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A decade of Systems Biology: where are we and where are we going to?

Manuel C. Peitsch, David de Graaf (

2014) Drug Discovery Today, 2014 Feb, 19:2, pp 105-107.


Systems diagnostics: anticipating the next generation of diagnostic tests based on mechanistic insight into disease.

David A. Fryburg, Diane H. Song, Daphna Laifenfeld, David de Graaf (2014) Drug Discovery Today, 2014 Feb, Volume 19, Issue 2, pp 108-112.


Reverse causal reasoning: applying qualitative causal knowledge to the interpretation of high-throughput data

Natalie L Catlett, Anthony J Bargnesi, Stephen Ungerer, Toby Seagaran, William Ladd, Keith O Elliston and Dexter Pratt

2013, BMC Bioinformatics, 14:340 doi:10.1186/1471-2105-14-340

Saved By The BEL

Slater T, Song D
Drug Discovery World, Fall 2012 Issue (Reproduction of Article Kindly Permitted by DDW)

Comparative Transcriptional Network Modeling of Three PPAR-α/γ Co-Agonists Reveals Distinct Metabolic Gene Signatures in Primary Human Hepatocytes

Deehan R, Maerz-Weiss P, Catlett NL, Steiner G, Wong B, Wright MB, Blander G, Elliston KO, Ladd W, Bobadilla M, Mizrahi J, Haefliger C, Edgar A
2012, PLoS One. 2012; 7(4): e35012

Genes associated with intestinal permeability in ulcerative colitis: Changes in expression following infliximab therapy

Toedter, G., Li, K., Sague, S., Ma, K., Marano, C., Macoritto, M., Park, J., Deehan, R., Matthews, A., Wu, G. D., Lewis, J. D., Arijs, I., Rutgeerts, P. and Baribaud, F.
2012, Inflammatory Bowel Diseases. doi: 10.1002/ibd.22853

Early patient stratification and predictive biomarkers in drug discovery and development

Laifenfeld D, Drubin DA, Catlett NL, Park JS, Van Hooser AA, Frushour BP, de Graaf D, Fryburg DA, Deehan R
2012, Adv Exp Med Biol. 2012;736:645-53

A network-based approach to quantifying the impact of biologically active substances

Hoeng J, Deehan R, Pratt D, Martin F, Sewer A, Thomson TM, Drubin DA, Waters CA, de Graaf D, Peitsch MC.
2011, Drug Discovery Today (December 2011)

A computable cellular stress network model for non-diseased pulmonary and cardiovascular tissue

Schlage WK, Westra JW, Gebel S, Catlett NL, Mathis C, Frushour BP, Hengstermann A, Van Hooser A, Poussin C, Wong B, Lietz M, Park J, Drubin D, Veljkovic E, Peitsch MC , Hoeng J, Deehan R
2011, BMC Systems Biology, Oct 19 5:168


Verification of systems biology research in the age of collaborative competition

Meyer P, Alexopoulos LG, Bonk T, Califano A, Cho CR, de la Fuente A, de Graaf D, Hartemink AJ, Hoeng J, Ivanov NV, Koeppl H, Linding R, Marbach D, Norel R, Peitsch MC, Rice JJ, Royyuru A, Schacherer F, Sprengel J, Stolle K, Vitkup D, Stolovitzky G
2011, Nat Biotechnol. Sep 8;29(9):811-5


Construction of a computable cell proliferation network focused on non-diseased lung cells

Westra JW, Schlage WK, Frushour BP, Gebel S, Catlett NL, Han W, Eddy SF, Hengstermann A, Matthews AL, Mathis C, Lichtner RB, Poussin C, Talikka M, Veljkovic E, Van Hooser AA, Wong B, Maria MJ, Peitsch MC, Deehan R, Hoeng J
2011, BMC Syst Biol. Jul 2;5(1):105

Causal reasoning identifies mechanisms of sensitivity for a novel AKT kinase inhibitor, GSK690693

Kumar R, Blakemore SJ, Ellis CE, Petricoin EF 3rd, Pratt D, Macoritto M, Matthews AL, Loureiro JJ, Elliston K
2010, BMC Genomics. Jul 6;11:419


The role of hypoxia in 2-butoxyethanol-induced hemangiosarcoma

Laifenfeld D, Gilchrist A, Drubin D, Jorge M, Eddy SF, Frushour BP, Ladd B, Obert LA, Gosink MM, Cook JC, Criswell K, Somps CJ, Koza-Taylor P, Elliston KO, Lawton MP
2010, Toxicol Sci. Jan;113(1):254-66

Small molecule activators of SIRT1 replicate signaling pathways triggered by calorie restriction in vivo

Smith JJ, Kenney RD, Gagne DJ, Frushour BP, Ladd W, Galonek HL, Israelian K, Song J, Razvadauskaite G, Lynch AV, Carney DP, Johnson RJ, Lavu S, Iffland A, Elliott PJ, Lambert PD, Elliston KO, Jirousek MR, Milne JC, Boss O
2009, BMC Syst Biol. Mar 10;3:31

SIRT1 promotes differentiation of normal human keratinocytes

Blander G, Bhimavarapu A, Mammone T, Maes D, Elliston K, Reich C, Matsui MS, Guarente L, Loureiro JJ
2009, J Invest Dermatol. Jan;129(1):41-9