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Items: 1 to 20 of 34

1.

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.

2.

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.

3.

SNiPer-HD: improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays.

Hua J, Craig DW, Brun M, Webster J, Zismann V, Tembe W, Joshipura K, Huentelman MJ, Dougherty ER, Stephan DA.

Bioinformatics. 2007 Jan 1;23(1):57-63. Epub 2006 Oct 24.

PMID:
17062589
4.
5.

Integrating genetic and network analysis to characterize genes related to mouse weight.

Ghazalpour A, Doss S, Zhang B, Wang S, Plaisier C, Castellanos R, Brozell A, Schadt EE, Drake TA, Lusis AJ, Horvath S.

PLoS Genet. 2006 Aug 18;2(8):e130. Epub 2006 Jul 5.

6.

Identification of inflammatory gene modules based on variations of human endothelial cell responses to oxidized lipids.

Gargalovic PS, Imura M, Zhang B, Gharavi NM, Clark MJ, Pagnon J, Yang WP, He A, Truong A, Patel S, Nelson SF, Horvath S, Berliner JA, Kirchgessner TG, Lusis AJ.

Proc Natl Acad Sci U S A. 2006 Aug 22;103(34):12741-6. Epub 2006 Aug 15.

7.

National Center for Biomedical Ontology: advancing biomedicine through structured organization of scientific knowledge.

Rubin DL, Lewis SE, Mungall CJ, Misra S, Westerfield M, Ashburner M, Sim I, Chute CG, Solbrig H, Storey MA, Smith B, Day-Richter J, Noy NF, Musen MA.

OMICS. 2006 Summer;10(2):185-98. Review.

PMID:
16901225
8.

A general framework for weighted gene co-expression network analysis.

Zhang B, Horvath S.

Stat Appl Genet Mol Biol. 2005;4:Article17. Epub 2005 Aug 12.

PMID:
16646834
9.

Gene connectivity, function, and sequence conservation: predictions from modular yeast co-expression networks.

Carlson MR, Zhang B, Fang Z, Mischel PS, Horvath S, Nelson SF.

BMC Genomics. 2006 Mar 3;7:40.

10.

The MGED Ontology: a resource for semantics-based description of microarray experiments.

Whetzel PL, Parkinson H, Causton HC, Fan L, Fostel J, Fragoso G, Game L, Heiskanen M, Morrison N, Rocca-Serra P, Sansone SA, Taylor C, White J, Stoeckert CJ Jr.

Bioinformatics. 2006 Apr 1;22(7):866-73. Epub 2006 Jan 21.

PMID:
16428806
11.

Visualization techniques for genomic data.

Loraine AE, Helt GA.

Proc IEEE Comput Soc Bioinform Conf. 2002;1:321-6. Review.

PMID:
15838148
12.

The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data.

Hayamizu TF, Mangan M, Corradi JP, Kadin JA, Ringwald M.

Genome Biol. 2005;6(3):R29. Epub 2005 Feb 15.

13.

An ontology for cell types.

Bard J, Rhee SY, Ashburner M.

Genome Biol. 2005;6(2):R21. Epub 2005 Jan 14.

14.

The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information.

Smith CL, Goldsmith CA, Eppig JT.

Genome Biol. 2005;6(1):R7. Epub 2004 Dec 15.

15.

NCBI GEO: mining millions of expression profiles--database and tools.

Barrett T, Suzek TO, Troup DB, Wilhite SE, Ngau WC, Ledoux P, Rudnev D, Lash AE, Fujibuchi W, Edgar R.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D562-6.

16.

The ArrayExpress gene expression database: a software engineering and implementation perspective.

Sarkans U, Parkinson H, Lara GG, Oezcimen A, Sharma A, Abeygunawardena N, Contrino S, Holloway E, Rocca-Serra P, Mukherjee G, Shojatalab M, Kapushesky M, Sansone SA, Farne A, Rayner T, Brazma A.

Bioinformatics. 2005 Apr 15;21(8):1495-501. Epub 2004 Nov 25.

PMID:
15564302
17.

Bioconductor: open software development for computational biology and bioinformatics.

Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J.

Genome Biol. 2004;5(10):R80. Epub 2004 Sep 15.

18.

Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression.

Rhodes DR, Yu J, Shanker K, Deshpande N, Varambally R, Ghosh D, Barrette T, Pandey A, Chinnaiyan AM.

Proc Natl Acad Sci U S A. 2004 Jun 22;101(25):9309-14. Epub 2004 Jun 7.

19.

Preprocessing of oligonucleotide array data.

Wu Z, Irizarry RA.

Nat Biotechnol. 2004 Jun;22(6):656-8; author reply 658. No abstract available.

PMID:
15175677
20.

Comparative analysis of protein domain organization.

Ye Y, Godzik A.

Genome Res. 2004 Mar;14(3):343-53.

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