Publications

Publications

Robust and sensitive analysis of xMap bead arrays using SAxCyB.

Won JH, Goldberger O, Shen-Orr SS, David MM, Olshen RA. Proc Natl Acad Sci U S A. 2012 Feb 21;109(8):2848-53. Epub 2012 Feb 9.

A systemic cytokine response defect stratifies older adults into distinct immune profiles.

Shen-Orr SS*,Furman D*,Kidd BA,Morgan A, Lovelace P, Rosenberg-Hasson Y, Maecker H, Mackey S, Dekker C,Butte AJ,Davis MM. Submitted.

Extracting Cell-Type-Specific Gene Expression Differences from Complex Tissues

Shen-Orr SS*, Tibshirani R*, Khatri P, Bodian DL, Staedtler F, Perry NM, Hastie T, Sarwal MM, Davis MM*, Butte AJ*. Nature Methods 2010 Apr;7(4):287-9.

Challenges and Promise for the Development of Human Immune Monitoring

Shen-Orr SS RMMJ October 2012, Volume 3, Issue 4

New tools for classification and monitoring of autoimmune diseases.

Maecker HT, Lindstrom TM, Robinson WH, Utz PJ, Hale M, Boyd SD, Shen-Orr SS, Fathman CG. Nat Rev Rheumatol. 2012 May 31;8(6):317-28

Towards a Cytokine-Cell Interaction Knowledgebase of the Adaptive Immune System.

Shen-Orr SS, Goldberger O,Garten Y,Rosenberg-Hasson Y,Lovelace PA,Hirschberg DL, Altman RB, Davis MM, Butte AJ. Pacific Symposium on Biocomputing 2009:439-450

Composition and regulation of maternal and zygotic transcriptomes reflects species specific reproductive mode

Shen-Orr SS, Pilpel Y, Hunter CP. Genome Biol. 2010 Jun 1;11:R58.

Pairing of competitive and topologically distinct regulatory modules enhances patterned gene expression

Yanai I, Baugh LR, Smith JJ, Roehrig C, Shen-Orr SS, Claggett JM, Hil AA, Slonim DK, Hunter CP Mol Syst Biol. 2008;4:163

Superfamilies of evolved and designed networks

Milo R, Itzkovitz S, Kashtan N, Levitt R, Shen-Orr S, Ayzenshtat I, Sheffer M, Alon U. Science. 2004 Mar 5;303(5663):1538

GeneCards(TM) 2002: towards a complete, object-oriented, human gene compendium

Safran M, Solomon I, Shmueli O, Lapidot M, Shen-Orr S, Adato A, Ben-Dor U, Esterman N, Rosen N, Peter I, Olender T, Chalifa-Caspi V, Lancet D. Bioinformatics. 2002 Nov;18(11):1542-3.

Network motifs: simple building blocks of complex networks

Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U. Science. 2002 Oct 25;298(5594):824.

Network motifs in the transcriptional regulation network of Escherichia coli

Shen-Orr SS, Milo R, Mangan S, Alon U. Nat Genet. 2002 May;31(1):64-8.

A relational schema for both array-based and SAGE gene expression experiments.

Stoeckert C, Pizarro A, Manduchi E, Gibson M, Brunk B, Crabtree J, Schug J, Shen-Orr S, Overton GC. Bioinformatics. 2001 Apr;17(4):300-8.