,
96
(6): 2907-12 .
Theilhaber , J. , T. Connolly , S. Roman-Roman , S. Bushnell , A. Jackson , K. Call , T .
Garcia and R. Baron ( 2002 ). ' Finding genes in the C2C12 osteogenic pathway
by k-nearest-neighbor classifi cation of expression data'.
Genome Res.
,
12
(1):
165-76 .
Thissen , H. , G. Johnson , G. McFarland , B.C.H. Verbiest , T. Gengenbach and N.H.
Voelcker (2006). 'Microarrays for the evaluation of cell-biomaterial surface
interactions'. Smart Materials IV, edited by Nicolas H. Voelcker,
Proc. of SPIE
,
6413
, 64130B, doi: 10.1117/12.696030
Tusher , V.G. , R. Tibshirani and G. Chu ( 2001 ). ' Signifi cance analysis of microarrays
applied to the ionizing radiation response'.
PNAS
,
98
: 5116-21 .
Wang , Y. , T. Joshi , X. Zhang , D. Xu and L. Chen ( 2006 ). ‚Inferring gene regulatory
networks from multiple microarray datasets'.
Bioinformatics
,
22
(19): 2413-20 .
doi:10.1093/bioinformatics/btl396
Werhli , A.V. , M. Grzegorczyk and D. Husmeier ( 2006 ). ' Comparative evaluation of
reverse engineering gene regulatory networks with relevance networks, graph-
ical gaussian models and bayesian networks.'
Bioinformatics,
22
(20): 2523-31 .
Westfall , P. and S. Young ( 1993 ).
Resampling-based Multiple Testing: Examples and
Methods for p-Value Adjustment
. John Wiley & Sons.
Wilson , C.L. and C.J. Miller ( 2005 ). ' Simpleaffy: a BioConductor package for
Affymetrix Quality Control and data analysis'.
Bioinformatics
,
21
(18): 3683-5 .
doi:10.1093/bioinformatics/bti605
W o l fi nger , R.D. , G. Gibson , E.D. Wolfi nger , L. Bennett , H. Hamadeh , P. Bushel ,
C. Afshari and R.S. Paules ( 2001 ). ' Assessing gene signifi cance from cDNA
microarray expression data via mixed models'.
J. Comput. Biol
.,
8
(6):
625-37 .
