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To What Extent is Blood a Reasonable Surrogate for Brain in Gene Expression Studies: Estimation from Mouse Hippocampus and Spleen.

Davies MN, Lawn S, Whatley S, Fernandes C, Williams RW, Schalkwyk LC.

Front Neurosci. 2009 Oct 9;3:54. doi: 10.3389/neuro.15.002.2009. eCollection 2009.


Coexpression network analysis of neural tissue reveals perturbations in developmental processes in schizophrenia.

Torkamani A, Dean B, Schork NJ, Thomas EA.

Genome Res. 2010 Apr;20(4):403-12. doi: 10.1101/gr.101956.109. Epub 2010 Mar 2.


Weighted gene co-expression network analysis of the peripheral blood from Amyotrophic Lateral Sclerosis patients.

Saris CG, Horvath S, van Vught PW, van Es MA, Blauw HM, Fuller TF, Langfelder P, DeYoung J, Wokke JH, Veldink JH, van den Berg LH, Ophoff RA.

BMC Genomics. 2009 Aug 27;10:405. doi: 10.1186/1471-2164-10-405.


Identification of brain transcriptional variation reproduced in peripheral blood: an approach for mapping brain expression traits.

Jasinska AJ, Service S, Choi OW, DeYoung J, Grujic O, Kong SY, Jorgensen MJ, Bailey J, Breidenthal S, Fairbanks LA, Woods RP, Jentsch JD, Freimer NB.

Hum Mol Genet. 2009 Nov 15;18(22):4415-27. doi: 10.1093/hmg/ddp397. Epub 2009 Aug 19.


Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells.

Mason MJ, Fan G, Plath K, Zhou Q, Horvath S.

BMC Genomics. 2009 Jul 20;10:327. doi: 10.1186/1471-2164-10-327.


WGCNA: an R package for weighted correlation network analysis.

Langfelder P, Horvath S.

BMC Bioinformatics. 2008 Dec 29;9:559. doi: 10.1186/1471-2105-9-559.


Integrated weighted gene co-expression network analysis with an application to chronic fatigue syndrome.

Presson AP, Sobel EM, Papp JC, Suarez CJ, Whistler T, Rajeevan MS, Vernon SD, Horvath S.

BMC Syst Biol. 2008 Nov 6;2:95. doi: 10.1186/1752-0509-2-95.


Functional organization of the transcriptome in human brain.

Oldham MC, Konopka G, Iwamoto K, Langfelder P, Kato T, Horvath S, Geschwind DH.

Nat Neurosci. 2008 Nov;11(11):1271-82. doi: 10.1038/nn.2207. Epub 2008 Oct 12.


Geometric interpretation of gene coexpression network analysis.

Horvath S, Dong J.

PLoS Comput Biol. 2008 Aug 15;4(8):e1000117. doi: 10.1371/journal.pcbi.1000117.


Fibroblast and lymphoblast gene expression profiles in schizophrenia: are non-neural cells informative?

Matigian NA, McCurdy RD, Féron F, Perry C, Smith H, Filippich C, McLean D, McGrath J, Mackay-Sim A, Mowry B, Hayward NK.

PLoS One. 2008 Jun 11;3(6):e2412. doi: 10.1371/journal.pone.0002412.


A gene expression network model of type 2 diabetes links cell cycle regulation in islets with diabetes susceptibility.

Keller MP, Choi Y, Wang P, Davis DB, Rabaglia ME, Oler AT, Stapleton DS, Argmann C, Schueler KL, Edwards S, Steinberg HA, Chaibub Neto E, Kleinhanz R, Turner S, Hellerstein MK, Schadt EE, Yandell BS, Kendziorski C, Attie AD.

Genome Res. 2008 May;18(5):706-16. doi: 10.1101/gr.074914.107. Epub 2008 Mar 17.


A systems level analysis of transcriptional changes in Alzheimer's disease and normal aging.

Miller JA, Oldham MC, Geschwind DH.

J Neurosci. 2008 Feb 6;28(6):1410-20. doi: 10.1523/JNEUROSCI.4098-07.2008.


Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R.

Langfelder P, Zhang B, Horvath S.

Bioinformatics. 2008 Mar 1;24(5):719-20. Epub 2007 Nov 16.


Discovery of expression QTLs using large-scale transcriptional profiling in human lymphocytes.

Göring HH, Curran JE, Johnson MP, Dyer TD, Charlesworth J, Cole SA, Jowett JB, Abraham LJ, Rainwater DL, Comuzzie AG, Mahaney MC, Almasy L, MacCluer JW, Kissebah AH, Collier GR, Moses EK, Blangero J.

Nat Genet. 2007 Oct;39(10):1208-16. Epub 2007 Sep 16.


Understanding network concepts in modules.

Dong J, Horvath S.

BMC Syst Biol. 2007 Jun 4;1:24.


Network neighborhood analysis with the multi-node topological overlap measure.

Li A, Horvath S.

Bioinformatics. 2007 Jan 15;23(2):222-31. Epub 2006 Nov 16.


Conservation and evolution of gene coexpression networks in human and chimpanzee brains.

Oldham MC, Horvath S, Geschwind DH.

Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):17973-8. Epub 2006 Nov 13.


Analysis of oncogenic signaling networks in glioblastoma identifies ASPM as a molecular target.

Horvath S, Zhang B, Carlson M, Lu KV, Zhu S, Felciano RM, Laurance MF, Zhao W, Qi S, Chen Z, Lee Y, Scheck AC, Liau LM, Wu H, Geschwind DH, Febbo PG, Kornblum HI, Cloughesy TF, Nelson SF, Mischel PS.

Proc Natl Acad Sci U S A. 2006 Nov 14;103(46):17402-7. Epub 2006 Nov 7.

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